diff --git a/pvactools/tools/pvacbind/example_data/results/MHC_Class_I/Test.all_epitopes.aggregated.tsv b/pvactools/tools/pvacbind/example_data/results/MHC_Class_I/Test.all_epitopes.aggregated.tsv index 4b6bd4b0..abf5bb99 100644 --- a/pvactools/tools/pvacbind/example_data/results/MHC_Class_I/Test.all_epitopes.aggregated.tsv +++ b/pvactools/tools/pvacbind/example_data/results/MHC_Class_I/Test.all_epitopes.aggregated.tsv @@ -36,14 +36,14 @@ ID A*02:01 B*35:01 Best Peptide Prob Pos Num Included Peptides Num Passing Pepti 27 1 SLLHTVSPEP None 1 0 3556.960 7.400 Poor Pending 35 2 NPETDYLTG None 2 0 3595.485 6.200 Poor Pending 20 1 DLIGKHGGV None 1 0 4145.685 12.500 Poor Pending -39 TSAKTTVVV None 0 0 5514.896 15.500 Poor Pending -40 TSAKTTVVV None 0 0 5514.896 15.500 Poor Pending -13 IANEDAAQG None 0 0 5541.375 8.587 Poor Pending -14 IANQDAAQG None 0 0 5738.350 12.249 Poor Pending -46 YESRVEPPH None 0 0 6159.300 13.850 Poor Pending -29 SAGQHWARL None 0 0 7663.630 12.785 Poor Pending -45 EASGSESRV None 0 0 10173.480 19.000 Poor Pending -8 SGGSHVWTH None 0 0 10761.968 23.096 Poor Pending -22 SPVKEEEKT None 0 0 12628.540 13.580 Poor Pending -21 SPVKEEEK None 0 0 14657.070 17.153 Poor Pending -7 WTRSRDPEG None 0 0 20800.365 35.287 Poor Pending +39 1 TSAKTTVVV None 1 0 5514.896 15.500 Poor Pending +40 1 TSAKTTVVV None 1 0 5514.896 15.500 Poor Pending +13 1 IANEDAAQG None 1 0 5541.375 8.587 Poor Pending +14 1 IANQDAAQG None 1 0 5738.350 12.249 Poor Pending +46 1 YESRVEPPH None 1 0 6159.300 13.850 Poor Pending +29 1 SAGQHWARL None 1 0 7663.630 12.785 Poor Pending +45 1 EASGSESRV None 1 0 10173.480 19.000 Poor Pending +8 1 SGGSHVWTH None 1 0 10761.968 23.096 Poor Pending +22 1 SPVKEEEKT None 1 0 12628.540 13.580 Poor Pending +21 1 SPVKEEEK None 1 0 14657.070 17.153 Poor Pending +7 1 WTRSRDPEG None 1 0 20800.365 35.287 Poor Pending diff --git a/pvactools/tools/pvacbind/example_data/results/MHC_Class_II/Test.all_epitopes.aggregated.tsv b/pvactools/tools/pvacbind/example_data/results/MHC_Class_II/Test.all_epitopes.aggregated.tsv index d1189e2c..8536b194 100644 --- a/pvactools/tools/pvacbind/example_data/results/MHC_Class_II/Test.all_epitopes.aggregated.tsv +++ b/pvactools/tools/pvacbind/example_data/results/MHC_Class_II/Test.all_epitopes.aggregated.tsv @@ -35,15 +35,15 @@ ID DRB1*11:01 Best Peptide Prob Pos Num Included Peptides Num Passing Peptides I 35 1 AIAGTLKFNPETDYL None 1 0 3844.535 65.000 Poor Pending 31 1 DDMDCLSDRCKILQV None 1 0 3900.880 64.000 Poor Pending 24 1 SLMVCELAGNLFNCE None 1 0 4781.440 70.000 Poor Pending -23 SLMVCELAGNPFNCE None 0 0 5518.185 74.000 Poor Pending -14 AVQGIANQDAAQGIA None 0 0 6113.120 70.000 Poor Pending -8 GGSHVWTHSRDPEGS None 0 0 6831.935 71.000 Poor Pending -4 SAAAAAAAVIPTVST None 0 0 6950.420 82.000 Poor Pending -3 AAAAAAAAVIPTVST None 0 0 7066.755 82.000 Poor Pending -27 SLLHTVSPEPPRPPQ None 0 0 7421.920 69.000 Poor Pending -12 NKSVNEALNNLLTEE None 0 0 7705.835 67.000 Poor Pending -13 AVQGIANEDAAQGIA None 0 0 8697.355 79.000 Poor Pending -22 EEEKTQEVKVKEPPK None 0 0 12127.835 86.410 Poor Pending -46 EASGYESRVEPPHEN None 0 0 14269.785 86.000 Poor Pending -21 EEEKPQEVKVKEPPK None 0 0 15116.485 83.650 Poor Pending -45 AREERTEASGSESRV None 0 0 25985.790 96.000 Poor Pending +23 1 SLMVCELAGNPFNCE None 1 0 5518.185 74.000 Poor Pending +14 1 AVQGIANQDAAQGIA None 1 0 6113.120 70.000 Poor Pending +8 1 GGSHVWTHSRDPEGS None 1 0 6831.935 71.000 Poor Pending +4 1 SAAAAAAAVIPTVST None 1 0 6950.420 82.000 Poor Pending +3 1 AAAAAAAAVIPTVST None 1 0 7066.755 82.000 Poor Pending +27 1 SLLHTVSPEPPRPPQ None 1 0 7421.920 69.000 Poor Pending +12 1 NKSVNEALNNLLTEE None 1 0 7705.835 67.000 Poor Pending +13 1 AVQGIANEDAAQGIA None 1 0 8697.355 79.000 Poor Pending +22 1 EEEKTQEVKVKEPPK None 1 0 12127.835 86.410 Poor Pending +46 1 EASGYESRVEPPHEN None 1 0 14269.785 86.000 Poor Pending +21 1 EEEKPQEVKVKEPPK None 1 0 15116.485 83.650 Poor Pending +45 1 AREERTEASGSESRV None 1 0 25985.790 96.000 Poor Pending diff --git a/pvactools/tools/pvacbind/example_data/results/combined/Test.all_epitopes.aggregated.tsv b/pvactools/tools/pvacbind/example_data/results/combined/Test.all_epitopes.aggregated.tsv index c752c75f..0c33e407 100644 --- a/pvactools/tools/pvacbind/example_data/results/combined/Test.all_epitopes.aggregated.tsv +++ b/pvactools/tools/pvacbind/example_data/results/combined/Test.all_epitopes.aggregated.tsv @@ -40,10 +40,10 @@ ID DRB1*11:01 A*02:01 B*35:01 Best Peptide Prob Pos Num Included Peptides Num Pa 36 4 1 AIAGTLKFNPQTDYL None 5 0 2466.625 57.000 Poor Pending 27 1 SLLHTVSPEP None 1 0 3556.960 7.400 Poor Pending 35 1 2 NPETDYLTG None 3 0 3595.485 6.200 Poor Pending -13 IANEDAAQG None 0 0 5541.375 8.587 Poor Pending -14 IANQDAAQG None 0 0 5738.350 12.249 Poor Pending -46 YESRVEPPH None 0 0 6159.300 13.850 Poor Pending -8 GGSHVWTHSRDPEGS None 0 0 6831.935 71.000 Poor Pending -45 EASGSESRV None 0 0 10173.480 19.000 Poor Pending -22 EEEKTQEVKVKEPPK None 0 0 12127.835 86.410 Poor Pending -21 SPVKEEEK None 0 0 14657.070 17.153 Poor Pending +13 1 IANEDAAQG None 1 0 5541.375 8.587 Poor Pending +14 1 IANQDAAQG None 1 0 5738.350 12.249 Poor Pending +46 1 YESRVEPPH None 1 0 6159.300 13.850 Poor Pending +8 1 GGSHVWTHSRDPEGS None 1 0 6831.935 71.000 Poor Pending +45 1 EASGSESRV None 1 0 10173.480 19.000 Poor Pending +22 1 EEEKTQEVKVKEPPK None 1 0 12127.835 86.410 Poor Pending +21 1 SPVKEEEK None 1 0 14657.070 17.153 Poor Pending diff --git a/pvactools/tools/pvacfuse/example_data/agfusion_results/MHC_Class_I/Test.all_epitopes.aggregated.tsv b/pvactools/tools/pvacfuse/example_data/agfusion_results/MHC_Class_I/Test.all_epitopes.aggregated.tsv index 7f99cf4b..99df3b74 100644 --- a/pvactools/tools/pvacfuse/example_data/agfusion_results/MHC_Class_I/Test.all_epitopes.aggregated.tsv +++ b/pvactools/tools/pvacfuse/example_data/agfusion_results/MHC_Class_I/Test.all_epitopes.aggregated.tsv @@ -22,15 +22,15 @@ ID A*02:01 B*35:01 Gene Best Peptide Best Transcript Allele Prob Pos Num Include 11.DNAJC7-CDK17.ENST00000457167-ENST00000261211.frameshift_fusion.25 1 1 DNAJC7-CDK17 LDDQEAKSF ENST00000457167-ENST00000261211 HLA-B*35:01 None 2 0 4488.075 14.000 NA NA Poor Pending 12.DNAJC7-CDK17.ENST00000457167-ENST00000261211.frameshift_fusion.25 1 1 DNAJC7-CDK17 LDDQEAKSF ENST00000457167-ENST00000261211 HLA-B*35:01 None 2 0 4488.075 14.000 NA NA Poor Pending 32.TIMP3-COL3A1.ENST00000266085-ENST00000304636.frameshift_fusion.211 1 TIMP3-COL3A1 NATDPGPEA ENST00000266085-ENST00000304636 HLA-B*35:01 None 1 0 4879.470 6.360 NA NA Poor Pending -36.TTC26-NDUFV2.ENST00000464848-ENST00000318388.inframe_fusion.239 TTC26-NDUFV2 RLYNGRAAEG ENST00000464848-ENST00000318388 HLA-A*02:01 None 0 0 5495.235 9.400 NA NA Poor Pending -5.CEP192-TMEM260.ENST00000506447-ENST00000261556.inframe_fusion.1724 CEP192-TMEM260 DPEACEESV ENST00000506447-ENST00000261556 HLA-B*35:01 None 0 0 5935.036 8.900 NA NA Poor Pending -15.LCORL-GNAS.ENST00000382226-ENST00000371100.inframe_fusion.143 LCORL-GNAS ALFRKKGA ENST00000382226-ENST00000371100 HLA-A*02:01 None 0 0 6647.795 23.226 NA NA Poor Pending -6.CLEC16A-RMI2.ENST00000409790-ENST00000312499.frameshift_fusion.242 CLEC16A-RMI2 CVQTDEEKV ENST00000409790-ENST00000312499 HLA-A*02:01 None 0 0 7223.131 19.000 NA NA Poor Pending -38.TUB-RIC3.ENST00000305253-ENST00000309737.frameshift_fusion.165 TUB-RIC3 APASAKRTK ENST00000305253-ENST00000309737 HLA-B*35:01 None 0 0 7902.902 19.000 NA NA Poor Pending -37.TTC39B-C6orf62.ENST00000512701-ENST00000378119.inframe_fusion.465 TTC39B-C6orf62 KWSKAKFEF ENST00000512701-ENST00000378119 HLA-B*35:01 None 0 0 8453.905 15.000 NA NA Poor Pending -17.MAX-TMEM260.ENST00000358664-ENST00000261556.frameshift_fusion.57 MAX-TMEM260 VPSLQGEKG ENST00000358664-ENST00000261556 HLA-B*35:01 None 0 0 12601.620 12.000 NA NA Poor Pending -21.PHTF1-YARS.ENST00000369604-ENST00000373477.inframe_fusion.15 PHTF1-YARS YQKKESKIDL ENST00000369604-ENST00000373477 HLA-A*02:01 None 0 0 13729.865 28.000 NA NA Poor Pending -41.ZC3H11A-KLHL12.ENST00000545588-ENST00000367261.frameshift_fusion.291 ZC3H11A-KLHL12 RLGKRKFSAG ENST00000545588-ENST00000367261 HLA-A*02:01 None 0 0 15600.145 33.268 NA NA Poor Pending -19.MIPOL1-PGAP1.ENST00000327441-ENST00000354764.frameshift_fusion.6 MIPOL1-PGAP1 NWSKVCCRL ENST00000327441-ENST00000354764 HLA-A*02:01 None 0 0 16894.461 34.000 NA NA Poor Pending -28.SNRPB2-METTL18.ENST00000246071-ENST00000310392.frameshift_fusion.215 SNRPB2-METTL18 QGFKITPSQ ENST00000246071-ENST00000310392 HLA-B*35:01 None 0 0 21917.167 36.000 NA NA Poor Pending -4.CDC37L1-BTG3.ENST00000381854-ENST00000339775.frameshift_fusion.169 CDC37L1-BTG3 KIRHFDEE ENST00000381854-ENST00000339775 HLA-A*02:01 None 0 0 35010.660 71.000 NA NA Poor Pending +36.TTC26-NDUFV2.ENST00000464848-ENST00000318388.inframe_fusion.239 1 TTC26-NDUFV2 RLYNGRAAEG ENST00000464848-ENST00000318388 HLA-A*02:01 None 1 0 5495.235 9.400 NA NA Poor Pending +5.CEP192-TMEM260.ENST00000506447-ENST00000261556.inframe_fusion.1724 1 CEP192-TMEM260 DPEACEESV ENST00000506447-ENST00000261556 HLA-B*35:01 None 1 0 5935.036 8.900 NA NA Poor Pending +15.LCORL-GNAS.ENST00000382226-ENST00000371100.inframe_fusion.143 1 LCORL-GNAS ALFRKKGA ENST00000382226-ENST00000371100 HLA-A*02:01 None 1 0 6647.795 23.226 NA NA Poor Pending +6.CLEC16A-RMI2.ENST00000409790-ENST00000312499.frameshift_fusion.242 1 CLEC16A-RMI2 CVQTDEEKV ENST00000409790-ENST00000312499 HLA-A*02:01 None 1 0 7223.131 19.000 NA NA Poor Pending +38.TUB-RIC3.ENST00000305253-ENST00000309737.frameshift_fusion.165 1 TUB-RIC3 APASAKRTK ENST00000305253-ENST00000309737 HLA-B*35:01 None 1 0 7902.902 19.000 NA NA Poor Pending +37.TTC39B-C6orf62.ENST00000512701-ENST00000378119.inframe_fusion.465 1 TTC39B-C6orf62 KWSKAKFEF ENST00000512701-ENST00000378119 HLA-B*35:01 None 1 0 8453.905 15.000 NA NA Poor Pending +17.MAX-TMEM260.ENST00000358664-ENST00000261556.frameshift_fusion.57 1 MAX-TMEM260 VPSLQGEKG ENST00000358664-ENST00000261556 HLA-B*35:01 None 1 0 12601.620 12.000 NA NA Poor Pending +21.PHTF1-YARS.ENST00000369604-ENST00000373477.inframe_fusion.15 1 PHTF1-YARS YQKKESKIDL ENST00000369604-ENST00000373477 HLA-A*02:01 None 1 0 13729.865 28.000 NA NA Poor Pending +41.ZC3H11A-KLHL12.ENST00000545588-ENST00000367261.frameshift_fusion.291 1 ZC3H11A-KLHL12 RLGKRKFSAG ENST00000545588-ENST00000367261 HLA-A*02:01 None 1 0 15600.145 33.268 NA NA Poor Pending +19.MIPOL1-PGAP1.ENST00000327441-ENST00000354764.frameshift_fusion.6 1 MIPOL1-PGAP1 NWSKVCCRL ENST00000327441-ENST00000354764 HLA-A*02:01 None 1 0 16894.461 34.000 NA NA Poor Pending +28.SNRPB2-METTL18.ENST00000246071-ENST00000310392.frameshift_fusion.215 1 SNRPB2-METTL18 QGFKITPSQ ENST00000246071-ENST00000310392 HLA-B*35:01 None 1 0 21917.167 36.000 NA NA Poor Pending +4.CDC37L1-BTG3.ENST00000381854-ENST00000339775.frameshift_fusion.169 1 CDC37L1-BTG3 KIRHFDEE ENST00000381854-ENST00000339775 HLA-A*02:01 None 1 0 35010.660 71.000 NA NA Poor Pending diff --git a/pvactools/tools/pvacfuse/example_data/agfusion_results/MHC_Class_II/Test.all_epitopes.aggregated.tsv b/pvactools/tools/pvacfuse/example_data/agfusion_results/MHC_Class_II/Test.all_epitopes.aggregated.tsv index 953a6f12..42c303e7 100644 --- a/pvactools/tools/pvacfuse/example_data/agfusion_results/MHC_Class_II/Test.all_epitopes.aggregated.tsv +++ b/pvactools/tools/pvacfuse/example_data/agfusion_results/MHC_Class_II/Test.all_epitopes.aggregated.tsv @@ -28,8 +28,8 @@ ID DRB1*11:01 Gene Best Peptide Best Transcript Allele Prob Pos Num Included Pep 29.TAOK3-MARCH1.ENST00000392533-ENST00000503008.frameshift_fusion.214 4 TAOK3-MARCH1 KVDIWSLGITCIELV ENST00000392533-ENST00000503008 DRB1*11:01 None 4 0 2887.565 61.000 NA NA Poor Pending 3.BTBD8-ELAVL4.ENST00000342818-ENST00000357083.frameshift_fusion.181 2 BTBD8-ELAVL4 DDDFISNGSPQLPLM ENST00000342818-ENST00000357083 DRB1*11:01 None 2 0 3275.675 44.690 NA NA Poor Pending 27.SMG1-PHF20.ENST00000446231-ENST00000374012.frameshift_fusion.3540 1 SMG1-PHF20 ATYQPSFAADDKAST ENST00000446231-ENST00000374012 DRB1*11:01 None 1 0 3853.640 45.070 NA NA Poor Pending -38.TUB-RIC3.ENST00000305253-ENST00000309737.frameshift_fusion.165 TUB-RIC3 TRPTAPASAKRTKAA ENST00000305253-ENST00000309737 DRB1*11:01 None 0 0 5064.720 69.000 NA NA Poor Pending -17.MAX-TMEM260.ENST00000358664-ENST00000261556.frameshift_fusion.57 MAX-TMEM260 HSLRDSVPSLQGEKG ENST00000358664-ENST00000261556 DRB1*11:01 None 0 0 5813.705 57.000 NA NA Poor Pending -5.CEP192-TMEM260.ENST00000506447-ENST00000261556.inframe_fusion.1724 CEP192-TMEM260 ESVCDQRTNYVIDKF ENST00000506447-ENST00000261556 DRB1*11:01 None 0 0 7719.265 81.000 NA NA Poor Pending -32.TIMP3-COL3A1.ENST00000266085-ENST00000304636.frameshift_fusion.211 TIMP3-COL3A1 PDKSIINATDPGPEA ENST00000266085-ENST00000304636 DRB1*11:01 None 0 0 13347.750 90.000 NA NA Poor Pending -6.CLEC16A-RMI2.ENST00000409790-ENST00000312499.frameshift_fusion.242 CLEC16A-RMI2 SHVIELDDCVQTDEE ENST00000409790-ENST00000312499 DRB1*11:01 None 0 0 14800.050 90.000 NA NA Poor Pending +38.TUB-RIC3.ENST00000305253-ENST00000309737.frameshift_fusion.165 1 TUB-RIC3 TRPTAPASAKRTKAA ENST00000305253-ENST00000309737 DRB1*11:01 None 1 0 5064.720 69.000 NA NA Poor Pending +17.MAX-TMEM260.ENST00000358664-ENST00000261556.frameshift_fusion.57 1 MAX-TMEM260 HSLRDSVPSLQGEKG ENST00000358664-ENST00000261556 DRB1*11:01 None 1 0 5813.705 57.000 NA NA Poor Pending +5.CEP192-TMEM260.ENST00000506447-ENST00000261556.inframe_fusion.1724 1 CEP192-TMEM260 ESVCDQRTNYVIDKF ENST00000506447-ENST00000261556 DRB1*11:01 None 1 0 7719.265 81.000 NA NA Poor Pending +32.TIMP3-COL3A1.ENST00000266085-ENST00000304636.frameshift_fusion.211 1 TIMP3-COL3A1 PDKSIINATDPGPEA ENST00000266085-ENST00000304636 DRB1*11:01 None 1 0 13347.750 90.000 NA NA Poor Pending +6.CLEC16A-RMI2.ENST00000409790-ENST00000312499.frameshift_fusion.242 1 CLEC16A-RMI2 SHVIELDDCVQTDEE ENST00000409790-ENST00000312499 DRB1*11:01 None 1 0 14800.050 90.000 NA NA Poor Pending diff --git a/pvactools/tools/pvacfuse/example_data/agfusion_results/combined/Test.all_epitopes.aggregated.tsv b/pvactools/tools/pvacfuse/example_data/agfusion_results/combined/Test.all_epitopes.aggregated.tsv index cceb73c5..06a68967 100644 --- a/pvactools/tools/pvacfuse/example_data/agfusion_results/combined/Test.all_epitopes.aggregated.tsv +++ b/pvactools/tools/pvacfuse/example_data/agfusion_results/combined/Test.all_epitopes.aggregated.tsv @@ -29,8 +29,8 @@ ID DRB1*11:01 A*02:01 B*35:01 Gene Best Peptide Best Transcript Allele Prob Pos 35.TRAPPC9-NUP50.ENST00000389328-ENST00000347635.frameshift_fusion.1034 8 2 1 TRAPPC9-NUP50 FSCCKWPYHL ENST00000389328-ENST00000347635 HLA-A*02:01 None 11 0 2130.755 6.400 NA NA Poor Pending 27.SMG1-PHF20.ENST00000446231-ENST00000374012.frameshift_fusion.3540 1 1 SMG1-PHF20 FAADDKAST ENST00000446231-ENST00000374012 HLA-B*35:01 None 2 0 2614.100 2.900 NA NA Poor Pending 32.TIMP3-COL3A1.ENST00000266085-ENST00000304636.frameshift_fusion.211 1 TIMP3-COL3A1 NATDPGPEA ENST00000266085-ENST00000304636 HLA-B*35:01 None 1 0 4879.470 6.360 NA NA Poor Pending -38.TUB-RIC3.ENST00000305253-ENST00000309737.frameshift_fusion.165 TUB-RIC3 TRPTAPASAKRTKAA ENST00000305253-ENST00000309737 DRB1*11:01 None 0 0 5064.720 69.000 NA NA Poor Pending -17.MAX-TMEM260.ENST00000358664-ENST00000261556.frameshift_fusion.57 MAX-TMEM260 HSLRDSVPSLQGEKG ENST00000358664-ENST00000261556 DRB1*11:01 None 0 0 5813.705 57.000 NA NA Poor Pending -5.CEP192-TMEM260.ENST00000506447-ENST00000261556.inframe_fusion.1724 CEP192-TMEM260 DPEACEESV ENST00000506447-ENST00000261556 HLA-B*35:01 None 0 0 5935.036 8.900 NA NA Poor Pending -6.CLEC16A-RMI2.ENST00000409790-ENST00000312499.frameshift_fusion.242 CLEC16A-RMI2 CVQTDEEKV ENST00000409790-ENST00000312499 HLA-A*02:01 None 0 0 7223.131 19.000 NA NA Poor Pending -19.MIPOL1-PGAP1.ENST00000327441-ENST00000354764.frameshift_fusion.6 MIPOL1-PGAP1 NWSKVCCRL ENST00000327441-ENST00000354764 HLA-A*02:01 None 0 0 16894.461 34.000 NA NA Poor Pending +38.TUB-RIC3.ENST00000305253-ENST00000309737.frameshift_fusion.165 1 TUB-RIC3 TRPTAPASAKRTKAA ENST00000305253-ENST00000309737 DRB1*11:01 None 1 0 5064.720 69.000 NA NA Poor Pending +17.MAX-TMEM260.ENST00000358664-ENST00000261556.frameshift_fusion.57 1 MAX-TMEM260 HSLRDSVPSLQGEKG ENST00000358664-ENST00000261556 DRB1*11:01 None 1 0 5813.705 57.000 NA NA Poor Pending +5.CEP192-TMEM260.ENST00000506447-ENST00000261556.inframe_fusion.1724 1 CEP192-TMEM260 DPEACEESV ENST00000506447-ENST00000261556 HLA-B*35:01 None 1 0 5935.036 8.900 NA NA Poor Pending +6.CLEC16A-RMI2.ENST00000409790-ENST00000312499.frameshift_fusion.242 1 CLEC16A-RMI2 CVQTDEEKV ENST00000409790-ENST00000312499 HLA-A*02:01 None 1 0 7223.131 19.000 NA NA Poor Pending +19.MIPOL1-PGAP1.ENST00000327441-ENST00000354764.frameshift_fusion.6 1 MIPOL1-PGAP1 NWSKVCCRL ENST00000327441-ENST00000354764 HLA-A*02:01 None 1 0 16894.461 34.000 NA NA Poor Pending diff --git a/pvactools/tools/pvacfuse/example_data/arriba_results/MHC_Class_I/Test.all_epitopes.aggregated.tsv b/pvactools/tools/pvacfuse/example_data/arriba_results/MHC_Class_I/Test.all_epitopes.aggregated.tsv index 2a97a314..d0df2e02 100644 --- a/pvactools/tools/pvacfuse/example_data/arriba_results/MHC_Class_I/Test.all_epitopes.aggregated.tsv +++ b/pvactools/tools/pvacfuse/example_data/arriba_results/MHC_Class_I/Test.all_epitopes.aggregated.tsv @@ -33,6 +33,22 @@ ID A*02:01 B*35:01 Gene Best Peptide Best Transcript Allele Prob Pos Num Include 64.SERINC3-BCAT2.ENST00000255175-..frameshift_fusion.36 6 3 SERINC3-BCAT2 KIQMGSHCV ENST00000255175-. HLA-A*02:01 None 9 1 435.940 3.300 NA 5 Pass Pending 8.PTEN-MED6P1(8171),ENSG00000275015(201135).ENST00000371953-..frameshift_fusion.52 3 5 PTEN-MED6P1(8171),ENSG00000275015(201135) TCNAVWSSY ENST00000371953-. HLA-B*35:01 None 8 1 438.793 0.848 NA 49 Pass Pending 56.ERO1A-FERMT2.ENST00000395686-ENST00000341590.inframe_fusion.42 1 ERO1A-FERMT2 FCEADGSIY ENST00000395686-ENST00000341590 HLA-B*35:01 None 1 1 478.077 1.200 NA 9 Pass Pending +91.STRBP-RHEB.ENST00000348403-ENST00000262187.frameshift_fusion.40 15 1 STRBP-RHEB FMLGDVILL ENST00000348403-ENST00000262187 HLA-A*02:01 None 15 5 3.680 0.022 NA 2 LowReadSupport Pending +21.E2F3-PKD2.ENST00000535432-ENST00000506727.frameshift_fusion.6 6 9 E2F3-PKD2 SLCEGCWYV ENST00000535432-ENST00000506727 HLA-A*02:01 None 15 5 3.740 0.110 NA 1 LowReadSupport Pending +33.EEFSEC-KPNA1.ENST00000254730-ENST00000344337.frameshift_fusion.39 5 1 EEFSEC-KPNA1 SLIRTIIGV ENST00000254730-ENST00000344337 HLA-A*02:01 None 6 3 12.281 0.090 NA 2 LowReadSupport Pending +51.BGN-ATP2B3.ENST00000331595-ENST00000263519.frameshift_fusion.12 10 6 BGN-ATP2B3 ALALRFWNL ENST00000331595-ENST00000263519 HLA-A*02:01 None 15 4 36.875 0.580 NA 0 LowReadSupport Pending +69.B4GALT1-ENSG00000271677(54939),ENOX2(20912).ENST00000535206-..frameshift_fusion.22 6 5 B4GALT1-ENSG00000271677(54939),ENOX2(20912) FVELLTPPF ENST00000535206-. HLA-B*35:01 None 11 5 40.180 0.600 NA 3 LowReadSupport Pending +37.MLLT10-AMD1P1.ENST00000631589-ENST00000457220.frameshift_fusion.49 14 3 MLLT10-AMD1P1 LLQDLSLGSV ENST00000631589-ENST00000457220 HLA-A*02:01 None 15 4 50.210 0.440 NA 4 LowReadSupport Pending +65.DGLUCY-ENSG00000227482(74932),ENSG00000214669(1207).ENST00000256324-..frameshift_fusion.69 2 2 DGLUCY-ENSG00000227482(74932),ENSG00000214669(1207) GAISETSIY ENST00000256324-. HLA-B*35:01 None 4 1 74.150 0.800 NA 4 LowReadSupport Pending +87.CRTC3-SNRPC.ENST00000268184-ENST00000244520.frameshift_fusion.48 4 CRTC3-SNRPC SPWYDASTPY ENST00000268184-ENST00000244520 HLA-B*35:01 None 4 1 107.216 0.098 NA 2 LowReadSupport Pending +66.DEAF1-ENSG00000269915.ENST00000683307-..frameshift_fusion.43 11 7 DEAF1-ENSG00000269915 YPLCSLSPV ENST00000683307-. HLA-B*35:01 None 15 2 120.514 0.790 NA 4 LowReadSupport Pending +67.PGAP1-PAX8.ENST00000354764-ENST00000681162.frameshift_fusion.11 9 7 PGAP1-PAX8 QILGQIFSA ENST00000354764-ENST00000681162 HLA-A*02:01 None 15 3 167.905 0.950 NA 3 LowReadSupport Pending +90.ASXL1-IMPDH2.ENST00000375687-ENST00000678920.frameshift_fusion.56 5 4 ASXL1-IMPDH2 ALTGGIGFI ENST00000375687-ENST00000678920 HLA-A*02:01 None 8 3 172.660 1.400 NA 2 LowReadSupport Pending +19.PDIA5-ENSG00000280441.ENST00000316218-ENST00000651813.frameshift_fusion.51 4 8 PDIA5-ENSG00000280441 MTRVGTTEF ENST00000316218-ENST00000651813 HLA-B*35:01 None 12 3 210.280 1.800 NA 1 LowReadSupport Pending +50.BGN-ATP2B3.ENST00000331595-ENST00000263519.frameshift_fusion.27 6 7 BGN-ATP2B3 KLYRCPRLAA ENST00000331595-ENST00000263519 HLA-A*02:01 None 12 2 249.185 2.300 NA 1 LowReadSupport Pending +63.UNC5C-STPG2.ENST00000453304-ENST00000522676.frameshift_fusion.18 3 5 UNC5C-STPG2 SPRGLRTYY ENST00000453304-ENST00000522676 HLA-B*35:01 None 8 1 364.050 1.970 NA 1 LowReadSupport Pending +70.GRIK2-GRIK2.ENST00000421544-..frameshift_fusion.34 1 GRIK2-GRIK2 SLKEEGLEKV ENST00000421544-. HLA-A*02:01 None 1 1 384.720 2.600 NA 2 LowReadSupport Pending +83.RBM46-RBM46.ENST00000281722-ENST00000281722.inframe_fusion.46 8 1 RBM46-RBM46 TLLHLGTATM ENST00000281722-ENST00000281722 HLA-A*02:01 None 8 1 441.230 3.000 NA 3 LowReadSupport Pending 14.ATG2B-ENSG00000285883(75498),CRAT37(26889).ENST00000359933-..frameshift_fusion.59 2 6 ATG2B-ENSG00000285883(75498),CRAT37(26889) QAILLPQPL ENST00000359933-. HLA-B*35:01 None 8 0 621.335 2.400 NA 24 Poor Pending 84.ST3GAL4-KIRREL3.ENST00000444328-..frameshift_fusion.20 1 2 ST3GAL4-KIRREL3 KQAWGDSKV ENST00000444328-. HLA-A*02:01 None 3 0 630.930 4.600 NA 3 Poor Pending 88.RAPGEF1-NUB1.ENST00000372195-ENST00000468404.frameshift_fusion.39 4 RAPGEF1-NUB1 MLEGVNSDPY ENST00000372195-ENST00000468404 HLA-B*35:01 None 4 0 664.640 1.000 NA 2 Poor Pending @@ -50,40 +66,24 @@ ID A*02:01 B*35:01 Gene Best Peptide Best Transcript Allele Prob Pos Num Include 38.TASP1-MACROD2.ENST00000337743-..frameshift_fusion.48 1 2 TASP1-MACROD2 FVLVHADDAW ENST00000337743-. HLA-B*35:01 None 3 0 3594.325 3.000 NA 4 Poor Pending 54.PCK2-LINC00596(469),DHRS4-AS1(3182).ENST00000559250-..frameshift_fusion.40 1 PCK2-LINC00596(469),DHRS4-AS1(3182) LVYEAFNWRS ENST00000559250-. HLA-A*02:01 None 1 0 4457.190 14.000 NA 12 Poor Pending 92.CLTC-LAMC1.ENST00000621829-ENST00000258341.inframe_fusion.55 1 CLTC-LAMC1 RTWKDSQAA ENST00000621829-ENST00000258341 HLA-A*02:01 None 1 0 4632.622 13.000 NA 2 Poor Pending -58.AGPAT5-MCPH1-AS1.ENST00000285518-..frameshift_fusion.68 AGPAT5-MCPH1-AS1 FFENYTGVQV ENST00000285518-. HLA-A*02:01 None 0 0 5086.370 8.000 NA 8 Poor Pending -81.ODF2-SPTAN1.ENST00000604420-ENST00000372731.frameshift_fusion.11 ODF2-SPTAN1 SSSGGSPRPV ENST00000604420-ENST00000372731 HLA-A*02:01 None 0 0 5439.649 14.000 NA 3 Poor Pending -42.HNRNPUL2-BSCL2-AHNAK.ENST00000403734-ENST00000257247.inframe_fusion.30 HNRNPUL2-BSCL2-AHNAK GQGYGDQIV ENST00000403734-ENST00000257247 HLA-A*02:01 None 0 0 5720.512 17.000 NA 0 Poor Pending -45.HNRNPUL2-AHNAK.ENST00000301785-ENST00000257247.inframe_fusion.30 HNRNPUL2-AHNAK GQGYGDQIV ENST00000301785-ENST00000257247 HLA-A*02:01 None 0 0 5720.512 17.000 NA 0 Poor Pending -72.SOX6-SOX6.ENST00000396356-ENST00000396356.inframe_fusion.56 SOX6-SOX6 LLGEIKDSS ENST00000396356-ENST00000396356 HLA-A*02:01 None 0 0 5825.477 18.000 NA 49 Poor Pending -24.LTBP1-BIRC6.ENST00000404816-ENST00000421745.inframe_fusion.60 LTBP1-BIRC6 LPQQIHSHD ENST00000404816-ENST00000421745 HLA-B*35:01 None 0 0 6591.350 7.674 NA 11 Poor Pending -89.CAMK2D-LUC7L2.ENST00000683023-ENST00000541170.inframe_fusion.34 CAMK2D-LUC7L2 KLSARGDTT ENST00000683023-ENST00000541170 HLA-A*02:01 None 0 0 6609.920 17.000 NA 2 Poor Pending -93.CAMK2D-FMC1-LUC7L2.ENST00000683023-ENST00000541515.inframe_fusion.34 CAMK2D-FMC1-LUC7L2 KLSARGDTT ENST00000683023-ENST00000541515 HLA-A*02:01 None 0 0 6609.920 17.000 NA 2 Poor Pending -74.IL13RA1-IL13RA1.ENST00000652600-ENST00000652600.frameshift_fusion.49 IL13RA1-IL13RA1 QTETHNVFYA ENST00000652600-ENST00000652600 HLA-A*02:01 None 0 0 7021.855 19.000 NA 17 Poor Pending -4.PLA2R1-RBMS1.ENST00000283243-ENST00000348849.inframe_fusion.72 PLA2R1-RBMS1 AQQEQDPTNL ENST00000283243-ENST00000348849 HLA-A*02:01 None 0 0 7061.555 13.000 NA 87 Poor Pending -82.ODF2-SPTAN1.ENST00000393533-ENST00000372731.frameshift_fusion.9 ODF2-SPTAN1 QQGPHQNRPV ENST00000393533-ENST00000372731 HLA-A*02:01 None 0 0 7637.935 18.000 NA 1 Poor Pending -25.WDR1-ENSG00000271544(16068),RAF1P1(623).ENST00000382452-..frameshift_fusion.35 WDR1-ENSG00000271544(16068),RAF1P1(623) FKFTVGGEL ENST00000382452-. HLA-B*35:01 None 0 0 8287.945 7.440 NA 11 Poor Pending -52.PDLIM5-ENSG00000287552.ENST00000615540-ENST00000667612.frameshift_fusion.47 PDLIM5-ENSG00000287552 NLNCRLLKS ENST00000615540-ENST00000667612 HLA-A*02:01 None 0 0 9285.000 19.000 NA 14 Poor Pending -3.EIF3K-CYP39A1.ENST00000614624-ENST00000275016.inframe_fusion.13 EIF3K-CYP39A1 KSSIPKNVFL ENST00000614624-ENST00000275016 HLA-A*02:01 None 0 0 10046.965 20.000 NA 1 Poor Pending -41.HNRNPUL2-BSCL2-AHNAK.ENST00000403734-ENST00000257247.frameshift_fusion.51 HNRNPUL2-BSCL2-AHNAK RLRGREEGGA ENST00000403734-ENST00000257247 HLA-A*02:01 None 0 0 12373.641 25.000 NA 40 Poor Pending -44.HNRNPUL2-AHNAK.ENST00000301785-ENST00000257247.frameshift_fusion.51 HNRNPUL2-AHNAK RLRGREEGGA ENST00000301785-ENST00000257247 HLA-A*02:01 None 0 0 12373.641 25.000 NA 40 Poor Pending -86.RALGPS2-TTC32.ENST00000367634-ENST00000333610.frameshift_fusion.69 RALGPS2-TTC32 CQSNKQQQM ENST00000367634-ENST00000333610 HLA-B*35:01 None 0 0 13864.710 15.000 NA 2 Poor Pending -34.EFTUD2-KIF18B.ENST00000426333-ENST00000593135.frameshift_fusion.44 EFTUD2-KIF18B KFFGEFTG ENST00000426333-ENST00000593135 HLA-A*02:01 None 0 0 15510.645 55.500 NA 8 Poor Pending -6.UNC5C-STPG2-AS1.ENST00000453304-..frameshift_fusion.53 UNC5C-STPG2-AS1 PPEGIPVAEI ENST00000453304-. HLA-B*35:01 None 0 0 21696.435 22.000 NA 59 Poor Pending -43.HNRNPUL2-BSCL2-AHNAK.ENST00000403734-ENST00000257247.frameshift_fusion.50 HNRNPUL2-BSCL2-AHNAK GQGYDGEG ENST00000403734-ENST00000257247 HLA-A*02:01 None 0 0 33260.560 69.486 NA 0 Poor Pending -46.HNRNPUL2-AHNAK.ENST00000301785-ENST00000257247.frameshift_fusion.50 HNRNPUL2-AHNAK GQGYDGEG ENST00000301785-ENST00000257247 HLA-A*02:01 None 0 0 33260.560 69.486 NA 0 Poor Pending -91.STRBP-RHEB.ENST00000348403-ENST00000262187.frameshift_fusion.40 15 1 STRBP-RHEB FMLGDVILL ENST00000348403-ENST00000262187 HLA-A*02:01 None 15 5 3.680 0.022 NA 2 LowReadSupport Pending -21.E2F3-PKD2.ENST00000535432-ENST00000506727.frameshift_fusion.6 6 9 E2F3-PKD2 SLCEGCWYV ENST00000535432-ENST00000506727 HLA-A*02:01 None 15 5 3.740 0.110 NA 1 LowReadSupport Pending -33.EEFSEC-KPNA1.ENST00000254730-ENST00000344337.frameshift_fusion.39 5 1 EEFSEC-KPNA1 SLIRTIIGV ENST00000254730-ENST00000344337 HLA-A*02:01 None 6 3 12.281 0.090 NA 2 LowReadSupport Pending -51.BGN-ATP2B3.ENST00000331595-ENST00000263519.frameshift_fusion.12 10 6 BGN-ATP2B3 ALALRFWNL ENST00000331595-ENST00000263519 HLA-A*02:01 None 15 4 36.875 0.580 NA 0 LowReadSupport Pending -69.B4GALT1-ENSG00000271677(54939),ENOX2(20912).ENST00000535206-..frameshift_fusion.22 6 5 B4GALT1-ENSG00000271677(54939),ENOX2(20912) FVELLTPPF ENST00000535206-. HLA-B*35:01 None 11 5 40.180 0.600 NA 3 LowReadSupport Pending -37.MLLT10-AMD1P1.ENST00000631589-ENST00000457220.frameshift_fusion.49 14 3 MLLT10-AMD1P1 LLQDLSLGSV ENST00000631589-ENST00000457220 HLA-A*02:01 None 15 4 50.210 0.440 NA 4 LowReadSupport Pending -65.DGLUCY-ENSG00000227482(74932),ENSG00000214669(1207).ENST00000256324-..frameshift_fusion.69 2 2 DGLUCY-ENSG00000227482(74932),ENSG00000214669(1207) GAISETSIY ENST00000256324-. HLA-B*35:01 None 4 1 74.150 0.800 NA 4 LowReadSupport Pending -87.CRTC3-SNRPC.ENST00000268184-ENST00000244520.frameshift_fusion.48 4 CRTC3-SNRPC SPWYDASTPY ENST00000268184-ENST00000244520 HLA-B*35:01 None 4 1 107.216 0.098 NA 2 LowReadSupport Pending -66.DEAF1-ENSG00000269915.ENST00000683307-..frameshift_fusion.43 11 7 DEAF1-ENSG00000269915 YPLCSLSPV ENST00000683307-. HLA-B*35:01 None 15 2 120.514 0.790 NA 4 LowReadSupport Pending -67.PGAP1-PAX8.ENST00000354764-ENST00000681162.frameshift_fusion.11 9 7 PGAP1-PAX8 QILGQIFSA ENST00000354764-ENST00000681162 HLA-A*02:01 None 15 3 167.905 0.950 NA 3 LowReadSupport Pending -90.ASXL1-IMPDH2.ENST00000375687-ENST00000678920.frameshift_fusion.56 5 4 ASXL1-IMPDH2 ALTGGIGFI ENST00000375687-ENST00000678920 HLA-A*02:01 None 8 3 172.660 1.400 NA 2 LowReadSupport Pending -19.PDIA5-ENSG00000280441.ENST00000316218-ENST00000651813.frameshift_fusion.51 4 8 PDIA5-ENSG00000280441 MTRVGTTEF ENST00000316218-ENST00000651813 HLA-B*35:01 None 12 3 210.280 1.800 NA 1 LowReadSupport Pending -50.BGN-ATP2B3.ENST00000331595-ENST00000263519.frameshift_fusion.27 6 7 BGN-ATP2B3 KLYRCPRLAA ENST00000331595-ENST00000263519 HLA-A*02:01 None 12 2 249.185 2.300 NA 1 LowReadSupport Pending -63.UNC5C-STPG2.ENST00000453304-ENST00000522676.frameshift_fusion.18 3 5 UNC5C-STPG2 SPRGLRTYY ENST00000453304-ENST00000522676 HLA-B*35:01 None 8 1 364.050 1.970 NA 1 LowReadSupport Pending -70.GRIK2-GRIK2.ENST00000421544-..frameshift_fusion.34 1 GRIK2-GRIK2 SLKEEGLEKV ENST00000421544-. HLA-A*02:01 None 1 1 384.720 2.600 NA 2 LowReadSupport Pending -83.RBM46-RBM46.ENST00000281722-ENST00000281722.inframe_fusion.46 8 1 RBM46-RBM46 TLLHLGTATM ENST00000281722-ENST00000281722 HLA-A*02:01 None 8 1 441.230 3.000 NA 3 LowReadSupport Pending +58.AGPAT5-MCPH1-AS1.ENST00000285518-..frameshift_fusion.68 1 AGPAT5-MCPH1-AS1 FFENYTGVQV ENST00000285518-. HLA-A*02:01 None 1 0 5086.370 8.000 NA 8 Poor Pending +81.ODF2-SPTAN1.ENST00000604420-ENST00000372731.frameshift_fusion.11 1 ODF2-SPTAN1 SSSGGSPRPV ENST00000604420-ENST00000372731 HLA-A*02:01 None 1 0 5439.649 14.000 NA 3 Poor Pending +42.HNRNPUL2-BSCL2-AHNAK.ENST00000403734-ENST00000257247.inframe_fusion.30 1 HNRNPUL2-BSCL2-AHNAK GQGYGDQIV ENST00000403734-ENST00000257247 HLA-A*02:01 None 1 0 5720.512 17.000 NA 0 Poor Pending +45.HNRNPUL2-AHNAK.ENST00000301785-ENST00000257247.inframe_fusion.30 1 HNRNPUL2-AHNAK GQGYGDQIV ENST00000301785-ENST00000257247 HLA-A*02:01 None 1 0 5720.512 17.000 NA 0 Poor Pending +72.SOX6-SOX6.ENST00000396356-ENST00000396356.inframe_fusion.56 1 SOX6-SOX6 LLGEIKDSS ENST00000396356-ENST00000396356 HLA-A*02:01 None 1 0 5825.477 18.000 NA 49 Poor Pending +24.LTBP1-BIRC6.ENST00000404816-ENST00000421745.inframe_fusion.60 1 LTBP1-BIRC6 LPQQIHSHD ENST00000404816-ENST00000421745 HLA-B*35:01 None 1 0 6591.350 7.674 NA 11 Poor Pending +89.CAMK2D-LUC7L2.ENST00000683023-ENST00000541170.inframe_fusion.34 1 CAMK2D-LUC7L2 KLSARGDTT ENST00000683023-ENST00000541170 HLA-A*02:01 None 1 0 6609.920 17.000 NA 2 Poor Pending +93.CAMK2D-FMC1-LUC7L2.ENST00000683023-ENST00000541515.inframe_fusion.34 1 CAMK2D-FMC1-LUC7L2 KLSARGDTT ENST00000683023-ENST00000541515 HLA-A*02:01 None 1 0 6609.920 17.000 NA 2 Poor Pending +74.IL13RA1-IL13RA1.ENST00000652600-ENST00000652600.frameshift_fusion.49 1 IL13RA1-IL13RA1 QTETHNVFYA ENST00000652600-ENST00000652600 HLA-A*02:01 None 1 0 7021.855 19.000 NA 17 Poor Pending +4.PLA2R1-RBMS1.ENST00000283243-ENST00000348849.inframe_fusion.72 1 PLA2R1-RBMS1 AQQEQDPTNL ENST00000283243-ENST00000348849 HLA-A*02:01 None 1 0 7061.555 13.000 NA 87 Poor Pending +82.ODF2-SPTAN1.ENST00000393533-ENST00000372731.frameshift_fusion.9 1 ODF2-SPTAN1 QQGPHQNRPV ENST00000393533-ENST00000372731 HLA-A*02:01 None 1 0 7637.935 18.000 NA 1 Poor Pending +25.WDR1-ENSG00000271544(16068),RAF1P1(623).ENST00000382452-..frameshift_fusion.35 1 WDR1-ENSG00000271544(16068),RAF1P1(623) FKFTVGGEL ENST00000382452-. HLA-B*35:01 None 1 0 8287.945 7.440 NA 11 Poor Pending +52.PDLIM5-ENSG00000287552.ENST00000615540-ENST00000667612.frameshift_fusion.47 1 PDLIM5-ENSG00000287552 NLNCRLLKS ENST00000615540-ENST00000667612 HLA-A*02:01 None 1 0 9285.000 19.000 NA 14 Poor Pending +3.EIF3K-CYP39A1.ENST00000614624-ENST00000275016.inframe_fusion.13 1 EIF3K-CYP39A1 KSSIPKNVFL ENST00000614624-ENST00000275016 HLA-A*02:01 None 1 0 10046.965 20.000 NA 1 Poor Pending +41.HNRNPUL2-BSCL2-AHNAK.ENST00000403734-ENST00000257247.frameshift_fusion.51 1 HNRNPUL2-BSCL2-AHNAK RLRGREEGGA ENST00000403734-ENST00000257247 HLA-A*02:01 None 1 0 12373.641 25.000 NA 40 Poor Pending +44.HNRNPUL2-AHNAK.ENST00000301785-ENST00000257247.frameshift_fusion.51 1 HNRNPUL2-AHNAK RLRGREEGGA ENST00000301785-ENST00000257247 HLA-A*02:01 None 1 0 12373.641 25.000 NA 40 Poor Pending +86.RALGPS2-TTC32.ENST00000367634-ENST00000333610.frameshift_fusion.69 1 RALGPS2-TTC32 CQSNKQQQM ENST00000367634-ENST00000333610 HLA-B*35:01 None 1 0 13864.710 15.000 NA 2 Poor Pending +34.EFTUD2-KIF18B.ENST00000426333-ENST00000593135.frameshift_fusion.44 1 EFTUD2-KIF18B KFFGEFTG ENST00000426333-ENST00000593135 HLA-A*02:01 None 1 0 15510.645 55.500 NA 8 Poor Pending +6.UNC5C-STPG2-AS1.ENST00000453304-..frameshift_fusion.53 1 UNC5C-STPG2-AS1 PPEGIPVAEI ENST00000453304-. HLA-B*35:01 None 1 0 21696.435 22.000 NA 59 Poor Pending +43.HNRNPUL2-BSCL2-AHNAK.ENST00000403734-ENST00000257247.frameshift_fusion.50 1 HNRNPUL2-BSCL2-AHNAK GQGYDGEG ENST00000403734-ENST00000257247 HLA-A*02:01 None 1 0 33260.560 69.486 NA 0 Poor Pending +46.HNRNPUL2-AHNAK.ENST00000301785-ENST00000257247.frameshift_fusion.50 1 HNRNPUL2-AHNAK GQGYDGEG ENST00000301785-ENST00000257247 HLA-A*02:01 None 1 0 33260.560 69.486 NA 0 Poor Pending diff --git a/pvactools/tools/pvacfuse/example_data/arriba_results/MHC_Class_II/Test.all_epitopes.aggregated.tsv b/pvactools/tools/pvacfuse/example_data/arriba_results/MHC_Class_II/Test.all_epitopes.aggregated.tsv index 769757e7..6f2e28d2 100644 --- a/pvactools/tools/pvacfuse/example_data/arriba_results/MHC_Class_II/Test.all_epitopes.aggregated.tsv +++ b/pvactools/tools/pvacfuse/example_data/arriba_results/MHC_Class_II/Test.all_epitopes.aggregated.tsv @@ -32,6 +32,25 @@ ID DRB1*11:01 Gene Best Peptide Best Transcript Allele Prob Pos Num Included Pep 25.WDR1-ENSG00000271544(16068),RAF1P1(623).ENST00000382452-..frameshift_fusion.35 3 WDR1-ENSG00000271544(16068),RAF1P1(623) EGPPFKFKFTVGGEL ENST00000382452-. DRB1*11:01 None 3 1 439.025 15.000 NA 11 Pass Pending 30.MFSD3-MROH1.ENST00000301327-ENST00000326134.inframe_fusion.48 12 MFSD3-MROH1 GMMRCSQLAPRALQI ENST00000301327-ENST00000326134 DRB1*11:01 None 12 1 454.615 28.000 NA 9 Pass Pending 73.FRMD3-FRMD3.ENST00000376438-ENST00000376438.inframe_fusion.40 10 FRMD3-FRMD3 PLLLLLLESGVPLPK ENST00000376438-ENST00000376438 DRB1*11:01 None 10 1 489.110 24.000 NA 30 Pass Pending +69.B4GALT1-ENSG00000271677(54939),ENOX2(20912).ENST00000535206-..frameshift_fusion.22 15 B4GALT1-ENSG00000271677(54939),ENOX2(20912) MGHFLYIRKNDSVDT ENST00000535206-. DRB1*11:01 None 15 15 17.400 0.590 NA 3 LowReadSupport Pending +50.BGN-ATP2B3.ENST00000331595-ENST00000263519.frameshift_fusion.27 15 BGN-ATP2B3 LRYSKLYRCPRLAAF ENST00000331595-ENST00000263519 DRB1*11:01 None 15 11 26.300 1.500 NA 1 LowReadSupport Pending +89.CAMK2D-LUC7L2.ENST00000683023-ENST00000541170.inframe_fusion.34 10 CAMK2D-LUC7L2 AAKIINTKKLSARGD ENST00000683023-ENST00000541170 DRB1*11:01 None 10 5 27.595 1.500 NA 2 LowReadSupport Pending +93.CAMK2D-FMC1-LUC7L2.ENST00000683023-ENST00000541515.inframe_fusion.34 10 CAMK2D-FMC1-LUC7L2 AAKIINTKKLSARGD ENST00000683023-ENST00000541515 DRB1*11:01 None 10 5 27.595 1.500 NA 2 LowReadSupport Pending +40.BRINP2-ASTN1.ENST00000361539-..frameshift_fusion.50 15 BRINP2-ASTN1 RYRIYSQSRRWTCLF ENST00000361539-. DRB1*11:01 None 15 12 38.190 3.000 NA 3 LowReadSupport Pending +51.BGN-ATP2B3.ENST00000331595-ENST00000263519.frameshift_fusion.12 15 BGN-ATP2B3 AACVFSRVKALALRF ENST00000331595-ENST00000263519 DRB1*11:01 None 15 15 38.300 2.700 NA 0 LowReadSupport Pending +80.FBXW10-FBXW10.ENST00000308799-ENST00000308799.frameshift_fusion.26 12 FBXW10-FBXW10 GSYDLSIRAQSRHHR ENST00000308799-ENST00000308799 DRB1*11:01 None 12 9 38.915 1.800 NA 4 LowReadSupport Pending +19.PDIA5-ENSG00000280441.ENST00000316218-ENST00000651813.frameshift_fusion.51 15 PDIA5-ENSG00000280441 DIVEWLKKRHLTCRG ENST00000316218-ENST00000651813 DRB1*11:01 None 15 10 46.600 5.800 NA 1 LowReadSupport Pending +91.STRBP-RHEB.ENST00000348403-ENST00000262187.frameshift_fusion.40 15 STRBP-RHEB DVILLQSLRTLGIYS ENST00000348403-ENST00000262187 DRB1*11:01 None 15 7 58.695 4.200 NA 2 LowReadSupport Pending +71.TMEM129-GUCY1B1.ENST00000303277-ENST00000264424.frameshift_fusion.44 15 TMEM129-GUCY1B1 DIWIRILSLESSKQW ENST00000303277-ENST00000264424 DRB1*11:01 None 15 10 74.855 6.000 NA 2 LowReadSupport Pending +83.RBM46-RBM46.ENST00000281722-ENST00000281722.inframe_fusion.46 10 RBM46-RBM46 AQFTLLHLGTATMNE ENST00000281722-ENST00000281722 DRB1*11:01 None 10 7 100.025 9.100 NA 3 LowReadSupport Pending +33.EEFSEC-KPNA1.ENST00000254730-ENST00000344337.frameshift_fusion.39 15 EEFSEC-KPNA1 KCCYSRRRNRRRSYV ENST00000254730-ENST00000344337 DRB1*11:01 None 15 14 102.100 7.700 NA 2 LowReadSupport Pending +21.E2F3-PKD2.ENST00000535432-ENST00000506727.frameshift_fusion.6 12 E2F3-PKD2 GCWYVNVCRFPWGVH ENST00000535432-ENST00000506727 DRB1*11:01 None 12 7 103.000 8.100 NA 1 LowReadSupport Pending +67.PGAP1-PAX8.ENST00000354764-ENST00000681162.frameshift_fusion.11 15 PGAP1-PAX8 AGWMGTNFRRRRDTG ENST00000354764-ENST00000681162 DRB1*11:01 None 15 4 285.500 19.000 NA 3 LowReadSupport Pending +90.ASXL1-IMPDH2.ENST00000375687-ENST00000678920.frameshift_fusion.56 15 ASXL1-IMPDH2 TPEFQANEVRKVKKY ENST00000375687-ENST00000678920 DRB1*11:01 None 15 6 298.140 15.000 NA 2 LowReadSupport Pending +37.MLLT10-AMD1P1.ENST00000631589-ENST00000457220.frameshift_fusion.49 15 MLLT10-AMD1P1 LGIFALLQDLSLGSV ENST00000631589-ENST00000457220 DRB1*11:01 None 15 6 390.745 26.000 NA 4 LowReadSupport Pending +3.EIF3K-CYP39A1.ENST00000614624-ENST00000275016.inframe_fusion.13 13 EIF3K-CYP39A1 ITGFEDSVRKSSIPK ENST00000614624-ENST00000275016 DRB1*11:01 None 13 1 426.055 16.000 NA 1 LowReadSupport Pending +65.DGLUCY-ENSG00000227482(74932),ENSG00000214669(1207).ENST00000256324-..frameshift_fusion.69 9 DGLUCY-ENSG00000227482(74932),ENSG00000214669(1207) ISETSIYKMLQDTAG ENST00000256324-. DRB1*11:01 None 9 1 434.850 24.000 NA 4 LowReadSupport Pending +66.DEAF1-ENSG00000269915.ENST00000683307-..frameshift_fusion.43 15 DEAF1-ENSG00000269915 GGCHRLYPLCSLSPV ENST00000683307-. DRB1*11:01 None 15 1 463.700 25.000 NA 4 LowReadSupport Pending 72.SOX6-SOX6.ENST00000396356-ENST00000396356.inframe_fusion.56 7 SOX6-SOX6 KDSSCMEKLLSKDWK ENST00000396356-ENST00000396356 DRB1*11:01 None 7 0 507.040 27.000 NA 49 Poor Pending 68.SHQ1-HNRNPA3P8(24281),ENSG00000242586(200566).ENST00000325599-..frameshift_fusion.64 3 SHQ1-HNRNPA3P8(24281),ENSG00000242586(200566) ISDYCVWIQKVNQVR ENST00000325599-. DRB1*11:01 None 3 0 528.680 28.000 NA 3 Poor Pending 57.GCLM-ABCA4.ENST00000370238-ENST00000370225.frameshift_fusion.61 13 GCLM-ABCA4 QFDIQLLTHNDPKAS ENST00000370238-ENST00000370225 DRB1*11:01 None 13 0 558.995 17.760 NA 8 Poor Pending @@ -60,28 +79,9 @@ ID DRB1*11:01 Gene Best Peptide Best Transcript Allele Prob Pos Num Included Pep 46.HNRNPUL2-AHNAK.ENST00000301785-ENST00000257247.frameshift_fusion.50 2 HNRNPUL2-AHNAK NKRNRQNRSRGQGYD ENST00000301785-ENST00000257247 DRB1*11:01 None 2 0 3727.845 51.000 NA 0 Poor Pending 87.CRTC3-SNRPC.ENST00000268184-ENST00000244520.frameshift_fusion.48 2 CRTC3-SNRPC SPWYDASTPYGGPSH ENST00000268184-ENST00000244520 DRB1*11:01 None 2 0 4070.710 52.000 NA 2 Poor Pending 92.CLTC-LAMC1.ENST00000621829-ENST00000258341.inframe_fusion.55 2 CLTC-LAMC1 GARKANSTRTWKDSQ ENST00000621829-ENST00000258341 DRB1*11:01 None 2 0 4320.290 61.000 NA 2 Poor Pending -62.UNC5C-STPG2.ENST00000453304-ENST00000506482.frameshift_fusion.79 UNC5C-STPG2 IPVAEVEVQLLQHQY ENST00000453304-ENST00000506482 DRB1*11:01 None 0 0 5301.650 69.000 NA 5 Poor Pending -88.RAPGEF1-NUB1.ENST00000372195-ENST00000468404.frameshift_fusion.39 RAPGEF1-NUB1 WSDQVMLEGVNSDPY ENST00000372195-ENST00000468404 DRB1*11:01 None 0 0 7021.200 77.000 NA 2 Poor Pending -59.ATAD1-ENSG00000224745.ENST00000680388-..frameshift_fusion.34 ATAD1-ENSG00000224745 MSLWDGLDTDHSCQV ENST00000680388-. DRB1*11:01 None 0 0 8431.535 65.000 NA 7 Poor Pending -24.LTBP1-BIRC6.ENST00000404816-ENST00000421745.inframe_fusion.60 LTBP1-BIRC6 KPSVGLPQQIHSHDD ENST00000404816-ENST00000421745 DRB1*11:01 None 0 0 9364.975 75.000 NA 11 Poor Pending -17.ATAD1-PTEN.ENST00000680388-..frameshift_fusion.57 ATAD1-PTEN LWDGLDTDHSCQATR ENST00000680388-. DRB1*11:01 None 0 0 9615.570 83.000 NA 16 Poor Pending -6.UNC5C-STPG2-AS1.ENST00000453304-..frameshift_fusion.53 UNC5C-STPG2-AS1 LLQCRPPEGIPVAEI ENST00000453304-. DRB1*11:01 None 0 0 13457.800 87.000 NA 59 Poor Pending -69.B4GALT1-ENSG00000271677(54939),ENOX2(20912).ENST00000535206-..frameshift_fusion.22 15 B4GALT1-ENSG00000271677(54939),ENOX2(20912) MGHFLYIRKNDSVDT ENST00000535206-. DRB1*11:01 None 15 15 17.400 0.590 NA 3 LowReadSupport Pending -50.BGN-ATP2B3.ENST00000331595-ENST00000263519.frameshift_fusion.27 15 BGN-ATP2B3 LRYSKLYRCPRLAAF ENST00000331595-ENST00000263519 DRB1*11:01 None 15 11 26.300 1.500 NA 1 LowReadSupport Pending -89.CAMK2D-LUC7L2.ENST00000683023-ENST00000541170.inframe_fusion.34 10 CAMK2D-LUC7L2 AAKIINTKKLSARGD ENST00000683023-ENST00000541170 DRB1*11:01 None 10 5 27.595 1.500 NA 2 LowReadSupport Pending -93.CAMK2D-FMC1-LUC7L2.ENST00000683023-ENST00000541515.inframe_fusion.34 10 CAMK2D-FMC1-LUC7L2 AAKIINTKKLSARGD ENST00000683023-ENST00000541515 DRB1*11:01 None 10 5 27.595 1.500 NA 2 LowReadSupport Pending -40.BRINP2-ASTN1.ENST00000361539-..frameshift_fusion.50 15 BRINP2-ASTN1 RYRIYSQSRRWTCLF ENST00000361539-. DRB1*11:01 None 15 12 38.190 3.000 NA 3 LowReadSupport Pending -51.BGN-ATP2B3.ENST00000331595-ENST00000263519.frameshift_fusion.12 15 BGN-ATP2B3 AACVFSRVKALALRF ENST00000331595-ENST00000263519 DRB1*11:01 None 15 15 38.300 2.700 NA 0 LowReadSupport Pending -80.FBXW10-FBXW10.ENST00000308799-ENST00000308799.frameshift_fusion.26 12 FBXW10-FBXW10 GSYDLSIRAQSRHHR ENST00000308799-ENST00000308799 DRB1*11:01 None 12 9 38.915 1.800 NA 4 LowReadSupport Pending -19.PDIA5-ENSG00000280441.ENST00000316218-ENST00000651813.frameshift_fusion.51 15 PDIA5-ENSG00000280441 DIVEWLKKRHLTCRG ENST00000316218-ENST00000651813 DRB1*11:01 None 15 10 46.600 5.800 NA 1 LowReadSupport Pending -91.STRBP-RHEB.ENST00000348403-ENST00000262187.frameshift_fusion.40 15 STRBP-RHEB DVILLQSLRTLGIYS ENST00000348403-ENST00000262187 DRB1*11:01 None 15 7 58.695 4.200 NA 2 LowReadSupport Pending -71.TMEM129-GUCY1B1.ENST00000303277-ENST00000264424.frameshift_fusion.44 15 TMEM129-GUCY1B1 DIWIRILSLESSKQW ENST00000303277-ENST00000264424 DRB1*11:01 None 15 10 74.855 6.000 NA 2 LowReadSupport Pending -83.RBM46-RBM46.ENST00000281722-ENST00000281722.inframe_fusion.46 10 RBM46-RBM46 AQFTLLHLGTATMNE ENST00000281722-ENST00000281722 DRB1*11:01 None 10 7 100.025 9.100 NA 3 LowReadSupport Pending -33.EEFSEC-KPNA1.ENST00000254730-ENST00000344337.frameshift_fusion.39 15 EEFSEC-KPNA1 KCCYSRRRNRRRSYV ENST00000254730-ENST00000344337 DRB1*11:01 None 15 14 102.100 7.700 NA 2 LowReadSupport Pending -21.E2F3-PKD2.ENST00000535432-ENST00000506727.frameshift_fusion.6 12 E2F3-PKD2 GCWYVNVCRFPWGVH ENST00000535432-ENST00000506727 DRB1*11:01 None 12 7 103.000 8.100 NA 1 LowReadSupport Pending -67.PGAP1-PAX8.ENST00000354764-ENST00000681162.frameshift_fusion.11 15 PGAP1-PAX8 AGWMGTNFRRRRDTG ENST00000354764-ENST00000681162 DRB1*11:01 None 15 4 285.500 19.000 NA 3 LowReadSupport Pending -90.ASXL1-IMPDH2.ENST00000375687-ENST00000678920.frameshift_fusion.56 15 ASXL1-IMPDH2 TPEFQANEVRKVKKY ENST00000375687-ENST00000678920 DRB1*11:01 None 15 6 298.140 15.000 NA 2 LowReadSupport Pending -37.MLLT10-AMD1P1.ENST00000631589-ENST00000457220.frameshift_fusion.49 15 MLLT10-AMD1P1 LGIFALLQDLSLGSV ENST00000631589-ENST00000457220 DRB1*11:01 None 15 6 390.745 26.000 NA 4 LowReadSupport Pending -3.EIF3K-CYP39A1.ENST00000614624-ENST00000275016.inframe_fusion.13 13 EIF3K-CYP39A1 ITGFEDSVRKSSIPK ENST00000614624-ENST00000275016 DRB1*11:01 None 13 1 426.055 16.000 NA 1 LowReadSupport Pending -65.DGLUCY-ENSG00000227482(74932),ENSG00000214669(1207).ENST00000256324-..frameshift_fusion.69 9 DGLUCY-ENSG00000227482(74932),ENSG00000214669(1207) ISETSIYKMLQDTAG ENST00000256324-. DRB1*11:01 None 9 1 434.850 24.000 NA 4 LowReadSupport Pending -66.DEAF1-ENSG00000269915.ENST00000683307-..frameshift_fusion.43 15 DEAF1-ENSG00000269915 GGCHRLYPLCSLSPV ENST00000683307-. DRB1*11:01 None 15 1 463.700 25.000 NA 4 LowReadSupport Pending +62.UNC5C-STPG2.ENST00000453304-ENST00000506482.frameshift_fusion.79 1 UNC5C-STPG2 IPVAEVEVQLLQHQY ENST00000453304-ENST00000506482 DRB1*11:01 None 1 0 5301.650 69.000 NA 5 Poor Pending +88.RAPGEF1-NUB1.ENST00000372195-ENST00000468404.frameshift_fusion.39 1 RAPGEF1-NUB1 WSDQVMLEGVNSDPY ENST00000372195-ENST00000468404 DRB1*11:01 None 1 0 7021.200 77.000 NA 2 Poor Pending +59.ATAD1-ENSG00000224745.ENST00000680388-..frameshift_fusion.34 1 ATAD1-ENSG00000224745 MSLWDGLDTDHSCQV ENST00000680388-. DRB1*11:01 None 1 0 8431.535 65.000 NA 7 Poor Pending +24.LTBP1-BIRC6.ENST00000404816-ENST00000421745.inframe_fusion.60 1 LTBP1-BIRC6 KPSVGLPQQIHSHDD ENST00000404816-ENST00000421745 DRB1*11:01 None 1 0 9364.975 75.000 NA 11 Poor Pending +17.ATAD1-PTEN.ENST00000680388-..frameshift_fusion.57 1 ATAD1-PTEN LWDGLDTDHSCQATR ENST00000680388-. DRB1*11:01 None 1 0 9615.570 83.000 NA 16 Poor Pending +6.UNC5C-STPG2-AS1.ENST00000453304-..frameshift_fusion.53 1 UNC5C-STPG2-AS1 LLQCRPPEGIPVAEI ENST00000453304-. DRB1*11:01 None 1 0 13457.800 87.000 NA 59 Poor Pending diff --git a/pvactools/tools/pvacfuse/example_data/arriba_results/combined/Test.all_epitopes.aggregated.tsv b/pvactools/tools/pvacfuse/example_data/arriba_results/combined/Test.all_epitopes.aggregated.tsv index 6b0876b7..2331f3ce 100644 --- a/pvactools/tools/pvacfuse/example_data/arriba_results/combined/Test.all_epitopes.aggregated.tsv +++ b/pvactools/tools/pvacfuse/example_data/arriba_results/combined/Test.all_epitopes.aggregated.tsv @@ -41,30 +41,6 @@ ID DRB1*11:01 A*02:01 B*35:01 Gene Best Peptide Best Transcript Allele Prob Pos 7.DTNB-Y_RNA(12184),ASXL2(24381).ENST00000288642-..frameshift_fusion.22 4 2 DTNB-Y_RNA(12184),ASXL2(24381) RQLFIEMLI ENST00000288642-. HLA-A*02:01 None 6 1 401.060 3.600 NA 53 Pass Pending 8.PTEN-MED6P1(8171),ENSG00000275015(201135).ENST00000371953-..frameshift_fusion.52 5 3 5 PTEN-MED6P1(8171),ENSG00000275015(201135) TCNAVWSSY ENST00000371953-. HLA-B*35:01 None 13 1 438.793 0.848 NA 49 Pass Pending 25.WDR1-ENSG00000271544(16068),RAF1P1(623).ENST00000382452-..frameshift_fusion.35 3 WDR1-ENSG00000271544(16068),RAF1P1(623) EGPPFKFKFTVGGEL ENST00000382452-. DRB1*11:01 None 3 1 439.025 15.000 NA 11 Pass Pending -72.SOX6-SOX6.ENST00000396356-ENST00000396356.inframe_fusion.56 7 SOX6-SOX6 KDSSCMEKLLSKDWK ENST00000396356-ENST00000396356 DRB1*11:01 None 7 0 507.040 27.000 NA 49 Poor Pending -68.SHQ1-HNRNPA3P8(24281),ENSG00000242586(200566).ENST00000325599-..frameshift_fusion.64 3 1 SHQ1-HNRNPA3P8(24281),ENSG00000242586(200566) ISDYCVWIQKVNQVR ENST00000325599-. DRB1*11:01 None 4 0 528.680 28.000 NA 3 Poor Pending -86.RALGPS2-TTC32.ENST00000367634-ENST00000333610.frameshift_fusion.69 1 RALGPS2-TTC32 FKHLSAACQSNKQQQ ENST00000367634-ENST00000333610 DRB1*11:01 None 1 0 589.090 22.000 NA 2 Poor Pending -85.SSBP4-ELL.ENST00000348495-..frameshift_fusion.36 11 3 1 SSBP4-ELL QDYRQGLALPPRLEL ENST00000348495-. DRB1*11:01 None 15 0 623.550 32.000 NA 3 Poor Pending -84.ST3GAL4-KIRREL3.ENST00000444328-..frameshift_fusion.20 10 1 2 ST3GAL4-KIRREL3 KQAWGDSKV ENST00000444328-. HLA-A*02:01 None 13 0 630.930 4.600 NA 3 Poor Pending -32.KPNA1-EEFSEC.ENST00000344337-ENST00000254730.frameshift_fusion.33 4 2 KPNA1-EEFSEC IDAGVCRRLVELLMG ENST00000344337-ENST00000254730 DRB1*11:01 None 6 0 655.800 27.000 NA 8 Poor Pending -88.RAPGEF1-NUB1.ENST00000372195-ENST00000468404.frameshift_fusion.39 4 RAPGEF1-NUB1 MLEGVNSDPY ENST00000372195-ENST00000468404 HLA-B*35:01 None 4 0 664.640 1.000 NA 2 Poor Pending -38.TASP1-MACROD2.ENST00000337743-..frameshift_fusion.48 7 1 2 TASP1-MACROD2 RGGFVLVHADDAWRM ENST00000337743-. DRB1*11:01 None 10 0 694.250 11.610 NA 4 Poor Pending -52.PDLIM5-ENSG00000287552.ENST00000615540-ENST00000667612.frameshift_fusion.47 2 PDLIM5-ENSG00000287552 DNTKKANLNCRLLKS ENST00000615540-ENST00000667612 DRB1*11:01 None 2 0 749.000 31.000 NA 14 Poor Pending -61.FOSL2-BABAM2.ENST00000264716-ENST00000344773.inframe_fusion.34 3 1 1 FOSL2-BABAM2 GGQQVQYVIQGYHKR ENST00000264716-ENST00000344773 DRB1*11:01 None 5 0 768.510 21.000 NA 1 Poor Pending -58.AGPAT5-MCPH1-AS1.ENST00000285518-..frameshift_fusion.68 4 AGPAT5-MCPH1-AS1 MVLFFFENYTGVQVT ENST00000285518-. DRB1*11:01 None 4 0 998.875 36.000 NA 8 Poor Pending -62.UNC5C-STPG2.ENST00000453304-ENST00000506482.frameshift_fusion.79 1 3 UNC5C-STPG2 IPVAEVEVQL ENST00000453304-ENST00000506482 HLA-B*35:01 None 4 0 1158.735 0.960 NA 5 Poor Pending -17.ATAD1-PTEN.ENST00000680388-..frameshift_fusion.57 1 ATAD1-PTEN GLDTDHSCQA ENST00000680388-. HLA-A*02:01 None 1 0 2388.535 6.300 NA 16 Poor Pending -41.HNRNPUL2-BSCL2-AHNAK.ENST00000403734-ENST00000257247.frameshift_fusion.51 8 HNRNPUL2-BSCL2-AHNAK NKRNRQNRSRGQGYG ENST00000403734-ENST00000257247 DRB1*11:01 None 8 0 3057.800 52.000 NA 40 Poor Pending -42.HNRNPUL2-BSCL2-AHNAK.ENST00000403734-ENST00000257247.inframe_fusion.30 2 HNRNPUL2-BSCL2-AHNAK NKRNRQNRSRGQGYG ENST00000403734-ENST00000257247 DRB1*11:01 None 2 0 3057.800 52.000 NA 0 Poor Pending -44.HNRNPUL2-AHNAK.ENST00000301785-ENST00000257247.frameshift_fusion.51 8 HNRNPUL2-AHNAK NKRNRQNRSRGQGYG ENST00000301785-ENST00000257247 DRB1*11:01 None 8 0 3057.800 52.000 NA 40 Poor Pending -45.HNRNPUL2-AHNAK.ENST00000301785-ENST00000257247.inframe_fusion.30 2 HNRNPUL2-AHNAK NKRNRQNRSRGQGYG ENST00000301785-ENST00000257247 DRB1*11:01 None 2 0 3057.800 52.000 NA 0 Poor Pending -43.HNRNPUL2-BSCL2-AHNAK.ENST00000403734-ENST00000257247.frameshift_fusion.50 2 HNRNPUL2-BSCL2-AHNAK NKRNRQNRSRGQGYD ENST00000403734-ENST00000257247 DRB1*11:01 None 2 0 3727.845 51.000 NA 0 Poor Pending -46.HNRNPUL2-AHNAK.ENST00000301785-ENST00000257247.frameshift_fusion.50 2 HNRNPUL2-AHNAK NKRNRQNRSRGQGYD ENST00000301785-ENST00000257247 DRB1*11:01 None 2 0 3727.845 51.000 NA 0 Poor Pending -92.CLTC-LAMC1.ENST00000621829-ENST00000258341.inframe_fusion.55 2 1 CLTC-LAMC1 GARKANSTRTWKDSQ ENST00000621829-ENST00000258341 DRB1*11:01 None 3 0 4320.290 61.000 NA 2 Poor Pending -81.ODF2-SPTAN1.ENST00000604420-ENST00000372731.frameshift_fusion.11 ODF2-SPTAN1 SSSGGSPRPV ENST00000604420-ENST00000372731 HLA-A*02:01 None 0 0 5439.649 14.000 NA 3 Poor Pending -24.LTBP1-BIRC6.ENST00000404816-ENST00000421745.inframe_fusion.60 LTBP1-BIRC6 LPQQIHSHD ENST00000404816-ENST00000421745 HLA-B*35:01 None 0 0 6591.350 7.674 NA 11 Poor Pending -82.ODF2-SPTAN1.ENST00000393533-ENST00000372731.frameshift_fusion.9 ODF2-SPTAN1 QQGPHQNRPV ENST00000393533-ENST00000372731 HLA-A*02:01 None 0 0 7637.935 18.000 NA 1 Poor Pending -6.UNC5C-STPG2-AS1.ENST00000453304-..frameshift_fusion.53 UNC5C-STPG2-AS1 LLQCRPPEGIPVAEI ENST00000453304-. DRB1*11:01 None 0 0 13457.800 87.000 NA 59 Poor Pending 91.STRBP-RHEB.ENST00000348403-ENST00000262187.frameshift_fusion.40 7 8 1 STRBP-RHEB FMLGDVILL ENST00000348403-ENST00000262187 HLA-A*02:01 None 15 12 3.680 0.022 NA 2 LowReadSupport Pending 21.E2F3-PKD2.ENST00000535432-ENST00000506727.frameshift_fusion.6 7 4 4 E2F3-PKD2 SLCEGCWYV ENST00000535432-ENST00000506727 HLA-A*02:01 None 15 12 3.740 0.110 NA 1 LowReadSupport Pending 33.EEFSEC-KPNA1.ENST00000254730-ENST00000344337.frameshift_fusion.39 12 3 EEFSEC-KPNA1 SLIRTIIGV ENST00000254730-ENST00000344337 HLA-A*02:01 None 15 15 12.281 0.090 NA 2 LowReadSupport Pending @@ -87,3 +63,27 @@ ID DRB1*11:01 A*02:01 B*35:01 Gene Best Peptide Best Transcript Allele Prob Pos 63.UNC5C-STPG2.ENST00000453304-ENST00000522676.frameshift_fusion.18 9 3 3 UNC5C-STPG2 SPRGLRTYY ENST00000453304-ENST00000522676 HLA-B*35:01 None 15 1 364.050 1.970 NA 1 LowReadSupport Pending 70.GRIK2-GRIK2.ENST00000421544-..frameshift_fusion.34 9 1 GRIK2-GRIK2 SLKEEGLEKV ENST00000421544-. HLA-A*02:01 None 10 1 384.720 2.600 NA 2 LowReadSupport Pending 3.EIF3K-CYP39A1.ENST00000614624-ENST00000275016.inframe_fusion.13 13 EIF3K-CYP39A1 ITGFEDSVRKSSIPK ENST00000614624-ENST00000275016 DRB1*11:01 None 13 1 426.055 16.000 NA 1 LowReadSupport Pending +72.SOX6-SOX6.ENST00000396356-ENST00000396356.inframe_fusion.56 7 SOX6-SOX6 KDSSCMEKLLSKDWK ENST00000396356-ENST00000396356 DRB1*11:01 None 7 0 507.040 27.000 NA 49 Poor Pending +68.SHQ1-HNRNPA3P8(24281),ENSG00000242586(200566).ENST00000325599-..frameshift_fusion.64 3 1 SHQ1-HNRNPA3P8(24281),ENSG00000242586(200566) ISDYCVWIQKVNQVR ENST00000325599-. DRB1*11:01 None 4 0 528.680 28.000 NA 3 Poor Pending +86.RALGPS2-TTC32.ENST00000367634-ENST00000333610.frameshift_fusion.69 1 RALGPS2-TTC32 FKHLSAACQSNKQQQ ENST00000367634-ENST00000333610 DRB1*11:01 None 1 0 589.090 22.000 NA 2 Poor Pending +85.SSBP4-ELL.ENST00000348495-..frameshift_fusion.36 11 3 1 SSBP4-ELL QDYRQGLALPPRLEL ENST00000348495-. DRB1*11:01 None 15 0 623.550 32.000 NA 3 Poor Pending +84.ST3GAL4-KIRREL3.ENST00000444328-..frameshift_fusion.20 10 1 2 ST3GAL4-KIRREL3 KQAWGDSKV ENST00000444328-. HLA-A*02:01 None 13 0 630.930 4.600 NA 3 Poor Pending +32.KPNA1-EEFSEC.ENST00000344337-ENST00000254730.frameshift_fusion.33 4 2 KPNA1-EEFSEC IDAGVCRRLVELLMG ENST00000344337-ENST00000254730 DRB1*11:01 None 6 0 655.800 27.000 NA 8 Poor Pending +88.RAPGEF1-NUB1.ENST00000372195-ENST00000468404.frameshift_fusion.39 4 RAPGEF1-NUB1 MLEGVNSDPY ENST00000372195-ENST00000468404 HLA-B*35:01 None 4 0 664.640 1.000 NA 2 Poor Pending +38.TASP1-MACROD2.ENST00000337743-..frameshift_fusion.48 7 1 2 TASP1-MACROD2 RGGFVLVHADDAWRM ENST00000337743-. DRB1*11:01 None 10 0 694.250 11.610 NA 4 Poor Pending +52.PDLIM5-ENSG00000287552.ENST00000615540-ENST00000667612.frameshift_fusion.47 2 PDLIM5-ENSG00000287552 DNTKKANLNCRLLKS ENST00000615540-ENST00000667612 DRB1*11:01 None 2 0 749.000 31.000 NA 14 Poor Pending +61.FOSL2-BABAM2.ENST00000264716-ENST00000344773.inframe_fusion.34 3 1 1 FOSL2-BABAM2 GGQQVQYVIQGYHKR ENST00000264716-ENST00000344773 DRB1*11:01 None 5 0 768.510 21.000 NA 1 Poor Pending +58.AGPAT5-MCPH1-AS1.ENST00000285518-..frameshift_fusion.68 4 AGPAT5-MCPH1-AS1 MVLFFFENYTGVQVT ENST00000285518-. DRB1*11:01 None 4 0 998.875 36.000 NA 8 Poor Pending +62.UNC5C-STPG2.ENST00000453304-ENST00000506482.frameshift_fusion.79 1 3 UNC5C-STPG2 IPVAEVEVQL ENST00000453304-ENST00000506482 HLA-B*35:01 None 4 0 1158.735 0.960 NA 5 Poor Pending +17.ATAD1-PTEN.ENST00000680388-..frameshift_fusion.57 1 ATAD1-PTEN GLDTDHSCQA ENST00000680388-. HLA-A*02:01 None 1 0 2388.535 6.300 NA 16 Poor Pending +41.HNRNPUL2-BSCL2-AHNAK.ENST00000403734-ENST00000257247.frameshift_fusion.51 8 HNRNPUL2-BSCL2-AHNAK NKRNRQNRSRGQGYG ENST00000403734-ENST00000257247 DRB1*11:01 None 8 0 3057.800 52.000 NA 40 Poor Pending +42.HNRNPUL2-BSCL2-AHNAK.ENST00000403734-ENST00000257247.inframe_fusion.30 2 HNRNPUL2-BSCL2-AHNAK NKRNRQNRSRGQGYG ENST00000403734-ENST00000257247 DRB1*11:01 None 2 0 3057.800 52.000 NA 0 Poor Pending +44.HNRNPUL2-AHNAK.ENST00000301785-ENST00000257247.frameshift_fusion.51 8 HNRNPUL2-AHNAK NKRNRQNRSRGQGYG ENST00000301785-ENST00000257247 DRB1*11:01 None 8 0 3057.800 52.000 NA 40 Poor Pending +45.HNRNPUL2-AHNAK.ENST00000301785-ENST00000257247.inframe_fusion.30 2 HNRNPUL2-AHNAK NKRNRQNRSRGQGYG ENST00000301785-ENST00000257247 DRB1*11:01 None 2 0 3057.800 52.000 NA 0 Poor Pending +43.HNRNPUL2-BSCL2-AHNAK.ENST00000403734-ENST00000257247.frameshift_fusion.50 2 HNRNPUL2-BSCL2-AHNAK NKRNRQNRSRGQGYD ENST00000403734-ENST00000257247 DRB1*11:01 None 2 0 3727.845 51.000 NA 0 Poor Pending +46.HNRNPUL2-AHNAK.ENST00000301785-ENST00000257247.frameshift_fusion.50 2 HNRNPUL2-AHNAK NKRNRQNRSRGQGYD ENST00000301785-ENST00000257247 DRB1*11:01 None 2 0 3727.845 51.000 NA 0 Poor Pending +92.CLTC-LAMC1.ENST00000621829-ENST00000258341.inframe_fusion.55 2 1 CLTC-LAMC1 GARKANSTRTWKDSQ ENST00000621829-ENST00000258341 DRB1*11:01 None 3 0 4320.290 61.000 NA 2 Poor Pending +81.ODF2-SPTAN1.ENST00000604420-ENST00000372731.frameshift_fusion.11 1 ODF2-SPTAN1 SSSGGSPRPV ENST00000604420-ENST00000372731 HLA-A*02:01 None 1 0 5439.649 14.000 NA 3 Poor Pending +24.LTBP1-BIRC6.ENST00000404816-ENST00000421745.inframe_fusion.60 1 LTBP1-BIRC6 LPQQIHSHD ENST00000404816-ENST00000421745 HLA-B*35:01 None 1 0 6591.350 7.674 NA 11 Poor Pending +82.ODF2-SPTAN1.ENST00000393533-ENST00000372731.frameshift_fusion.9 1 ODF2-SPTAN1 QQGPHQNRPV ENST00000393533-ENST00000372731 HLA-A*02:01 None 1 0 7637.935 18.000 NA 1 Poor Pending +6.UNC5C-STPG2-AS1.ENST00000453304-..frameshift_fusion.53 1 UNC5C-STPG2-AS1 LLQCRPPEGIPVAEI ENST00000453304-. DRB1*11:01 None 1 0 13457.800 87.000 NA 59 Poor Pending diff --git a/pvactools/tools/pvacseq/example_data/results/MHC_Class_I/HCC1395_TUMOR_DNA.all_epitopes.aggregated.metrics.json b/pvactools/tools/pvacseq/example_data/results/MHC_Class_I/HCC1395_TUMOR_DNA.all_epitopes.aggregated.metrics.json index 695224f2..8069eb31 100644 --- a/pvactools/tools/pvacseq/example_data/results/MHC_Class_I/HCC1395_TUMOR_DNA.all_epitopes.aggregated.metrics.json +++ b/pvactools/tools/pvacseq/example_data/results/MHC_Class_I/HCC1395_TUMOR_DNA.all_epitopes.aggregated.metrics.json @@ -1236,11 +1236,236 @@ "best_hla_allele": "HLA-A*29:02" }, "chr1-13318693-13318694-G-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "LLTQGVHPR": { + "ic50s_MT": [ + 11195.1201171875, + "X" + ], + "percentiles_MT": [ + 10.630000114440918, + "X" + ], + "ic50s_WT": [ + 22722.072, + "X" + ], + "percentiles_WT": [ + 20.5, + "X" + ], + "hla_types": [ + "HLA-A*29:02", + "HLA-B*45:01" + ], + "mutation_position": "7", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 13753.661082486446, + 5697.83, + 16217.4, + 8342.39, + 16811.45, + 3000.81, + 13701.24, + 8689.0 + ] + }, + "WT": { + "HLA-A*29:02": [ + 21095.25354673594, + 5679.88, + 26073.82, + 16946.23, + 24348.89, + 5500.22, + 38793.59, + 25940.0 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 6.917250156402588, + 11.460000038146973, + 14.0, + 9.5, + 9.800000190734863, + 5.800000190734863, + 23.0, + 17.0 + ] + }, + "WT": { + "HLA-A*29:02": [ + 12.580124999999995, + 10.62, + 27.0, + 22.0, + 19.0, + 14.0, + 43.0, + 34.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "HLA-A*29:02": [ + 0.1470492705702781, + 0.0119867991044704, + 0.00191, + 0.0030534756, + 0.01640218 + ] + }, + "WT": { + "HLA-A*29:02": [ + 0.1148582734167575, + 0.007094782407419, + 0.000718, + 0.0009946094, + 0.0059910337 + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "HLA-A*29:02": [ + "NA", + 20.2322554347826, + 7.0, + "NA", + "NA" + ] + }, + "WT": { + "HLA-A*29:02": [ + "NA", + 31.64317934782608, + 12.0, + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "MHCflurryEL Presentation", + "NetMHCpanEL" + ], + "MT": { + "HLA-A*29:02": [ + 6.917250156402588, + 11.460000038146973, + 14.0, + 9.5, + 9.800000190734863, + 5.800000190734863, + 23.0, + 17.0, + 20.2322554347826, + 7.0 + ] + }, + "WT": { + "HLA-A*29:02": [ + 12.580124999999995, + 10.62, + 27.0, + 22.0, + 19.0, + 14.0, + 43.0, + 34.0, + 31.64317934782608, + 12.0 + ] + } + }, + "wt_peptide": "LLTQGVRPR" + } + }, + "transcripts": [ + "ENST00000376152.2-PRAMEF15-R/H-96" + ], + "transcript_expr": [ + 0.0 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 478 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0.0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0.0 + ], "DNA VAF": 0.098, "RNA VAF": 0.0, "gene_expr": 0.0, @@ -1249,11 +1474,236 @@ "best_hla_allele": "HLA-A*29:02" }, "chr1-16006133-16006134-G-T": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "PMGWGCLAQ": { + "ic50s_MT": [ + 8033.18017578125, + "X" + ], + "percentiles_MT": [ + 17.44499969482422, + "X" + ], + "ic50s_WT": [ + 10860.41, + "X" + ], + "percentiles_WT": [ + 16.06, + "X" + ], + "hla_types": [ + "HLA-A*29:02", + "HLA-B*45:01" + ], + "mutation_position": "4", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 24631.87043569525, + 5777.9, + 8660.05, + 7406.31, + 24866.19, + 13212.86, + 2527.9, + 4942.77 + ] + }, + "WT": { + "HLA-A*29:02": [ + 22814.62120158952, + 5780.91, + 12221.82, + 9499.0, + 29415.4, + 13947.35, + 2305.47, + 4623.49 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 17.79974937438965, + 17.09000015258789, + 6.599999904632568, + 8.5, + 20.0, + 34.0, + 6.3, + 10.0 + ] + }, + "WT": { + "HLA-A*29:02": [ + 14.730749999999995, + 17.39, + 9.0, + 12.0, + 29.0, + 35.0, + 5.9, + 9.6 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "HLA-A*29:02": [ + 0.0015490807691094, + 0.0040997088158493, + 5e-05, + 0.0006987037, + 0.042544775 + ] + }, + "WT": { + "HLA-A*29:02": [ + 0.0028514973819255, + 0.0044354582913652, + 0.000136, + 0.00035014004, + 0.020470437 + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "HLA-A*29:02": [ + "NA", + 62.74467391304348, + 35.0, + "NA", + "NA" + ] + }, + "WT": { + "HLA-A*29:02": [ + "NA", + 62.74467391304348, + 24.0, + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "MHCflurryEL Presentation", + "NetMHCpanEL" + ], + "MT": { + "HLA-A*29:02": [ + 17.79974937438965, + 17.09000015258789, + 6.599999904632568, + 8.5, + 20.0, + 34.0, + 6.3, + 10.0, + 62.74467391304348, + 35.0 + ] + }, + "WT": { + "HLA-A*29:02": [ + 14.730749999999995, + 17.39, + 9.0, + 12.0, + 29.0, + 35.0, + 5.9, + 9.6, + 62.74467391304348, + 24.0 + ] + } + }, + "wt_peptide": "PMGGGCLAQ" + } + }, + "transcripts": [ + "ENST00000329454.2-SRARP-G/W-100" + ], + "transcript_expr": [ + 0.082 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 169 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0.082 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0.082 + ], "DNA VAF": 1.0, "RNA VAF": 0.0, "gene_expr": 0.082, @@ -1262,11 +1712,236 @@ "best_hla_allele": "HLA-A*29:02" }, "chr1-16972417-16972418-C-G": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "SSAPFCPPS": { + "ic50s_MT": [ + "X", + 13779.64453125 + ], + "percentiles_MT": [ + "X", + 15.5 + ], + "ic50s_WT": [ + "X", + 13580.41 + ], + "percentiles_WT": [ + "X", + 12.04 + ], + "hla_types": [ + "HLA-A*29:02", + "HLA-B*45:01" + ], + "mutation_position": "6", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*45:01": [ + 22489.3987938728, + 17180.0, + 10379.29, + 25982.58, + 18180.55, + 6469.41, + 5678.19, + 1939.19 + ] + 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"individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "HLA-B*45:01": [ + "NA", + 62.74467391304348, + 20.0, + "NA", + "NA" + ] + }, + "WT": { + "HLA-B*45:01": [ + "NA", + 37.35904891304347, + 8.8, + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "MHCflurryEL Presentation", + "NetMHCpanEL" + ], + "MT": { + "HLA-B*45:01": [ + 8.125499725341797, + 18.459999084472656, + 7.300000190734863, + 14.0, + 7.199999809265137, + 19.0, + 17.0, + 7.3, + 62.74467391304348, + 20.0 + ] + }, + "WT": { + "HLA-B*45:01": [ + 7.239375, + 14.28, + 9.2, + 16.0, + 7.0, + 17.0, + 17.0, + 9.8, + 37.35904891304347, + 8.8 + ] + } + }, + "wt_peptide": "SSAPFSPPS" + } + }, + "transcripts": [ + "ENST00000375541.10-CROCC-S/C-2009" + ], + "transcript_expr": 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Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "HLA-A*29:02": [ + 0.0740617662668228, + 0.0135546274022154, + 0.00253, + 0.0043244446, + 0.10322578 + ] + }, + "WT": { + "HLA-A*29:02": [ + 0.2137247584760189, + 0.0134967446504942, + 0.00143, + 0.0030485208, + 0.0652511 + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "HLA-A*29:02": [ + "NA", + 17.305597826086952, + 6.1, + "NA", + "NA" + ] + }, + "WT": { + "HLA-A*29:02": [ + "NA", + 17.305597826086952, + 8.1, + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "MHCflurryEL Presentation", + "NetMHCpanEL" + ], + "MT": { + "HLA-A*29:02": [ + 4.896999835968018, + 4.110000133514404, + 9.600000381469727, + 7.199999809265137, + 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"best_peptide_mt": "FEQELQDDDF", - "best_peptide_wt": "CEQELQDDDF", - "best_hla_allele": "HLA-B*45:01" - }, - "chr4-154491218-154491219-G-C": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 0.963, - "RNA VAF": 1.0, - "gene_expr": 2.425, - "best_peptide_mt": "TQRCLLWLLV", - "best_peptide_wt": "TQRSLLWLLV", - "best_hla_allele": "HLA-B*45:01" - }, - "chr4-176120050-176120052-AG-GA": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 0.508, - "RNA VAF": "NA", - "gene_expr": 0.514, - "best_peptide_mt": "HTHQKGKIVF", - "best_peptide_wt": "HTHQKGKVVF", - "best_hla_allele": "HLA-A*29:02" - }, - "chr4-176120051-176120052-G-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 0.489, - "RNA VAF": 0.0, - "gene_expr": 0.514, - "best_peptide_mt": "HTHQKGKIVF", - "best_peptide_wt": 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3551.864062697033, - 5587.22, - 1999.03, - 1525.99, - 5371.77, - 2842.78, - 1129.17, - 1156.03 + "HLA-B*45:01": [ + 1458.997457565957, + 19070.94, + 24646.01, + 10699.58, + 19898.48, + 2781.92, + 2347.96, + 2971.19 ] }, "WT": { - "HLA-A*29:02": [ - 10580.04477899484, - 5764.61, - 8945.77, - 7486.88, - 12599.12, - 5210.57, - 3197.13, - 3451.2 + "HLA-B*45:01": [ + 1361.4055663970328, + 11361.94, + 8757.29, + 7131.08, + 15173.55, + 2077.17, + 670.95, + 1051.79 ] } }, @@ -123649,27 +141354,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 2.8884999752044678, - 7.559999942779541, - 2.4000000953674316, - 3.4000000953674316, - 3.0999999046325684, - 5.400000095367432, - 3.8, - 3.9 + "HLA-B*45:01": [ + 1.3198750019073486, + 21.09000015258789, + 18.0, + 5.900000095367432, + 8.199999809265137, + 4.099999904632568, + 8.7, + 12.0 ] }, "WT": { - "HLA-A*29:02": [ - 5.429374999999998, - 15.85, - 6.8, - 8.6, - 6.8, - 14.0, - 7.4, - 7.8 + "HLA-B*45:01": [ + 1.2857499999999982, + 11.8, + 6.3, + 4.7, + 5.8, + 3.0, + 2.6, + 4.3 ] } }, @@ -123682,21 +141387,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.1040278747677803, - 0.0373608314927562, - 0.0174, - 0.02474969, - 0.011770672 + "HLA-B*45:01": [ + 0.0208648219704628, + 0.064220218696069, + 0.00252, + 0.0015444646, + 0.0014195822 ] }, "WT": { - "HLA-A*29:02": [ - 0.1143431104719638, - 0.013751121021206, - 0.00498, - 0.0058935573, - 0.0070516155 + "HLA-B*45:01": [ + 0.0023408867418766, + 0.0643229695957479, + 0.00181, + 0.00025495805, + 0.00041126544 ] } }, @@ -123709,19 +141414,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 6.63130434782606, - 2.4, + 4.102010869565163, + 6.5, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 17.305597826086952, - 4.4, + 4.102010869565163, + 7.5, "NA", "NA" ] @@ -123741,55 +141446,55 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 2.8884999752044678, - 7.559999942779541, - 2.4000000953674316, - 3.4000000953674316, - 3.0999999046325684, - 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0.013751121021206, + 0.00498, + 0.0058935573, + 0.0070516155 ] } }, @@ -124772,19 +142604,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 1.9827717391303563, - 3.5, + 6.63130434782606, + 2.4, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 1.7785054347825593, - 1.7, + 17.305597826086952, + 4.4, "NA", "NA" ] @@ -124804,107 +142636,102 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 0.8831250071525574, - 12.6899995803833, - 6.900000095367432, - 2.5999999046325684, - 1.399999976158142, - 1.2000000476837158, - 28.0, - 19.0, - 1.9827717391303563, - 3.5 + "HLA-A*29:02": [ + 2.8884999752044678, + 7.559999942779541, + 2.4000000953674316, + 3.4000000953674316, + 3.0999999046325684, + 5.400000095367432, + 3.8, + 3.9, + 6.63130434782606, + 2.4 ] }, "WT": { - "HLA-B*45:01": [ - 0.9513749999999992, - 21.51, + "HLA-A*29:02": [ + 5.429374999999998, + 15.85, + 6.8, + 8.6, + 6.8, + 14.0, + 7.4, 7.8, - 2.8, - 1.6, - 1.5, - 26.0, - 19.0, - 1.7785054347825593, - 1.7 + 17.305597826086952, + 4.4 ] } }, - "wt_peptide": "LEMADQGRLL" + "wt_peptide": "MLGQPARPH" } }, "transcripts": [ - "ENST00000344204.9-TRIO-R/C-2876", - "ENST00000344135.5-TRIO-R/C-375" + "ENST00000469176.1-NDUFS6-R/H-118" ], "transcript_expr": [ - 11.522, - 0.395 + 0.592 ], "tsl": [ - 1, 2 ], "biotype": [ - "protein_coding", "protein_coding" ], "transcript_length": [ - 3097, - 596 + 172 ], - "transcript_count": 2, - "peptide_count": 2, - "total_expr": 11.917 + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0.592 } }, "sets": [ "Transcript Set 1" ], "transcript_counts": [ - 2 + 1 ], "peptide_counts": [ - 2 + 1 ], "set_expr": [ - 11.917 + 0.592 ], - "DNA VAF": 0.259, - "RNA VAF": 0.25, - "gene_expr": 74.348, - "best_peptide_mt": "LEMADQGCL", - "best_peptide_wt": "LEMADQGRL", - "best_hla_allele": "HLA-B*45:01" + "DNA VAF": 0.41, + "RNA VAF": 0.5, + "gene_expr": 181.433, + "best_peptide_mt": "MLGQPAHPH", + "best_peptide_wt": "MLGQPARPH", + 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2241.135009765625 + 1833.72998046875, + "X" ], "percentiles_MT": [ - "X", - 3.200000047683716 + 5.25, + "X" ], "ic50s_WT": [ - "X", - "NA" + 2056.685, + "X" ], "percentiles_WT": [ - "X", - "NA" + 4.95, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "1-9", + "mutation_position": "9", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -125162,27 +142940,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 274.7085988589157, - 5383.96, - 4428.2, - 2858.2, - 1890.36, - 1073.58, - 1714.79, - 2591.91 + "HLA-A*29:02": [ + 15576.249878393372, + 5141.36, + 1963.22, + 1517.76, + 1368.18, + 6539.79, + 1622.86, + 1704.24 ] }, "WT": { - "HLA-B*45:01": [ - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA" + "HLA-A*29:02": [ + 17508.408486088672, + 5176.49, + 1579.15, + 1332.95, + 1115.53, + 5681.68, + 2266.1, + 1847.27 ] } }, @@ -125198,27 +142976,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 0.6054999828338623, - 6.210000038146973, - 3.9000000953674316, - 3.0, - 0.949999988079071, + "HLA-A*29:02": [ + 7.990749835968018, + 2.7300000190734863, + 2.4000000953674316, 3.4000000953674316, - 6.5, - 9.5 + 1.2999999523162842, + 5.199999809265137, + 5.3, + 5.4 ] }, "WT": { - "HLA-B*45:01": [ - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA" + "HLA-A*29:02": [ + 9.323624999999996, + 2.88, + 2.1, + 3.2, + 1.2, + 4.1, + 6.7, + 5.8 ] } }, @@ -125231,21 +143009,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.3943346478044987, - 0.5656886653290315, - 0.113, - 0.0024359177, - 7.706582e-05 + "HLA-A*29:02": [ + 0.0011878125369548, + 0.0063758335308919, + 0.00148, + 0.0027240731, + 0.43099037 ] }, "WT": { - "HLA-B*45:01": [ - "NA", - "NA", - "NA", - "NA", - "NA" + "HLA-A*29:02": [ + 0.0010899901390075, + 0.0056931935497964, + 0.00122, + 0.0041984087, + 0.51934564 ] } }, @@ -125258,19 +143036,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.6837228260868784, - 0.92, + 37.35904891304347, + 7.9, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ - "NA", - "NA", + "HLA-A*29:02": [ "NA", + 46.22467391304348, + 8.7, "NA", "NA" ] @@ -125290,60 +143068,60 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 0.6054999828338623, - 6.210000038146973, - 3.9000000953674316, - 3.0, - 0.949999988079071, + "HLA-A*29:02": [ + 7.990749835968018, + 2.7300000190734863, + 2.4000000953674316, 3.4000000953674316, - 6.5, - 9.5, - 0.6837228260868784, - 0.92 + 1.2999999523162842, + 5.199999809265137, + 5.3, + 5.4, + 37.35904891304347, + 7.9 ] }, "WT": { - "HLA-B*45:01": [ - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA" + "HLA-A*29:02": [ + 9.323624999999996, + 2.88, + 2.1, + 3.2, + 1.2, + 4.1, + 6.7, + 5.8, + 46.22467391304348, + 8.7 ] } }, - "wt_peptide": "FS-NA" + "wt_peptide": "QFIFTWCLEI" }, - "QEWLRSPRDV": { + "QFIFTWCLQ": { "ic50s_MT": [ - "X", - 1189.7750244140625 + 2880.35498046875, + "X" ], "percentiles_MT": [ - "X", - 1.6540000438690186 + 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@@ -125891,27 +143607,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 4.029749870300293, - 1.4600000381469727, - 2.0999999046325684, - 3.700000047683716, - 3.299999952316284, - 14.0, - 4.3, - 4.4 + "HLA-B*45:01": [ + 0.8831250071525574, + 12.6899995803833, + 6.900000095367432, + 2.5999999046325684, + 1.399999976158142, + 1.2000000476837158, + 28.0, + 19.0 ] }, "WT": { - "HLA-A*29:02": [ - 3.553624999999999, - 2.29, + "HLA-B*45:01": [ + 0.9513749999999992, + 21.51, + 7.8, 2.8, - 4.5, - 3.8, - 19.0, - 5.3, - 5.6 + 1.6, + 1.5, + 26.0, + 19.0 ] } }, @@ -125924,21 +143640,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.0551944859325885, - 0.0169845077350593, - 0.0198, - 0.0055641322, - 0.10912829 + "HLA-B*45:01": [ + 0.0839122161269187, + 0.1785565638428305, + 0.00992, + 0.0020671953, + 0.00015078652 ] }, "WT": { - "HLA-A*29:02": [ - 0.0700401104986667, - 0.0220620292146439, - 0.012, - 0.0035674244, - 0.08904667 + "HLA-B*45:01": [ + 0.1860126815736293, + 0.209414064085149, + 0.0452, + 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192.23500061035156, - "X" + "X", + 2241.135009765625 ], "percentiles_MT": [ - 0.5559999942779541, - "X" + "X", + 3.200000047683716 ], "ic50s_WT": [ - 144.45, - "X" + "X", + "NA" ], "percentiles_WT": [ - 0.514, - "X" + "X", + "NA" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "8", + "mutation_position": "1-9", "problematic_positions": "None", - "anchor_fails": "HLA-A*29:02", + "anchor_fails": "None", "individual_ic50_calls": { "algorithms": [ "MHCflurry", @@ -126292,27 +144057,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 55.285696721707, - 1283.82, - 423.26, - 237.32, - 86.33, - 3567.97, - 147.15, - 117.21 + "HLA-B*45:01": [ + 274.7085988589157, + 5383.96, + 4428.2, + 2858.2, + 1890.36, + 1073.58, + 1714.79, + 2591.91 ] }, "WT": { - "HLA-A*29:02": [ - 60.49081581246877, - 1767.97, - 268.14, - 162.5, - 82.89, - 3066.45, - 126.4, - 92.89 + "HLA-B*45:01": [ + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -126328,27 +144093,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 0.2082500010728836, - 0.15000000596046448, - 0.9900000095367432, - 1.5, - 0.1899999976158142, - 7.599999904632568, - 1.0, - 0.8 + "HLA-B*45:01": [ + 0.6054999828338623, + 6.210000038146973, + 3.9000000953674316, + 3.0, + 0.949999988079071, + 3.4000000953674316, + 6.5, + 9.5 ] }, "WT": { - "HLA-A*29:02": [ - 0.2389999999999999, - 0.24, - 0.75, - 1.2, - 0.19, - 6.0, - 0.8, - 0.7 + "HLA-B*45:01": [ + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -126361,21 +144126,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.2349477522075176, - 0.7786163108437211, - 0.69, - 0.8373448, - 0.7657297 + "HLA-B*45:01": [ + 0.3943346478044987, + 0.5656886653290315, + 0.113, + 0.0024359177, + 7.706582e-05 ] }, "WT": { - "HLA-A*29:02": [ - 0.2433972582221031, - 0.7685455466961161, - 0.59, - 0.8229329, - 0.7114665 + "HLA-B*45:01": [ + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -126388,19 +144153,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 0.3123641304347586, - 0.1, + 0.6837228260868784, + 0.92, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ + "NA", + "NA", "NA", - 0.3283152173912782, - 0.15, "NA", "NA" ] @@ -126420,60 +144185,60 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 0.2082500010728836, - 0.15000000596046448, - 0.9900000095367432, - 1.5, - 0.1899999976158142, - 7.599999904632568, - 1.0, - 0.8, - 0.3123641304347586, - 0.1 + "HLA-B*45:01": [ + 0.6054999828338623, + 6.210000038146973, + 3.9000000953674316, + 3.0, + 0.949999988079071, + 3.4000000953674316, + 6.5, + 9.5, + 0.6837228260868784, + 0.92 ] }, "WT": { - "HLA-A*29:02": [ - 0.2389999999999999, - 0.24, - 0.75, - 1.2, - 0.19, - 6.0, - 0.8, - 0.7, - 0.3283152173912782, - 0.15 + "HLA-B*45:01": [ + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, - "wt_peptide": "GLPFLAIAY" + "wt_peptide": "FS-NA" }, - "IGLPFLAITY": { + "QEWLRSPRDV": { "ic50s_MT": [ - 529.9099731445312, - "X" + "X", + 1189.7750244140625 ], "percentiles_MT": [ - 1.277999997138977, - "X" + "X", + 1.6540000438690186 ], "ic50s_WT": [ - 292.38, - "X" + "X", + 293.61 ], "percentiles_WT": [ - 0.952, - "X" + "X", + 0.547 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "9", + "mutation_position": "10", "problematic_positions": "None", - "anchor_fails": "HLA-A*29:02", + "anchor_fails": "HLA-B*45:01", "individual_ic50_calls": { "algorithms": [ "MHCflurry", @@ -126486,27 +144251,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 163.79657220977694, - 2350.28, - 1279.55, - 403.25, - 152.3, - 9865.62, - 656.57, - 377.16 + "HLA-B*45:01": [ + 1720.1786418379672, + 4886.74, + 734.45, + 747.17, + 1094.47, + 1584.89, + 525.64, + 1285.08 ] }, "WT": { - "HLA-A*29:02": [ - 162.72021846810276, - 2914.36, - 837.91, - 246.48, - 139.19, - 8664.37, - 338.28, - 184.73 + "HLA-B*45:01": [ + 337.2743967239948, + 975.98, + 126.85, + 254.61, + 187.57, + 751.22, + 119.31, + 332.61 ] } }, @@ -126522,27 +144287,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 0.6608750224113464, - 0.3400000035762787, - 1.899999976158142, - 1.899999976158142, - 0.30000001192092896, - 9.5, - 2.8, - 1.7 + "HLA-B*45:01": [ + 1.4078749418258667, + 5.769999980926514, + 0.9800000190734863, + 0.9700000286102295, + 0.6499999761581421, + 2.0999999046325684, + 1.9, + 5.1 ] }, "WT": { - "HLA-A*29:02": [ - 0.6608749999999998, - 0.48, - 1.6, - 1.5, - 0.28, - 7.8, - 1.5, - 0.9 + "HLA-B*45:01": [ + 0.6848749999999995, + 1.94, + 0.18, + 0.41, + 0.18, + 0.8, + 0.3, + 1.1 ] } }, @@ -126555,21 +144320,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.1594298034906387, - 0.4838634322759273, - 0.235, - 0.07661538, - 0.68724126 + "HLA-B*45:01": [ + 0.023054338991642, + 0.0556572731532938, + 0.0709, + 0.00016902528, + 5.2158135e-05 ] }, "WT": { - "HLA-A*29:02": [ - 0.086044255644083, - 0.4212090338487597, - 0.164, - 0.06041771, - 0.6782407 + "HLA-B*45:01": [ + 0.0299073792994022, + 0.2271601377098881, + 0.312, + 0.0006926119, + 0.00020675892 ] } }, @@ -126582,19 +144347,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 0.8561956521737955, - 0.47, + 4.657581521739076, + 1.3, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 1.0039945652172406, - 0.66, + 1.68184782608688, + 0.37, "NA", "NA" ] @@ -126614,65 +144379,65 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 0.6608750224113464, - 0.3400000035762787, - 1.899999976158142, - 1.899999976158142, - 0.30000001192092896, - 9.5, - 2.8, - 1.7, - 0.8561956521737955, - 0.47 + "HLA-B*45:01": [ + 1.4078749418258667, + 5.769999980926514, + 0.9800000190734863, + 0.9700000286102295, + 0.6499999761581421, + 2.0999999046325684, + 1.9, + 5.1, + 4.657581521739076, + 1.3 ] }, "WT": { - "HLA-A*29:02": [ - 0.6608749999999998, - 0.48, - 1.6, - 1.5, - 0.28, - 7.8, - 1.5, - 0.9, - 1.0039945652172406, - 0.66 + "HLA-B*45:01": [ + 0.6848749999999995, + 1.94, + 0.18, + 0.41, + 0.18, + 0.8, + 0.3, + 1.1, + 1.68184782608688, + 0.37 ] } }, - "wt_peptide": "IGLPFLAIAY" + "wt_peptide": "QEWLRSPRDA" } }, "transcripts": [ - "ENST00000513104.6-TRPC7-A/T-368", - "ENST00000378459.7-TRPC7-A/T-307", - "ENST00000503275.6-TRPC7-A/T-368" + "ENST00000282369.7-TRIM36-AVS/X-607-609", + "ENST00000514154.1-TRIM36-AVS/X-452-454", + "ENST00000513154.6-TRIM36-AVS/X-595-597" ], "transcript_expr": [ 0.0, - 0.0, - 0.0 + 0.456, + 0.317 ], "tsl": [ - 5, - 5, - 5 + 1, + 1, + 2 ], "biotype": [ "protein_coding", "protein_coding", - "nonsense_mediated_decay" + "protein_coding" ], "transcript_length": [ - 862, - 801, - 380 + 728, + 573, + 716 ], "transcript_count": 3, - "peptide_count": 3, - "total_expr": 0.0 + "peptide_count": 2, + "total_expr": 0.773 } }, "sets": [ @@ -126682,57 +144447,44 @@ 3 ], "peptide_counts": [ - 3 + 2 ], "set_expr": [ - 0.0 + 0.773 ], - "DNA VAF": 0.366, - "RNA VAF": 0.0, - "gene_expr": 0.005, - "best_peptide_mt": "PFLAITYWI", - "best_peptide_wt": "PFLAIAYWI", - "best_hla_allele": "HLA-A*29:02" - }, - "chr5-141123692-141123693-G-C": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 0.307, + "DNA VAF": 0.92, "RNA VAF": 0.0, - "gene_expr": 1.436, - "best_peptide_mt": "SPFVLYPLH", - "best_peptide_wt": "SPFVLYPLQ", - "best_hla_allele": "HLA-A*29:02" + "gene_expr": 1.136, + "best_peptide_mt": "VEVRMPVLI", + "best_peptide_wt": "NA", + "best_hla_allele": "HLA-B*45:01" }, - "chr5-141332647-141332648-C-T": { + "chr5-133103958-133103959-T-C": { "good_binders": { "Transcript Set 1": { "peptides": { - "LFATVTLTV": { + "MEWMNNKLNP": { "ic50s_MT": [ - 2028.9659423828125, - "X" + "X", + 992.1630249023438 ], "percentiles_MT": [ - 3.200000047683716, - "X" + "X", + 1.7999999523162842 ], "ic50s_WT": [ - 8022.44, - "X" + "X", + 1329.71 ], "percentiles_WT": [ - 12.65, - "X" + "X", + 2.932 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "2", + "mutation_position": "10", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -126747,27 +144499,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 2003.1127156542263, - 4946.57, - 2681.35, - 2054.82, - 1818.54, - 2264.98, - 1018.03, - 1294.11 + "HLA-B*45:01": [ + 964.046930954678, + 1020.28, + 9795.1, + 1028.11, + 238.04, + 2077.17, + 900.93, + 461.24 ] }, "WT": { - "HLA-A*29:02": [ - 6886.719383618843, - 5694.71, - 12111.11, - 11730.27, - 11833.27, - 6903.33, - 7494.8, - 8550.08 + "HLA-B*45:01": [ + 1348.069348570758, + 4442.9, + 5112.06, + 973.97, + 1311.35, + 1050.6, + 1278.47, + 1523.81 ] } }, @@ -126783,27 +144535,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 2.2634999752044678, - 2.049999952316284, - 2.9000000953674316, - 3.9000000953674316, - 1.5, - 3.799999952316284, - 3.5, - 4.2 + "HLA-B*45:01": [ + 1.11899995803833, + 2.0, + 6.900000095367432, + 1.399999976158142, + 0.20999999344348907, + 3.0, + 3.6, + 1.6 ] }, "WT": { - "HLA-A*29:02": [ - 4.029749999999998, - 11.3, - 8.9, - 14.0, - 6.4, - 19.0, - 15.0, - 17.0 + "HLA-B*45:01": [ + 1.279499999999998, + 5.390000000000001, + 4.3, + 1.3, + 0.74, + 1.3, + 5.1, + 5.9 ] } }, @@ -126816,21 +144568,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.0503360070288181, - 0.0530173104473194, - 0.0457, - 0.04756546, - 0.23731641 + "HLA-B*45:01": [ + 0.0413418300449848, + 0.0993813760421554, + 0.145, + 0.011427677, + 0.0013917775 ] }, "WT": { - "HLA-A*29:02": [ - 0.0468250475823879, - 0.0163893016921467, - 0.00268, - 0.018266868, - 0.37207314 + "HLA-B*45:01": [ + 0.0318974666297435, + 0.07154360076845, + 0.029, + 0.0015529776, + 0.00024679472 ] } }, @@ -126843,19 +144595,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 4.887418478260841, - 1.6, + 2.9306793478260005, + 0.78, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 14.277038043478257, - 6.0, + 3.764592391304277, + 2.1, "NA", "NA" ] @@ -126875,101 +144627,96 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 2.2634999752044678, - 2.049999952316284, - 2.9000000953674316, - 3.9000000953674316, - 1.5, - 3.799999952316284, - 3.5, - 4.2, - 4.887418478260841, - 1.6 + "HLA-B*45:01": [ + 1.11899995803833, + 2.0, + 6.900000095367432, + 1.399999976158142, + 0.20999999344348907, + 3.0, + 3.6, + 1.6, + 2.9306793478260005, + 0.78 ] }, "WT": { - "HLA-A*29:02": [ - 4.029749999999998, - 11.3, - 8.9, - 14.0, - 6.4, - 19.0, - 15.0, - 17.0, - 14.277038043478257, - 6.0 + "HLA-B*45:01": [ + 1.279499999999998, + 5.390000000000001, + 4.3, + 1.3, + 0.74, + 1.3, + 5.1, + 5.9, + 3.764592391304277, + 2.1 ] } }, - "wt_peptide": "LSATVTLTV" + "wt_peptide": "MEWMNNKLNL" } }, "transcripts": [ - "ENST00000517417.3-PCDHGA1-S/F-655", - "ENST00000378105.4-PCDHGA1-S/F-655" + "ENST00000304858.7-HSPA4-L/P-751" ], "transcript_expr": [ - 0.037, - 0.289 + 83.59 ], "tsl": [ - 1, - "NA" + 1 ], "biotype": [ - "protein_coding", "protein_coding" ], "transcript_length": [ - 931, - 823 + 840 ], - "transcript_count": 2, + "transcript_count": 1, "peptide_count": 1, - "total_expr": 0.32599999999999996 + "total_expr": 83.59 } }, "sets": [ "Transcript Set 1" ], "transcript_counts": [ - 2 + 1 ], "peptide_counts": [ 1 ], "set_expr": [ - 0.32599999999999996 + 83.59 ], - "DNA VAF": 0.681, - "RNA VAF": 0.571, - "gene_expr": 0.326, - "best_peptide_mt": "LFATVTLTV", - "best_peptide_wt": "LSATVTLTV", - "best_hla_allele": "HLA-A*29:02" + "DNA VAF": 1.0, + "RNA VAF": 0.996, + "gene_expr": 114.662, + "best_peptide_mt": "MEWMNNKLNP", + "best_peptide_wt": "MEWMNNKLNL", + "best_hla_allele": "HLA-B*45:01" }, - "chr5-145817966-145817967-A-G": { + "chr5-134703847-134703848-G-T": { "good_binders": { "Transcript Set 1": { "peptides": { - "RSHRLTWTQY": { + "AGYSVQMSV": { "ic50s_MT": [ - 655.4849853515625, - "X" + "X", + 11899.8447265625 ], "percentiles_MT": [ - 1.7899999618530273, - "X" + "X", + 11.399999618530273 ], "ic50s_WT": [ - 580.445, - "X" + "X", + 10023.73 ], "percentiles_WT": [ - 1.5, - "X" + "X", + 9.7 ], "hla_types": [ "HLA-A*29:02", @@ -126990,27 +144737,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 263.8904177510411, - 4958.4, - 1977.5, - 588.9, - 682.14, - 4242.33, - 342.2, - 628.83 + "HLA-B*45:01": [ + 20422.086931947822, + 4343.49, + 13817.86, + 26123.53, + 26487.26, + 1804.62, + 9981.83, + 3553.2 ] }, "WT": { - "HLA-A*29:02": [ - 128.8940583208034, - 5060.81, - 938.09, - 579.42, - 278.29, - 3646.02, - 292.6, - 581.47 + "HLA-B*45:01": [ + 20488.41908915825, + 3491.23, + 11551.55, + 23318.07, + 25329.99, + 1844.1, + 8495.91, + 2252.27 ] } }, @@ -127026,27 +144773,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 0.8957499861717224, - 2.0799999237060547, - 2.4000000953674316, - 2.200000047683716, - 0.7599999904632568, - 2.5, - 1.5, - 2.6 + "HLA-B*45:01": [ + 6.4070000648498535, + 5.300000190734863, + 9.399999618530273, + 14.0, + 15.0, + 5.800000190734863, + 22.0, + 13.0 ] }, "WT": { - "HLA-A*29:02": [ - 0.5483749999999997, - 2.41, - 1.7, - 2.2, - 0.43, - 2.0, - 1.3, - 2.4 + "HLA-B*45:01": [ + 6.407, + 4.53, + 8.0, + 12.0, + 14.0, + 5.9, + 20.0, + 8.4 ] } }, @@ -127059,21 +144806,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.4911752939224243, - 0.6560956434499866, - 0.114, - 0.06279274, - 0.7067126 + "HLA-B*45:01": [ + 0.1159412562847137, + 0.0073480741115983, + 0.000953, + 0.00028894292, + 0.009656238 ] }, "WT": { - "HLA-A*29:02": [ - 0.4077710434794426, - 0.7401723305572829, - 0.068, - 0.10669507, - 0.818892 + "HLA-B*45:01": [ + 0.1195611767470836, + 0.0074188554409356, + 0.00084, + 0.00047302077, + 0.015415172 ] } }, @@ -127086,19 +144833,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 0.5143749999999585, - 0.88, + 31.64317934782608, + 9.8, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 0.37358695652172, - 1.3, + 31.64317934782608, + 11.0, "NA", "NA" ] @@ -127118,58 +144865,102 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 0.8957499861717224, - 2.0799999237060547, - 2.4000000953674316, - 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"best_peptide_wt": "RSHCLTWTQY", + "DNA VAF": 0.993, + "RNA VAF": 0.996, + "gene_expr": 42.95, + "best_peptide_mt": "FLALDAPQH", + "best_peptide_wt": "FLALDASQH", "best_hla_allele": "HLA-A*29:02" }, - "chr5-150120064-150120065-G-A": { + "chr5-136274698-136274699-C-T": { "good_binders": { "Transcript Set 1": { "peptides": { - "YTILSDVWSF": { + "PFLAITYWI": { "ic50s_MT": [ - 685.1439819335938, + 4831.51513671875, "X" ], "percentiles_MT": [ - 1.600000023841858, + 5.849999904632568, "X" ], "ic50s_WT": [ - 1367.35, + 5173.105, "X" ], "percentiles_WT": [ - 2.973, + 6.35, "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "3", + "mutation_position": "6", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -127443,26 +145219,26 @@ ], "MT": { "HLA-A*29:02": [ - 868.1785230874556, - 4515.77, - 1107.17, - 326.55, - 502.11, - 4936.17, - 408.58, - 352.8 + 17349.44965236745, + 5466.35, + 5563.3, + 4196.68, + 7724.52, + 3890.57, + 1748.88, 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"percentiles_MT": [ - 3.563999891281128, + 1.277999997138977, "X" ], "ic50s_WT": [ - 8291.985, + 292.38, "X" ], "percentiles_WT": [ - 9.32, + 0.952, "X" ], "hla_types": [ @@ -127817,7 +145593,7 @@ ], "mutation_position": "9", "problematic_positions": "None", - "anchor_fails": "None", + "anchor_fails": "HLA-A*29:02", "individual_ic50_calls": { "algorithms": [ "MHCflurry", @@ -127831,26 +145607,26 @@ ], "MT": { "HLA-A*29:02": [ - 5060.531627648274, - 4503.24, - 3992.7, - 4883.05, - 3820.57, - 1746.99, - 2784.58, - 2735.08 + 163.79657220977694, + 2350.28, + 1279.55, + 403.25, + 152.3, + 9865.62, + 656.57, + 377.16 ] }, "WT": { "HLA-A*29:02": [ - 18694.452209816827, - 5133.35, - 9950.21, - 12584.95, - 12291.44, - 2693.07, - 6633.76, - 6515.83 + 162.72021846810276, + 2914.36, + 837.91, + 246.48, + 139.19, + 8664.37, + 338.28, + 184.73 ] } }, @@ -127867,26 +145643,26 @@ ], "MT": { "HLA-A*29:02": [ - 3.427375078201294, - 1.2699999809265137, - 3.700000047683716, - 6.199999809265137, - 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"total_expr": 0.32599999999999996 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 2 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0.32599999999999996 + ], + "DNA VAF": 0.681, + "RNA VAF": 0.571, + "gene_expr": 0.326, + "best_peptide_mt": "LFATVTLTV", + "best_peptide_wt": "LSATVTLTV", + "best_hla_allele": "HLA-A*29:02" + }, + "chr5-145817966-145817967-A-G": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "RSHRLTWTQY": { "ic50s_MT": [ - "X", - 94.55500030517578 + 655.4849853515625, + "X" ], "percentiles_MT": [ - "X", - 0.21400000154972076 + 1.7899999618530273, + "X" ], "ic50s_WT": [ - "X", - 97.43 + 580.445, + "X" ], "percentiles_WT": [ - "X", - 0.24 + 1.5, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "3", + "mutation_position": "4", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -128456,27 +146335,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 51.17860205825851, - 40.74, - 99.91, - 99.86, - 88.7, - 209.55, - 141.97, - 89.25 + "HLA-A*29:02": [ + 263.8904177510411, + 4958.4, + 1977.5, + 588.9, + 682.14, + 4242.33, + 342.2, + 628.83 ] }, "WT": { - "HLA-B*45:01": [ - 54.12954231947754, - 20.05, - 92.95, - 107.72, - 106.83, - 241.2, - 101.91, - 83.68 + "HLA-A*29:02": [ + 128.8940583208034, + 5060.81, + 938.09, + 579.42, + 278.29, + 3646.02, + 292.6, + 581.47 ] } }, @@ -128492,27 +146371,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 0.04062499850988388, - 0.20000000298023224, - 0.15000000596046448, - 0.3400000035762787, - 0.10000000149011612, - 0.4000000059604645, - 0.6, - 0.4 + "HLA-A*29:02": [ + 0.8957499861717224, + 2.0799999237060547, + 2.4000000953674316, + 2.200000047683716, + 0.7599999904632568, + 2.5, + 1.5, + 2.6 ] }, "WT": { - "HLA-B*45:01": [ - 0.054, - 0.0699999999999999, - 0.14, - 0.34, - 0.12, - 0.5, - 0.4, - 0.4 + "HLA-A*29:02": [ + 0.5483749999999997, + 2.41, + 1.7, + 2.2, + 0.43, + 2.0, + 1.3, + 2.4 ] } }, @@ -128525,21 +146404,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.3087762370705604, - 0.8311524734522843, - 0.703, - 0.16062121, - 0.0094778435 + "HLA-A*29:02": [ + 0.4911752939224243, + 0.6560956434499866, + 0.114, + 0.06279274, + 0.7067126 ] }, "WT": { - "HLA-B*45:01": [ - 0.1902814395725727, - 0.7540099616231987, - 0.598, - 0.3904945, - 0.07911669 + "HLA-A*29:02": [ + 0.4077710434794426, + 0.7401723305572829, + 0.068, + 0.10669507, + 0.818892 ] } }, @@ -128552,19 +146431,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.2287228260869653, - 0.09, + 0.5143749999999585, + 0.88, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.3513586956521664, - 0.12, + 0.37358695652172, + 1.3, "NA", "NA" ] @@ -128584,58 +146463,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 0.04062499850988388, - 0.20000000298023224, - 0.15000000596046448, - 0.3400000035762787, - 0.10000000149011612, - 0.4000000059604645, - 0.6, - 0.4, - 0.2287228260869653, - 0.09 + 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3.2, + 0.97, + 8.3, + 1.4, + 1.4 ] } }, @@ -128719,21 +146598,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.7114333435893059, - 0.9510477320354396, - 0.687, - 0.029503217, - 0.0009166083 + "HLA-A*29:02": [ + 0.3127920627593994, + 0.2982224928276516, + 0.147, + 0.048111122, + 0.66774 ] }, "WT": { - "HLA-B*45:01": [ - 0.2610307559370994, - 0.7873932550871853, - 0.661, - 0.009215982, - 0.00059353217 + "HLA-A*29:02": [ + 0.3157375603914261, + 0.5523154353205899, + 0.248, + 0.096463144, + 0.8559009 ] } }, @@ -128746,19 +146625,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.0451630434782828, - 0.1, + 1.372880434782516, + 0.72, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.2977989130434366, - 0.11, + 0.7129891304346785, + 0.44, "NA", "NA" ] @@ -128778,58 +146657,122 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 0.05400000140070915, - 0.8899999856948853, - 0.7099999785423279, - 0.5899999737739563, - 0.23000000417232513, - 0.4000000059604645, - 1.5, + "HLA-A*29:02": [ + 1.397125005722046, + 3.4600000381469727, + 1.2999999523162842, + 4.400000095367432, + 1.899999976158142, + 13.0, 1.9, - 0.0451630434782828, - 0.1 + 2.3, + 1.372880434782516, + 0.72 ] }, "WT": { - "HLA-B*45:01": [ - 0.071375, - 0.67, - 0.69, - 0.72, - 0.18, - 0.4, - 1.5, - 1.7, - 0.2977989130434366, - 0.11 + "HLA-A*29:02": [ + 0.8028749999999999, + 2.94, + 1.2, + 3.2, + 0.97, + 8.3, + 1.4, + 1.4, + 0.7129891304346785, + 0.44 ] } }, - "wt_peptide": "SEVEEAAAI" - }, - "SEVEKAAA": { + "wt_peptide": "SHCLTWTQY" + } + }, + "transcripts": [ + "ENST00000394450.6-PRELID2-C/R-70", + "ENST00000334744.8-PRELID2-C/R-111", + "ENST00000511435.1-PRELID2-C/R-99", + "ENST00000505416.5-PRELID2-C/R-99", + "ENST00000683046.1-PRELID2-C/R-99" + ], + "transcript_expr": [ + 3.292, + 0.664, + 0.256, + 0.197, + 0.664 + ], + "tsl": [ + 1, + 2, + 2, + 3, + "NA" + ], + "biotype": [ + "protein_coding", + "protein_coding", + "protein_coding", + "protein_coding", + "protein_coding" + ], + "transcript_length": [ + 148, + 189, + 164, + 177, + 177 + ], + "transcript_count": 5, + "peptide_count": 2, + "total_expr": 5.0729999999999995 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 5 + ], + "peptide_counts": [ + 2 + ], + "set_expr": [ + 5.0729999999999995 + ], + "DNA VAF": 0.324, + "RNA VAF": 0.386, + "gene_expr": 7.144, + "best_peptide_mt": "RSHRLTWTQY", + "best_peptide_wt": "RSHCLTWTQY", + "best_hla_allele": "HLA-A*29:02" + }, + "chr5-150120064-150120065-G-A": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "YTILSDVWSF": { "ic50s_MT": [ - "X", - 296.5249938964844 + 685.1439819335938, + "X" ], "percentiles_MT": [ - "X", - 0.22699999809265137 + 1.600000023841858, + "X" ], "ic50s_WT": [ - "X", - 291.525 + 1367.35, + "X" ], "percentiles_WT": [ - "X", - 0.255 + 2.973, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "5", + "mutation_position": "3", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -128844,27 +146787,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 103.58685483900194, - 18.81, - 403.63, - 41.57, - 576.74, - 283.7, - 309.35, - 736.61 + "HLA-A*29:02": [ + 868.1785230874556, + 4515.77, + 1107.17, + 326.55, + 502.11, + 4936.17, + 408.58, + 352.8 ] }, "WT": { - "HLA-B*45:01": [ - 87.56056248829839, - 10.48, - 333.66, - 52.18, - 787.6, - 254.61, - 328.44, - 855.54 + "HLA-A*29:02": [ + 4553.999798027952, + 5120.99, + 1717.21, + 947.98, + 882.05, + 8297.38, + 918.92, + 1017.49 ] } }, @@ -128880,27 +146823,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 0.2538749873638153, - 0.07000000029802322, - 0.5799999833106995, - 0.15000000596046448, - 0.4300000071525574, - 0.20000000298023224, - 0.2, - 0.3 + "HLA-A*29:02": [ + 1.5966249704360962, + 1.2899999618530273, + 1.7999999523162842, + 1.600000023841858, + 0.6299999952316284, + 3.299999952316284, + 1.8, + 1.6 ] }, "WT": { - "HLA-B*45:01": [ - 0.19575, - 0.02, - 0.48, - 0.23, - 0.52, - 0.2, - 0.2, - 0.3 + "HLA-A*29:02": [ + 3.2467499999999987, + 2.65, + 2.2, + 2.7, + 0.9, + 7.5, + 3.6, + 3.9 ] } }, @@ -128913,21 +146856,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.0713391900062561, - 0.5172041430551221, - 0.536, - 0.037593316, - 0.03722801 + "HLA-A*29:02": [ + 0.1655117645859718, + 0.1593535608494873, + 0.0546, + 0.033417463, + 0.494358 ] }, "WT": { - "HLA-B*45:01": [ - 0.0124877020716667, - 0.5059708083975577, - 0.394, - 0.0031070502, - 0.0038311502 + "HLA-A*29:02": [ + 0.0414019338786602, + 0.0238449692372816, + 0.0393, + 0.010150576, + 0.417809 ] } }, @@ -128940,19 +146883,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.7859510869564019, - 0.16, + 2.1379619565216643, + 1.4, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.8087499999998755, - 0.28, + 10.23198369565216, + 1.7, "NA", "NA" ] @@ -128972,58 +146915,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 0.2538749873638153, - 0.07000000029802322, - 0.5799999833106995, - 0.15000000596046448, - 0.4300000071525574, - 0.20000000298023224, - 0.2, - 0.3, - 0.7859510869564019, - 0.16 + "HLA-A*29:02": [ + 1.5966249704360962, + 1.2899999618530273, + 1.7999999523162842, + 1.600000023841858, + 0.6299999952316284, + 3.299999952316284, + 1.8, + 1.6, + 2.1379619565216643, + 1.4 ] }, "WT": { - "HLA-B*45:01": [ - 0.19575, - 0.02, - 0.48, - 0.23, - 0.52, - 0.2, - 0.2, - 0.3, - 0.8087499999998755, - 0.28 + "HLA-A*29:02": [ + 3.2467499999999987, + 2.65, + 2.2, + 2.7, + 0.9, + 7.5, + 3.6, + 3.9, + 10.23198369565216, + 1.7 ] } }, - "wt_peptide": "SEVEEAAA" + "wt_peptide": "YTTLSDVWSF" }, - "SEVEKAAAII": { + "TILSDVWSF": { "ic50s_MT": [ - "X", - 762.7999877929688 + 2773.2900390625, + "X" ], "percentiles_MT": [ - "X", - 0.824999988079071 + 1.8450000286102295, + "X" ], "ic50s_WT": [ - "X", - 707.635 + 2209.355, + "X" ], "percentiles_WT": [ - "X", - 0.785 + 1.645, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "5", + "mutation_position": "2", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -129038,27 +146981,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 106.06209769444212, - 599.45, - 1503.83, - 649.13, - 813.94, - 711.66, - 3233.63, - 2605.73 + "HLA-A*29:02": [ + 112.0082840571392, + 3435.29, + 2583.39, + 1103.02, + 856.14, + 4478.16, + 2963.19, + 3523.47 ] }, "WT": { - "HLA-B*45:01": [ - 81.11995356878876, - 415.26, - 1994.88, - 663.33, - 741.08, - 674.19, - 2358.79, - 1725.56 + "HLA-A*29:02": [ + 106.47386509660512, + 3747.13, + 2160.52, + 989.9, + 714.64, + 3033.45, + 2258.19, + 3111.5 ] } }, @@ -129074,27 +147017,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 0.2605000138282776, - 1.440000057220459, - 1.7999999523162842, - 0.8500000238418579, - 0.5400000214576721, - 0.800000011920929, - 13.0, - 9.6 + "HLA-A*29:02": [ + 0.4827499985694885, + 0.6299999952316284, + 2.799999952316284, + 2.9000000953674316, + 0.8899999856948853, + 11.0, + 7.0, + 7.9 ] }, "WT": { - "HLA-B*45:01": [ - 0.172625, - 1.15, - 2.2, - 0.87, - 0.5, - 0.7, - 8.7, - 6.6 + "HLA-A*29:02": [ + 0.4591249999999997, + 0.75, + 2.5, + 2.8, + 0.79, + 5.9, + 5.8, + 7.3 ] } }, @@ -129107,21 +147050,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.4738117158412933, - 0.8130430678085877, - 0.14, - 0.0053676004, - 0.00032111714 + "HLA-A*29:02": [ + 0.1096737571060657, + 0.5320940919681094, + 0.197, + 0.10497052, + 0.4472055 ] }, "WT": { - "HLA-B*45:01": [ - 0.2192848809063434, - 0.6963068496216679, - 0.171, - 0.005917755, - 0.00038468078 + "HLA-A*29:02": [ + 0.0887319557368755, + 0.525896796251894, + 0.231, + 0.075033136, + 0.41401687 ] } }, @@ -129134,19 +147077,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.2572826086956468, - 0.8, + 0.7532880434781362, + 0.57, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.4438315217391135, - 0.67, + 0.7659510869564059, + 0.48, "NA", "NA" ] @@ -129166,58 +147109,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 0.2605000138282776, - 1.440000057220459, - 1.7999999523162842, - 0.8500000238418579, - 0.5400000214576721, - 0.800000011920929, - 13.0, - 9.6, - 0.2572826086956468, - 0.8 - ] - }, - "WT": { - "HLA-B*45:01": [ - 0.172625, - 1.15, - 2.2, - 0.87, - 0.5, - 0.7, - 8.7, - 6.6, - 0.4438315217391135, - 0.67 + "HLA-A*29:02": [ + 0.4827499985694885, + 0.6299999952316284, + 2.799999952316284, + 2.9000000953674316, + 0.8899999856948853, + 11.0, + 7.0, + 7.9, + 0.7532880434781362, + 0.57 + ] + }, + "WT": { + "HLA-A*29:02": [ + 0.4591249999999997, + 0.75, + 2.5, + 2.8, + 0.79, + 5.9, + 5.8, + 7.3, + 0.7659510869564059, + 0.48 ] } }, - "wt_peptide": "SEVEEAAAII" + "wt_peptide": "TTLSDVWSF" }, - "SESEVEKA": { + "SIFNSLYTI": { "ic50s_MT": [ - "X", - 777.1900024414062 + 3906.635009765625, + "X" ], "percentiles_MT": [ - "X", - 0.5559999942779541 + 3.563999891281128, + "X" ], "ic50s_WT": [ - "X", - 524.045 + 8291.985, + "X" ], "percentiles_WT": [ - "X", - 0.43 + 9.32, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "7", + "mutation_position": "9", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -129232,27 +147175,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 48.671520544584325, - 109.37, - 1498.81, - 131.59, - 1028.72, - 525.66, - 2309.14, - 3700.33 + "HLA-A*29:02": [ + 5060.531627648274, + 4503.24, + 3992.7, + 4883.05, + 3820.57, + 1746.99, + 2784.58, + 2735.08 ] }, "WT": { - "HLA-B*45:01": [ - 50.40651159923456, - 18.33, - 663.24, - 95.12, - 651.33, - 396.76, - 1700.0, - 1968.97 + "HLA-A*29:02": [ + 18694.452209816827, + 5133.35, + 9950.21, + 12584.95, + 12291.44, + 2693.07, + 6633.76, + 6515.83 ] } }, @@ -129268,27 +147211,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 0.029999999329447746, - 0.4699999988079071, - 1.7999999523162842, - 0.49000000953674316, - 0.6200000047683716, - 0.6000000238418579, - 1.4, - 2.9 + "HLA-A*29:02": [ 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"HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.5583152173912822, - 0.11, + 46.22467391304348, + 8.4, "NA", "NA" ] @@ -129360,58 +147303,102 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 0.029999999329447746, - 0.4699999988079071, - 1.7999999523162842, - 0.49000000953674316, - 0.6200000047683716, - 0.6000000238418579, - 1.4, - 2.9, - 0.5128260869564798, - 0.11 + "HLA-A*29:02": [ + 3.427375078201294, + 1.2699999809265137, + 3.700000047683716, + 6.199999809265137, + 2.4000000953674316, + 2.4000000953674316, + 6.8, + 6.7, + 9.15535326086956, + 3.0 ] }, "WT": { - "HLA-B*45:01": [ - 0.036375, - 0.06, - 0.91, - 0.36, - 0.46, - 0.4, - 0.8, - 1.0, - 0.5583152173912822, - 0.11 + "HLA-A*29:02": [ + 10.239624999999997, + 2.7, + 7.4, + 16.0, + 6.6, + 5.1, + 14.0, + 14.0, + 46.22467391304348, + 8.4 ] } }, - "wt_peptide": "SESEVEEA" - }, - "EVEKAAAIIA": { + "wt_peptide": "SIFNSLYTT" + } + }, + "transcripts": [ + "ENST00000261799.9-PDGFRB-T/I-882" + ], + "transcript_expr": [ + 0.129 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 1106 + ], + "transcript_count": 1, + "peptide_count": 3, + "total_expr": 0.129 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 3 + ], + "set_expr": [ + 0.129 + ], + "DNA VAF": 0.291, + "RNA VAF": 0.0, + "gene_expr": 0.28, + "best_peptide_mt": "YTILSDVWSF", + "best_peptide_wt": "YTTLSDVWSF", + "best_hla_allele": "HLA-A*29:02" + }, + "chr5-177460554-177460555-C-T": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "SESEVEKAA": { "ic50s_MT": [ "X", - 799.344970703125 + 58.84000015258789 ], "percentiles_MT": [ "X", - 3.1500000953674316 + 0.20000000298023224 ], "ic50s_WT": [ "X", - 1022.51 + 48.155 ], "percentiles_WT": [ "X", - 3.525 + 0.145 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "4", + "mutation_position": "7", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -129427,26 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- 5.5 + 0.17 ] } }, - "wt_peptide": "SFTFWVPLC" + "wt_peptide": "KSESEVEEAA" }, - "FIFWVPLCGH": { + "VEKAAAII": { "ic50s_MT": [ - 2365.72998046875, - "X" + "X", + 3184.550048828125 ], "percentiles_MT": [ - 3.549999952316284, - "X" + "X", + 3.015000104904175 ], "ic50s_WT": [ - 1599.23, - "X" + "X", + 2781.588 ], "percentiles_WT": [ - 2.55, - "X" + "X", + 2.6 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "2", + "mutation_position": "3", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -131324,27 +149159,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 12944.171142038967, - 4317.95, - 1068.87, - 1794.89, - 1025.14, - 2936.57, - 3078.08, - 1043.59 + "HLA-B*45:01": [ + 3161.060632899992, + 1488.85, + 12495.8, + 1269.61, + 10960.05, + 1017.05, + 4565.1, + 3208.04 ] }, "WT": { - "HLA-A*29:02": [ - 8812.951461515693, - 4782.41, - 1204.96, - 1209.27, - 667.15, - 1989.19, - 2214.52, - 996.62 + "HLA-B*45:01": [ + 2617.126197714122, 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0.8, - 6.6, - 3.8, - 17.305597826086952, - 2.0 + 2.1, + 6.18413043478256, + 3.5 ] } }, - "wt_peptide": "FTFWVPLCGH" + "wt_peptide": "VEEAAAII" }, - "IFWVPLCGH": { + "VEKAAAIIAQ": { "ic50s_MT": [ - 2986.4619140625, - "X" + "X", + 4286.134765625 ], "percentiles_MT": [ - 2.8959999084472656, - "X" + "X", + 3.434000015258789 ], "ic50s_WT": [ - 3024.8, - "X" + "X", + 2599.724 ], "percentiles_WT": [ - 3.285, - "X" + "X", + 3.2 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "1", + "mutation_position": "3", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -131518,27 +149353,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 3759.974417135593, - 5191.81, - 2212.95, - 6504.5, - 4505.13, - 1691.19, - 1179.67, - 1336.5 + "HLA-B*45:01": [ + 12013.90025795406, + 2243.14, + 1111.31, + 3786.74, + 5398.69, + 2145.7, + 8466.23, + 4785.53 ] }, "WT": { - "HLA-A*29:02": [ - 3656.1133546155775, - 5279.48, - 2507.17, - 6978.43, - 3542.43, - 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0.115, - 0.013199693, - 0.22209296 + 0.0255310051143169, + 0.0161535943735426, + 0.0017, + 0.0020825819, + 0.09304715 ] } }, @@ -132247,8 +150141,8 @@ "MT": { "HLA-A*29:02": [ "NA", - 2.3018478260868847, - 1.9, + 2.356766304347744, + 1.8, "NA", "NA" ] @@ -132256,8 +150150,8 @@ "WT": { "HLA-A*29:02": [ "NA", - 0.9620652173911992, - 0.88, + 14.277038043478257, + 7.4, "NA", "NA" ] @@ -132278,57 +150172,101 @@ ], "MT": { "HLA-A*29:02": [ - 1.3158750534057617, - 5.539999961853027, - 1.899999976158142, - 3.5, - 1.2999999523162842, - 7.699999809265137, - 6.5, - 5.1, - 2.3018478260868847, - 1.9 + 1.3537499904632568, + 8.3100004196167, + 13.0, + 6.400000095367432, + 4.699999809265137, + 26.0, + 7.8, + 13.0, + 2.356766304347744, + 1.8 ] }, "WT": { "HLA-A*29:02": [ - 0.6408749999999998, - 1.78, - 0.89, - 2.1, - 0.44, - 2.2, - 4.0, - 3.1, - 0.9620652173911992, - 0.88 + 3.902999999999999, + 29.43, + 33.0, + 27.0, + 21.0, + 47.0, + 28.0, + 38.0, + 14.277038043478257, + 7.4 ] } }, - "wt_peptide": "CLFYGPVGF" - }, - "LYGPVGFTYI": { + "wt_peptide": "HESPRRGANF" + } + }, + "transcripts": [ + "ENST00000380815.5-GMDS-F/Y-218" + ], + "transcript_expr": [ + 28.948 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 372 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 28.948 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 28.948 + ], + "DNA VAF": 0.212, + "RNA VAF": 0.02, + "gene_expr": 52.423, + "best_peptide_mt": "HESPRRGANY", + "best_peptide_wt": "HESPRRGANF", + "best_hla_allele": "HLA-A*29:02" + }, + "chr6-3723707-3723708-C-G": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "SEFPSQLEDG": { "ic50s_MT": [ - 2491.844970703125, - "X" + "X", + 1952.7249755859375 ], "percentiles_MT": [ - 2.365000009536743, - "X" + "X", + 2.799999952316284 ], "ic50s_WT": [ - 1313.535, - "X" + "X", + 2692.965 ], "percentiles_WT": [ - 1.265, - "X" + "X", + 3.05 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "1", + "mutation_position": "6", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -132343,27 +150281,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 8114.768554338346, - 5066.36, - 612.96, - 4062.65, - 560.82, - 13648.77, - 921.04, - 552.75 + "HLA-B*45:01": [ + 201.12069034142945, + 6952.84, + 3287.7, + 2469.77, + 1805.68, + 2099.77, + 1681.47, + 1422.1 ] }, "WT": { - "HLA-A*29:02": [ - 2902.3455575294624, - 4154.8, - 200.67, - 2077.17, - 137.38, - 9654.43, - 549.9, - 280.24 + "HLA-B*45:01": [ + 204.72796441601048, + 5541.86, + 3502.15, + 2889.29, + 3124.62, + 2496.64, + 983.31, + 1013.75 ] } }, @@ -132379,27 +150317,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 4.486249923706055, - 2.430000066757202, - 1.2999999523162842, - 5.400000095367432, - 0.6800000071525574, - 15.0, - 3.6, - 2.3 + "HLA-B*45:01": [ + 0.48750001192092896, + 7.619999885559082, + 3.0999999046325684, + 2.5, + 0.8999999761581421, + 3.0999999046325684, + 6.5, + 5.6 ] }, "WT": { - "HLA-A*29:02": [ - 2.654999999999999, - 0.97, - 0.62, - 3.8, - 0.27, - 9.2, - 2.3, - 1.3 + "HLA-B*45:01": [ + 0.4953749999999998, + 6.34, + 3.3, + 2.8, + 1.5, + 3.7, + 4.0, + 4.1 ] } }, @@ -132412,21 +150350,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.7634405754506588, - 0.1520627864764565, - 0.149, - 0.010538288, - 0.17445208 + "HLA-B*45:01": [ + 0.0505678281188011, + 0.3431843134807561, + 0.0889, + 9.7441785e-05, + 4.4091306e-05 ] }, "WT": { - "HLA-A*29:02": [ - 0.7786610201001167, - 0.3394046619845349, - 0.357, - 0.058572385, - 0.34763685 + "HLA-B*45:01": [ + 0.0463449135422706, + 0.3359612531551675, + 0.0473, + 7.379708e-05, + 3.691524e-05 ] } }, @@ -132439,19 +150377,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 2.211847826086881, - 0.71, + 1.2209510869564042, + 1.1, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 1.230081521738995, - 0.31, + 1.2431249999998784, + 1.6, "NA", "NA" ] @@ -132471,58 +150409,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 4.486249923706055, - 2.430000066757202, - 1.2999999523162842, - 5.400000095367432, - 0.6800000071525574, - 15.0, - 3.6, - 2.3, - 2.211847826086881, - 0.71 + "HLA-B*45:01": [ + 0.48750001192092896, + 7.619999885559082, + 3.0999999046325684, + 2.5, + 0.8999999761581421, + 3.0999999046325684, + 6.5, + 5.6, + 1.2209510869564042, + 1.1 ] }, "WT": { - "HLA-A*29:02": [ - 2.654999999999999, - 0.97, - 0.62, - 3.8, - 0.27, - 9.2, - 2.3, - 1.3, - 1.230081521738995, - 0.31 + "HLA-B*45:01": [ + 0.4953749999999998, + 6.34, + 3.3, + 2.8, + 1.5, + 3.7, + 4.0, + 4.1, + 1.2431249999998784, + 1.6 ] } }, - "wt_peptide": "FYGPVGFTYI" + "wt_peptide": "SEFPSELEDG" }, - "HFMVVCLLYG": { + "SEFPSQLED": { "ic50s_MT": [ - 2572.889892578125, - "X" + "X", + 2200.85498046875 ], "percentiles_MT": [ - 2.799999952316284, - "X" + "X", + 2.25 ], "ic50s_WT": [ - 2115.76, - "X" + "X", + 2216.3 ], "percentiles_WT": [ - 2.55, - "X" + "X", + 2.4 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "8", + "mutation_position": "6", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -132537,27 +150475,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 22179.740075071528, - 5415.14, - 133.23, - 9865.62, - 191.22, - 4478.16, - 406.71, - 667.62 + "HLA-B*45:01": [ + 151.32691159227738, + 4436.22, + 2922.08, + 2192.64, + 2242.96, + 638.68, + 2209.07, + 691.23 ] }, "WT": { - "HLA-A*29:02": [ - 21111.886183898485, - 5449.36, - 191.28, - 10933.64, - 313.06, - 3646.02, - 391.99, - 585.5 + "HLA-B*45:01": [ + 172.6859685493537, + 2313.21, + 3087.86, + 3587.33, + 4364.69, + 864.68, + 2119.39, + 564.44 ] } }, @@ -132573,27 +150511,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 13.71875, - 4.659999847412109, - 0.47999998927116394, - 12.0, - 0.3499999940395355, + "HLA-B*45:01": [ + 0.3863750100135803, + 5.380000114440918, + 2.9000000953674316, 2.799999952316284, - 1.8, - 2.8 + 1.2000000476837158, + 2.0, + 8.2, + 2.5 ] }, "WT": { - "HLA-A*29:02": [ - 12.580124999999995, - 5.08, - 0.6, - 13.0, - 0.46, - 2.0, - 1.8, - 2.4 + "HLA-B*45:01": [ + 0.4336249999999997, + 3.41, + 3.0, + 3.4, + 1.9, + 2.8, + 7.9, + 2.0 ] } }, @@ -132606,21 +150544,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.0063188076019287, - 0.004614174959331, - 0.0252, - 0.01351472, - 0.373487 + "HLA-B*45:01": [ + 0.0493033304810524, + 0.4067792415544211, + 0.163, + 0.00051207596, + 2.412473e-05 ] }, "WT": { - "HLA-A*29:02": [ - 0.002848457545042, - 0.0047808416737538, - 0.0141, - 0.0057845223, - 0.43725058 + "HLA-B*45:01": [ + 0.0282067582011222, + 0.3588892586299282, + 0.0867, + 0.00024191305, + 1.7483295e-05 ] } }, @@ -132633,19 +150571,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 62.74467391304348, - 2.1, + 1.0393749999998647, + 0.69, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 62.74467391304348, - 2.7, + 1.1706249999998732, + 1.1, "NA", "NA" ] @@ -132665,58 +150603,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 13.71875, - 4.659999847412109, - 0.47999998927116394, - 12.0, - 0.3499999940395355, + "HLA-B*45:01": [ + 0.3863750100135803, + 5.380000114440918, + 2.9000000953674316, 2.799999952316284, - 1.8, - 2.8, - 62.74467391304348, - 2.1 + 1.2000000476837158, + 2.0, + 8.2, + 2.5, + 1.0393749999998647, + 0.69 ] }, "WT": { - "HLA-A*29:02": [ - 12.580124999999995, - 5.08, - 0.6, - 13.0, - 0.46, + "HLA-B*45:01": [ + 0.4336249999999997, + 3.41, + 3.0, + 3.4, + 1.9, + 2.8, + 7.9, 2.0, - 1.8, - 2.4, - 62.74467391304348, - 2.7 + 1.1706249999998732, + 1.1 ] } }, - "wt_peptide": "HFMVVCLFYG" + "wt_peptide": "SEFPSELED" }, - "FMVVCLLYG": { + "FENGSEFPSQ": { "ic50s_MT": [ - 3692.97509765625, - "X" + "X", + 3773.7109375 ], "percentiles_MT": [ - 5.900000095367432, - "X" + "X", + 6.5 ], "ic50s_WT": [ - 3746.815, - "X" + "X", + 3730.899 ], "percentiles_WT": [ - 5.3, - "X" + "X", + 5.65 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "7", + "mutation_position": "10", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -132731,27 +150669,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 18092.30207443289, - 4916.18, - 2261.97, - 6229.0, - 14080.17, - 2469.77, - 899.0, - 442.56 + "HLA-B*45:01": [ + 3485.89228853872, + 16384.96, + 6781.99, + 3254.47, + 15764.12, + 2192.64, + 4061.53, + 2709.75 ] }, "WT": { - "HLA-A*29:02": [ - 15753.553325944104, - 5069.06, - 2424.57, - 7446.48, - 12162.07, - 1785.2, - 1232.42, - 517.57 + "HLA-B*45:01": [ + 4136.13867148239, + 14621.54, + 6484.62, + 3325.66, + 14441.05, + 1584.89, + 2016.93, + 1541.45 ] } }, @@ -132767,27 +150705,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 9.764249801635742, - 1.9800000190734863, - 2.5999999046325684, - 7.400000095367432, - 7.800000190734863, - 4.400000095367432, - 3.3, - 2.1 + "HLA-B*45:01": [ + 1.8927500247955322, + 17.440000534057617, + 5.199999809265137, + 3.0, + 6.099999904632568, + 3.200000047683716, + 16.0, + 10.0 ] }, "WT": { - "HLA-A*29:02": [ - 8.091874999999998, - 2.44, - 2.7, - 8.5, - 6.6, - 2.5, - 4.0, - 2.4 + "HLA-B*45:01": [ + 2.032125, + 15.32, + 5.0, + 3.1, + 5.4, + 2.1, + 7.7, + 5.9 ] } }, @@ -132800,21 +150738,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.000414203852415, - 0.0055025220445944, - 3.1e-05, - 0.05972474, - 0.81575596 - ] - }, + "HLA-B*45:01": [ + 0.0310472846031188, + 0.0296251398737464, + 0.0022, + 0.0021445858, + 0.00090230803 + ] + }, "WT": { - "HLA-A*29:02": [ - 0.0004966221749782, - 0.0062912516252914, - 2.3e-05, - 0.026595948, - 0.8077242 + "HLA-B*45:01": [ + 0.0171150751411914, + 0.024021483377448, + 0.00179, + 0.0016754934, + 0.0009789811 ] } }, @@ -132827,19 +150765,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 46.22467391304348, - 42.0, + 8.269211956521715, + 6.9, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 37.35904891304347, - 46.0, + 10.23198369565216, + 7.5, "NA", "NA" ] @@ -132859,60 +150797,109 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 9.764249801635742, - 1.9800000190734863, - 2.5999999046325684, - 7.400000095367432, - 7.800000190734863, - 4.400000095367432, - 3.3, - 2.1, - 46.22467391304348, - 42.0 + "HLA-B*45:01": [ + 1.8927500247955322, + 17.440000534057617, + 5.199999809265137, + 3.0, + 6.099999904632568, + 3.200000047683716, + 16.0, + 10.0, + 8.269211956521715, + 6.9 ] }, "WT": { - "HLA-A*29:02": [ - 8.091874999999998, - 2.44, - 2.7, - 8.5, - 6.6, - 2.5, - 4.0, - 2.4, - 37.35904891304347, - 46.0 + "HLA-B*45:01": [ + 2.032125, + 15.32, + 5.0, + 3.1, + 5.4, + 2.1, + 7.7, + 5.9, + 10.23198369565216, + 7.5 ] } }, - "wt_peptide": "FMVVCLFYG" - }, - "HFMVVCLLY": { + "wt_peptide": "FENGSEFPSE" + } + }, + "transcripts": [ + "ENST00000380283.5-PXDC1-E/Q-203", + "ENST00000380277.6-PXDC1-E/Q-151" + ], + "transcript_expr": [ + 12.155, + 5.998 + ], + "tsl": [ + 1, + 3 + ], + "biotype": [ + "protein_coding", + "protein_coding" + ], + "transcript_length": [ + 231, + 179 + ], + "transcript_count": 2, + "peptide_count": 3, + "total_expr": 18.153 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 2 + ], + "peptide_counts": [ + 3 + ], + "set_expr": [ + 18.153 + ], + "DNA VAF": 0.418, + "RNA VAF": 0.539, + "gene_expr": 22.483, + "best_peptide_mt": "SEFPSQLEDG", + "best_peptide_wt": "SEFPSELEDG", + "best_hla_allele": "HLA-B*45:01" + }, + "chr6-10801907-10801908-C-G": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "NWDPKKPPTA": { "ic50s_MT": [ - 7.215000152587891, - "X" + "X", + 22818.2421875 ], "percentiles_MT": [ - 0.06499999761581421, - "X" + "X", + 25.5 ], "ic50s_WT": [ - 11.27, - "X" + "X", + 29208.615 ], "percentiles_WT": [ - 0.095, - "X" + "X", + 33.0 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "8", + "mutation_position": "7", "problematic_positions": "None", - "anchor_fails": "HLA-A*29:02", + "anchor_fails": "None", "individual_ic50_calls": { "algorithms": [ "MHCflurry", @@ -132925,27 +150912,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 25.47472477827301, - 586.87, - 7.04, - 4.4, - 7.39, - 188.06, - 6.51, - 5.35 + "HLA-B*45:01": [ + 21393.90322775185, + 24242.58, + 40435.86, + 38150.11, + 35256.96, + 21040.32, + 4771.89, + 7276.63 ] }, "WT": { - "HLA-A*29:02": [ - 25.09662235396695, - 576.61, - 9.47, - 5.65, - 10.13, - 209.55, - 12.41, - 9.98 + "HLA-B*45:01": [ + 24585.521032728648, + 32293.7, + 41427.85, + 38984.65, + 35027.31, + 26123.53, + 4771.89, + 6697.77 ] } }, @@ -132961,27 +150948,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 0.014624999836087227, - 0.009999999776482582, - 0.029999999329447746, - 0.07000000029802322, - 0.019999999552965164, - 0.10000000149011612, - 0.2, - 0.2 + "HLA-B*45:01": [ + 7.0551252365112305, + 29.889999389648438, + 44.0, + 47.0, + 34.0, + 27.0, + 18.0, + 24.0 ] }, "WT": { - "HLA-A*29:02": [ - 0.0132499999999999, - 0.01, - 0.05, - 0.1, - 0.03, - 0.2, - 0.2, - 0.2 + "HLA-B*45:01": [ + 10.885249999999996, + 52.59, + 48.0, + 51.0, + 33.0, + 33.0, + 18.0, + 23.0 ] } }, @@ -132994,21 +150981,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.1179754547774791, - 0.8315131016562805, - 0.8, - 0.9577649, - 0.9472173 + "HLA-B*45:01": [ + 0.2312996760010719, + 0.010529948943739, + 0.00197, + 0.003857199, + 0.18275487 ] }, "WT": { - "HLA-A*29:02": [ - 0.0581217817962169, - 0.8020480441378723, - 0.709, - 0.88869923, - 0.91494805 + "HLA-B*45:01": [ + 0.11194659024477, + 0.006057988734953, + 0.00108, + 0.0012843385, + 0.12717906 ] } }, @@ -133021,19 +151008,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 0.2287228260869653, - 0.06, + 22.19230978260869, + 7.2, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 0.274510869565205, - 0.09, + 37.35904891304347, + 9.3, "NA", "NA" ] @@ -133053,60 +151040,104 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 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0.47594354 ] }, "WT": { "HLA-A*29:02": [ - 0.9503531157970428, - 0.9908807864381948, - 0.985, - 0.9951738, - 0.929759 + 0.0043031983077526, + 0.0059103354205932, + 0.00316, + 0.0872932, + 0.4748859 ] } }, @@ -133217,8 +151248,8 @@ "MT": { "HLA-A*29:02": [ "NA", - 0.0016847826086774, - 0.01, + 24.57923913043477, + 4.2, "NA", "NA" ] @@ -133226,8 +151257,8 @@ "WT": { "HLA-A*29:02": [ "NA", - 0.0011141304347574, - 0.01, + 46.22467391304348, + 5.5, "NA", "NA" ] @@ -133248,59 +151279,59 @@ ], "MT": { "HLA-A*29:02": [ - 0.017124999314546585, - 0.05000000074505806, - 0.18000000715255737, - 0.3799999952316284, - 0.05000000074505806, - 0.699999988079071, - 0.4, - 0.3, - 0.0016847826086774, - 0.01 + 5.903625011444092, + 2.0899999141693115, + 2.200000047683716, + 4.199999809265137, + 3.5999999046325684, + 3.0999999046325684, + 2.0, + 1.7, + 24.57923913043477, + 4.2 ] }, "WT": { "HLA-A*29:02": [ - 0.003125, - 0.01, - 0.08, - 0.2, - 0.02, - 0.4, - 0.3, - 0.2, - 0.0011141304347574, - 0.01 + 8.916624999999996, + 2.42, + 4.1, + 7.5, + 4.9, + 7.1, + 3.4, + 2.9, + 46.22467391304348, + 5.5 ] } }, - "wt_peptide": "FYGPVGFTY" + "wt_peptide": "SFTFWVPLC" }, - "SHFMVVCLLY": { + "FIFWVPLCGH": { "ic50s_MT": [ - 44.005001068115234, + 2365.72998046875, "X" ], "percentiles_MT": [ - 0.26499998569488525, + 3.549999952316284, "X" ], "ic50s_WT": [ - 41.735, + 1599.23, "X" ], "percentiles_WT": [ - 0.36, + 2.55, "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "9", + "mutation_position": "2", "problematic_positions": "None", - "anchor_fails": "HLA-A*29:02", + "anchor_fails": "None", "individual_ic50_calls": { "algorithms": [ "MHCflurry", @@ -133314,26 +151345,26 @@ ], "MT": { "HLA-A*29:02": [ - 167.53107868406028, - 1673.01, - 19.8, - 52.18, - 17.14, - 1290.38, - 35.83, - 22.88 + 12944.171142038967, + 4317.95, + 1068.87, + 1794.89, + 1025.14, + 2936.57, + 3078.08, + 1043.59 ] }, "WT": { "HLA-A*29:02": [ - 131.2589287964622, - 2193.81, - 25.96, - 57.51, - 23.38, - 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0.0515662990510463, + 0.0131591853360683, + 0.026, + 0.018082896, + 0.32514498 ] } }, @@ -133411,8 +151442,8 @@ "MT": { "HLA-A*29:02": [ "NA", - 1.036603260869441, - 0.32, + 24.57923913043477, + 3.5, "NA", "NA" ] @@ -133420,8 +151451,8 @@ "WT": { "HLA-A*29:02": [ "NA", - 0.9296739130433592, - 0.45, + 17.305597826086952, + 2.0, "NA", "NA" ] @@ -133442,59 +151473,59 @@ ], "MT": { "HLA-A*29:02": [ - 0.6694999933242798, - 0.23000000417232513, - 0.12999999523162842, - 0.4399999976158142, - 0.05999999865889549, - 0.30000001192092896, - 0.2, - 0.2, - 1.036603260869441, - 0.32 + 6.538374900817871, + 1.090000033378601, + 1.7999999523162842, + 3.5999999046325684, + 0.9900000095367432, + 1.2999999523162842, + 8.3, + 3.9, + 24.57923913043477, + 3.5 ] }, "WT": { "HLA-A*29:02": [ - 0.5577499999999996, - 0.32, - 0.15, - 0.48, - 0.08, - 0.4, - 0.2, - 0.2, - 0.9296739130433592, - 0.45 + 4.718624999999999, + 1.69, + 1.9, + 3.1, + 0.75, + 0.8, + 6.6, + 3.8, + 17.305597826086952, + 2.0 ] } }, - "wt_peptide": "SHFMVVCLFY" + "wt_peptide": "FTFWVPLCGH" }, - "LLYGPVGFTY": { + "IFWVPLCGH": { "ic50s_MT": [ - 78.76499938964844, + 2986.4619140625, "X" ], "percentiles_MT": [ - 0.07500000298023224, + 2.8959999084472656, "X" ], "ic50s_WT": [ - 29.894, + 3024.8, "X" ], "percentiles_WT": [ - 0.035, + 3.285, "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "2", + "mutation_position": "1", "problematic_positions": "None", - "anchor_fails": "HLA-A*29:02", + "anchor_fails": "None", "individual_ic50_calls": { "algorithms": [ "MHCflurry", @@ -133508,26 +151539,26 @@ ], "MT": { "HLA-A*29:02": [ - 29.13970333120221, - 741.76, - 29.13, - 18.97, - 12.76, - 883.6, - 160.8, - 128.39 + 3759.974417135593, + 5191.81, + 2212.95, + 6504.5, + 4505.13, + 1691.19, + 1179.67, + 1336.5 ] }, "WT": { "HLA-A*29:02": [ - 24.98773487002895, - 567.93, - 9.35, - 8.75, - 5.74, - 520.0, - 36.41, - 34.8 + 3656.1133546155775, + 5279.48, + 2507.17, + 6978.43, + 3542.43, + 2010.83, + 1326.66, + 1827.97 ] } }, @@ -133544,26 +151575,26 @@ ], "MT": { "HLA-A*29:02": [ - 0.03175000101327896, - 0.05000000074505806, - 0.17000000178813934, - 0.10000000149011612, - 0.03999999910593033, - 0.20000000298023224, - 0.8, - 0.6 + 2.9744999408721924, + 2.9600000381469727, + 2.5999999046325684, + 7.599999904632568, + 2.700000047683716, + 2.200000047683716, + 3.9, + 4.3 ] }, "WT": { "HLA-A*29:02": [ - 0.0132499999999999, - 0.01, - 0.05, - 0.02, - 0.02, - 0.2, - 0.2, - 0.2 + 2.9311249999999984, + 3.47, + 2.7, + 8.1, + 2.3, + 3.1, + 4.3, + 5.0 ] } }, @@ -133577,20 +151608,20 @@ ], "MT": { "HLA-A*29:02": [ - 0.5768589898943901, - 0.9564539694063896, - 0.846, - 0.9048465, - 0.9454332 + 0.4324104785919189, + 0.1050337683636792, + 0.0178, + 0.010522689, + 0.20256114 ] }, "WT": { "HLA-A*29:02": [ - 0.4810018204152584, - 0.9478252791536952, - 0.944, - 0.985465, - 0.9089304 + 0.1944323033094406, + 0.0493929717682249, + 0.0329, + 0.018638264, + 0.19563405 ] } }, @@ -133605,8 +151636,8 @@ "MT": { "HLA-A*29:02": [ "NA", - 0.0383152173913146, - 0.04, + 2.832907608695578, + 2.4, "NA", "NA" ] @@ -133614,8 +151645,8 @@ "WT": { "HLA-A*29:02": [ "NA", - 0.0509510869565446, - 0.02, + 5.149211956521697, + 1.8, "NA", "NA" ] @@ -133636,59 +151667,59 @@ ], "MT": { "HLA-A*29:02": [ - 0.03175000101327896, - 0.05000000074505806, - 0.17000000178813934, - 0.10000000149011612, - 0.03999999910593033, - 0.20000000298023224, - 0.8, - 0.6, - 0.0383152173913146, - 0.04 + 2.9744999408721924, + 2.9600000381469727, + 2.5999999046325684, + 7.599999904632568, + 2.700000047683716, + 2.200000047683716, + 3.9, + 4.3, + 2.832907608695578, + 2.4 ] }, "WT": { "HLA-A*29:02": [ - 0.0132499999999999, - 0.01, - 0.05, - 0.02, - 0.02, - 0.2, - 0.2, - 0.2, - 0.0509510869565446, - 0.02 + 2.9311249999999984, + 3.47, + 2.7, + 8.1, + 2.3, + 3.1, + 4.3, + 5.0, + 5.149211956521697, + 1.8 ] } }, - "wt_peptide": "LFYGPVGFTY" + "wt_peptide": "TFWVPLCGH" }, - "FMVVCLLY": { + "ISALHSSFIF": { "ic50s_MT": [ - 421.3380126953125, + 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"WT": { - "HLA-B*45:01": [ - 71.34989046488244, - 1391.96, - 280.91, - 621.64, - 185.81, - 330.1, - 1365.24, - 947.59 + "HLA-A*29:02": [ + 15753.553325944104, + 5069.06, + 2424.57, + 7446.48, + 12162.07, + 1785.2, + 1232.42, + 517.57 ] } }, @@ -134800,27 +152787,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 0.1626249998807907, - 2.8399999141693115, - 0.5299999713897705, - 1.7999999523162842, - 0.17000000178813934, - 0.8999999761581421, - 6.1, - 4.5 + "HLA-A*29:02": [ + 9.764249801635742, + 1.9800000190734863, + 2.5999999046325684, + 7.400000095367432, + 7.800000190734863, + 4.400000095367432, + 3.3, + 2.1 ] }, "WT": { - "HLA-B*45:01": [ - 0.135625, - 2.42, - 0.42, - 1.2, - 0.18, - 0.8, - 5.2, - 3.6 + "HLA-A*29:02": [ + 8.091874999999998, + 2.44, + 2.7, + 8.5, + 6.6, + 2.5, + 4.0, + 2.4 ] } }, @@ -134833,21 +152820,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.0151928216218948, - 0.536615942271981, - 0.32, - 0.000117507836, - 1.6514434e-05 + "HLA-A*29:02": [ + 0.000414203852415, + 0.0055025220445944, + 3.1e-05, + 0.05972474, + 0.81575596 ] }, "WT": { - "HLA-B*45:01": [ - 0.0619797892868518, - 0.5981742772454897, - 0.374, - 0.00049899245, - 3.8871727e-05 + "HLA-A*29:02": [ + 0.0004966221749782, + 0.0062912516252914, + 2.3e-05, + 0.026595948, + 0.8077242 ] } }, @@ -134860,19 +152847,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.7437499999998778, - 0.35, + 46.22467391304348, + 42.0, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.61907608695644, - 0.29, + 37.35904891304347, + 46.0, "NA", "NA" ] @@ -134892,60 +152879,60 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 0.1626249998807907, - 2.8399999141693115, - 0.5299999713897705, - 1.7999999523162842, - 0.17000000178813934, - 0.8999999761581421, - 6.1, - 4.5, - 0.7437499999998778, - 0.35 + "HLA-A*29:02": [ + 9.764249801635742, + 1.9800000190734863, + 2.5999999046325684, + 7.400000095367432, + 7.800000190734863, + 4.400000095367432, + 3.3, + 2.1, + 46.22467391304348, + 42.0 ] }, "WT": { - "HLA-B*45:01": [ - 0.135625, - 2.42, - 0.42, - 1.2, - 0.18, - 0.8, - 5.2, - 3.6, - 0.61907608695644, - 0.29 + "HLA-A*29:02": [ + 8.091874999999998, + 2.44, + 2.7, + 8.5, + 6.6, + 2.5, + 4.0, + 2.4, + 37.35904891304347, + 46.0 ] } }, - "wt_peptide": "SEFSTVSSG" + "wt_peptide": "FMVVCLFYG" }, - "SEFSTASS": { + "HFMVVCLLY": { "ic50s_MT": [ - "X", - 2438.4599609375 + 7.215000152587891, + "X" ], "percentiles_MT": [ - "X", - 1.4500000476837158 + 0.06499999761581421, + "X" ], "ic50s_WT": [ - "X", - 1567.61 + 11.27, + "X" ], "percentiles_WT": [ - "X", - 1.091 + 0.095, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "6", + "mutation_position": "8", "problematic_positions": "None", - "anchor_fails": "None", + "anchor_fails": "HLA-A*29:02", "individual_ic50_calls": { "algorithms": [ "MHCflurry", @@ -134958,27 +152945,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 2761.1301078608776, - 280.83, - 3031.74, - 356.07, - 2225.67, - 681.52, - 2651.25, - 8170.34 + "HLA-A*29:02": [ + 25.47472477827301, + 586.87, + 7.04, + 4.4, + 7.39, + 188.06, + 6.51, + 5.35 ] }, "WT": { - "HLA-B*45:01": [ - 1299.959054888819, - 149.69, - 2616.7, - 265.87, - 1835.26, - 652.65, - 6523.04, - 14231.15 + "HLA-A*29:02": [ + 25.09662235396695, + 576.61, + 9.47, + 5.65, + 10.13, + 209.55, + 12.41, + 9.98 ] } }, @@ -134994,27 +152981,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 1.718000054359436, - 0.8999999761581421, - 3.0, - 0.8100000023841858, - 1.2000000476837158, - 0.8999999761581421, - 1.7, - 8.6 + "HLA-A*29:02": [ + 0.014624999836087227, + 0.009999999776482582, + 0.029999999329447746, + 0.07000000029802322, + 0.019999999552965164, + 0.10000000149011612, + 0.2, + 0.2 ] }, "WT": { - "HLA-B*45:01": [ - 1.2624999999999982, - 0.59, - 2.6, - 0.73, - 0.92, - 0.8, - 6.2, - 19.0 + "HLA-A*29:02": [ + 0.0132499999999999, + 0.01, + 0.05, + 0.1, + 0.03, + 0.2, + 0.2, + 0.2 ] } }, @@ -135027,21 +153014,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.0088712982833385, - 0.0341873642186582, - 0.0901, - 0.0009710548, - 0.0014565507 + "HLA-A*29:02": [ + 0.1179754547774791, + 0.8315131016562805, + 0.8, + 0.9577649, + 0.9472173 ] }, "WT": { - "HLA-B*45:01": [ - 0.0255561433732509, - 0.0724027651445963, - 0.15, - 0.0035708647, - 0.0015503152 + "HLA-A*29:02": [ + 0.0581217817962169, + 0.8020480441378723, + 0.709, + 0.88869923, + 0.91494805 ] } }, @@ -135054,19 +153041,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 7.147065217391287, - 1.1, + 0.2287228260869653, + 0.06, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 3.720108695652101, - 0.75, + 0.274510869565205, + 0.09, "NA", "NA" ] @@ -135086,104 +153073,60 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 1.718000054359436, - 0.8999999761581421, - 3.0, - 0.8100000023841858, - 1.2000000476837158, - 0.8999999761581421, - 1.7, - 8.6, - 7.147065217391287, - 1.1 + "HLA-A*29:02": [ + 0.014624999836087227, + 0.009999999776482582, + 0.029999999329447746, + 0.07000000029802322, + 0.019999999552965164, + 0.10000000149011612, + 0.2, + 0.2, + 0.2287228260869653, + 0.06 ] }, "WT": { - "HLA-B*45:01": [ - 1.2624999999999982, - 0.59, - 2.6, - 0.73, - 0.92, - 0.8, - 6.2, - 19.0, - 3.720108695652101, - 0.75 + "HLA-A*29:02": [ + 0.0132499999999999, + 0.01, + 0.05, + 0.1, + 0.03, + 0.2, + 0.2, + 0.2, + 0.274510869565205, + 0.09 ] } }, - "wt_peptide": "SEFSTVSS" - } - }, - "transcripts": [ - "ENST00000376296.3-MUC21-V/A-98" - ], - "transcript_expr": [ - 0.025 - ], - "tsl": [ - 1 - ], - "biotype": [ - "protein_coding" - ], - "transcript_length": [ - 566 - ], - "transcript_count": 1, - "peptide_count": 3, - "total_expr": 0.025 - } - }, - "sets": [ - "Transcript Set 1" - ], - "transcript_counts": [ - 1 - ], - "peptide_counts": [ - 3 - ], - "set_expr": [ - 0.025 - ], - "DNA VAF": 0.662, - "RNA VAF": 0.0, - "gene_expr": 0.123, - "best_peptide_mt": "SEFSTASSGI", - "best_peptide_wt": "SEFSTVSSGI", - "best_hla_allele": "HLA-B*45:01" - }, - "chr6-32181195-32181196-G-T": { - "good_binders": { - "Transcript Set 1": { - "peptides": { - "AEMNQSEEP": { + "wt_peptide": "HFMVVCLFY" + }, + "LYGPVGFTY": { "ic50s_MT": [ - "X", - 262.30999755859375 + 34.56999969482422, + "X" ], "percentiles_MT": [ - "X", - 0.6000000238418579 + 0.11500000208616257, + "X" ], "ic50s_WT": [ - "X", - 415.285 + 19.881, + "X" ], "percentiles_WT": [ - "X", - 1.095 + 0.05, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "3", + "mutation_position": "1", "problematic_positions": "None", - "anchor_fails": "None", + "anchor_fails": "HLA-A*29:02", "individual_ic50_calls": { "algorithms": [ "MHCflurry", @@ -135196,27 +153139,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 43.86322346022311, - 130.12, - 994.52, - 282.17, - 51.02, - 418.82, - 283.28, - 242.45 + "HLA-A*29:02": [ + 25.95760568092118, + 747.54, + 32.83, + 27.86, + 14.4, + 864.68, + 50.32, + 36.31 ] }, "WT": { - "HLA-B*45:01": [ - 47.43452142494411, - 229.28, - 4113.33, - 917.7, - 263.14, - 681.52, - 448.96, - 381.61 + "HLA-A*29:02": [ + 21.902413590693968, + 562.83, + 13.62, + 11.35, + 7.32, + 611.63, + 24.53, + 17.86 ] } }, @@ -135232,27 +153175,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 0.01412499975413084, - 0.5400000214576721, - 1.2999999523162842, - 0.6600000262260437, - 0.07000000029802322, - 1.100000023841858, - 1.1, - 1.0 + "HLA-A*29:02": [ + 0.017124999314546585, + 0.05000000074505806, + 0.18000000715255737, + 0.3799999952316284, + 0.05000000074505806, + 0.699999988079071, + 0.4, + 0.3 ] }, "WT": { - "HLA-B*45:01": [ - 0.02575, - 0.79, - 3.7, - 1.6, - 0.23, - 2.2, - 1.6, - 1.4 + "HLA-A*29:02": [ + 0.003125, + 0.01, + 0.08, + 0.2, + 0.02, + 0.4, + 0.3, + 0.2 ] } }, @@ -135265,21 +153208,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.0682407319545745, - 0.7094260309442599, - 0.935, - 0.10140984, - 0.0094343545 + "HLA-A*29:02": [ + 0.9201952368021012, + 0.9880677509472188, + 0.964, + 0.9834265, + 0.8918852 ] }, "WT": { - "HLA-B*45:01": [ - 0.0702307745814323, - 0.6950015459613194, - 0.831, - 0.02680006, - 0.002382436 + "HLA-A*29:02": [ + 0.9503531157970428, + 0.9908807864381948, + 0.985, + 0.9951738, + 0.929759 ] } }, @@ -135292,19 +153235,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.4232336956521578, + 0.0016847826086774, 0.01, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.4456249999999784, - 0.04, + 0.0011141304347574, + 0.01, "NA", "NA" ] @@ -135324,60 +153267,60 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 0.01412499975413084, - 0.5400000214576721, - 1.2999999523162842, - 0.6600000262260437, - 0.07000000029802322, - 1.100000023841858, - 1.1, - 1.0, - 0.4232336956521578, + "HLA-A*29:02": [ + 0.017124999314546585, + 0.05000000074505806, + 0.18000000715255737, + 0.3799999952316284, + 0.05000000074505806, + 0.699999988079071, + 0.4, + 0.3, + 0.0016847826086774, 0.01 ] }, "WT": { - "HLA-B*45:01": [ - 0.02575, - 0.79, - 3.7, - 1.6, - 0.23, - 2.2, - 1.6, - 1.4, - 0.4456249999999784, - 0.04 + "HLA-A*29:02": [ + 0.003125, + 0.01, + 0.08, + 0.2, + 0.02, + 0.4, + 0.3, + 0.2, + 0.0011141304347574, + 0.01 ] } }, - "wt_peptide": "AELNQSEEP" + "wt_peptide": "FYGPVGFTY" }, - "AEMNQSEEPE": { + "SHFMVVCLLY": { "ic50s_MT": [ - "X", - 1243.594970703125 + 44.005001068115234, + "X" ], "percentiles_MT": [ - "X", - 1.5499999523162842 + 0.26499998569488525, + "X" ], "ic50s_WT": [ - "X", - 2271.165 + 41.735, + "X" ], "percentiles_WT": [ - "X", - 3.47 + 0.36, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "3", + "mutation_position": "9", "problematic_positions": "None", - "anchor_fails": "None", + "anchor_fails": "HLA-A*29:02", "individual_ic50_calls": { "algorithms": [ "MHCflurry", @@ -135390,27 +153333,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 1680.4338430168684, - 1523.7, - 2182.09, - 963.49, - 3112.71, - 625.01, - 584.37, - 465.51 + "HLA-A*29:02": [ + 167.53107868406028, + 1673.01, + 19.8, + 52.18, + 17.14, + 1290.38, + 35.83, + 22.88 ] }, "WT": { - "HLA-B*45:01": [ - 2819.04941662414, - 2045.44, - 5276.21, - 2483.17, - 9960.76, - 1017.05, - 2059.16, - 1595.62 + "HLA-A*29:02": [ + 131.2589287964622, + 2193.81, + 25.96, + 57.51, + 23.38, + 1407.05, + 21.49, + 12.4 ] } }, @@ -135426,27 +153369,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 1.3954999446868896, - 2.569999933242798, - 2.299999952316284, - 1.2999999523162842, - 1.5, - 0.6000000238418579, - 2.2, - 1.6 + "HLA-A*29:02": [ + 0.6694999933242798, + 0.23000000417232513, + 0.12999999523162842, + 0.4399999976158142, + 0.05999999865889549, + 0.30000001192092896, + 0.2, + 0.2 ] }, "WT": { - "HLA-B*45:01": [ - 1.7331249999999985, - 3.14, - 4.3, - 2.5, - 3.8, - 1.2, - 7.8, - 6.2 + "HLA-A*29:02": [ + 0.5577499999999996, + 0.32, + 0.15, + 0.48, + 0.08, + 0.4, + 0.2, + 0.2 ] } }, @@ -135459,21 +153402,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.008710578083992, - 0.054201550225973, - 0.0573, - 0.00035590006, - 0.00011967833 + "HLA-A*29:02": [ + 0.0787721164524555, + 0.4080955545697046, + 0.339, + 0.33517784, + 0.97072506 ] }, "WT": { - "HLA-B*45:01": [ - 0.011358980089426, - 0.0338141453110785, - 0.019, - 0.00025093034, - 6.0612983e-05 + "HLA-A*29:02": [ + 0.0622620210051536, + 0.4518369264852817, + 0.245, + 0.16830172, + 0.96454734 ] } }, @@ -135486,19 +153429,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 4.732201086956479, - 1.5, + 1.036603260869441, + 0.32, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 7.348016304347794, - 2.7, + 0.9296739130433592, + 0.45, "NA", "NA" ] @@ -135518,60 +153461,60 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 1.3954999446868896, - 2.569999933242798, - 2.299999952316284, - 1.2999999523162842, - 1.5, - 0.6000000238418579, - 2.2, - 1.6, - 4.732201086956479, - 1.5 + "HLA-A*29:02": [ + 0.6694999933242798, + 0.23000000417232513, + 0.12999999523162842, + 0.4399999976158142, + 0.05999999865889549, + 0.30000001192092896, + 0.2, + 0.2, + 1.036603260869441, + 0.32 ] }, "WT": { - "HLA-B*45:01": [ - 1.7331249999999985, - 3.14, - 4.3, - 2.5, - 3.8, - 1.2, - 7.8, - 6.2, - 7.348016304347794, - 2.7 + "HLA-A*29:02": [ + 0.5577499999999996, + 0.32, + 0.15, + 0.48, + 0.08, + 0.4, + 0.2, + 0.2, + 0.9296739130433592, + 0.45 ] } }, - "wt_peptide": "AELNQSEEPE" + "wt_peptide": "SHFMVVCLFY" }, - "EERAEMNQS": { + "LLYGPVGFTY": { "ic50s_MT": [ - "X", - 2193.93994140625 + 78.76499938964844, + "X" ], "percentiles_MT": [ - "X", - 2.9000000953674316 + 0.07500000298023224, + "X" ], "ic50s_WT": [ - "X", - 1655.97 + 29.894, + "X" ], "percentiles_WT": [ - "X", - 2.55 + 0.035, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "6", + "mutation_position": "2", "problematic_positions": "None", - "anchor_fails": "None", + "anchor_fails": "HLA-A*29:02", "individual_ic50_calls": { "algorithms": [ "MHCflurry", @@ -135584,27 +153527,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 369.15640159157255, - 6245.93, - 3197.68, - 3472.75, - 3909.18, - 1097.07, - 741.67, - 1190.2 + "HLA-A*29:02": [ + 29.13970333120221, + 741.76, + 29.13, + 18.97, + 12.76, + 883.6, + 160.8, + 128.39 ] }, "WT": { - "HLA-B*45:01": [ - 242.75997314893348, - 7406.05, - 2167.43, - 3848.7, - 2827.14, - 1097.07, - 760.69, - 1144.51 + "HLA-A*29:02": [ + 24.98773487002895, + 567.93, + 9.35, + 8.75, + 5.74, + 520.0, + 36.41, + 34.8 ] } }, @@ -135620,27 +153563,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 0.7160000205039978, - 6.980000019073486, - 3.0999999046325684, - 3.299999952316284, - 1.7000000476837158, - 3.5, - 2.7, - 4.5 + "HLA-A*29:02": [ + 0.03175000101327896, + 0.05000000074505806, + 0.17000000178813934, + 0.10000000149011612, + 0.03999999910593033, + 0.20000000298023224, + 0.8, + 0.6 ] }, "WT": { - "HLA-B*45:01": [ - 0.5606249999999997, - 8.03, - 2.3, - 3.5, - 1.4, - 3.5, - 2.8, - 4.4 + "HLA-A*29:02": [ + 0.0132499999999999, + 0.01, + 0.05, + 0.02, + 0.02, + 0.2, + 0.2, + 0.2 ] } }, @@ -135653,21 +153596,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.0020373798906803, - 0.196114148482402, - 0.155, - 0.0014924536, - 0.0006789122 + "HLA-A*29:02": [ + 0.5768589898943901, + 0.9564539694063896, + 0.846, + 0.9048465, + 0.9454332 ] }, "WT": { - "HLA-B*45:01": [ - 0.0030843429267406, - 0.2689579161354511, - 0.217, - 0.0047267494, - 0.004187298 + "HLA-A*29:02": [ + 0.4810018204152584, + 0.9478252791536952, + 0.944, + 0.985465, + 0.9089304 ] } }, @@ -135680,19 +153623,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 1.864429347826018, - 0.74, + 0.0383152173913146, + 0.04, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 1.486277173912967, - 0.53, + 0.0509510869565446, + 0.02, "NA", "NA" ] @@ -135712,60 +153655,60 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 0.7160000205039978, - 6.980000019073486, - 3.0999999046325684, - 3.299999952316284, - 1.7000000476837158, - 3.5, - 2.7, - 4.5, - 1.864429347826018, - 0.74 + "HLA-A*29:02": [ + 0.03175000101327896, + 0.05000000074505806, + 0.17000000178813934, + 0.10000000149011612, + 0.03999999910593033, + 0.20000000298023224, + 0.8, + 0.6, + 0.0383152173913146, + 0.04 ] }, "WT": { - "HLA-B*45:01": [ - 0.5606249999999997, - 8.03, - 2.3, - 3.5, - 1.4, - 3.5, - 2.8, - 4.4, - 1.486277173912967, - 0.53 + "HLA-A*29:02": [ + 0.0132499999999999, + 0.01, + 0.05, + 0.02, + 0.02, + 0.2, + 0.2, + 0.2, + 0.0509510869565446, + 0.02 ] } }, - "wt_peptide": "EERAELNQS" + "wt_peptide": "LFYGPVGFTY" }, - "AEMNQSEE": { + "FMVVCLLY": { "ic50s_MT": [ - "X", - 4015.465087890625 + 421.3380126953125, + "X" ], "percentiles_MT": [ - "X", - 2.325000047683716 + 0.4699999988079071, + "X" ], "ic50s_WT": [ - "X", - 5529.875 + 425.176, + "X" ], "percentiles_WT": [ - "X", - 3.192 + 0.518, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "3", + "mutation_position": "7", "problematic_positions": "None", - "anchor_fails": "None", + "anchor_fails": "HLA-A*29:02", "individual_ic50_calls": { "algorithms": [ "MHCflurry", @@ -135778,27 +153721,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 8155.316030894908, - 5625.24, - 6075.44, - 423.37, - 9475.7, - 767.66, - 2048.57, - 2405.69 + "HLA-A*29:02": [ + 190.02544538429828, + 1830.15, + 13.38, + 3.78, + 114.85, + 652.65, + 8642.71, + 17336.04 ] }, "WT": { - "HLA-B*45:01": [ - 9479.170035688749, - 7864.9, - 15677.55, - 1453.47, - 20206.55, - 1249.17, - 3194.85, - 3042.57 + "HLA-A*29:02": [ + 183.42293242080527, + 1783.79, + 17.89, + 4.45, + 173.52, + 666.93, + 8642.71, + 20509.26 ] } }, @@ -135814,27 +153757,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 2.75, - 6.409999847412109, - 4.800000190734863, - 0.9200000166893005, - 3.5999999046325684, - 1.0, - 1.1, - 1.5 + "HLA-A*29:02": [ + 0.7323750257492065, + 0.25, + 0.07999999821186066, + 0.009999999776482582, + 0.23999999463558197, + 0.20000000298023224, + 8.1, + 17.0 ] }, "WT": { - "HLA-B*45:01": [ - 2.9838749999999994, - 8.43, - 12.0, - 2.1, - 8.4, - 1.8, - 2.3, - 2.2 + "HLA-A*29:02": [ + 0.7158749999999999, + 0.25, + 0.11, + 0.02, + 0.32, + 0.2, + 8.1, + 19.0 ] } }, @@ -135847,21 +153790,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.0048203654587268, - 0.0120394845456089, - 0.0361, - 0.00018548543, - 0.0006353288 + "HLA-A*29:02": [ + 0.0129121541976928, + 0.3257996145154553, + 0.159, + 0.43661252, + 0.9933954 ] }, "WT": { - "HLA-B*45:01": [ - 0.0050631612539291, - 0.0104287061954013, - 0.0109, - 0.00021734227, - 0.00039251853 + "HLA-A*29:02": [ + 0.0127069279551506, + 0.3332281303155582, + 0.0977, + 0.2671113, + 0.9907799 ] } }, @@ -135874,19 +153817,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 18.61798913043478, - 1.9, + 1.2760054347825047, + 0.69, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 22.19230978260869, - 3.4, + 1.2529347826086052, + 0.98, "NA", "NA" ] @@ -135906,58 +153849,102 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 2.75, - 6.409999847412109, - 4.800000190734863, - 0.9200000166893005, - 3.5999999046325684, - 1.0, - 1.1, - 1.5, - 18.61798913043478, - 1.9 + "HLA-A*29:02": [ + 0.7323750257492065, + 0.25, + 0.07999999821186066, + 0.009999999776482582, + 0.23999999463558197, + 0.20000000298023224, + 8.1, + 17.0, + 1.2760054347825047, + 0.69 ] }, "WT": { - "HLA-B*45:01": [ - 2.9838749999999994, - 8.43, - 12.0, - 2.1, - 8.4, - 1.8, - 2.3, - 2.2, - 22.19230978260869, - 3.4 + "HLA-A*29:02": [ + 0.7158749999999999, + 0.25, + 0.11, + 0.02, + 0.32, + 0.2, + 8.1, + 19.0, + 1.2529347826086052, + 0.98 ] } }, - "wt_peptide": "AELNQSEE" - }, - "EEEEERAEM": { + "wt_peptide": "FMVVCLFY" + } + }, + "transcripts": [ + "ENST00000396806.3-OR12D3-F/L-250" + ], + "transcript_expr": [ + 0.001 + ], + "tsl": [ + "NA" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 316 + ], + "transcript_count": 1, + "peptide_count": 9, + "total_expr": 0.001 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 9 + ], + "set_expr": [ + 0.001 + ], + "DNA VAF": 0.398, + "RNA VAF": 0.0, + "gene_expr": 0.006, + "best_peptide_mt": "CLLYGPVGF", + "best_peptide_wt": "CLFYGPVGF", + "best_hla_allele": "HLA-A*29:02" + }, + "chr6-29726902-29726904-AA-CT": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "YSVVSGLLM": { "ic50s_MT": [ - "X", - 4346.3349609375 + 688.260009765625, + "X" ], "percentiles_MT": [ - "X", - 3.75 + 2.325000047683716, + "X" ], "ic50s_WT": [ - "X", - 3516.215 + 3512.527, + "X" ], "percentiles_WT": [ - "X", - 3.25 + 4.996, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "9", + "mutation_position": "7", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -135972,27 +153959,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 112.5052777551844, - 9509.46, - 12695.45, - 4219.45, - 7093.07, - 1209.27, - 1582.01, - 4473.22 + "HLA-A*29:02": [ + 1283.3772494238476, + 5042.62, + 92.14, + 688.93, + 687.59, + 3202.08, + 517.32, + 504.63 ] }, "WT": { - "HLA-B*45:01": [ - 82.13807739343383, - 7676.56, - 8712.03, - 4242.33, - 5642.6, - 1006.1, - 875.41, - 2790.1 + "HLA-A*29:02": [ + 3872.034274819901, + 5726.62, + 1109.61, + 4676.23, + 3153.02, + 5210.57, + 2348.33, + 2147.68 ] } }, @@ -136008,27 +153995,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 0.28349998593330383, - 9.960000038146973, - 8.699999809265137, - 3.700000047683716, - 2.700000047683716, - 3.799999952316284, - 6.1, - 15.0 + "HLA-A*29:02": [ + 1.8792500495910645, + 2.3499999046325684, + 0.3799999952316284, + 2.4000000953674316, + 0.7699999809265137, + 6.5, + 2.4, + 2.3 ] }, "WT": { - "HLA-B*45:01": [ - 0.18, - 8.260000000000002, - 6.3, - 3.7, - 2.3, - 3.3, - 3.2, - 10.0 + "HLA-A*29:02": [ + 3.0063749999999985, + 13.05, + 1.8, + 6.0, + 2.2, + 14.0, + 6.0, + 5.6 ] } }, @@ -136041,21 +154028,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.0052969343960285, - 0.4390432039424092, - 0.254, - 0.008255103, - 0.0014695702 + "HLA-A*29:02": [ + 0.2211716622114181, + 0.1363702918748753, + 0.07, + 0.061763797, + 0.7037029 ] }, "WT": { - "HLA-B*45:01": [ - 0.031882919371128, - 0.538574393352932, - 0.349, - 0.02546205, - 0.003424886 + "HLA-A*29:02": [ + 0.2672895230352878, + 0.0597908353370689, + 0.018, + 0.0074723274, + 0.2987122 ] } }, @@ -136068,19 +154055,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.9595108695650936, - 0.46, + 2.3670380434781606, + 1.3, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.7398913043477222, - 0.31, + 4.391929347826036, + 2.4, "NA", "NA" ] @@ -136100,58 +154087,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 0.28349998593330383, - 9.960000038146973, - 8.699999809265137, - 3.700000047683716, - 2.700000047683716, - 3.799999952316284, - 6.1, - 15.0, - 0.9595108695650936, - 0.46 + "HLA-A*29:02": [ + 1.8792500495910645, + 2.3499999046325684, + 0.3799999952316284, + 2.4000000953674316, + 0.7699999809265137, + 6.5, + 2.4, + 2.3, + 2.3670380434781606, + 1.3 ] }, "WT": { - "HLA-B*45:01": [ - 0.18, - 8.260000000000002, - 6.3, - 3.7, - 2.3, - 3.3, - 3.2, - 10.0, - 0.7398913043477222, - 0.31 + "HLA-A*29:02": [ + 3.0063749999999985, + 13.05, + 1.8, + 6.0, + 2.2, + 14.0, + 6.0, + 5.6, + 4.391929347826036, + 2.4 ] } }, - "wt_peptide": "EEEEERAEL" + "wt_peptide": "YSVVSGNLM" }, - "EEERAEMNQS": { + "AYSVVSGLLM": { "ic50s_MT": [ - "X", - 4467.35986328125 + 1821.531005859375, + "X" ], "percentiles_MT": [ - "X", - 3.9000000953674316 + 1.878999948501587, + "X" ], "ic50s_WT": [ - "X", - 4482.31 + 4243.938, + "X" ], "percentiles_WT": [ - "X", - 3.413 + 3.6, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "7", + "mutation_position": "8", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -136166,27 +154153,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 1550.7287277730184, - 6186.52, - 7983.08, - 5044.15, - 10033.67, - 3890.57, - 781.07, - 466.58 + "HLA-A*29:02": [ + 2389.4826012500625, + 4916.14, + 884.2, + 2456.44, + 1253.58, + 5997.52, + 428.82, + 327.74 ] }, "WT": { - "HLA-B*45:01": [ - 1119.5861012981418, - 7090.99, - 6972.24, - 5238.84, - 8715.33, - 3725.78, - 781.07, - 475.26 + "HLA-A*29:02": [ + 4572.775035999453, + 5573.99, + 3469.97, + 6755.55, + 3915.1, + 9245.51, + 1486.89, + 1010.49 ] } }, @@ -136202,27 +154189,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 1.3567500114440918, - 6.920000076293945, - 5.900000095367432, + "HLA-A*29:02": [ + 2.4483749866485596, + 1.9800000190734863, + 1.600000023841858, 4.0, - 3.799999952316284, - 5.400000095367432, - 3.0, - 1.6 + 1.2000000476837158, + 4.5, + 1.9, + 1.5 ] }, "WT": { - "HLA-B*45:01": [ - 1.1893749999999983, - 7.739999999999999, - 5.3, - 4.1, + "HLA-A*29:02": [ + 3.263249999999999, + 7.249999999999999, 3.3, - 5.2, - 3.0, - 1.7 + 7.4, + 2.5, + 8.6, + 5.1, + 3.9 ] } }, @@ -136235,21 +154222,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.0019620992243289, - 0.0570453809375052, - 0.0214, - 0.00056374987, - 0.0005841363 + "HLA-A*29:02": [ + 0.5162727423012257, + 0.1969543106613679, + 0.0341, + 0.44001397, + 0.4887762 ] }, "WT": { - "HLA-B*45:01": [ - 0.0047572813928127, - 0.0773544119301606, - 0.034, - 0.002392533, - 0.0015463942 + "HLA-A*29:02": [ + 0.5258885063230991, + 0.1190068897222027, + 0.013, + 0.19763789, + 0.13845529 ] } }, @@ -136262,19 +154249,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 4.585733695652138, - 2.5, + 1.858124999999916, + 1.8, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 3.526929347825998, - 2.0, + 2.6017663043477626, + 2.9, "NA", "NA" ] @@ -136294,58 +154281,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 1.3567500114440918, - 6.920000076293945, - 5.900000095367432, + "HLA-A*29:02": [ + 2.4483749866485596, + 1.9800000190734863, + 1.600000023841858, 4.0, - 3.799999952316284, - 5.400000095367432, - 3.0, - 1.6, - 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20745.32, - 6978.43, - 13383.79, - 2443.19, - 2492.81, - 2327.72 + "HLA-A*29:02": [ + 9816.567336188324, + 4931.24, + 3076.25, + 3848.7, + 7336.68, + 3890.57, + 1917.61, + 1678.69 ] }, "WT": { - "HLA-B*45:01": [ - 89.75750535783621, - 6652.61, - 16119.96, - 6539.79, - 12034.7, - 2032.71, - 1258.03, - 1617.82 + "HLA-A*29:02": [ + 12143.674171540866, + 5425.29, + 4663.95, + 4883.05, + 10209.32, + 4062.65, + 2252.99, + 1936.29 ] } }, @@ -136396,27 +154383,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 0.28349998593330383, - 8.979999542236328, - 15.0, - 4.599999904632568, - 5.0, - 3.5999999046325684, - 9.1, - 8.6 + "HLA-A*29:02": [ + 5.104374885559082, + 2.009999990463257, + 3.0999999046325684, + 5.400000095367432, + 3.9000000953674316, + 8.5, + 5.1, + 4.8 ] }, "WT": { - "HLA-B*45:01": [ - 0.2065, - 7.340000000000001, - 12.0, - 4.5, - 4.5, - 2.9, - 5.1, - 6.2 + "HLA-A*29:02": [ + 6.140374999999998, + 4.78, + 4.1, + 6.2, + 5.4, + 9.1, + 5.8, + 5.2 ] } }, @@ -136429,21 +154416,21 @@ 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} }, "sets": [ "Transcript Set 1" ], "transcript_counts": [ - 3 + 2 ], "peptide_counts": [ - 7 + 3 ], "set_expr": [ - 0.0 + 0.09 ], - "DNA VAF": 0.51, - "RNA VAF": 0.462, - "gene_expr": 2.211, - "best_peptide_mt": "AEMNQSEEP", - "best_peptide_wt": "AELNQSEEP", - "best_hla_allele": "HLA-B*45:01" + "DNA VAF": 0.648, + "RNA VAF": "NA", + "gene_expr": 74.251, + "best_peptide_mt": "YSVVSGLLM", + "best_peptide_wt": "YSVVSGNLM", + "best_hla_allele": "HLA-A*29:02" }, - "chr6-32223881-32223881-T-TAGCAGC": { + "chr6-30986467-30986468-T-C": { "good_binders": { "Transcript Set 1": { "peptides": { - "LLLLLLLLL": { + "SEFSTASSGI": { "ic50s_MT": [ - 3852.572998046875, - "X" + "X", + 557.875 ], "percentiles_MT": [ - 5.400000095367432, - "X" + "X", + 0.7360000014305115 ], "ic50s_WT": [ - 7483.75, - "X" + "X", + 495.655 ], "percentiles_WT": [ - 13.975, - "X" + "X", + 0.692 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "9", + "mutation_position": "6", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -136608,27 +154590,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 4093.406864537241, - 5186.99, - 3611.74, - 6095.65, - 12435.24, - 3416.85, - 1272.8, - 1247.3 + "HLA-B*45:01": [ + 96.80698712737728, + 1620.44, + 762.73, + 371.82, + 331.17, + 531.38, + 584.37, + 699.73 ] }, "WT": { - "HLA-A*29:02": [ - 18192.84843805777, - 5765.81, - 9201.69, - 14722.66, - 31624.25, - 4625.9, - 1348.22, - 1279.29 + "HLA-B*45:01": [ + 91.15897349468258, + 1148.79, + 576.13, + 311.03, + 312.67, + 531.38, + 459.93, + 704.58 ] } }, @@ -136644,27 +154626,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 3.084625005722046, - 2.930000066757202, - 3.4000000953674316, - 7.300000190734863, - 6.699999809265137, - 7.199999809265137, - 4.1, - 4.1 + "HLA-B*45:01": [ + 0.22937500476837158, + 2.680000066757202, + 1.100000023841858, + 0.5299999713897705, + 0.2800000011920929, + 0.5, + 2.2, + 2.7 ] }, "WT": { - "HLA-A*29:02": [ - 9.764249999999995, - 15.95, 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3.084625005722046, - 2.930000066757202, - 3.4000000953674316, - 7.300000190734863, - 6.699999809265137, - 7.199999809265137, - 4.1, - 4.1, - 10.23198369565216, - 11.0 + "HLA-B*45:01": [ + 0.22937500476837158, + 2.680000066757202, + 1.100000023841858, + 0.5299999713897705, + 0.2800000011920929, + 0.5, + 2.2, + 2.7, + 0.8515489130433593, + 0.62 ] }, "WT": { - "HLA-A*29:02": [ - 9.764249999999995, - 15.95, - 6.9, - 19.0, - 34.0, - 12.0, - 4.3, - 4.1, - 46.22467391304348, - 32.0 + "HLA-B*45:01": [ + 0.209125, + 2.15, + 0.8, + 0.48, + 0.27, + 0.5, + 1.6, + 2.7, + 0.7638043478259533, + 0.62 ] } }, - "wt_peptide": "LLLLLLLLC" - } - }, - "transcripts": [ - "ENST00000375023.3-NOTCH4-L/LLL-16" - ], - "transcript_expr": [ - 0.024 - ], - "tsl": [ - 1 - ], - "biotype": [ - "protein_coding" - ], - "transcript_length": [ - 2003 - ], - "transcript_count": 1, - "peptide_count": 1, - "total_expr": 0.024 - } - }, - "sets": [ - "Transcript Set 1" - ], - "transcript_counts": [ - 1 - ], - "peptide_counts": [ - 1 - ], - "set_expr": [ - 0.024 - ], - "DNA VAF": 0.187, - "RNA VAF": 0.0, - "gene_expr": 1.26, - "best_peptide_mt": "LLLLLLLLL", - "best_peptide_wt": "LLLLLLLLC", - "best_hla_allele": "HLA-A*29:02" - }, - "chr6-33211510-33211511-C-A": { - "good_binders": { - "Transcript Set 1": { - "peptides": { - "HLLVEKGEY": { + "wt_peptide": "SEFSTVSSGI" + }, + "SEFSTASSG": { "ic50s_MT": [ - 616.364990234375, - "X" + "X", + 698.52001953125 ], "percentiles_MT": [ - 1.600000023841858, - "X" + "X", + 0.8220000267028809 ], "ic50s_WT": [ - 2296.565, - "X" + "X", + 475.87 ], "percentiles_WT": [ - 2.35, - "X" + "X", + 0.71 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "1", + "mutation_position": "6", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -136846,27 +154784,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 70.21508970501182, - 5128.89, - 695.77, - 598.54, - 634.19, - 3416.85, - 352.18, - 389.92 + "HLA-B*45:01": [ + 77.92284314828022, + 1764.73, + 368.93, + 1028.11, + 178.61, + 344.7, + 1600.33, + 1182.01 ] }, "WT": { - "HLA-A*29:02": [ - 717.5665963920558, - 5484.29, - 1855.99, - 2737.14, - 3748.63, - 11112.54, - 424.38, - 659.13 + "HLA-B*45:01": [ + 71.34989046488244, + 1391.96, + 280.91, + 621.64, + 185.81, + 330.1, + 1365.24, + 947.59 ] } }, @@ -136882,27 +154820,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 0.2919999957084656, - 2.680000066757202, - 1.399999976158142, - 2.200000047683716, - 0.7300000190734863, - 7.199999809265137, - 1.8, - 1.9 + "HLA-B*45:01": [ + 0.1626249998807907, + 2.8399999141693115, + 0.5299999713897705, + 1.7999999523162842, + 0.17000000178813934, + 0.8999999761581421, + 6.1, + 4.5 ] }, "WT": { - "HLA-A*29:02": [ - 1.4738749999999996, - 5.58, - 2.3, - 4.6, - 2.4, - 29.0, - 2.0, - 2.8 + "HLA-B*45:01": [ + 0.135625, + 2.42, + 0.42, + 1.2, + 0.18, + 0.8, + 5.2, + 3.6 ] } }, @@ -136915,21 +154853,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.3650634028017521, - 0.8154449340397167, - 0.305, - 0.31749794, - 0.7372598 + "HLA-B*45:01": [ + 0.0151928216218948, + 0.536615942271981, + 0.32, + 0.000117507836, + 1.6514434e-05 ] }, "WT": { - "HLA-A*29:02": [ - 0.1002534218132495, - 0.1533110206736332, - 0.0383, - 0.0733022, - 0.5397011 + "HLA-B*45:01": [ + 0.0619797892868518, + 0.5981742772454897, + 0.374, + 0.00049899245, + 3.8871727e-05 ] } }, @@ -136942,19 +154880,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 0.2542934782608625, - 0.37, + 0.7437499999998778, + 0.35, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 2.192336956521657, - 1.7, + 0.61907608695644, + 0.29, "NA", "NA" ] @@ -136974,52 +154912,52 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 0.2919999957084656, - 2.680000066757202, - 1.399999976158142, - 2.200000047683716, - 0.7300000190734863, - 7.199999809265137, - 1.8, - 1.9, - 0.2542934782608625, - 0.37 + "HLA-B*45:01": [ + 0.1626249998807907, + 2.8399999141693115, + 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2651.25, + 8170.34 ] }, "WT": { - "HLA-A*29:02": [ - 1691.9695960978706, - 3725.83, - 982.48, - 1189.81, - 2409.25, - 3167.62, - 709.19, - 849.12 + "HLA-B*45:01": [ + 1299.959054888819, + 149.69, + 2616.7, + 265.87, + 1835.26, + 652.65, + 6523.04, + 14231.15 ] } }, @@ -137076,27 +155014,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 2.680375099182129, - 0.75, - 1.2999999523162842, - 2.700000047683716, - 1.899999976158142, - 5.5, - 2.6, - 2.9 + "HLA-B*45:01": [ + 1.718000054359436, + 0.8999999761581421, + 3.0, + 0.8100000023841858, + 1.2000000476837158, + 0.8999999761581421, + 1.7, + 8.6 ] }, "WT": { - "HLA-A*29:02": [ - 2.11575, - 0.75, - 1.7, - 3.0, - 1.8, - 6.3, - 2.9, - 3.2 + "HLA-B*45:01": [ + 1.2624999999999982, + 0.59, + 2.6, + 0.73, + 0.92, + 0.8, + 6.2, + 19.0 ] } }, @@ -137109,21 +155047,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.3069544658064842, - 0.0865161652941525, - 0.0449, - 0.049581226, - 0.3311746 + "HLA-B*45:01": [ + 0.0088712982833385, + 0.0341873642186582, + 0.0901, + 0.0009710548, + 0.0014565507 ] }, "WT": { - "HLA-A*29:02": [ - 0.8229466900229454, - 0.5037267962474673, - 0.083, - 0.41557696, - 0.47232655 + "HLA-B*45:01": [ + 0.0255561433732509, + 0.0724027651445963, + 0.15, + 0.0035708647, + 0.0015503152 ] } }, @@ -137136,19 +155074,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 3.238749999999925, - 1.6, + 7.147065217391287, + 1.1, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 0.8127173913042185, - 1.1, + 3.720108695652101, + 0.75, "NA", "NA" ] @@ -137168,58 +155106,102 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 2.680375099182129, - 0.75, - 1.2999999523162842, - 2.700000047683716, - 1.899999976158142, - 5.5, - 2.6, - 2.9, - 3.238749999999925, - 1.6 + "HLA-B*45:01": [ + 1.718000054359436, + 0.8999999761581421, + 3.0, + 0.8100000023841858, + 1.2000000476837158, + 0.8999999761581421, + 1.7, + 8.6, + 7.147065217391287, + 1.1 ] }, "WT": { - "HLA-A*29:02": [ - 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"MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 5.054048913043445, - 1.5, + 0.4232336956521578, + 0.01, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 9.15535326086956, - 2.1, + 0.4456249999999784, + 0.04, "NA", "NA" ] @@ -137362,58 +155344,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 2.2972500324249268, - 1.850000023841858, - 3.0, - 4.099999904632568, - 2.0, - 0.800000011920929, - 3.5, - 3.6, - 5.054048913043445, - 1.5 + "HLA-B*45:01": [ + 0.01412499975413084, + 0.5400000214576721, + 1.2999999523162842, + 0.6600000262260437, + 0.07000000029802322, + 1.100000023841858, + 1.1, + 1.0, + 0.4232336956521578, + 0.01 ] }, "WT": { - "HLA-A*29:02": [ - 3.464249999999999, - 2.52, - 3.6, - 5.7, - 3.1, - 1.2, - 4.4, - 4.6, - 9.15535326086956, - 2.1 + "HLA-B*45:01": [ + 0.02575, + 0.79, + 3.7, + 1.6, + 0.23, + 2.2, + 1.6, + 1.4, + 0.4456249999999784, + 0.04 ] } }, - "wt_peptide": "LVFRPHPLL" + "wt_peptide": "AELNQSEEP" }, - "IELVFRPHHL": { + "AEMNQSEEPE": { 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6.962798913043457, - 4.1, + 7.348016304347794, + 2.7, "NA", "NA" ] @@ -137557,57 +155539,57 @@ ], "MT": { "HLA-B*45:01": [ - 1.9192500114440918, - 16.389999389648438, - 12.0, - 3.0999999046325684, - 3.5, - 3.5999999046325684, - 7.7, - 12.0, - 7.147065217391287, - 3.4 + 1.3954999446868896, + 2.569999933242798, + 2.299999952316284, + 1.2999999523162842, + 1.5, + 0.6000000238418579, + 2.2, + 1.6, + 4.732201086956479, + 1.5 ] }, "WT": { "HLA-B*45:01": [ - 1.7916249999999985, - 17.76, - 6.5, - 2.3, - 1.8, - 1.6, - 6.0, - 7.7, - 6.962798913043457, - 4.1 + 1.7331249999999985, + 3.14, + 4.3, + 2.5, + 3.8, + 1.2, + 7.8, + 6.2, + 7.348016304347794, + 2.7 ] } }, - "wt_peptide": "IELVFRPHPL" + "wt_peptide": "AELNQSEEPE" }, - "HHLLVEKGEY": { + "EERAEMNQS": { "ic50s_MT": [ - 3597.594970703125, - "X" + "X", + 2193.93994140625 ], "percentiles_MT": [ - 3.1500000953674316, - "X" + "X", + 2.9000000953674316 ], "ic50s_WT": [ - 4467.68, - "X" + "X", + 1655.97 ], "percentiles_WT": [ - 4.9, - "X" + "X", + 2.55 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "2", + "mutation_position": "6", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -137622,27 +155604,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 1368.7113905880874, - 5421.76, - 3419.21, - 4752.74, - 3775.98, - 15208.39, - 830.39, - 730.35 + "HLA-B*45:01": [ + 369.15640159157255, + 6245.93, + 3197.68, + 3472.75, + 3909.18, + 1097.07, + 741.67, + 1190.2 ] }, "WT": { - "HLA-A*29:02": [ - 2780.34804670408, - 5693.42, - 4772.73, - 6610.93, - 4162.63, - 18679.43, - 1746.95, - 2379.74 + "HLA-B*45:01": [ + 242.75997314893348, + 7406.05, + 2167.43, + 3848.7, + 2827.14, + 1097.07, + 760.69, + 1144.51 ] } }, @@ -137658,27 +155640,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 1.933750033378601, - 4.739999771118164, + "HLA-B*45:01": [ + 0.7160000205039978, + 6.980000019073486, + 3.0999999046325684, 3.299999952316284, - 5.900000095367432, - 2.4000000953674316, - 17.0, - 3.3, - 3.0 + 1.7000000476837158, + 3.5, + 2.7, + 4.5 ] }, "WT": { - "HLA-A*29:02": [ - 2.608124999999999, - 11.24, - 4.2, - 7.3, - 2.6, - 21.0, - 5.6, - 7.0 + "HLA-B*45:01": [ + 0.5606249999999997, + 8.03, + 2.3, + 3.5, + 1.4, + 3.5, + 2.8, + 4.4 ] } }, @@ -137691,21 +155673,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.5528523735702038, - 0.3241485525502999, - 0.0316, - 0.05935677, - 0.69807494 + "HLA-B*45:01": [ + 0.0020373798906803, + 0.196114148482402, + 0.155, + 0.0014924536, + 0.0006789122 ] }, "WT": { - "HLA-A*29:02": [ - 0.5886714048683643, - 0.2147642137642702, - 0.0286, - 0.06868215, - 0.32047445 + "HLA-B*45:01": [ + 0.0030843429267406, + 0.2689579161354511, + 0.217, + 0.0047267494, + 0.004187298 ] } }, @@ -137718,19 +155700,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 1.2827717391303397, - 1.9, + 1.864429347826018, + 0.74, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 1.7490489130433955, - 1.9, + 1.486277173912967, + 0.53, "NA", "NA" ] @@ -137750,58 +155732,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 1.933750033378601, - 4.739999771118164, + "HLA-B*45:01": [ + 0.7160000205039978, + 6.980000019073486, + 3.0999999046325684, 3.299999952316284, - 5.900000095367432, - 2.4000000953674316, - 17.0, - 3.3, - 3.0, - 1.2827717391303397, - 1.9 + 1.7000000476837158, + 3.5, + 2.7, + 4.5, + 1.864429347826018, + 0.74 ] }, "WT": { - "HLA-A*29:02": [ - 2.608124999999999, - 11.24, - 4.2, - 7.3, - 2.6, - 21.0, - 5.6, - 7.0, - 1.7490489130433955, - 1.9 + "HLA-B*45:01": [ + 0.5606249999999997, + 8.03, + 2.3, + 3.5, + 1.4, + 3.5, + 2.8, + 4.4, + 1.486277173912967, + 0.53 ] } }, - "wt_peptide": "HPLLVEKGEY" + "wt_peptide": "EERAELNQS" }, - "LVFRPHHLLV": { + "AEMNQSEE": { "ic50s_MT": [ - 3671.294921875, - "X" + "X", + 4015.465087890625 ], "percentiles_MT": [ - 4.0, - "X" + "X", + 2.325000047683716 ], "ic50s_WT": [ - 3591.575, - "X" + "X", + 5529.875 ], "percentiles_WT": [ - 3.7, - "X" + "X", + 3.192 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "7", + "mutation_position": "3", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -137816,27 +155798,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 23546.897259866884, - 3931.43, - 1744.66, - 1925.66, - 3411.16, - 2443.19, - 20430.55, - 15189.03 + "HLA-B*45:01": [ + 8155.316030894908, + 5625.24, + 6075.44, + 423.37, + 9475.7, + 767.66, + 2048.57, + 2405.69 ] }, "WT": { - "HLA-A*29:02": [ - 20959.773152519727, - 3714.42, - 3468.73, - 2469.77, - 3295.68, - 2751.98, - 20383.56, - 16577.92 + "HLA-B*45:01": [ + 9479.170035688749, + 7864.9, + 15677.55, + 1453.47, + 20206.55, + 1249.17, + 3194.85, + 3042.57 ] } }, @@ -137852,27 +155834,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 15.90262508392334, - 0.8399999737739563, - 2.299999952316284, - 3.700000047683716, - 2.299999952316284, + "HLA-B*45:01": [ + 2.75, + 6.409999847412109, + 4.800000190734863, + 0.9200000166893005, + 3.5999999046325684, 1.0, - 35.0, - 28.0 + 1.1, + 1.5 ] }, "WT": { - "HLA-A*29:02": [ - 12.320249999999994, - 0.74, - 3.3, - 4.1, - 2.2, - 1.2, - 34.0, - 30.0 + "HLA-B*45:01": [ + 2.9838749999999994, + 8.43, + 12.0, + 2.1, + 8.4, + 1.8, + 2.3, + 2.2 ] } }, @@ -137885,21 +155867,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.0928400121629238, - 0.0059053398981215, - 0.00524, - 0.009582157, - 0.15009701 + "HLA-B*45:01": [ + 0.0048203654587268, + 0.0120394845456089, + 0.0361, + 0.00018548543, + 0.0006353288 ] }, "WT": { - "HLA-A*29:02": [ - 0.4582127593457699, - 0.0236563164828247, - 0.0103, - 0.057056215, - 0.1782657 + "HLA-B*45:01": [ + 0.0050631612539291, + 0.0104287061954013, + 0.0109, + 0.00021734227, + 0.00039251853 ] } }, @@ -137912,19 +155894,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 46.22467391304348, - 4.3, + 18.61798913043478, + 1.9, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 10.23198369565216, - 3.1, + 22.19230978260869, + 3.4, "NA", "NA" ] @@ -137944,102 +155926,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 15.90262508392334, - 0.8399999737739563, - 2.299999952316284, - 3.700000047683716, - 2.299999952316284, + "HLA-B*45:01": [ + 2.75, + 6.409999847412109, + 4.800000190734863, + 0.9200000166893005, + 3.5999999046325684, 1.0, - 35.0, - 28.0, - 46.22467391304348, - 4.3 + 1.1, + 1.5, + 18.61798913043478, + 1.9 ] }, "WT": { - "HLA-A*29:02": [ - 12.320249999999994, - 0.74, - 3.3, - 4.1, + "HLA-B*45:01": [ + 2.9838749999999994, + 8.43, + 12.0, + 2.1, + 8.4, + 1.8, + 2.3, 2.2, - 1.2, - 34.0, - 30.0, - 10.23198369565216, - 3.1 + 22.19230978260869, + 3.4 ] } }, - "wt_peptide": "LVFRPHPLLV" - } - }, - "transcripts": [ - "ENST00000374656.5-RING1-P/H-270" - ], - "transcript_expr": [ - 2.529 - ], - "tsl": [ - 1 - ], - "biotype": [ - "protein_coding" - ], - "transcript_length": [ - 406 - ], - "transcript_count": 1, - "peptide_count": 6, - "total_expr": 2.529 - } - }, - "sets": [ - "Transcript Set 1" - ], - 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@@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 56.5001781651594, - 2658.32, - 259.89, - 185.03, - 250.83, - 1946.61, - 216.15, - 315.48 + "HLA-B*45:01": [ + 1550.7287277730184, + 6186.52, + 7983.08, + 5044.15, + 10033.67, + 3890.57, + 781.07, + 466.58 ] }, "WT": { - "HLA-A*29:02": [ - 57.407941876661006, - 1996.49, - 129.53, - 96.68, - 189.42, - 1158.05, - 119.33, - 190.09 + "HLA-B*45:01": [ + 1119.5861012981418, + 7090.99, + 6972.24, + 5238.84, + 8715.33, + 3725.78, + 781.07, + 475.26 ] } }, @@ -138284,27 +156222,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 0.21562500298023224, - 0.4099999964237213, - 0.7300000190734863, - 1.2999999523162842, - 0.4000000059604645, + "HLA-B*45:01": [ + 1.3567500114440918, + 6.920000076293945, + 5.900000095367432, + 4.0, + 3.799999952316284, + 5.400000095367432, 3.0, - 1.3, - 1.7 + 1.6 ] }, "WT": { - "HLA-A*29:02": [ - 0.219375, - 0.2799999999999999, - 0.48, - 0.84, - 0.35, - 1.2, - 0.8, - 1.2 + "HLA-B*45:01": [ + 1.1893749999999983, + 7.739999999999999, + 5.3, + 4.1, + 3.3, + 5.2, + 3.0, + 1.7 ] } }, @@ -138317,21 +156255,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.7282090783119202, - 0.9517421836143808, - 0.61, - 0.5210376, - 0.523324 + "HLA-B*45:01": [ + 0.0019620992243289, + 0.0570453809375052, + 0.0214, + 0.00056374987, + 0.0005841363 ] }, "WT": { - "HLA-A*29:02": [ - 0.8399943709373474, - 0.9664879883288984, - 0.716, - 0.7086426, - 0.5832198 + "HLA-B*45:01": [ + 0.0047572813928127, + 0.0773544119301606, + 0.034, + 0.002392533, + 0.0015463942 ] } }, @@ -138344,19 +156282,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 0.0451630434782828, - 0.14, + 4.585733695652138, + 2.5, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 0.0240489130435008, - 0.09, + 3.526929347825998, + 2.0, "NA", "NA" ] @@ -138376,107 +156314,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 0.21562500298023224, - 0.4099999964237213, - 0.7300000190734863, - 1.2999999523162842, - 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}, + "chr6-32223881-32223881-T-TAGCAGC": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "LLLLLLLLL": { "ic50s_MT": [ - "X", - 3328.2099609375 + 3852.572998046875, + "X" ], "percentiles_MT": [ - "X", - 3.950000047683716 + 5.400000095367432, + "X" ], "ic50s_WT": [ - "X", - 1943.335 + 7483.75, + "X" ], "percentiles_WT": [ - "X", - 2.1 + 13.975, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "1", + "mutation_position": "9", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -138685,27 +156628,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 224.2790999722926, - 6173.43, - 12941.34, - 3548.72, - 3488.8, - 3167.62, - 1437.77, - 1573.73 + "HLA-A*29:02": [ + 4093.406864537241, + 5186.99, + 3611.74, + 6095.65, + 12435.24, + 3416.85, + 1272.8, + 1247.3 ] }, "WT": { - "HLA-B*45:01": [ - 186.62437767656004, - 3248.82, - 5717.14, - 1646.06, - 2283.56, - 2240.61, - 614.74, - 668.24 + "HLA-A*29:02": [ + 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} }, - "wt_peptide": "AFCDCAQSD" - } - }, - "transcripts": [ - "ENST00000340465.2-GFRAL-D/H-195" - ], - "transcript_expr": [ - 0.013 - ], - "tsl": [ - 1 - ], - "biotype": [ - "protein_coding" - ], - "transcript_length": [ - 394 - ], - "transcript_count": 1, - "peptide_count": 1, - "total_expr": 0.013 - } - }, - "sets": [ - "Transcript Set 1" - ], - "transcript_counts": [ - 1 - ], - "peptide_counts": [ - 1 - ], - "set_expr": [ - 0.013 - ], - "DNA VAF": 0.511, - "RNA VAF": 0.0, - "gene_expr": 0.013, - "best_peptide_mt": "AFCDCAQSH", - "best_peptide_wt": "AFCDCAQSD", - "best_hla_allele": "HLA-A*29:02" - }, - "chr6-70190343-70190344-G-C": { - "good_binders": { - "Transcript Set 1": { - "peptides": { - "VSFEEINKY": { + "wt_peptide": "LVFRPHPLL" + }, + "IELVFRPHHL": { "ic50s_MT": [ - 536.8900146484375, - "X" + "X", + 3489.194091796875 ], "percentiles_MT": [ - 1.0149999856948853, - "X" + "X", + 5.374000072479248 ], "ic50s_WT": [ - 1078.04, - "X" + "X", + 2647.138 ], "percentiles_WT": [ - 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6955.83, + 3126.92, + 1915.27, + 1493.28, + 446.91, + 897.86, + 1488.06 ] } }, @@ -140728,27 +158547,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 0.840624988079071, - 11.970000267028809, - 4.800000190734863, - 2.5, - 0.8199999928474426, - 12.0, - 4.2, - 5.5 + "HLA-B*45:01": [ + 0.32087498903274536, + 11.119999885559082, + 5.900000095367432, + 4.199999809265137, + 1.399999976158142, + 2.0, + 8.8, + 9.2 ] }, "WT": { - "HLA-A*29:02": [ - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA" + "HLA-B*45:01": [ + 0.15875, + 7.62, + 3.0, + 2.6, + 0.8, + 1.2, + 3.3, + 5.6 ] } }, @@ -140761,21 +158580,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.2196164838969707, - 0.4493059103567223, - 0.0579, - 0.0054298355, - 0.15225407 + "HLA-B*45:01": [ + 0.0716228820383548, + 0.4704434990347859, + 0.156, + 0.00091129687, + 5.6408287e-05 ] }, "WT": { - "HLA-A*29:02": [ - "NA", - "NA", - "NA", - "NA", - "NA" + "HLA-B*45:01": [ + 0.0872749462723732, + 0.6014842248564666, + 0.37, + 0.0012324984, + 0.000101855374 ] } }, @@ -140788,19 +158607,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 0.9356793478259532, - 1.4, + 0.8884239130433542, + 0.72, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ - "NA", - "NA", + "HLA-B*45:01": [ "NA", + 0.6137228260868852, + 0.29, "NA", "NA" ] @@ -140820,58 +158639,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 0.840624988079071, - 11.970000267028809, - 4.800000190734863, - 2.5, - 0.8199999928474426, - 12.0, - 4.2, - 5.5, - 0.9356793478259532, - 1.4 + "HLA-B*45:01": [ + 0.32087498903274536, + 11.119999885559082, + 5.900000095367432, + 4.199999809265137, + 1.399999976158142, + 2.0, + 8.8, + 9.2, + 0.8884239130433542, + 0.72 ] }, "WT": { - "HLA-A*29:02": [ - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA" + "HLA-B*45:01": [ + 0.15875, + 7.62, + 3.0, + 2.6, + 0.8, + 1.2, + 3.3, + 5.6, + 0.6137228260868852, + 0.29 ] } }, - "wt_peptide": "FS-NA" + "wt_peptide": "EEFSAGGEL" }, - 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"SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 6.758500099182129, - 4.380000114440918, - 2.0, - 3.9000000953674316, - 2.9000000953674316, - 4.699999809265137, - 3.4, - 3.4 + "HLA-B*45:01": [ + 0.5297499895095825, + 6.909999847412109, + 8.899999618530273, + 3.299999952316284, + 1.600000023841858, + 4.5, + 5.6, + 6.1 ] }, "WT": { - "HLA-A*29:02": [ - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA" + "HLA-B*45:01": [ + 0.4592499999999998, + 4.31, + 4.6, + 1.9, + 1.2, + 3.3, + 2.3, + 2.5 ] } }, @@ -140955,21 +158774,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.0133323892951011, - 0.0076923383745988, - 0.00821, - 0.036688503, - 0.2946052 + "HLA-B*45:01": [ + 0.0195622965693473, + 0.2963580361729832, + 0.0106, + 0.00012793233, + 4.5822413e-05 ] }, "WT": { - "HLA-A*29:02": [ - "NA", - "NA", - "NA", - "NA", - "NA" + "HLA-B*45:01": [ + 0.0324939787387847, + 0.3451518008190138, + 0.0401, + 0.00019069905, + 4.0315073e-05 ] } }, @@ -140982,19 +158801,19 @@ "BigMHC_IM" ], "MT": { - 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"chr6-43587456-43587457-G-A": { "good_binders": { "Transcript Set 1": { "peptides": { - "GELRSWYLG": { + "IEGLPQDPT": { "ic50s_MT": [ "X", - 1001.989990234375 + 2977.985107421875 ], "percentiles_MT": [ "X", - 1.899999976158142 + 2.9000000953674316 ], "ic50s_WT": [ "X", - "NA" + 3031.475 ], "percentiles_WT": [ "X", - "NA" + 2.898 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "3-9", + "mutation_position": "7", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -141319,26 +159182,26 @@ ], "MT": { "HLA-B*45:01": [ - 1660.677992464929, - 2557.05, - 1010.16, - 841.61, - 993.82, - 719.41, - 1200.08, - 421.33 + 581.8085473317885, + 6845.79, + 8053.96, + 4478.16, + 5645.71, + 1062.03, + 665.59, + 1477.81 ] }, "WT": { "HLA-B*45:01": [ - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA" + 793.0344365410981, + 9279.43, + 6252.56, + 5712.5, + 5033.47, + 932.72, + 531.14, + 1029.48 ] } }, @@ -141355,26 +159218,26 @@ ], "MT": { 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- "HLA-A*29:02": [ - 13401.58304249547, - 5389.75, - 1345.21, - 1967.79, - 4871.39, - 2607.06, - 932.74, - 933.19 + "HLA-B*45:01": [ + 4168.162238698939, + 5266.21, + 16492.21, + 11666.98, + 19265.88, + 3236.91, + 2839.29, + 3270.54 ] }, "WT": { - "HLA-A*29:02": [ - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA" + "HLA-B*45:01": [ + 22737.23982864917, + 37167.92, + 42938.42, + 36337.11, + 34975.44, + 13797.25, + 38477.78, + 28159.18 ] } }, @@ -141548,27 +159460,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 6.758500099182129, - 4.380000114440918, - 2.0, - 3.9000000953674316, - 2.9000000953674316, - 4.699999809265137, - 3.4, - 3.4 + "HLA-B*45:01": [ + 2.041874885559082, + 6.110000133514404, + 12.0, + 6.400000095367432, + 7.800000190734863, + 9.600000381469727, + 11.0, + 12.0 ] }, "WT": { - "HLA-A*29:02": [ - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA" + "HLA-B*45:01": [ + 8.390625, + 78.2, + 56.0, + 30.0, + 33.0, + 37.0, + 50.0, + 41.0 ] } }, @@ 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@@ -141900,27 +159910,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 8997.593831534588, - 4475.17, - 3947.81, - 1414.68, - 4034.44, - 2010.83, - 8865.23, - 5247.23 + "HLA-A*29:02": [ + 3538.386210527465, + 4997.88, + 7106.43, + 7860.43, + 8609.33, + 4429.97, + 3386.57, + 2937.45 ] }, "WT": { - "HLA-B*45:01": [ - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA" + "HLA-A*29:02": [ + 25854.37461152546, + 5805.05, + 27211.15, + 29266.51, + 35785.8, + 13212.86, + 19044.08, + 17578.02 ] } }, @@ -141936,27 +159946,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 2.900624990463257, - 5.420000076293945, - 3.5999999046325684, - 1.7000000476837158, - 1.7999999523162842, - 2.9000000953674316, - 28.0, - 19.0 + "HLA-A*29:02": [ + 2.8884999752044678, + 2.200000047683716, + 5.599999904632568, + 9.0, + 4.599999904632568, + 10.0, + 7.7, + 7.0 ] }, "WT": { - "HLA-B*45:01": [ - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA" + "HLA-A*29:02": [ + 20.969124999999995, + 20.25, + 30.0, + 55.0, + 48.0, + 34.0, + 28.0, + 27.0 ] } }, @@ -141969,21 +159979,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.1279685609042644, - 0.0168367953617748, - 0.000673, - 0.0002963775, - 0.0005029607 + "HLA-A*29:02": [ + 0.0240382440388202, + 0.028515526732186, + 0.0226, + 0.011861186, + 0.28716844 ] }, "WT": { - "HLA-B*45:01": [ - "NA", - "NA", - "NA", - "NA", - "NA" + "HLA-A*29:02": [ + 0.0034171305596828, + 0.0039378575297865, + 1.5e-05, + 0.0011168577, + 0.17009401 ] } }, @@ -141996,19 +160006,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 14.277038043478257, - 12.0, + 8.545326086956507, + 2.2, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ - "NA", - "NA", + "HLA-A*29:02": [ "NA", + 99.28660326086955, + 53.0, "NA", "NA" ] @@ -142028,58 +160038,102 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 2.900624990463257, - 5.420000076293945, - 3.5999999046325684, - 1.7000000476837158, - 1.7999999523162842, - 2.9000000953674316, - 28.0, - 19.0, - 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"AFCDCAQSH", + "best_peptide_wt": "AFCDCAQSD", + "best_hla_allele": "HLA-A*29:02" + }, + "chr6-70190343-70190344-G-C": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "VSFEEINKY": { "ic50s_MT": [ - "X", - 4674.3251953125 + 536.8900146484375, + "X" ], "percentiles_MT": [ - "X", - 2.700000047683716 + 1.0149999856948853, + "X" ], "ic50s_WT": [ - "X", - "NA" + 1078.04, + "X" ], "percentiles_WT": [ - "X", - "NA" + 1.41, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "3-8", + "mutation_position": "7", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -142094,27 +160148,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 1757.3459518376474, - 4167.22, - 9867.33, - 953.12, - 7499.53, - 953.12, - 5181.43, - 24391.58 + "HLA-A*29:02": [ + 38.35101107160436, + 2019.54, + 956.84, + 592.1, + 180.17, + 3380.08, + 481.68, + 449.75 ] }, "WT": { - "HLA-B*45:01": [ - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA" + "HLA-A*29:02": [ + 44.01406094993045, + 2824.89, + 1556.96, + 1477.25, + 629.21, + 4830.5, + 678.83, + 633.83 ] } }, @@ -142130,27 +160184,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 1.418874979019165, - 5.139999866485596, - 7.0, + "HLA-A*29:02": [ + 0.0988750010728836, + 0.28999999165534973, 1.7000000476837158, - 2.799999952316284, - 1.2999999523162842, - 4.6, - 33.0 + 2.200000047683716, + 0.33000001311302185, + 7.099999904632568, + 2.3, + 2.2 ] }, "WT": { - "HLA-B*45:01": [ - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA" + "HLA-A*29:02": [ + 0.138, + 0.4599999999999999, + 2.1, + 3.4, + 0.72, + 12.0, + 2.8, + 2.7 ] } }, @@ -142163,21 +160217,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.7748331055045128, - 0.4521097614408699, - 0.0206, - 0.003787931, - 0.0009359125 + "HLA-A*29:02": [ + 0.4517743848264217, + 0.9152923795643008, + 0.799, + 0.3319033, + 0.668888 ] }, "WT": { - "HLA-B*45:01": [ - "NA", - "NA", - "NA", - "NA", - "NA" + "HLA-A*29:02": [ + 0.3191943652927875, + 0.8553470575129185, + 0.665, + 0.21672902, + 0.5843306 ] } }, @@ -142190,19 +160244,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.9296739130433592, - 2.6, + 0.0978804347825956, + 0.06, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ - "NA", - "NA", + "HLA-A*29:02": [ "NA", + 0.1914673913043429, + 0.12, "NA", "NA" ] @@ -142222,115 +160276,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 1.418874979019165, - 5.139999866485596, - 7.0, + "HLA-A*29:02": [ + 0.0988750010728836, + 0.28999999165534973, 1.7000000476837158, - 2.799999952316284, - 1.2999999523162842, - 4.6, - 33.0, - 0.9296739130433592, - 2.6 + 2.200000047683716, + 0.33000001311302185, + 7.099999904632568, + 2.3, + 2.2, + 0.0978804347825956, + 0.06 ] }, "WT": { - "HLA-B*45:01": [ - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA", - "NA" + "HLA-A*29:02": [ + 0.138, + 0.4599999999999999, + 2.1, + 3.4, + 0.72, + 12.0, + 2.8, + 2.7, + 0.1914673913043429, + 0.12 ] 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0.51769274 ] } }, @@ -142441,19 +160438,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.4698369565216751, - 0.42, + 0.6333423913042822, + 0.19, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.2334510869565207, - 0.37, + 1.049592391304202, + 0.33, "NA", "NA" ] @@ -142473,58 +160470,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 0.27687498927116394, - 2.259999990463257, - 3.799999952316284, - 1.2000000476837158, - 0.5400000214576721, - 2.5, - 15.0, - 12.0, - 0.4698369565216751, - 0.42 + "HLA-A*29:02": [ + 0.5091249942779541, + 0.4300000071525574, + 3.0999999046325684, + 2.0, + 0.7599999904632568, + 6.199999809265137, + 3.3, + 4.2, + 0.6333423913042822, + 0.19 ] }, "WT": { - "HLA-B*45:01": [ - 0.091625, - 1.55, + "HLA-A*29:02": [ + 0.758875, + 0.96, + 3.9, 2.7, - 1.1, - 0.52, - 1.3, - 12.0, - 7.9, - 0.2334510869565207, - 0.37 + 1.5, + 8.6, + 2.9, + 4.4, + 1.049592391304202, + 0.33 ] } }, - "wt_peptide": "GEFEQKLAST" + "wt_peptide": 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"HLA-B*45:01": [ "NA", - 3.2967934782607813, - 2.5, + 2.32364130434776, + 2.4, "NA", "NA" ] @@ -142668,57 +160665,57 @@ ], "MT": { "HLA-B*45:01": [ - 1.1706249713897705, - 16.290000915527344, - 2.5999999046325684, - 2.200000047683716, - 2.200000047683716, + 1.455875039100647, + 9.010000228881836, + 4.599999904632568, 2.200000047683716, - 5.6, - 6.5, - 2.9511413043477432, - 2.9 + 6.599999904632568, + 8.0, + 2.8, + 5.5, + 1.9268749999999244, + 2.3 ] }, "WT": { "HLA-B*45:01": [ - 1.1431249999999988, - 16.06, - 4.8, - 3.8, - 3.4, - 3.2, - 9.5, - 12.0, - 3.2967934782607813, - 2.5 + 1.325249999999998, + 12.55, + 4.2, + 2.3, + 7.0, + 9.0, + 3.1, + 6.5, + 2.32364130434776, + 2.4 ] } }, - "wt_peptide": "FEQKLASTE" + "wt_peptide": "EEIKKYINQ" }, - "GEFEQKLAF": { + "SFEEINKY": { "ic50s_MT": [ - "X", - 2197.0400390625 + 4721.06005859375, + "X" ], "percentiles_MT": [ - "X", - 1.649999976158142 + 2.0999999046325684, + "X" ], "ic50s_WT": [ - "X", - 744.21 + 6947.055, + "X" ], "percentiles_WT": [ - "X", - 1.47 + 3.2, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "9", + "mutation_position": "6", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -142733,27 +160730,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 204.09630813167652, - 2606.7, - 8337.16, - 1804.62, - 1370.32, - 344.7, - 2589.46, - 3644.35 + "HLA-A*29:02": [ + 133.10752554329028, + 3129.5, + 5370.32, + 350.34, + 4071.8, + 6610.93, + 7025.06, + 27286.64 ] }, "WT": { - "HLA-B*45:01": [ - 56.8202591182147, - 745.28, - 5488.69, - 663.33, - 229.94, - 743.14, - 1274.12, - 1724.33 + "HLA-A*29:02": [ + 201.7531362982054, + 3593.38, + 6869.05, + 739.13, + 7696.99, + 9447.76, + 7025.06, + 34749.62 ] } }, @@ -142769,27 +160766,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 0.49537500739097595, - 3.700000047683716, - 6.099999904632568, - 2.4000000953674316, - 0.75, - 0.8999999761581421, - 9.5, - 13.0 + "HLA-A*29:02": [ + 0.562375009059906, + 0.5400000214576721, + 4.599999904632568, + 1.7000000476837158, + 2.5, + 5.099999904632568, + 6.8, + 27.0 ] }, "WT": { - "HLA-B*45:01": [ - 0.069375, - 1.64, - 4.5, - 1.3, - 0.21, - 2.4, - 4.8, - 6.6 + "HLA-A*29:02": [ + 0.76425, + 0.69, + 5.5, + 2.3, + 4.1, + 8.9, + 6.8, + 36.0 ] } }, @@ -142802,21 +160799,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.8704978078603745, - 0.9035769974463784, - 0.494, - 0.039413683, - 0.0024513204 + "HLA-A*29:02": [ + 0.1202741712331771, + 0.4996045763549182, + 0.192, + 0.28415093, + 0.37006226 ] }, "WT": { - "HLA-B*45:01": [ - 0.2008855007588863, - 0.7522241760368635, - 0.634, - 0.0051574283, - 0.0009296623 + "HLA-A*29:02": [ + 0.0404683463275432, + 0.3344962088898499, + 0.142, + 0.35194066, + 0.4617443 ] } }, @@ -142829,19 +160826,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.1168206521739136, - 0.19, + 0.8208423913042395, + 0.58, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.3542391304347632, - 0.11, + 1.246494565217276, + 0.74, "NA", "NA" ] @@ -142861,58 +160858,102 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 0.49537500739097595, - 3.700000047683716, - 6.099999904632568, - 2.4000000953674316, - 0.75, - 0.8999999761581421, - 9.5, - 13.0, - 0.1168206521739136, - 0.19 + "HLA-A*29:02": [ + 0.562375009059906, + 0.5400000214576721, + 4.599999904632568, + 1.7000000476837158, + 2.5, + 5.099999904632568, + 6.8, + 27.0, + 0.8208423913042395, + 0.58 ] }, "WT": { - "HLA-B*45:01": [ - 0.069375, - 1.64, - 4.5, - 1.3, - 0.21, - 2.4, - 4.8, - 6.6, - 0.3542391304347632, - 0.11 + "HLA-A*29:02": [ + 0.76425, + 0.69, + 5.5, + 2.3, + 4.1, + 8.9, + 6.8, + 36.0, + 1.246494565217276, + 0.74 ] } }, - "wt_peptide": "GEFEQKLAS" - }, - "FEQKLAFTEK": { + "wt_peptide": "SFEEIKKY" + } + }, + "transcripts": [ + "ENST00000620364.5-COL19A1-K/N-1019" + ], + "transcript_expr": [ + 6.012 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 1142 + ], + "transcript_count": 1, + "peptide_count": 4, + "total_expr": 6.012 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 4 + ], + "set_expr": [ + 6.012 + ], + "DNA VAF": 0.255, + "RNA VAF": 0.269, + "gene_expr": 10.708, + "best_peptide_mt": "VSFEEINKY", + "best_peptide_wt": "VSFEEIKKY", + "best_hla_allele": "HLA-A*29:02" + }, + "chr6-73363141-73363172-CTTGATTCACGTGAATCGATTGGACCCTAACG-C": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "QIARLRSWY": { "ic50s_MT": [ - "X", - 4779.8701171875 + 423.6700134277344, + "X" ], "percentiles_MT": [ - "X", - 5.300000190734863 + 1.5499999523162842, + "X" ], "ic50s_WT": [ - "X", - 4417.687 + "NA", + "X" ], "percentiles_WT": [ - "X", - 6.25 + "NA", + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "7", + "mutation_position": "3-9", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -142927,34 +160968,34 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 5752.459372109569, - 28071.96, - 8646.39, - 2216.49, - 8766.49, - 3807.28, - 3301.34, - 1299.96 + "HLA-A*29:02": [ + 130.25148777588305, + 5215.85, + 2075.33, + 337.32, + 386.05, + 3307.72, + 212.7, + 461.29 ] }, "WT": { - "HLA-B*45:01": [ - 4772.723425098626, - 25649.63, - 12819.26, - 3548.72, - 13220.57, - 4062.65, - 3316.58, - 1819.41 - ] - } - }, - "individual_ic50_percentile_calls": { - "algorithms": [ - "MHCflurry", - "MHCnuggetsI", + "HLA-A*29:02": [ + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", "NetMHC", "NetMHCcons", "NetMHCpan", @@ -142963,27 +161004,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 2.337125062942505, - 38.72999954223633, - 6.300000190734863, - 2.299999952316284, - 3.299999952316284, - 5.400000095367432, - 13.0, - 5.2 + "HLA-A*29:02": [ + 0.5532500147819519, + 3.0899999141693115, + 2.5, + 1.7999999523162842, + 0.5299999713897705, + 6.900000095367432, + 1.3, + 2.2 ] }, "WT": { - "HLA-B*45:01": [ - 2.16325, - 32.86, - 8.8, - 3.3, - 4.9, - 5.6, - 14.0, - 6.9 + "HLA-A*29:02": [ + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -142996,21 +161037,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.1121042966842651, - 0.0243915848981582, - 0.00492, - 0.0005659539, - 0.0005913895 + "HLA-A*29:02": [ + 0.1129569746553897, + 0.4983994866980877, + 0.199, + 0.15043029, + 0.5651005 ] }, "WT": { - "HLA-B*45:01": [ - 0.0125643424689769, - 0.0206404397814736, - 0.0064, - 0.00078439096, - 0.00023941827 + "HLA-A*29:02": [ + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -143023,19 +161064,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 9.849456521739114, - 4.8, + 0.8247010869563951, + 0.55, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ + "NA", + "NA", "NA", - 11.6303260869565, - 4.3, "NA", "NA" ] @@ -143055,58 +161096,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 2.337125062942505, - 38.72999954223633, - 6.300000190734863, - 2.299999952316284, - 3.299999952316284, - 5.400000095367432, - 13.0, - 5.2, - 9.849456521739114, - 4.8 + "HLA-A*29:02": [ + 0.5532500147819519, + 3.0899999141693115, + 2.5, + 1.7999999523162842, + 0.5299999713897705, + 6.900000095367432, + 1.3, + 2.2, + 0.8247010869563951, + 0.55 ] }, "WT": { - "HLA-B*45:01": [ - 2.16325, - 32.86, - 8.8, - 3.3, - 4.9, - 5.6, - 14.0, - 6.9, - 11.6303260869565, - 4.3 + "HLA-A*29:02": [ + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, - "wt_peptide": "FEQKLASTEK" + "wt_peptide": "FS-NA" }, - "FEQKLAFT": { + "SQIARLRSWY": { "ic50s_MT": [ - "X", - 4979.9208984375 + 1445.1300048828125, + "X" ], "percentiles_MT": [ - "X", - 3.5 + 3.3499999046325684, + "X" ], "ic50s_WT": [ - "X", - 3025.335 + "NA", + "X" ], "percentiles_WT": [ - "X", - 3.05 + "NA", + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "7", + "mutation_position": "4-10", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -143121,27 +161162,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 5630.892003062949, - 6479.05, - 4328.95, - 704.01, - 8469.44, - 2077.17, - 3527.36, - 9665.85 + "HLA-A*29:02": [ + 235.29900748033492, + 5707.54, + 5678.18, + 792.98, + 770.39, + 11112.54, + 1170.25, + 1720.01 ] }, "WT": { - "HLA-B*45:01": [ - 1704.6466672946867, - 3564.96, - 4533.44, - 883.6, - 9342.75, - 1362.11, - 2485.71, - 8002.76 + "HLA-A*29:02": [ + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -143157,27 +161198,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 2.315624952316284, - 7.179999828338623, - 3.799999952316284, - 1.399999976158142, - 3.200000047683716, - 3.200000047683716, - 2.8, - 12.0 + "HLA-A*29:02": [ + 0.840624988079071, + 11.970000267028809, + 4.800000190734863, + 2.5, + 0.8199999928474426, + 12.0, + 4.2, + 5.5 ] }, "WT": { - "HLA-B*45:01": [ - 1.4078749999999978, - 4.590000000000001, - 3.9, - 1.6, - 3.5, - 2.0, - 1.6, - 8.4 + "HLA-A*29:02": [ + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -143190,21 +161231,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.0157344937324523, - 0.0178271592432843, - 0.0077, - 0.0012308314, - 0.002358466 + "HLA-A*29:02": [ + 0.2196164838969707, + 0.4493059103567223, + 0.0579, + 0.0054298355, + 0.15225407 ] }, "WT": { - "HLA-B*45:01": [ - 0.0275617614388465, - 0.0569729650120957, - 0.0199, - 0.005198356, - 0.0044463836 + "HLA-A*29:02": [ + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -143217,19 +161258,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 13.500896739130424, - 4.0, + 0.9356793478259532, + 1.4, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ + "NA", + "NA", "NA", - 4.585733695652138, - 2.6, "NA", "NA" ] @@ -143249,127 +161290,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 2.315624952316284, - 7.179999828338623, - 3.799999952316284, - 1.399999976158142, - 3.200000047683716, - 3.200000047683716, - 2.8, + "HLA-A*29:02": [ + 0.840624988079071, + 11.970000267028809, + 4.800000190734863, + 2.5, + 0.8199999928474426, 12.0, - 13.500896739130424, - 4.0 + 4.2, + 5.5, + 0.9356793478259532, + 1.4 ] }, "WT": { - "HLA-B*45:01": [ - 1.4078749999999978, - 4.590000000000001, - 3.9, - 1.6, - 3.5, - 2.0, - 1.6, - 8.4, - 4.585733695652138, - 2.6 + "HLA-A*29:02": [ + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, - "wt_peptide": "FEQKLAST" - } - }, - "transcripts": [ - "ENST00000368491.8-CEP85L-S/F-450", - "ENST00000434604.5-CEP85L-S/F-453", - "ENST00000392500.7-CEP85L-S/F-453", - "ENST00000419517.2-CEP85L-S/F-450", - "ENST00000360290.7-CEP85L-S/F-348", - "ENST00000368488.9-CEP85L-S/F-453" - ], - "transcript_expr": [ - 5.216, - 5.765, - 0.698, - 0.644, - 0.202, - 0.0 - ], - "tsl": [ - 1, - 1, - 1, - 1, - 1, - 5 - ], - "biotype": [ - "protein_coding", - "protein_coding", - "protein_coding", - "protein_coding", - "protein_coding", - "protein_coding" - ], - "transcript_length": [ - 805, - 576, - 499, - 496, - 394, - 808 - ], - "transcript_count": 6, - "peptide_count": 5, - "total_expr": 12.525 - } - }, - "sets": [ - "Transcript Set 1" - ], - "transcript_counts": [ - 6 - ], - "peptide_counts": [ - 5 - ], - "set_expr": [ - 12.525 - ], - "DNA VAF": 0.581, - "RNA VAF": 0.421, - "gene_expr": 16.147, - "best_peptide_mt": "GEFEQKLAFT", - "best_peptide_wt": "GEFEQKLAST", - "best_hla_allele": "HLA-B*45:01" - }, - "chr6-122781239-122781240-C-G": { - "good_binders": { - "Transcript Set 1": { - "peptides": { - "FFSSAHTSH": { + "wt_peptide": "FS-NA" + }, + "SWYLGGLLT": { "ic50s_MT": [ - 1003.8150024414062, + 2287.425048828125, "X" ], "percentiles_MT": [ - 1.7990000247955322, + 3.700000047683716, "X" ], "ic50s_WT": [ - 955.04, + "NA", "X" ], "percentiles_WT": [ - 1.709, + "NA", "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "5", + "mutation_position": "1-9", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -143385,26 +161357,26 @@ ], "MT": { "HLA-A*29:02": [ - 736.4850260812453, - 3893.4, - 453.02, - 963.49, - 877.6, - 2032.71, - 1044.14, - 1503.04 + 13401.58304249547, + 5389.75, + 1345.21, + 1967.79, + 4871.39, + 2607.06, + 932.74, + 933.19 ] }, "WT": { "HLA-A*29:02": [ - 607.9783030994745, - 3817.19, - 506.12, - 1000.67, - 853.66, - 2077.17, - 909.41, - 1227.35 + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -143421,26 +161393,26 @@ ], "MT": { "HLA-A*29:02": [ - 1.4872499704360962, - 0.8199999928474426, - 1.100000023841858, - 2.700000047683716, - 0.8999999761581421, - 3.200000047683716, - 3.6, - 4.6 + 6.758500099182129, + 4.380000114440918, + 2.0, + 3.9000000953674316, + 2.9000000953674316, + 4.699999809265137, + 3.4, + 3.4 ] }, "WT": { "HLA-A*29:02": [ - 1.359, - 0.7799999999999999, - 1.2, - 2.8, - 0.89, - 3.3, - 3.3, - 4.0 + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -143454,20 +161426,20 @@ ], "MT": { "HLA-A*29:02": [ - 0.127112828195095, - 0.1625861523296328, - 0.184, - 0.42189744, - 0.27783856 + 0.0133323892951011, + 0.0076923383745988, + 0.00821, + 0.036688503, + 0.2946052 ] }, "WT": { "HLA-A*29:02": [ - 0.0869543813169002, - 0.1686900864084002, - 0.317, - 0.5321022, - 0.32184002 + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -143482,8 +161454,8 @@ "MT": { "HLA-A*29:02": [ "NA", - 2.1113315217390607, - 0.6, + 31.64317934782608, + 3.5, "NA", "NA" ] @@ -143491,8 +161463,8 @@ "WT": { "HLA-A*29:02": [ "NA", - 2.059347826086878, - 0.35, + "NA", + "NA", "NA", "NA" ] @@ -143513,57 +161485,57 @@ ], "MT": { "HLA-A*29:02": [ - 1.4872499704360962, - 0.8199999928474426, - 1.100000023841858, - 2.700000047683716, - 0.8999999761581421, - 3.200000047683716, - 3.6, - 4.6, - 2.1113315217390607, - 0.6 + 6.758500099182129, + 4.380000114440918, + 2.0, + 3.9000000953674316, + 2.9000000953674316, + 4.699999809265137, + 3.4, + 3.4, + 31.64317934782608, + 3.5 ] }, "WT": { "HLA-A*29:02": [ - 1.359, - 0.7799999999999999, - 1.2, - 2.8, - 0.89, - 3.3, - 3.3, - 4.0, - 2.059347826086878, - 0.35 + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, - "wt_peptide": "FFSSPHTSH" + "wt_peptide": "FS-NA" }, - "FFLVFFSSAH": { + "WYLGGLLTR": { "ic50s_MT": [ - 1541.074951171875, + 2301.27294921875, "X" ], "percentiles_MT": [ - 2.700000047683716, + 2.4630000591278076, "X" ], "ic50s_WT": [ - 1747.775, + "NA", "X" ], "percentiles_WT": [ - 3.5, + "NA", "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "9", + "mutation_position": "1-9", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -143579,26 +161551,26 @@ ], "MT": { "HLA-A*29:02": [ - 10536.97886807888, - 4718.52, - 819.97, - 1384.4, - 1697.75, - 3848.7, - 1143.62, - 526.66 + 2337.565412890759, + 5126.78, + 1980.5, + 2264.98, + 3996.46, + 1437.83, + 2759.05, + 1922.96 ] }, "WT": { "HLA-A*29:02": [ - 13399.133464146264, - 4550.19, - 640.57, - 1158.05, - 1380.7, - 3766.31, - 2114.85, - 1060.55 + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -143615,26 +161587,26 @@ ], "MT": { "HLA-A*29:02": [ - 5.429375171661377, - 1.5700000524520874, - 1.5, - 3.200000047683716, - 1.5, - 2.200000047683716, - 4.2, - 2.2 + 2.426374912261963, + 2.6700000762939453, + 2.4000000953674316, + 4.099999904632568, + 2.5, + 1.7000000476837158, + 6.7, + 5.2 ] }, "WT": { "HLA-A*29:02": [ - 6.758499999999998, - 1.34, - 1.4, - 3.0, - 1.3, - 2.2, - 6.4, - 4.0 + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -143648,20 +161620,20 @@ ], "MT": { "HLA-A*29:02": [ - 0.0160654224455356, - 0.0097900966155016, - 0.00536, - 0.046165906, - 0.19587693 + 0.4777794666588306, + 0.1794178750206876, + 0.0331, + 0.021865984, + 0.11701535 ] }, "WT": { "HLA-A*29:02": [ - 0.0227832533419132, - 0.0079532274455885, - 0.00252, - 0.048903536, - 0.12040087 + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -143676,8 +161648,8 @@ "MT": { "HLA-A*29:02": [ "NA", - 24.57923913043477, - 4.3, + 1.975027173912963, + 1.8, "NA", "NA" ] @@ -143685,8 +161657,8 @@ "WT": { "HLA-A*29:02": [ "NA", - 31.64317934782608, - 6.2, + "NA", + "NA", "NA", "NA" ] @@ -143707,57 +161679,101 @@ ], "MT": { "HLA-A*29:02": [ - 5.429375171661377, - 1.5700000524520874, - 1.5, - 3.200000047683716, - 1.5, - 2.200000047683716, - 4.2, - 2.2, - 24.57923913043477, - 4.3 + 2.426374912261963, + 2.6700000762939453, + 2.4000000953674316, + 4.099999904632568, + 2.5, + 1.7000000476837158, + 6.7, + 5.2, + 1.975027173912963, + 1.8 ] }, "WT": { "HLA-A*29:02": [ - 6.758499999999998, - 1.34, - 1.4, - 3.0, - 1.3, - 2.2, - 6.4, - 4.0, - 31.64317934782608, - 6.2 + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, - "wt_peptide": "FFLVFFSSPH" - }, - "FLVFFSSAH": { + "wt_peptide": "FS-NA" + } + }, + "transcripts": [ + "ENST00000370367.4-KHDC3L-LIHVNRLDPNG/X-73-83" + ], + "transcript_expr": [ + 0.0 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 217 + ], + "transcript_count": 1, + "peptide_count": 4, + "total_expr": 0.0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 4 + ], + "set_expr": [ + 0.0 + ], + "DNA VAF": 0.113, + "RNA VAF": 0.0, + "gene_expr": 0.0, + "best_peptide_mt": "QIARLRSWY", + "best_peptide_wt": "NA", + "best_hla_allele": "HLA-A*29:02" + }, + "chr6-73363176-73363177-AG-A": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "GELRSWYLG": { "ic50s_MT": [ - 2185.2099609375, - "X" + "X", + 1001.989990234375 ], "percentiles_MT": [ - 3.2330000400543213, - "X" + "X", + 1.899999976158142 ], "ic50s_WT": [ - 1735.855, - "X" + "X", + "NA" ], "percentiles_WT": [ - 3.096, - "X" + "X", + "NA" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "8", + "mutation_position": "3-9", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -143772,27 +161788,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 4305.2013082165295, - 5206.99, - 580.48, - 1050.6, - 2547.53, - 3272.12, - 1822.89, - 1044.65 + "HLA-B*45:01": [ + 1660.677992464929, + 2557.05, + 1010.16, + 841.61, + 993.82, + 719.41, + 1200.08, + 421.33 ] }, "WT": { - "HLA-A*29:02": [ - 3831.814536362014, - 5124.58, - 408.72, - 670.55, - 1854.52, - 3202.08, - 1617.19, - 831.71 + "HLA-B*45:01": [ + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -143808,27 +161824,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 3.1665000915527344, - 3.0299999713897705, - 1.2999999523162842, - 2.799999952316284, - 1.899999976158142, - 6.800000190734863, - 5.0, - 3.6 + "HLA-B*45:01": [ + 1.3887499570846558, + 3.6500000953674316, + 1.399999976158142, + 1.5, + 0.6100000143051147, + 2.299999952316284, + 4.6, + 1.5 ] }, "WT": { - "HLA-A*29:02": [ - 2.9913749999999983, - 2.66, - 0.98, - 2.3, - 1.5, - 6.5, - 4.8, - 3.2 + "HLA-B*45:01": [ + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -143841,21 +161857,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.0125104449689388, - 0.0227606733207784, - 0.00956, - 0.020124925, - 0.29780468 + "HLA-B*45:01": [ + 0.1719816476106643, + 0.0936247585824729, + 0.0108, + 0.0035540275, + 0.0013085513 ] }, "WT": { - "HLA-A*29:02": [ - 0.0323308929800987, - 0.0272142912177654, - 0.0055, - 0.035013203, - 0.18965495 + "HLA-B*45:01": [ + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -143868,19 +161884,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 10.655842391304333, - 3.3, + 3.0595108695651447, + 3.4, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ + "NA", + "NA", "NA", - 8.839293478260856, - 4.2, "NA", "NA" ] @@ -143900,58 +161916,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 3.1665000915527344, - 3.0299999713897705, - 1.2999999523162842, - 2.799999952316284, - 1.899999976158142, - 6.800000190734863, - 5.0, - 3.6, - 10.655842391304333, - 3.3 + "HLA-B*45:01": [ + 1.3887499570846558, + 3.6500000953674316, + 1.399999976158142, + 1.5, + 0.6100000143051147, + 2.299999952316284, + 4.6, + 1.5, + 3.0595108695651447, + 3.4 ] }, "WT": { - "HLA-A*29:02": [ - 2.9913749999999983, - 2.66, - 0.98, - 2.3, - 1.5, - 6.5, - 4.8, - 3.2, - 8.839293478260856, - 4.2 + "HLA-B*45:01": [ + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, - "wt_peptide": "FLVFFSSPH" + "wt_peptide": "FS-NA" }, - "VFFSSAHTSH": { + "SWYLGGLLT": { "ic50s_MT": [ - 2295.6201171875, + 2287.425048828125, "X" ], "percentiles_MT": [ - 2.5859999656677246, + 3.700000047683716, "X" ], "ic50s_WT": [ - 2096.945, + "NA", "X" ], "percentiles_WT": [ - 2.424, + "NA", "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "6", + "mutation_position": "1-9", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -143967,26 +161983,26 @@ ], "MT": { "HLA-A*29:02": [ - 3508.899569095868, - 4723.81, - 1761.09, - 1854.1, - 2151.86, - 2904.96, - 2439.38, - 1248.91 + 13401.58304249547, + 5389.75, + 1345.21, + 1967.79, + 4871.39, + 2607.06, + 932.74, + 933.19 ] }, "WT": { "HLA-A*29:02": [ - 2395.801409038965, - 4094.41, - 1922.98, - 1672.99, - 2054.55, - 2873.7, - 2139.34, - 1170.93 + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -144003,26 +162019,26 @@ ], "MT": { "HLA-A*29:02": [ - 2.872999906539917, - 1.5800000429153442, - 2.299999952316284, - 3.700000047683716, - 1.7000000476837158, - 1.2999999523162842, - 7.1, - 4.4 + 6.758500099182129, + 4.380000114440918, + 2.0, + 3.9000000953674316, + 2.9000000953674316, + 4.699999809265137, + 3.4, + 3.4 ] }, "WT": { "HLA-A*29:02": [ - 2.4483749999999995, - 0.93, - 2.4, - 3.5, - 1.6, - 1.3, - 6.5, - 4.2 + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -144036,20 +162052,20 @@ ], "MT": { "HLA-A*29:02": [ - 0.2560442611575126, - 0.0630099105570002, - 0.0643, - 0.12086106, - 0.12443195 + 0.0133323892951011, + 0.0076923383745988, + 0.00821, + 0.036688503, + 0.2946052 ] }, "WT": { "HLA-A*29:02": [ - 0.3264539018273353, - 0.1110945986358765, - 0.126, - 0.19592223, - 0.14429672 + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -144064,8 +162080,8 @@ "MT": { "HLA-A*29:02": [ "NA", - 4.213478260869522, - 1.3, + 31.64317934782608, + 3.5, "NA", "NA" ] @@ -144073,8 +162089,8 @@ "WT": { "HLA-A*29:02": [ "NA", - 2.7245652173912447, - 0.82, + "NA", + "NA", "NA", "NA" ] @@ -144095,57 +162111,57 @@ ], "MT": { "HLA-A*29:02": [ - 2.872999906539917, - 1.5800000429153442, - 2.299999952316284, - 3.700000047683716, - 1.7000000476837158, - 1.2999999523162842, - 7.1, - 4.4, - 4.213478260869522, - 1.3 + 6.758500099182129, + 4.380000114440918, + 2.0, + 3.9000000953674316, + 2.9000000953674316, + 4.699999809265137, + 3.4, + 3.4, + 31.64317934782608, + 3.5 ] }, "WT": { "HLA-A*29:02": [ - 2.4483749999999995, - 0.93, - 2.4, - 3.5, - 1.6, - 1.3, - 6.5, - 4.2, - 2.7245652173912447, - 0.82 - ] + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" + ] } }, - "wt_peptide": "VFFSSPHTSH" + "wt_peptide": "FS-NA" }, - "FFSSAHTSHL": { + "WYLGGLLTR": { "ic50s_MT": [ - 3484.659912109375, + 2301.27294921875, "X" ], "percentiles_MT": [ - 4.699999809265137, + 2.4630000591278076, "X" ], "ic50s_WT": [ - 5199.69, + "NA", "X" ], "percentiles_WT": [ - 4.8, + "NA", "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "5", + "mutation_position": "1-9", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -144161,26 +162177,26 @@ ], "MT": { "HLA-A*29:02": [ - 3163.169193737719, - 5291.88, - 5456.06, - 3398.41, - 3570.91, - 8853.9, - 2159.14, - 2145.51 + 2337.565412890759, + 5126.78, + 1980.5, + 2264.98, + 3996.46, + 1437.83, + 2759.05, + 1922.96 ] }, "WT": { "HLA-A*29:02": [ - 2589.331490405233, - 4925.69, - 5696.27, - 3416.85, - 3974.73, - 8950.22, - 5473.69, - 6019.08 + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -144197,26 +162213,26 @@ ], "MT": { "HLA-A*29:02": [ - 2.7577500343322754, - 3.559999942779541, - 4.599999904632568, - 4.800000190734863, - 2.299999952316284, - 8.0, - 6.5, - 6.5 + 2.426374912261963, + 2.6700000762939453, + 2.4000000953674316, + 4.099999904632568, + 2.5, + 1.7000000476837158, + 6.7, + 5.2 ] }, "WT": { "HLA-A*29:02": [ - 2.521999999999999, - 2.0, - 4.8, - 4.8, - 2.5, - 8.1, - 14.0, - 15.0 + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -144230,20 +162246,20 @@ ], "MT": { "HLA-A*29:02": [ - 0.1046364977955818, - 0.0417134040624105, - 0.0118, - 0.038347084, - 0.08678936 + 0.4777794666588306, + 0.1794178750206876, + 0.0331, + 0.021865984, + 0.11701535 ] }, "WT": { "HLA-A*29:02": [ - 0.1003083027899265, - 0.0494914258241473, - 0.025, - 0.08616217, - 0.08758639 + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ 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5.800000190734863, - "X" + "X", + 4.510000228881836 ], "ic50s_WT": [ - 4416.04, - "X" + "X", + "NA" ], "percentiles_WT": [ - 5.09, - "X" + "X", + "NA" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "6", + "mutation_position": "3-10", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -144354,27 +162370,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 15171.40272761222, - 4877.68, - 3772.18, - 5530.06, - 6988.4, - 2693.07, - 2616.74, - 3459.15 + "HLA-B*45:01": [ + 8997.593831534588, + 4475.17, + 3947.81, + 1414.68, + 4034.44, + 2010.83, + 8865.23, + 5247.23 ] }, "WT": { - "HLA-A*29:02": [ - 10697.757128067768, - 4514.87, - 4317.21, - 5324.55, - 6326.12, - 2607.06, - 2842.89, - 3740.85 + "HLA-B*45:01": [ + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -144390,27 +162406,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 7.69350004196167, - 1.8899999856948853, - 3.5, - 6.800000190734863, - 3.799999952316284, - 5.099999904632568, - 6.5, - 7.8 + "HLA-B*45:01": [ + 2.900624990463257, + 5.420000076293945, + 3.5999999046325684, + 1.7000000476837158, + 1.7999999523162842, + 2.9000000953674316, + 28.0, + 19.0 ] }, "WT": { - "HLA-A*29:02": [ - 5.479374999999997, - 1.28, - 3.9, - 6.6, - 3.5, - 4.7, - 6.9, - 8.1 + "HLA-B*45:01": [ + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -144423,21 +162439,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.0316912941634655, - 0.0072798518045899, - 0.00557, - 0.019772014, - 0.14681952 + "HLA-B*45:01": [ + 0.1279685609042644, + 0.0168367953617748, + 0.000673, + 0.0002963775, + 0.0005029607 ] }, "WT": { - "HLA-A*29:02": [ - 0.0688785053789615, - 0.0116078776425116, - 0.0143, - 0.04003129, - 0.15117237 + "HLA-B*45:01": [ + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -144450,19 +162466,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 31.64317934782608, - 4.2, + 14.277038043478257, + 12.0, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ + "NA", + "NA", "NA", - 20.2322554347826, - 2.7, "NA", "NA" ] @@ -144482,58 +162498,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 7.69350004196167, - 1.8899999856948853, - 3.5, - 6.800000190734863, - 3.799999952316284, - 5.099999904632568, - 6.5, - 7.8, - 31.64317934782608, - 4.2 + "HLA-B*45:01": [ + 2.900624990463257, + 5.420000076293945, + 3.5999999046325684, + 1.7000000476837158, + 1.7999999523162842, + 2.9000000953674316, + 28.0, + 19.0, + 14.277038043478257, + 12.0 ] }, "WT": { - "HLA-A*29:02": [ - 5.479374999999997, - 1.28, - 3.9, - 6.6, - 3.5, - 4.7, - 6.9, - 8.1, - 20.2322554347826, - 2.7 + "HLA-B*45:01": [ + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, - "wt_peptide": "VFFSSPHTS" + "wt_peptide": "FS-NA" }, - "FFLVFFSSA": { + "GELRSWYL": { "ic50s_MT": [ - 4594.2548828125, - "X" + "X", + 4674.3251953125 ], "percentiles_MT": [ - 7.800000190734863, - "X" + "X", + 2.700000047683716 ], "ic50s_WT": [ - 11750.735, - "X" + "X", + "NA" ], "percentiles_WT": [ - 16.0, - "X" + "X", + "NA" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "9", + "mutation_position": "3-8", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -144548,27 +162564,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 11000.434509699957, - 4543.68, - 3693.51, - 7092.61, - 10423.63, - 3807.28, - 3988.04, - 4644.83 + "HLA-B*45:01": [ + 1757.3459518376474, + 4167.22, + 9867.33, + 953.12, + 7499.53, + 953.12, + 5181.43, + 24391.58 ] }, "WT": { - "HLA-A*29:02": [ - 23337.76821310461, - 5729.22, - 8210.58, - 15290.89, - 22019.23, - 7609.38, - 6994.55, - 18705.53 + "HLA-B*45:01": [ + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -144584,27 +162600,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 5.632500171661377, - 1.3300000429153442, - 3.5, - 8.199999809265137, - 5.599999904632568, - 8.300000190734863, - 8.5, - 9.6 + "HLA-B*45:01": [ + 1.418874979019165, + 5.139999866485596, + 7.0, + 1.7000000476837158, + 2.799999952316284, + 1.2999999523162842, + 4.6, + 33.0 ] }, "WT": { - "HLA-A*29:02": [ - 15.483874999999996, - 13.22, - 6.3, - 20.0, - 16.0, - 20.0, - 15.0, - 28.0 + "HLA-B*45:01": [ + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -144617,21 +162633,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.0602556690573692, - 0.0109651702027473, - 0.00169, - 0.020766232, - 0.20470336 + "HLA-B*45:01": [ + 0.7748331055045128, + 0.4521097614408699, + 0.0206, + 0.003787931, + 0.0009359125 ] }, "WT": { - "HLA-A*29:02": [ - 0.0403822287917137, - 0.0049524291500086, - 0.000361, - 0.026071528, - 0.21330644 + "HLA-B*45:01": [ + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, @@ -144644,19 +162660,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 22.19230978260869, - 7.4, + 0.9296739130433592, + 2.6, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ + "NA", + "NA", "NA", - 62.74467391304348, - 16.0, "NA", "NA" ] @@ -144676,42 +162692,42 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 5.632500171661377, - 1.3300000429153442, - 3.5, - 8.199999809265137, - 5.599999904632568, - 8.300000190734863, - 8.5, - 9.6, - 22.19230978260869, - 7.4 + "HLA-B*45:01": [ + 1.418874979019165, + 5.139999866485596, + 7.0, + 1.7000000476837158, + 2.799999952316284, + 1.2999999523162842, + 4.6, + 33.0, + 0.9296739130433592, + 2.6 ] }, "WT": { - "HLA-A*29:02": [ - 15.483874999999996, - 13.22, - 6.3, - 20.0, - 16.0, - 20.0, - 15.0, - 28.0, - 62.74467391304348, - 16.0 + "HLA-B*45:01": [ + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA", + "NA" ] } }, - "wt_peptide": "FFLVFFSSP" + "wt_peptide": "FS-NA" } }, "transcripts": [ - "ENST00000356535.4-FABP7-P/A-132" + "ENST00000370367.4-KHDC3L-E/X-84" ], "transcript_expr": [ - 0.206 + 0.0 ], "tsl": [ 1 @@ -144720,11 +162736,11 @@ "protein_coding" ], "transcript_length": [ - 166 + 217 ], "transcript_count": 1, - "peptide_count": 7, - "total_expr": 0.206 + "peptide_count": 5, + "total_expr": 0.0 } }, "sets": [ @@ -144734,44 +162750,44 @@ 1 ], "peptide_counts": [ - 7 + 5 ], "set_expr": [ - 0.206 + 0.0 ], - "DNA VAF": 0.362, + "DNA VAF": 0.085, "RNA VAF": 0.0, - "gene_expr": 0.317, - "best_peptide_mt": "FFSSAHTSH", - "best_peptide_wt": "FFSSPHTSH", - "best_hla_allele": "HLA-A*29:02" + "gene_expr": 0.0, + "best_peptide_mt": "GELRSWYLG", + "best_peptide_wt": "NA", + "best_hla_allele": "HLA-B*45:01" }, - "chr6-131710718-131710719-T-C": { + "chr6-109451607-109451608-G-T": { "good_binders": { "Transcript Set 1": { "peptides": { - "KFSLIRKEY": { + "VMRQPFWPL": { "ic50s_MT": [ - 321.42498779296875, + 5082.77978515625, "X" ], "percentiles_MT": [ - 0.6299999952316284, + 6.25, "X" ], "ic50s_WT": [ - 157.385, + 10672.89, "X" ], "percentiles_WT": [ - 0.41, + 12.903, "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "6", + "mutation_position": "2", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -144787,26 +162803,26 @@ ], "MT": { "HLA-A*29:02": [ - 84.53076639585404, - 2947.21, - 259.64, - 418.82, - 383.21, - 1407.05, - 133.28, - 173.77 + 3667.474164693132, + 5780.56, + 6680.53, + 6030.06, + 6944.76, + 2032.71, + 4312.81, + 4385.0 ] }, "WT": { "HLA-A*29:02": [ - 51.58122789950227, - 2187.76, - 139.11, - 264.44, - 175.66, - 1290.38, - 110.6, - 121.89 + 6537.873138608217, + 5844.47, + 11708.33, + 10081.44, + 11264.34, + 5044.15, + 15731.13, + 14189.6 ] } }, @@ -144823,26 +162839,26 @@ ], "MT": { "HLA-A*29:02": [ - 0.36399999260902405, - 0.47999998927116394, - 0.7300000190734863, - 1.899999976158142, - 0.5299999713897705, - 1.600000023841858, - 0.9, - 1.1 + 2.9311249256134033, + 17.350000381469727, + 5.300000190734863, + 7.199999809265137, + 3.700000047683716, + 3.200000047683716, + 9.0, + 9.1 ] }, "WT": { "HLA-A*29:02": [ - 0.186625, - 0.31, - 0.5, - 1.6, - 0.32, - 1.4, - 0.8, - 0.8 + 3.927999999999999, + 27.11, + 8.6, + 13.0, + 6.0, + 13.0, + 25.0, + 23.0 ] } }, @@ -144856,20 +162872,20 @@ ], "MT": { "HLA-A*29:02": [ - 0.5540553331375122, - 0.8780644183444019, - 0.538, - 0.6274907, - 0.6074363 + 0.0383649691939353, + 0.0289588582880735, + 0.00677, + 0.0035537998, + 0.06264497 ] }, "WT": { "HLA-A*29:02": [ - 0.4824101515114307, - 0.9002984072622726, - 0.765, - 0.5980585, - 0.70125645 + 0.0716062635183334, + 0.018772183869569, + 0.00471, + 0.0031240988, + 0.0959278 ] } }, @@ -144884,8 +162900,8 @@ "MT": { "HLA-A*29:02": [ "NA", - 0.156630434782599, - 0.18, + 8.545326086956507, + 3.8, "NA", "NA" ] @@ -144893,8 +162909,8 @@ "WT": { "HLA-A*29:02": [ "NA", - 0.1211956521739239, - 0.07, + 12.805461956521723, + 4.6, "NA", "NA" ] @@ -144915,57 +162931,101 @@ ], "MT": { "HLA-A*29:02": [ - 0.36399999260902405, - 0.47999998927116394, - 0.7300000190734863, - 1.899999976158142, - 0.5299999713897705, - 1.600000023841858, - 0.9, - 1.1, - 0.156630434782599, - 0.18 + 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"best_peptide_wt": "VLRQPFWPL", + "best_hla_allele": "HLA-A*29:02" + }, + "chr6-118491773-118491774-G-A": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "GEFEQKLAFT": { "ic50s_MT": [ - 681.3049926757812, - "X" + "X", + 1514.3399658203125 ], "percentiles_MT": [ - 1.100000023841858, - "X" + "X", + 1.7300000190734863 ], "ic50s_WT": [ - 561.54, - "X" + "X", + 919.75 ], "percentiles_WT": [ - 0.715, - "X" + "X", + 1.2 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "4", + "mutation_position": "9", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -144980,27 +163040,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 186.3349782223501, - 3733.85, - 715.06, - 373.84, - 647.55, - 4106.84, - 724.9, - 613.1 + "HLA-B*45:01": [ + 110.01588415490504, + 1243.48, + 4344.06, + 823.59, + 835.2, + 1785.2, + 3878.73, + 2792.09 ] }, "WT": { - "HLA-A*29:02": [ - 87.03980528230635, - 2789.99, - 283.77, - 216.47, - 536.23, - 4062.65, 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0.8377520315683549, - 0.262, - 0.18658176, - 0.6814748 + "HLA-B*45:01": [ + 0.355692483484745, + 0.8280411053774164, + 0.312, + 0.002464711, + 0.00013740764 ] } }, @@ -145076,19 +163136,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 0.3445108695651981, - 0.8, + 0.4698369565216751, + 0.42, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 0.2196739130434792, - 0.43, + 0.2334510869565207, + 0.37, "NA", "NA" ] @@ -145108,58 +163168,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 0.721875011920929, - 0.75, - 1.399999976158142, - 1.7000000476837158, - 0.7300000190734863, - 2.4000000953674316, - 3.0, - 2.6, - 0.3445108695651981, - 0.8 + "HLA-B*45:01": [ + 0.27687498927116394, + 2.259999990463257, + 3.799999952316284, + 1.2000000476837158, + 0.5400000214576721, + 2.5, + 15.0, + 12.0, + 0.4698369565216751, + 0.42 ] }, "WT": { - "HLA-A*29:02": [ - 0.3756249999999998, - 0.4499999999999999, - 0.77, - 1.5, - 0.66, - 2.4, - 2.6, - 2.4, - 0.2196739130434792, - 0.43 + "HLA-B*45:01": [ + 0.091625, + 1.55, + 2.7, + 1.1, + 0.52, + 1.3, + 12.0, + 7.9, + 0.2334510869565207, + 0.37 ] } }, - "wt_peptide": "SLIQKEYEGY" + "wt_peptide": "GEFEQKLAST" }, - "LIRKEYEGY": { + "FEQKLAFTE": { "ic50s_MT": [ - 1732.14501953125, - "X" + "X", + 1613.56494140625 ], "percentiles_MT": [ - 3.4000000953674316, - "X" + "X", + 2.75 ], "ic50s_WT": [ - 899.505, - "X" + "X", + 3835.415 ], "percentiles_WT": [ - 2.75, - "X" + "X", + 3.6 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "3", + "mutation_position": "7", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -145174,27 +163234,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 121.3845003181506, - 5746.75, - 4680.38, - 1559.37, - 1904.92, - 5500.22, - 905.23, - 1076.39 + "HLA-B*45:01": [ + 1070.7501838576547, + 15444.45, + 2592.13, + 1534.27, + 5497.6, + 681.52, + 1503.87, + 1692.86 ] }, "WT": { - "HLA-A*29:02": [ - 91.30908007027712, - 5509.04, - 3105.11, - 907.82, - 813.01, - 6062.77, - 666.44, - 891.19 + "HLA-B*45:01": [ + 1015.786430480265, + 15248.39, + 6074.78, + 4576.12, + 9120.91, + 995.27, + 2595.43, + 3094.71 ] } }, @@ -145210,27 +163270,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 0.5224999785423279, - 14.430000305175781, - 4.099999904632568, - 3.5, - 1.5, - 14.0, - 3.3, - 3.7 + "HLA-B*45:01": [ + 1.1706249713897705, + 16.290000915527344, + 2.5999999046325684, + 2.200000047683716, + 2.200000047683716, + 2.200000047683716, + 5.6, + 6.5 ] }, "WT": { - "HLA-A*29:02": [ - 0.3922499999999997, - 5.96, - 3.1, - 2.7, - 0.85, - 16.0, - 2.8, - 3.3 + "HLA-B*45:01": [ + 1.1431249999999988, + 16.06, + 4.8, + 3.8, + 3.4, + 3.2, + 9.5, + 12.0 ] } }, @@ -145243,21 +163303,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.3800892867147922, - 0.7324778665246917, - 0.104, - 0.59430176, - 0.7850766 + "HLA-B*45:01": [ + 0.0679298229515552, + 0.0986768911953965, + 0.0162, + 0.005530614, + 0.00026956983 ] }, "WT": { - "HLA-A*29:02": [ - 0.2957241646945476, - 0.7281571906817849, - 0.21, - 0.34595346, - 0.81213343 + "HLA-B*45:01": [ + 0.0065367519855499, + 0.0848624368105714, + 0.0214, + 0.0015735009, + 8.4620624e-05 ] } }, @@ -145270,19 +163330,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 0.3866032608695633, - 0.94, + 2.9511413043477432, + 2.9, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 0.392527173913038, - 0.52, + 3.2967934782607813, + 2.5, "NA", "NA" ] @@ -145302,58 +163362,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 0.5224999785423279, - 14.430000305175781, - 4.099999904632568, - 3.5, - 1.5, - 14.0, - 3.3, - 3.7, - 0.3866032608695633, - 0.94 + "HLA-B*45:01": [ + 1.1706249713897705, + 16.290000915527344, + 2.5999999046325684, + 2.200000047683716, + 2.200000047683716, + 2.200000047683716, + 5.6, + 6.5, + 2.9511413043477432, + 2.9 ] }, "WT": { - "HLA-A*29:02": [ - 0.3922499999999997, - 5.96, - 3.1, - 2.7, - 0.85, - 16.0, - 2.8, - 3.3, - 0.392527173913038, - 0.52 - ] - } - }, - "wt_peptide": "LIQKEYEGY" + "HLA-B*45:01": [ + 1.1431249999999988, + 16.06, + 4.8, + 3.8, + 3.4, + 3.2, + 9.5, + 12.0, + 3.2967934782607813, + 2.5 + ] + } + }, + "wt_peptide": "FEQKLASTE" }, - "EKFSLIRKEY": { + "GEFEQKLAF": { "ic50s_MT": [ - 3325.6220703125, - "X" + "X", + 2197.0400390625 ], "percentiles_MT": [ - 2.9089999198913574, - "X" + "X", + 1.649999976158142 ], "ic50s_WT": [ - 1736.752, - "X" + "X", + 744.21 ], "percentiles_WT": [ - 2.573, - "X" + "X", + 1.47 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "7", + "mutation_position": "9", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -145368,27 +163428,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 3353.744298082096, - 5807.06, - 960.13, - 6469.41, - 3297.5, - 31398.89, - 736.68, - 761.25 + "HLA-B*45:01": [ + 204.09630813167652, + 2606.7, + 8337.16, + 1804.62, + 1370.32, + 344.7, + 2589.46, + 3644.35 ] }, "WT": { - "HLA-A*29:02": [ - 1648.2634353474696, - 5774.68, - 566.46, - 5965.16, - 1825.24, - 28178.94, - 741.79, - 770.07 + "HLA-B*45:01": [ + 56.8202591182147, + 745.28, + 5488.69, + 663.33, + 229.94, + 743.14, + 1274.12, + 1724.33 ] } }, @@ -145404,27 +163464,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 2.8178749084472656, - 20.530000686645508, - 1.7000000476837158, - 7.199999809265137, - 2.200000047683716, - 34.0, - 3.0, - 3.1 + "HLA-B*45:01": [ + 0.49537500739097595, + 3.700000047683716, + 6.099999904632568, + 2.4000000953674316, + 0.75, + 0.8999999761581421, + 9.5, + 13.0 ] }, "WT": { - "HLA-A*29:02": [ - 2.088375, - 16.78, + "HLA-B*45:01": [ + 0.069375, + 1.64, + 4.5, 1.3, - 6.7, - 1.5, - 31.0, - 3.0, - 3.1 + 0.21, + 2.4, + 4.8, + 6.6 ] } }, @@ -145437,21 +163497,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.509595587849617, - 0.1469966386786509, - 0.0394, - 0.00672204, - 0.13658519 + "HLA-B*45:01": [ + 0.8704978078603745, + 0.9035769974463784, + 0.494, + 0.039413683, + 0.0024513204 ] }, "WT": { - "HLA-A*29:02": [ - 0.3400879018008709, - 0.1586792481645993, - 0.108, - 0.01873131, - 0.26519105 + "HLA-B*45:01": [ + 0.2008855007588863, + 0.7522241760368635, + 0.634, + 0.0051574283, + 0.0009296623 ] } }, @@ -145464,19 +163524,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 2.2610597826086405, - 1.7, + 0.1168206521739136, + 0.19, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 2.1463315217390573, - 0.92, + 0.3542391304347632, + 0.11, "NA", "NA" ] @@ -145496,58 +163556,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 2.8178749084472656, - 20.530000686645508, - 1.7000000476837158, - 7.199999809265137, - 2.200000047683716, - 34.0, - 3.0, - 3.1, - 2.2610597826086405, - 1.7 + "HLA-B*45:01": [ + 0.49537500739097595, + 3.700000047683716, + 6.099999904632568, + 2.4000000953674316, + 0.75, + 0.8999999761581421, + 9.5, + 13.0, + 0.1168206521739136, + 0.19 ] }, "WT": { - "HLA-A*29:02": [ - 2.088375, - 16.78, + "HLA-B*45:01": [ + 0.069375, + 1.64, + 4.5, 1.3, - 6.7, - 1.5, - 31.0, - 3.0, - 3.1, - 2.1463315217390573, - 0.92 + 0.21, + 2.4, + 4.8, + 6.6, + 0.3542391304347632, + 0.11 ] } }, - "wt_peptide": "EKFSLIQKEY" + "wt_peptide": "GEFEQKLAS" }, - "FSLIRKEY": { + "FEQKLAFTEK": { "ic50s_MT": [ - 4606.85986328125, - "X" + "X", + 4779.8701171875 ], "percentiles_MT": [ - 2.8429999351501465, - "X" + "X", + 5.300000190734863 ], "ic50s_WT": [ - 3459.16, - "X" + "X", + 4417.687 ], "percentiles_WT": [ - 2.212, - "X" + "X", + 6.25 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "5", + "mutation_position": "7", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -145562,27 +163622,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 2027.1990717495328, - 5629.11, - 3584.61, - 418.82, - 8491.01, - 8297.38, - 722.19, - 9245.92 + "HLA-B*45:01": [ + 5752.459372109569, + 28071.96, + 8646.39, + 2216.49, + 8766.49, + 3807.28, + 3301.34, + 1299.96 ] }, "WT": { - "HLA-A*29:02": [ - 1352.436314373153, - 5521.48, - 2112.94, - 242.51, - 4805.38, - 8032.38, - 400.54, - 9098.09 + "HLA-B*45:01": [ + 4772.723425098626, + 25649.63, + 12819.26, + 3548.72, + 13220.57, + 4062.65, + 3316.58, + 1819.41 ] } }, @@ -145598,27 +163658,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 2.286250114440918, - 8.720000267028809, - 3.4000000953674316, - 1.899999976158142, - 4.5, - 7.300000190734863, - 0.2, - 8.7 + "HLA-B*45:01": [ + 2.337125062942505, + 38.72999954223633, + 6.300000190734863, + 2.299999952316284, + 3.299999952316284, + 5.400000095367432, + 13.0, + 5.2 ] }, "WT": { - "HLA-A*29:02": [ - 1.9247499999999995, - 6.18, - 2.5, - 1.4, - 2.8, - 6.9, - 0.2, - 8.5 + "HLA-B*45:01": [ + 2.16325, + 32.86, + 8.8, + 3.3, + 4.9, + 5.6, + 14.0, + 6.9 ] } }, @@ -145631,21 +163691,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.916014663875103, - 0.5420530326732657, - 0.0262, - 0.49678013, - 0.7372356 + "HLA-B*45:01": [ + 0.1121042966842651, + 0.0243915848981582, + 0.00492, + 0.0005659539, + 0.0005913895 ] }, "WT": { - "HLA-A*29:02": [ - 0.7879234254360199, - 0.5271133278777707, - 0.0687, - 0.3869215, - 0.7965805 + "HLA-B*45:01": [ + 0.0125643424689769, + 0.0206404397814736, + 0.0064, + 0.00078439096, + 0.00023941827 ] } }, @@ -145658,19 +163718,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 0.7328804347824871, - 2.0, + 9.849456521739114, + 4.8, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 0.7638043478259533, - 1.3, + 11.6303260869565, + 4.3, "NA", "NA" ] @@ -145690,115 +163750,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 2.286250114440918, - 8.720000267028809, - 3.4000000953674316, - 1.899999976158142, - 4.5, - 7.300000190734863, - 0.2, - 8.7, - 0.7328804347824871, - 2.0 + "HLA-B*45:01": [ + 2.337125062942505, + 38.72999954223633, + 6.300000190734863, + 2.299999952316284, + 3.299999952316284, + 5.400000095367432, + 13.0, + 5.2, + 9.849456521739114, + 4.8 ] }, "WT": { - "HLA-A*29:02": [ - 1.9247499999999995, - 6.18, - 2.5, - 1.4, - 2.8, + "HLA-B*45:01": [ + 2.16325, + 32.86, + 8.8, + 3.3, + 4.9, + 5.6, + 14.0, 6.9, - 0.2, - 8.5, - 0.7638043478259533, - 1.3 + 11.6303260869565, + 4.3 ] } }, - "wt_peptide": "FSLIQKEY" - } - }, - "transcripts": [ - "ENST00000314099.10-CTAGE9-Q/R-100" - ], - "transcript_expr": [ - 0.0 - ], - "tsl": [ - "NA" - ], - "biotype": [ - "protein_coding" - ], - "transcript_length": [ - 777 - ], - "transcript_count": 1, - "peptide_count": 5, - "total_expr": 0.0 - } - }, - "sets": [ - "Transcript Set 1" - ], - "transcript_counts": [ - 1 - ], - "peptide_counts": [ - 5 - ], - "set_expr": [ - 0.0 - ], - "DNA VAF": 0.103, - "RNA VAF": 0.0, - "gene_expr": 0.0, - "best_peptide_mt": "KFSLIRKEY", - "best_peptide_wt": "KFSLIQKEY", - "best_hla_allele": "HLA-A*29:02" - }, - "chr6-152325133-152325134-C-T": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 0.323, - "RNA VAF": 0.286, - "gene_expr": 5.739, - "best_peptide_mt": "DQKKILEDA", - "best_peptide_wt": "DQEKILEDA", - "best_hla_allele": "HLA-B*45:01" - }, - "chr6-157133135-157133136-G-C": { - "good_binders": { - "Transcript Set 1": { - "peptides": { - "QMHAAISSF": { + "wt_peptide": "FEQKLASTEK" + }, + "FEQKLAFT": { "ic50s_MT": [ - 2963.5048828125, - "X" + "X", + 4979.9208984375 ], "percentiles_MT": [ - 4.099999904632568, - "X" + "X", + 3.5 ], "ic50s_WT": [ - 1896.095, - "X" + "X", + 3025.335 ], "percentiles_WT": [ - 3.0, - "X" + "X", + 3.05 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "5", + "mutation_position": "7", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -145813,27 +163816,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 399.4423836119613, - 5764.32, - 3672.95, - 2858.2, - 2450.87, - 3202.08, - 1613.47, - 3068.81 + "HLA-B*45:01": [ + 5630.892003062949, + 6479.05, + 4328.95, + 704.01, + 8469.44, + 2077.17, + 3527.36, + 9665.85 ] }, "WT": { - "HLA-A*29:02": [ - 315.8049628029705, - 5657.47, - 2001.71, - 1654.99, - 2018.9, - 3975.68, - 1088.33, - 1790.48 + "HLA-B*45:01": [ + 1704.6466672946867, + 3564.96, + 4533.44, + 883.6, + 9342.75, + 1362.11, + 2485.71, + 8002.76 ] } }, @@ -145849,27 +163852,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 1.121500015258789, - 15.829999923706055, - 3.5, - 4.699999809265137, - 1.7999999523162842, - 6.5, - 4.7, - 7.2 + "HLA-B*45:01": [ + 2.315624952316284, + 7.179999828338623, + 3.799999952316284, + 1.399999976158142, + 3.200000047683716, + 3.200000047683716, + 2.8, + 12.0 ] }, "WT": { - "HLA-A*29:02": [ - 0.99075, - 9.73, - 2.4, - 3.6, + "HLA-B*45:01": [ + 1.4078749999999978, + 4.590000000000001, + 3.9, 1.6, - 8.8, - 3.7, - 5.0 + 3.5, + 2.0, + 1.6, + 8.4 ] } }, @@ -145882,21 +163885,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.3821356259286403, - 0.4644316881101775, - 0.0751, - 0.043661483, - 0.10409398 + "HLA-B*45:01": [ + 0.0157344937324523, + 0.0178271592432843, + 0.0077, + 0.0012308314, + 0.002358466 ] }, "WT": { - "HLA-A*29:02": [ - 0.5206898152828217, - 0.6401287503094367, - 0.106, - 0.04887751, - 0.085765004 + "HLA-B*45:01": [ + 0.0275617614388465, + 0.0569729650120957, + 0.0199, + 0.005198356, + 0.0044463836 ] } }, @@ -145909,19 +163912,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 0.9014130434781435, - 1.2, + 13.500896739130424, + 4.0, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 0.5419293478260414, - 0.93, + 4.585733695652138, + 2.6, "NA", "NA" ] @@ -145941,69 +163944,60 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 1.121500015258789, - 15.829999923706055, - 3.5, - 4.699999809265137, - 1.7999999523162842, - 6.5, - 4.7, - 7.2, - 0.9014130434781435, - 1.2 + "HLA-B*45:01": [ + 2.315624952316284, + 7.179999828338623, + 3.799999952316284, + 1.399999976158142, + 3.200000047683716, + 3.200000047683716, + 2.8, + 12.0, + 13.500896739130424, + 4.0 ] }, "WT": { - "HLA-A*29:02": [ - 0.99075, - 9.73, - 2.4, - 3.6, + "HLA-B*45:01": [ + 1.4078749999999978, + 4.590000000000001, + 3.9, 1.6, - 8.8, - 3.7, - 5.0, - 0.5419293478260414, - 0.93 + 3.5, + 2.0, + 1.6, + 8.4, + 4.585733695652138, + 2.6 ] } }, - "wt_peptide": "QMHAGISSF" + "wt_peptide": "FEQKLAST" } }, "transcripts": [ - "ENST00000346085.10-ARID1B-G/A-910", - "ENST00000350026.10-ARID1B-G/A-814", - "ENST00000637810.1-ARID1B-G/A-64", - "ENST00000636930.2-ARID1B-G/A-897", - "ENST00000319584.11-ARID1B-G/A-235", - "ENST00000414678.7-ARID1B-G/A-283", - "ENST00000637904.1-ARID1B-G/A-64", - "ENST00000637003.1-ARID1B-G/A-64", - "ENST00000647938.1-ARID1B-G/A-827" + "ENST00000368491.8-CEP85L-S/F-450", + "ENST00000434604.5-CEP85L-S/F-453", + "ENST00000392500.7-CEP85L-S/F-453", + "ENST00000419517.2-CEP85L-S/F-450", + "ENST00000360290.7-CEP85L-S/F-348", + "ENST00000368488.9-CEP85L-S/F-453" ], "transcript_expr": [ - 0.097, - 0.0, - 0.51, - 0.479, - 0.797, - 5.811, - 3.524, - 0.976, - 1.723 + 5.216, + 5.765, + 0.698, + 0.644, + 0.202, + 0.0 ], "tsl": [ 1, 1, 1, - 2, - 2, - 5, - 5, - 5, - "NA" + 1, + 1, + 5 ], "biotype": [ "protein_coding", @@ -146011,111 +164005,66 @@ "protein_coding", "protein_coding", "protein_coding", - "protein_coding", - "protein_coding", - "protein_coding", "protein_coding" ], "transcript_length": [ - 2332, - 2236, - 1486, - 2372, - 727, - 1758, - 1539, - 97, - 2249 + 805, + 576, + 499, + 496, + 394, + 808 ], - "transcript_count": 9, - "peptide_count": 1, - "total_expr": 13.917 + "transcript_count": 6, + "peptide_count": 5, + "total_expr": 12.525 } }, "sets": [ "Transcript Set 1" ], "transcript_counts": [ - 9 + 6 ], "peptide_counts": [ - 1 + 5 ], "set_expr": [ - 13.917 + 12.525 ], - "DNA VAF": 1.0, - "RNA VAF": 1.0, - "gene_expr": 39.757, - "best_peptide_mt": "QMHAAISSF", - "best_peptide_wt": "QMHAGISSF", - "best_hla_allele": "HLA-A*29:02" - }, - "chr7-27130623-27130624-C-T": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - 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"good_binders": { "Transcript Set 1": { "peptides": { - "MEGGVKITA": { + "FFSSAHTSH": { "ic50s_MT": [ - "X", - 61.46500015258789 + 1003.8150024414062, + "X" ], "percentiles_MT": [ - "X", - 0.15000000596046448 + 1.7990000247955322, + "X" ], "ic50s_WT": [ - "X", - 53.445 + 955.04, + "X" ], "percentiles_WT": [ - "X", - 0.15 + 1.709, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "6", + "mutation_position": "5", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -146130,27 +164079,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 43.087156465526704, - 91.42, - 65.11, - 57.82, - 56.72, - 165.16, - 46.69, - 91.75 + "HLA-A*29:02": [ + 736.4850260812453, + 3893.4, + 453.02, + 963.49, + 877.6, + 2032.71, + 1044.14, + 1503.04 ] }, "WT": { - "HLA-B*45:01": [ - 44.04870151626124, - 52.99, - 69.33, - 53.9, - 41.96, - 174.34, - 52.75, - 107.06 + "HLA-A*29:02": [ + 607.9783030994745, + 3817.19, + 506.12, + 1000.67, + 853.66, + 2077.17, + 909.41, + 1227.35 ] } }, @@ -146166,27 +164115,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 0.011500000022351742, - 0.4099999964237213, - 0.10000000149011612, - 0.20000000298023224, - 0.07999999821186066, - 0.30000001192092896, - 0.3, - 0.4 + "HLA-A*29:02": [ + 1.4872499704360962, + 0.8199999928474426, + 1.100000023841858, + 2.700000047683716, + 0.8999999761581421, + 3.200000047683716, + 3.6, + 4.6 ] }, "WT": { - "HLA-B*45:01": [ - 0.014125, - 0.26, - 0.11, - 0.19, - 0.07, - 0.3, - 0.3, - 0.4 + "HLA-A*29:02": [ + 1.359, + 0.7799999999999999, + 1.2, + 2.8, + 0.89, + 3.3, + 3.3, + 4.0 ] } }, @@ -146199,21 +164148,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.7363156080245972, - 0.9635145255511188, - 0.87, - 0.94133085, - 0.11244655 + "HLA-A*29:02": [ + 0.127112828195095, + 0.1625861523296328, + 0.184, + 0.42189744, + 0.27783856 ] }, "WT": { - "HLA-B*45:01": [ - 0.7228128388524055, - 0.9610017756888022, - 0.832, - 0.8328333, - 0.07014678 + "HLA-A*29:02": [ + 0.0869543813169002, + 0.1686900864084002, + 0.317, + 0.5321022, + 0.32184002 ] } }, @@ -146226,19 +164175,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.0282065217391647, - 0.03, + 2.1113315217390607, + 0.6, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.031548913043494, - 0.04, + 2.059347826086878, + 0.35, "NA", "NA" ] @@ -146258,58 +164207,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 0.011500000022351742, - 0.4099999964237213, - 0.10000000149011612, - 0.20000000298023224, - 0.07999999821186066, - 0.30000001192092896, - 0.3, - 0.4, - 0.0282065217391647, - 0.03 + "HLA-A*29:02": [ + 1.4872499704360962, + 0.8199999928474426, + 1.100000023841858, + 2.700000047683716, + 0.8999999761581421, + 3.200000047683716, + 3.6, + 4.6, + 2.1113315217390607, + 0.6 ] }, "WT": { - "HLA-B*45:01": [ - 0.014125, - 0.26, - 0.11, - 0.19, - 0.07, - 0.3, - 0.3, - 0.4, - 0.031548913043494, - 0.04 + "HLA-A*29:02": [ + 1.359, + 0.7799999999999999, + 1.2, + 2.8, + 0.89, + 3.3, + 3.3, + 4.0, + 2.059347826086878, + 0.35 ] } }, - "wt_peptide": "MEGGVRITA" + "wt_peptide": "FFSSPHTSH" }, - "MEGGVKITAE": { + "FFLVFFSSAH": { "ic50s_MT": [ - "X", - 1680.1650390625 + 1541.074951171875, + "X" ], "percentiles_MT": [ - "X", - 2.200000047683716 + 2.700000047683716, + "X" ], "ic50s_WT": [ - "X", - 1632.045 + 1747.775, + "X" ], "percentiles_WT": [ - "X", - 2.2 + 3.5, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "6", + "mutation_position": "9", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -146324,27 +164273,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 3049.998123289672, - 6364.92, - 651.2, - 2111.16, - 3098.87, - 1249.17, - 1065.84, - 563.55 + "HLA-A*29:02": [ + 10536.97886807888, + 4718.52, + 819.97, + 1384.4, + 1697.75, + 3848.7, + 1143.62, + 526.66 ] }, "WT": { - "HLA-B*45:01": [ - 3974.2174677671815, - 5597.18, - 690.9, - 2054.82, - 2175.86, - 1209.27, - 846.62, - 554.54 + "HLA-A*29:02": [ + 13399.133464146264, + 4550.19, + 640.57, + 1158.05, + 1380.7, + 3766.31, + 2114.85, + 1060.55 ] } }, @@ -146360,27 +164309,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 1.784999966621399, - 7.079999923706055, - 0.8899999856948853, - 2.299999952316284, + "HLA-A*29:02": [ + 5.429375171661377, + 1.5700000524520874, 1.5, - 1.600000023841858, - 4.3, - 2.1 + 3.200000047683716, + 1.5, + 2.200000047683716, + 4.2, + 2.2 ] }, "WT": { - "HLA-B*45:01": [ - 2.002124999999999, - 6.38, - 0.94, - 2.3, - 1.2, - 1.6, - 3.3, - 2.1 + "HLA-A*29:02": [ + 6.758499999999998, + 1.34, + 1.4, + 3.0, + 1.3, + 2.2, + 6.4, + 4.0 ] } }, @@ -146393,21 +164342,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.0996569022536277, - 0.0424295975551177, - 0.022, - 0.002890248, - 0.00029853877 + "HLA-A*29:02": [ + 0.0160654224455356, + 0.0097900966155016, + 0.00536, + 0.046165906, + 0.19587693 ] }, "WT": { - "HLA-B*45:01": [ - 0.0704126954078674, - 0.0299700810900165, - 0.0167, - 0.0024896802, - 0.00032450655 + "HLA-A*29:02": [ + 0.0227832533419132, + 0.0079532274455885, + 0.00252, + 0.048903536, + 0.12040087 ] } }, @@ -146420,19 +164369,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 5.913749999999965, - 2.5, + 24.57923913043477, + 4.3, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 8.269211956521715, - 2.8, + 31.64317934782608, + 6.2, "NA", "NA" ] @@ -146452,58 +164401,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 1.784999966621399, - 7.079999923706055, - 0.8899999856948853, - 2.299999952316284, + "HLA-A*29:02": [ + 5.429375171661377, + 1.5700000524520874, 1.5, - 1.600000023841858, - 4.3, - 2.1, - 5.913749999999965, - 2.5 + 3.200000047683716, + 1.5, + 2.200000047683716, + 4.2, + 2.2, + 24.57923913043477, + 4.3 ] }, "WT": { - "HLA-B*45:01": [ - 2.002124999999999, - 6.38, - 0.94, - 2.3, - 1.2, - 1.6, - 3.3, - 2.1, - 8.269211956521715, - 2.8 - ] - } - }, - "wt_peptide": "MEGGVRITAE" - }, - "TMEGGVKITA": { - "ic50s_MT": [ - "X", - 4747.48486328125 + "HLA-A*29:02": [ + 6.758499999999998, + 1.34, + 1.4, + 3.0, + 1.3, + 2.2, + 6.4, + 4.0, + 31.64317934782608, + 6.2 + ] + } + }, + "wt_peptide": "FFLVFFSSPH" + }, + "FLVFFSSAH": { + "ic50s_MT": [ + 2185.2099609375, + "X" ], "percentiles_MT": [ - "X", - 4.6519999504089355 + 3.2330000400543213, + "X" ], "ic50s_WT": [ - "X", - 4657.905 + 1735.855, + "X" ], "percentiles_WT": [ - "X", - 5.117 + 3.096, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "7", + "mutation_position": "8", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -146518,27 +164467,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 18222.41839646241, - 21333.01, - 420.22, - 30232.07, - 788.52, - 8478.89, - 597.98, - 1016.08 + "HLA-A*29:02": [ + 4305.2013082165295, + 5206.99, + 580.48, + 1050.6, + 2547.53, + 3272.12, + 1822.89, + 1044.65 ] }, "WT": { - "HLA-B*45:01": [ - 20016.767565120863, - 20058.31, - 449.35, - 30726.73, - 514.95, - 8297.38, - 597.98, - 1018.43 + "HLA-A*29:02": [ + 3831.814536362014, + 5124.58, + 408.72, + 670.55, + 1854.52, + 3202.08, + 1617.19, + 831.71 ] } }, @@ -146554,27 +164503,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 5.204249858856201, - 24.649999618530273, - 0.6100000143051147, - 21.0, - 0.5199999809265137, - 13.0, - 2.2, - 4.1 + "HLA-A*29:02": [ + 3.1665000915527344, + 3.0299999713897705, + 1.2999999523162842, + 2.799999952316284, + 1.899999976158142, + 6.800000190734863, + 5.0, + 3.6 ] }, "WT": { - "HLA-B*45:01": [ - 6.133875, - 22.57, - 0.65, - 22.0, - 0.39, - 12.0, - 2.2, - 4.1 + "HLA-A*29:02": [ + 2.9913749999999983, + 2.66, + 0.98, + 2.3, + 1.5, + 6.5, + 4.8, + 3.2 ] } }, @@ -146587,21 +164536,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.4030416458845138, - 0.0223255756938413, - 0.414, - 0.022765892, - 0.24184537 + "HLA-A*29:02": [ + 0.0125104449689388, + 0.0227606733207784, + 0.00956, + 0.020124925, + 0.29780468 ] }, "WT": { - "HLA-B*45:01": [ - 0.5299620032310486, - 0.0316268701660848, - 0.349, - 0.010790621, - 0.19968383 + "HLA-A*29:02": [ + 0.0323308929800987, + 0.0272142912177654, + 0.0055, + 0.035013203, + 0.18965495 ] } }, @@ -146614,19 +164563,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", 10.655842391304333, - 0.25, + 3.3, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 7.778097826086963, - 0.31, + 8.839293478260856, + 4.2, "NA", "NA" ] @@ -146646,102 +164595,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 5.204249858856201, - 24.649999618530273, - 0.6100000143051147, - 21.0, - 0.5199999809265137, - 13.0, - 2.2, - 4.1, + "HLA-A*29:02": [ + 3.1665000915527344, + 3.0299999713897705, + 1.2999999523162842, + 2.799999952316284, + 1.899999976158142, + 6.800000190734863, + 5.0, + 3.6, 10.655842391304333, - 0.25 + 3.3 ] }, "WT": { - "HLA-B*45:01": [ - 6.133875, - 22.57, - 0.65, - 22.0, - 0.39, - 12.0, - 2.2, - 4.1, - 7.778097826086963, - 0.31 + "HLA-A*29:02": [ + 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2.5859999656677246, + "X" ], "ic50s_WT": [ - "X", - 5566.405 + 2096.945, + "X" ], "percentiles_WT": [ - "X", - 4.75 + 2.424, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "9", + "mutation_position": "6", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -146756,27 +164661,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 278.752774435432, - 17097.24, - 4895.86, - 3997.24, - 3702.63, - 6469.41, - 5684.47, - 3810.04 + "HLA-A*29:02": [ + 3508.899569095868, + 4723.81, + 1761.09, + 1854.1, + 2151.86, + 2904.96, + 2439.38, + 1248.91 ] }, "WT": { - "HLA-B*45:01": [ - 262.7008143715017, - 10548.98, - 7518.13, - 4856.71, - 4840.81, - 6539.79, - 6276.1, - 4284.79 + "HLA-A*29:02": [ + 2395.801409038965, + 4094.41, + 1922.98, + 1672.99, + 2054.55, + 2873.7, + 2139.34, + 1170.93 ] } }, @@ -146792,27 +164697,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 0.6088749766349792, - 18.350000381469727, - 4.199999809265137, - 3.5, + "HLA-A*29:02": [ + 2.872999906539917, + 1.5800000429153442, + 2.299999952316284, + 3.700000047683716, 1.7000000476837158, - 8.600000381469727, - 20.0, - 15.0 + 1.2999999523162842, + 7.1, + 4.4 ] }, "WT": { - "HLA-B*45:01": [ - 0.5892499999999997, - 10.98, - 5.6, - 3.9, - 2.0, - 8.7, - 22.0, - 16.0 + "HLA-A*29:02": [ + 2.4483749999999995, + 0.93, + 2.4, + 3.5, + 1.6, + 1.3, + 6.5, + 4.2 ] } }, @@ -146825,21 +164730,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.0462082549929618, - 0.2725685283242328, - 0.0679, - 0.013650162, - 0.049173675 + "HLA-A*29:02": [ + 0.2560442611575126, + 0.0630099105570002, + 0.0643, + 0.12086106, + 0.12443195 ] }, "WT": { - "HLA-B*45:01": [ - 0.0654609911143779, - 0.2981965370673585, - 0.0836, - 0.006710503, - 0.044957794 + "HLA-A*29:02": [ + 0.3264539018273353, + 0.1110945986358765, + 0.126, + 0.19592223, + 0.14429672 ] } }, @@ -146852,19 +164757,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 1.4691847826085933, + 4.213478260869522, 1.3, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 1.372880434782516, - 1.2, + 2.7245652173912447, + 0.82, "NA", "NA" ] @@ -146884,116 +164789,52 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 0.6088749766349792, - 18.350000381469727, - 4.199999809265137, - 3.5, + "HLA-A*29:02": [ + 2.872999906539917, + 1.5800000429153442, + 2.299999952316284, + 3.700000047683716, 1.7000000476837158, - 8.600000381469727, - 20.0, - 15.0, - 1.4691847826085933, + 1.2999999523162842, + 7.1, + 4.4, + 4.213478260869522, 1.3 ] }, "WT": { - "HLA-B*45:01": [ - 0.5892499999999997, - 10.98, - 5.6, - 3.9, - 2.0, - 8.7, - 22.0, - 16.0, - 1.372880434782516, - 1.2 + "HLA-A*29:02": [ + 2.4483749999999995, + 0.93, + 2.4, + 3.5, + 1.6, + 1.3, + 6.5, + 4.2, + 2.7245652173912447, + 0.82 ] } }, - "wt_peptide": "HEDVPICIHC" - } - }, - "transcripts": [ - "ENST00000248594.11-PTPN12-H/Y-230", - "ENST00000435495.6-PTPN12-H/Y-100", - "ENST00000415482.6-PTPN12-H/Y-111", - "ENST00000522115.6-PTPN12-H/Y-169", - "ENST00000447995.2-PTPN12-H/Y-111" - ], - "transcript_expr": [ - 14.21, - 35.285, - 46.053, - 0.28, - 1.021 - ], - "tsl": [ - 1, - 2, - 5, - 5, - 3 - ], - "biotype": [ - "protein_coding", - "protein_coding", - "protein_coding", - "protein_coding", - "nonsense_mediated_decay" - ], - "transcript_length": [ - 780, - 650, - 661, - 214, - 113 - ], - "transcript_count": 5, - "peptide_count": 1, - "total_expr": 96.849 - } - }, - "sets": [ - "Transcript Set 1" - ], - "transcript_counts": [ - 5 - ], - "peptide_counts": [ - 1 - ], - "set_expr": [ - 96.849 - ], - "DNA VAF": 0.203, - "RNA VAF": 0.161, - "gene_expr": 128.676, - "best_peptide_mt": "HEDVPICIYC", - "best_peptide_wt": "HEDVPICIHC", - "best_hla_allele": "HLA-B*45:01" - }, - "chr7-82908982-82908983-C-G": { - "good_binders": { - "Transcript Set 1": { - "peptides": { - "EETDSFDKP": { + "wt_peptide": "VFFSSPHTSH" + }, + "FFSSAHTSHL": { "ic50s_MT": [ - "X", - 1687.1099853515625 + 3484.659912109375, + "X" ], "percentiles_MT": [ - "X", - 3.75 + 4.699999809265137, + "X" ], "ic50s_WT": [ - "X", - 1650.12 + 5199.69, + "X" ], "percentiles_WT": [ - "X", - 3.6 + 4.8, + "X" ], "hla_types": [ "HLA-A*29:02", @@ -147014,27 +164855,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 75.21630326402004, - 12836.03, - 12298.36, - 2551.25, - 1336.14, - 2010.83, - 1230.86, - 1363.39 + "HLA-A*29:02": [ + 3163.169193737719, + 5291.88, + 5456.06, + 3398.41, + 3570.91, + 8853.9, + 2159.14, + 2145.51 ] }, "WT": { - "HLA-B*45:01": [ - 76.95703778172935, - 13201.66, - 9383.57, - 1989.19, - 1190.11, - 2077.17, - 1230.86, - 1311.05 + "HLA-A*29:02": [ + 2589.331490405233, + 4925.69, + 5696.27, + 3416.85, + 3974.73, + 8950.22, + 5473.69, + 6019.08 ] } }, @@ -147050,27 +164891,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 0.14637500047683716, - 13.329999923706055, - 8.5, - 2.9000000953674316, - 0.75, - 6.400000095367432, - 4.6, - 5.2 + "HLA-A*29:02": [ + 2.7577500343322754, + 3.559999942779541, + 4.599999904632568, + 4.800000190734863, + 2.299999952316284, + 8.0, + 6.5, + 6.5 ] }, "WT": { - "HLA-B*45:01": [ - 0.15875, - 13.72, - 6.7, - 2.6, - 0.7, - 6.6, - 4.6, - 5.0 + "HLA-A*29:02": [ + 2.521999999999999, + 2.0, + 4.8, + 4.8, + 2.5, + 8.1, + 14.0, + 15.0 ] } }, @@ -147083,21 +164924,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.1627701744437217, - 0.6688996748160927, - 0.575, - 0.20712815, - 0.026346518 + "HLA-A*29:02": [ + 0.1046364977955818, + 0.0417134040624105, + 0.0118, + 0.038347084, + 0.08678936 ] }, "WT": { - "HLA-B*45:01": [ - 0.6044212281703949, - 0.9040976909700456, - 0.469, - 0.5226737, - 0.16768046 + "HLA-A*29:02": [ + 0.1003083027899265, + 0.0494914258241473, + 0.025, + 0.08616217, + 0.08758639 ] } }, @@ -147110,19 +164951,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.4916032608695388, - 0.13, + 6.047907608695624, + 3.0, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.1149184782608756, - 0.2, + 5.149211956521697, + 2.1, "NA", "NA" ] @@ -147142,52 +164983,52 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 0.14637500047683716, - 13.329999923706055, - 8.5, - 2.9000000953674316, - 0.75, - 6.400000095367432, - 4.6, - 5.2, - 0.4916032608695388, - 0.13 + "HLA-A*29:02": [ + 2.7577500343322754, + 3.559999942779541, + 4.599999904632568, + 4.800000190734863, + 2.299999952316284, + 8.0, + 6.5, + 6.5, + 6.047907608695624, + 3.0 ] }, "WT": { - "HLA-B*45:01": [ - 0.15875, - 13.72, - 6.7, - 2.6, - 0.7, - 6.6, - 4.6, - 5.0, - 0.1149184782608756, - 0.2 + "HLA-A*29:02": [ + 2.521999999999999, + 2.0, + 4.8, + 4.8, + 2.5, + 8.1, + 14.0, + 15.0, + 5.149211956521697, + 2.1 ] } }, - "wt_peptide": "EETDWFDKP" + "wt_peptide": "FFSSPHTSHL" }, - "REETDSFDKP": { + "VFFSSAHTS": { "ic50s_MT": [ - "X", - 3646.544921875 + 4324.93017578125, + "X" ], "percentiles_MT": [ - "X", - 4.25 + 5.800000190734863, + "X" ], "ic50s_WT": [ - "X", - 3892.605 + 4416.04, + "X" ], "percentiles_WT": [ - "X", - 3.7 + 5.09, + "X" ], "hla_types": [ "HLA-A*29:02", @@ -147208,27 +165049,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 177.6312469302498, - 6187.2, - 17103.17, - 6539.79, - 2462.59, - 4830.5, - 2447.32, - 1002.14 + "HLA-A*29:02": [ + 15171.40272761222, + 4877.68, + 3772.18, + 5530.06, + 6988.4, + 2693.07, + 2616.74, + 3459.15 ] }, "WT": { - "HLA-B*45:01": [ - 336.9722349416143, - 5915.85, - 10088.75, - 5411.67, - 2686.18, - 5099.03, - 2391.61, - 839.32 + "HLA-A*29:02": [ + 10697.757128067768, + 4514.87, + 4317.21, + 5324.55, + 6326.12, + 2607.06, + 2842.89, + 3740.85 ] } }, @@ -147244,27 +165085,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 0.4440000057220459, - 6.920000076293945, - 13.0, - 4.5, - 1.2999999523162842, - 6.599999904632568, - 9.0, - 4.0 + "HLA-A*29:02": [ + 7.69350004196167, + 1.8899999856948853, + 3.5, + 6.800000190734863, + 3.799999952316284, + 5.099999904632568, + 6.5, + 7.8 ] }, "WT": { - "HLA-B*45:01": [ - 0.6848749999999995, - 6.68, - 7.1, - 4.2, - 1.4, + "HLA-A*29:02": [ + 5.479374999999997, + 1.28, + 3.9, + 6.6, + 3.5, + 4.7, 6.9, - 8.8, - 3.2 + 8.1 ] } }, @@ -147277,21 +165118,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.3598996847867965, - 0.6378299805722337, - 0.204, - 0.0014232798, - 0.004757184 + "HLA-A*29:02": [ + 0.0316912941634655, + 0.0072798518045899, + 0.00557, + 0.019772014, + 0.14681952 ] }, "WT": { - "HLA-B*45:01": [ - 0.5557462610304356, - 0.6540614165298912, - 0.0835, - 0.0036248222, - 0.016851041 + "HLA-A*29:02": [ + 0.0688785053789615, + 0.0116078776425116, + 0.0143, + 0.04003129, + 0.15117237 ] } }, @@ -147304,19 +165145,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.5453532608695184, - 0.57, + 31.64317934782608, + 4.2, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.5181249999999551, - 1.2, + 20.2322554347826, + 2.7, "NA", "NA" ] @@ -147336,107 +165177,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 0.4440000057220459, - 6.920000076293945, - 13.0, - 4.5, - 1.2999999523162842, - 6.599999904632568, - 9.0, - 4.0, - 0.5453532608695184, - 0.57 + "HLA-A*29:02": [ + 7.69350004196167, + 1.8899999856948853, + 3.5, + 6.800000190734863, + 3.799999952316284, + 5.099999904632568, + 6.5, + 7.8, + 31.64317934782608, + 4.2 ] }, "WT": { - "HLA-B*45:01": [ - 0.6848749999999995, - 6.68, - 7.1, - 4.2, - 1.4, + "HLA-A*29:02": [ + 5.479374999999997, + 1.28, + 3.9, + 6.6, + 3.5, + 4.7, 6.9, - 8.8, - 3.2, - 0.5181249999999551, - 1.2 + 8.1, + 20.2322554347826, + 2.7 ] } }, - "wt_peptide": "REETDWFDKP" - } - }, - "transcripts": [ - "ENST00000333891.14-PCLO-W/S-4444", - "ENST00000423517.6-PCLO-W/S-4444" - ], - "transcript_expr": [ - 0.037, - 2.087 - ], - "tsl": [ - 2, - 5 - ], - "biotype": [ - "protein_coding", - "protein_coding" - ], - "transcript_length": [ - 5142, - 4935 - ], - "transcript_count": 2, - "peptide_count": 2, - "total_expr": 2.124 - } - }, - "sets": [ - "Transcript Set 1" - ], - "transcript_counts": [ - 2 - ], - "peptide_counts": [ - 2 - ], - "set_expr": [ - 2.124 - ], 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7092.61, + 10423.63, + 3807.28, + 3988.04, + 4644.83 ] }, "WT": { - "HLA-B*45:01": [ - 1223.166361042498, - 164.56, - 2643.02, - 444.5, - 14376.51, - 1062.03, - 2814.82, - 6141.01 + "HLA-A*29:02": [ + 23337.76821310461, + 5729.22, + 8210.58, + 15290.89, + 22019.23, + 7609.38, + 6994.55, + 18705.53 ] } }, @@ -147487,27 +165279,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 0.5892500281333923, - 0.5899999737739563, - 1.7999999523162842, - 0.5400000214576721, - 2.200000047683716, - 1.100000023841858, - 7.5, - 16.0 + "HLA-A*29:02": [ + 5.632500171661377, + 1.3300000429153442, + 3.5, + 8.199999809265137, + 5.599999904632568, + 8.300000190734863, + 8.5, + 9.6 ] }, "WT": { - "HLA-B*45:01": [ - 1.2303749999999982, - 0.63, - 2.7, - 0.95, - 5.4, - 1.5, - 1.9, - 5.8 + "HLA-A*29:02": [ + 15.483874999999996, + 13.22, + 6.3, + 20.0, + 16.0, + 20.0, + 15.0, + 28.0 ] } }, @@ -147520,21 +165312,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.0435947887599468, - 0.2827763753820894, - 0.195, - 0.022002842, - 0.049310774 + "HLA-A*29:02": [ + 0.0602556690573692, + 0.0109651702027473, + 0.00169, + 0.020766232, + 0.20470336 ] }, "WT": { - "HLA-B*45:01": [ - 0.0016422607004642, - 0.0707110446549687, - 0.0474, - 0.0046397415, - 0.009228548 + "HLA-A*29:02": [ + 0.0403822287917137, + 0.0049524291500086, + 0.000361, + 0.026071528, + 0.21330644 ] } }, @@ -147547,19 +165339,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 1.4288858695651214, - 0.58, + 22.19230978260869, + 7.4, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 3.80744565217384, - 1.6, + 62.74467391304348, + 16.0, "NA", "NA" ] @@ -147579,58 +165371,102 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 0.5892500281333923, - 0.5899999737739563, - 1.7999999523162842, - 0.5400000214576721, - 2.200000047683716, - 1.100000023841858, - 7.5, - 16.0, - 1.4288858695651214, - 0.58 + "HLA-A*29:02": [ + 5.632500171661377, + 1.3300000429153442, + 3.5, + 8.199999809265137, + 5.599999904632568, + 8.300000190734863, + 8.5, + 9.6, + 22.19230978260869, + 7.4 ] }, "WT": { - "HLA-B*45:01": [ - 1.2303749999999982, - 0.63, - 2.7, - 0.95, - 5.4, - 1.5, - 1.9, - 5.8, - 3.80744565217384, - 1.6 - ] - } - }, - "wt_peptide": "EEEKEIDA" - }, - "KEIYAKLRY": { - "ic50s_MT": [ - 1205.125, + "HLA-A*29:02": [ + 15.483874999999996, + 13.22, + 6.3, + 20.0, + 16.0, + 20.0, + 15.0, + 28.0, + 62.74467391304348, + 16.0 + ] + } + }, + "wt_peptide": "FFLVFFSSP" + } + }, + "transcripts": [ + "ENST00000356535.4-FABP7-P/A-132" + ], + "transcript_expr": [ + 0.206 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 166 + ], + "transcript_count": 1, + "peptide_count": 7, + "total_expr": 0.206 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 7 + ], + "set_expr": [ + 0.206 + ], + "DNA VAF": 0.362, + "RNA VAF": 0.0, + "gene_expr": 0.317, + "best_peptide_mt": "FFSSAHTSH", + "best_peptide_wt": "FFSSPHTSH", + "best_hla_allele": "HLA-A*29:02" + }, + "chr6-131710718-131710719-T-C": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "KFSLIRKEY": { + "ic50s_MT": [ + 321.42498779296875, "X" ], "percentiles_MT": [ - 2.200000047683716, + 0.6299999952316284, "X" ], "ic50s_WT": [ - 1219.36, + 157.385, "X" ], "percentiles_WT": [ - 2.16, + 0.41, "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "4", + "mutation_position": "6", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -147646,26 +165482,26 @@ ], "MT": { "HLA-A*29:02": [ - 110.0201909186694, - 5163.97, - 1386.74, - 1215.83, - 1194.42, - 4288.48, - 526.94, - 781.57 + 84.53076639585404, + 2947.21, + 259.64, + 418.82, + 383.21, + 1407.05, + 133.28, + 173.77 ] }, "WT": { "HLA-A*29:02": [ - 64.63834870877959, - 4969.86, - 2094.03, - 1276.5, - 1162.22, - 4727.1, - 457.89, - 699.79 + 51.58122789950227, + 2187.76, + 139.11, + 264.44, + 175.66, + 1290.38, + 110.6, + 121.89 ] } }, @@ -147682,26 +165518,26 @@ ], "MT": { "HLA-A*29:02": [ - 0.4790000021457672, - 2.8299999237060547, - 2.0, - 3.0999999046325684, - 1.2000000476837158, - 9.699999809265137, - 2.4, - 3.1 + 0.36399999260902405, + 0.47999998927116394, + 0.7300000190734863, + 1.899999976158142, + 0.5299999713897705, + 1.600000023841858, + 0.9, + 1.1 ] }, "WT": { "HLA-A*29:02": [ - 0.2599999999999999, - 2.12, - 2.5, - 3.2, - 1.2, - 12.0, - 2.2, - 2.9 + 0.186625, + 0.31, + 0.5, + 1.6, + 0.32, + 1.4, + 0.8, + 0.8 ] } }, @@ -147715,20 +165551,20 @@ ], "MT": { "HLA-A*29:02": [ - 0.4960987605154514, - 0.8195306276303905, - 0.344, - 0.6071485, - 0.96655124 + 0.5540553331375122, + 0.8780644183444019, + 0.538, + 0.6274907, + 0.6074363 ] }, "WT": { "HLA-A*29:02": [ - 0.8461986482143402, - 0.9633318523722464, - 0.579, - 0.8810333, - 0.96438557 + 0.4824101515114307, + 0.9002984072622726, + 0.765, + 0.5980585, + 0.70125645 ] } }, @@ -147743,8 +165579,8 @@ "MT": { "HLA-A*29:02": [ "NA", - 0.2481521739130414, - 0.32, + 0.156630434782599, + 0.18, "NA", "NA" ] @@ -147752,8 +165588,8 @@ "WT": { "HLA-A*29:02": [ "NA", - 0.0282065217391647, - 0.16, + 0.1211956521739239, + 0.07, "NA", "NA" ] @@ -147774,57 +165610,57 @@ ], "MT": { "HLA-A*29:02": [ - 0.4790000021457672, - 2.8299999237060547, - 2.0, - 3.0999999046325684, - 1.2000000476837158, - 9.699999809265137, - 2.4, - 3.1, - 0.2481521739130414, - 0.32 + 0.36399999260902405, + 0.47999998927116394, + 0.7300000190734863, + 1.899999976158142, + 0.5299999713897705, + 1.600000023841858, + 0.9, + 1.1, + 0.156630434782599, + 0.18 ] }, "WT": { "HLA-A*29:02": [ - 0.2599999999999999, - 2.12, - 2.5, - 3.2, - 1.2, - 12.0, - 2.2, - 2.9, - 0.0282065217391647, - 0.16 + 0.186625, + 0.31, + 0.5, + 1.6, + 0.32, + 1.4, + 0.8, + 0.8, + 0.1211956521739239, + 0.07 ] } }, - "wt_peptide": "KEIDAKLRY" + "wt_peptide": "KFSLIQKEY" }, - "EEEKEIYAK": { + "SLIRKEYEGY": { "ic50s_MT": [ - "X", - 1359.010009765625 + 681.3049926757812, + "X" ], "percentiles_MT": [ - "X", - 2.9000000953674316 + 1.100000023841858, + "X" ], "ic50s_WT": [ - "X", - 4351.27 + 561.54, + "X" ], "percentiles_WT": [ - "X", - 7.15 + 0.715, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "7", + "mutation_position": "4", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -147839,27 +165675,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 935.0334916803008, - 10959.29, - 6549.42, - 1602.13, - 8660.15, - 963.49, - 748.53, - 1115.89 + "HLA-A*29:02": [ + 186.3349782223501, + 3733.85, + 715.06, + 373.84, + 647.55, + 4106.84, + 724.9, + 613.1 ] }, "WT": { - "HLA-B*45:01": [ - 1025.6811639917576, - 14202.63, - 14401.26, - 4651.0, - 17461.8, - 2443.19, - 2099.96, - 4051.54 + "HLA-A*29:02": [ + 87.03980528230635, + 2789.99, + 283.77, + 216.47, + 536.23, + 4062.65, + 627.02, + 586.85 ] } }, @@ -147875,27 +165711,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 1.106124997138977, - 11.390000343322754, - 5.0, - 2.299999952316284, - 3.299999952316284, - 3.0999999046325684, - 2.7, - 4.3 + "HLA-A*29:02": [ + 0.721875011920929, + 0.75, + 1.399999976158142, + 1.7000000476837158, + 0.7300000190734863, + 2.4000000953674316, + 3.0, + 2.6 ] }, "WT": { - "HLA-B*45:01": [ - 1.1483749999999988, - 14.829999999999998, - 9.7, - 3.9, - 6.8, - 7.5, - 7.8, - 14.0 + "HLA-A*29:02": [ + 0.3756249999999998, + 0.4499999999999999, + 0.77, + 1.5, + 0.66, + 2.4, + 2.6, + 2.4 ] } }, @@ -147908,21 +165744,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.1518077254295349, - 0.1438601283396859, - 0.0941, - 0.01814803, - 0.009855283 + "HLA-A*29:02": [ + 0.5357473120093346, + 0.7579849751883281, + 0.129, + 0.116455436, + 0.6532463 ] }, "WT": { - "HLA-B*45:01": [ - 0.0029355138540267, - 0.0831574000628316, - 0.0373, - 0.0010590215, - 0.00062758994 + "HLA-A*29:02": [ + 0.4680724143981933, + 0.8377520315683549, + 0.262, + 0.18658176, + 0.6814748 ] } }, @@ -147935,19 +165771,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 2.2920108695651606, - 1.1, + 0.3445108695651981, + 0.8, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 3.326576086956436, - 1.9, + 0.2196739130434792, + 0.43, "NA", "NA" ] @@ -147967,58 +165803,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 1.106124997138977, - 11.390000343322754, - 5.0, - 2.299999952316284, - 3.299999952316284, - 3.0999999046325684, - 2.7, - 4.3, - 2.2920108695651606, - 1.1 + "HLA-A*29:02": [ + 0.721875011920929, + 0.75, + 1.399999976158142, + 1.7000000476837158, + 0.7300000190734863, + 2.4000000953674316, + 3.0, + 2.6, + 0.3445108695651981, + 0.8 ] }, "WT": { - "HLA-B*45:01": [ - 1.1483749999999988, - 14.829999999999998, - 9.7, - 3.9, - 6.8, - 7.5, - 7.8, - 14.0, - 3.326576086956436, - 1.9 + "HLA-A*29:02": [ + 0.3756249999999998, + 0.4499999999999999, + 0.77, + 1.5, + 0.66, + 2.4, + 2.6, + 2.4, + 0.2196739130434792, + 0.43 ] } }, - "wt_peptide": "EEEKEIDAK" + "wt_peptide": "SLIQKEYEGY" }, - "EEKEIYAKL": { + "LIRKEYEGY": { "ic50s_MT": [ - "X", - 1390.074951171875 + 1732.14501953125, + "X" ], "percentiles_MT": [ - "X", - 1.7999999523162842 + 3.4000000953674316, + "X" ], "ic50s_WT": [ - "X", - 3058.35 + 899.505, + "X" ], "percentiles_WT": [ - "X", - 2.95 + 2.75, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "6", + "mutation_position": "3", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -148033,27 +165869,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 74.68094175638734, - 11367.6, - 2239.13, - 995.27, - 2738.59, - 611.63, - 1423.02, - 1357.13 + "HLA-A*29:02": [ + 121.3845003181506, + 5746.75, + 4680.38, + 1559.37, + 1904.92, + 5500.22, + 905.23, + 1076.39 ] }, "WT": { - "HLA-B*45:01": [ - 79.00953203663147, - 14505.15, - 6963.72, - 3975.68, - 5745.36, - 735.14, - 1637.61, - 2141.02 + "HLA-A*29:02": [ + 91.30908007027712, + 5509.04, + 3105.11, + 907.82, + 813.01, + 6062.77, + 666.44, + 891.19 ] } }, @@ -148069,27 +165905,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 0.14637500047683716, - 11.800000190734863, - 2.4000000953674316, - 1.7000000476837158, - 1.399999976158142, - 1.899999976158142, - 5.5, - 5.2 + "HLA-A*29:02": [ + 0.5224999785423279, + 14.430000305175781, + 4.099999904632568, + 3.5, + 1.5, + 14.0, + 3.3, + 3.7 ] }, "WT": { - "HLA-B*45:01": [ - 0.166125, - 15.19, - 5.3, - 3.6, - 2.3, - 2.3, - 6.3, - 8.0 + "HLA-A*29:02": [ + 0.3922499999999997, + 5.96, + 3.1, + 2.7, + 0.85, + 16.0, + 2.8, + 3.3 ] } }, @@ -148102,21 +165938,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.37980667501688, - 0.8142785205316942, - 0.449, - 0.10798913, - 0.0023683817 + "HLA-A*29:02": [ + 0.3800892867147922, + 0.7324778665246917, + 0.104, + 0.59430176, + 0.7850766 ] }, "WT": { - "HLA-B*45:01": [ - 0.3239262774586677, - 0.7730497802180148, - 0.377, - 0.028616026, - 0.0011004362 + "HLA-A*29:02": [ + 0.2957241646945476, + 0.7281571906817849, + 0.21, + 0.34595346, + 0.81213343 ] } }, @@ -148129,19 +165965,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.2556793478260744, - 0.22, + 0.3866032608695633, + 0.94, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.3199456521738852, - 0.29, + 0.392527173913038, + 0.52, "NA", "NA" ] @@ -148161,58 +165997,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 0.14637500047683716, - 11.800000190734863, - 2.4000000953674316, - 1.7000000476837158, - 1.399999976158142, - 1.899999976158142, - 5.5, - 5.2, - 0.2556793478260744, - 0.22 + "HLA-A*29:02": [ + 0.5224999785423279, + 14.430000305175781, + 4.099999904632568, + 3.5, + 1.5, + 14.0, + 3.3, + 3.7, + 0.3866032608695633, + 0.94 ] }, "WT": { - "HLA-B*45:01": [ - 0.166125, - 15.19, - 5.3, - 3.6, - 2.3, - 2.3, - 6.3, - 8.0, - 0.3199456521738852, - 0.29 + "HLA-A*29:02": [ + 0.3922499999999997, + 5.96, + 3.1, + 2.7, + 0.85, + 16.0, + 2.8, + 3.3, + 0.392527173913038, + 0.52 ] } }, - "wt_peptide": "EEKEIDAKL" + "wt_peptide": "LIQKEYEGY" }, - "IYAKLRYLEM": { + "EKFSLIRKEY": { "ic50s_MT": [ - 1607.449951171875, + 3325.6220703125, "X" ], "percentiles_MT": [ - 3.9000000953674316, + 2.9089999198913574, "X" ], "ic50s_WT": [ - 15033.22, + 1736.752, "X" ], "percentiles_WT": [ - 26.0, + 2.573, "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "2", + "mutation_position": "7", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -148228,26 +166064,26 @@ ], "MT": { "HLA-A*29:02": [ - 17451.217786654117, - 5381.39, - 1317.31, - 1700.36, - 982.14, - 4936.17, - 1514.54, - 1460.6 + 3353.744298082096, + 5807.06, + 960.13, + 6469.41, + 3297.5, + 31398.89, + 736.68, + 761.25 ] }, "WT": { "HLA-A*29:02": [ - 28207.4028782035, - 6031.45, - 14772.13, - 10815.98, - 18932.97, - 26985.39, - 11648.77, - 15294.31 + 1648.2634353474696, + 5774.68, + 566.46, + 5965.16, + 1825.24, + 28178.94, + 741.79, + 770.07 ] } }, @@ -148264,26 +166100,26 @@ ], "MT": { "HLA-A*29:02": [ - 9.185375213623047, 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46.22467391304348, - 19.0, + 2.1463315217390573, + 0.92, "NA", "NA" ] @@ -148356,57 +166192,57 @@ ], "MT": { "HLA-A*29:02": [ - 9.185375213623047, - 4.300000190734863, - 2.0, - 3.5, - 0.9700000286102295, - 3.299999952316284, - 5.1, - 5.0, - 5.346684782608634, - 2.5 + 2.8178749084472656, + 20.530000686645508, + 1.7000000476837158, + 7.199999809265137, + 2.200000047683716, + 34.0, + 3.0, + 3.1, + 2.2610597826086405, + 1.7 ] }, "WT": { "HLA-A*29:02": [ - 29.365875, - 99.08, - 12.0, - 13.0, - 13.0, - 30.0, - 24.0, - 28.0, - 46.22467391304348, - 19.0 + 2.088375, + 16.78, + 1.3, + 6.7, + 1.5, + 31.0, + 3.0, + 3.1, + 2.1463315217390573, + 0.92 ] } }, - "wt_peptide": "IDAKLRYLEM" + "wt_peptide": "EKFSLIQKEY" }, - "EEEKEIYAKL": { + "FSLIRKEY": { "ic50s_MT": [ - "X", - 1800.1199951171875 + 4606.85986328125, + "X" ], "percentiles_MT": [ - "X", - 2.450000047683716 + 2.8429999351501465, + "X" ], "ic50s_WT": [ - "X", - 4016.555 + 3459.16, + "X" ], "percentiles_WT": [ - "X", - 4.45 + 2.212, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "7", + "mutation_position": "5", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -148421,27 +166257,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 190.5272776420719, - 12088.08, - 4935.53, - 2065.97, - 6562.68, - 1534.27, - 1484.88, - 952.64 + "HLA-A*29:02": [ + 2027.1990717495328, + 5629.11, + 3584.61, + 418.82, + 8491.01, + 8297.38, + 722.19, + 9245.92 ] }, "WT": { - "HLA-B*45:01": [ - 164.27682104941437, - 14658.24, - 12842.73, - 5743.49, - 12350.5, - 2289.62, - 1491.73, - 1285.08 + "HLA-A*29:02": [ + 1352.436314373153, + 5521.48, + 2112.94, + 242.51, + 4805.38, + 8032.38, + 400.54, + 9098.09 ] } }, @@ -148457,27 +166293,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 0.4673750102519989, - 12.550000190734863, - 4.199999809265137, - 2.299999952316284, - 2.5999999046325684, - 2.0, - 5.8, - 3.8 + "HLA-A*29:02": [ + 2.286250114440918, + 8.720000267028809, + 3.4000000953674316, 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0.7638043478259533, + 1.3, "NA", "NA" ] @@ -148549,58 +166385,102 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 0.4673750102519989, - 12.550000190734863, - 4.199999809265137, - 2.299999952316284, - 2.5999999046325684, - 2.0, - 5.8, - 3.8, - 1.0576086956520356, - 1.2 + "HLA-A*29:02": [ + 2.286250114440918, + 8.720000267028809, + 3.4000000953674316, + 1.899999976158142, + 4.5, + 7.300000190734863, + 0.2, + 8.7, + 0.7328804347824871, + 2.0 ] }, "WT": { - "HLA-B*45:01": [ - 0.4182499999999997, - 15.37, - 8.8, - 4.3, - 4.6, - 3.4, - 5.8, - 5.1, - 1.0090760869563835, - 1.1 + "HLA-A*29:02": [ + 1.9247499999999995, + 6.18, + 2.5, + 1.4, + 2.8, + 6.9, + 0.2, + 8.5, + 0.7638043478259533, + 1.3 ] } }, - "wt_peptide": "EEEKEIDAKL" - }, - "DEEEKEIYA": { + "wt_peptide": "FSLIQKEY" + } + }, + "transcripts": [ + "ENST00000314099.10-CTAGE9-Q/R-100" + ], + "transcript_expr": [ + 0.0 + ], + "tsl": [ + "NA" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 777 + ], + 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1.2019836956520606, - 0.49 - ] - } - }, - "wt_peptide": "DEEEKEIDA" - }, - "KEIYAKLRYL": { + 1.5447499999999983, + 12.79, + 21.0, + 17.0, + 8.9, + 13.0, + 19.0, + 14.0, + 5.788070652173886, + 3.8 + ] + } + }, + "wt_peptide": "DQEKILEDA" + } + }, + "transcripts": [ + "ENST00000367255.10-SYNE1-E/K-5203" + ], + "transcript_expr": [ + 0.02 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 8797 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0.02 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0.02 + ], + "DNA VAF": 0.323, + "RNA VAF": 0.286, + "gene_expr": 5.739, + "best_peptide_mt": "DQKKILEDA", + "best_peptide_wt": "DQEKILEDA", + "best_hla_allele": "HLA-B*45:01" + }, + "chr6-157133135-157133136-G-C": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "QMHAAISSF": { "ic50s_MT": [ - "X", - 3122.43408203125 + 2963.5048828125, + "X" ], 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13.850000381469727, - 6.199999809265137, - 2.5, - 2.0, + "HLA-A*29:02": [ + 1.121500015258789, + 15.829999923706055, + 3.5, 4.699999809265137, - 8.3, - 8.6 + 1.7999999523162842, + 6.5, + 4.7, + 7.2 ] }, "WT": { - "HLA-B*45:01": [ - 0.3784999999999997, - 21.51, - 9.1, - 2.8, - 1.8, - 4.4, - 14.0, - 13.0 + "HLA-A*29:02": [ + 0.99075, + 9.73, + 2.4, + 3.6, + 1.6, + 8.8, + 3.7, + 5.0 ] } }, @@ -148878,21 +166802,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.2575856000185013, - 0.0735863451980626, - 0.0218, - 0.0017175546, - 0.00025983536 + "HLA-A*29:02": [ + 0.3821356259286403, + 0.4644316881101775, + 0.0751, + 0.043661483, + 0.10409398 ] }, "WT": { - "HLA-B*45:01": [ - 0.545869093388319, - 0.8022390561141856, - 0.133, - 0.014151591, - 0.0014146676 + "HLA-A*29:02": [ + 0.5206898152828217, + 0.6401287503094367, + 0.106, + 0.04887751, + 0.085765004 ] } }, @@ -148905,19 +166829,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 3.679429347826016, - 2.5, + 0.9014130434781435, + 1.2, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.274510869565205, - 0.82, + 0.5419293478260414, + 0.93, "NA", "NA" ] @@ -148937,58 +166861,142 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 1.768625020980835, - 13.850000381469727, - 6.199999809265137, - 2.5, - 2.0, + "HLA-A*29:02": [ + 1.121500015258789, + 15.829999923706055, + 3.5, 4.699999809265137, - 8.3, - 8.6, - 3.679429347826016, - 2.5 + 1.7999999523162842, + 6.5, + 4.7, + 7.2, + 0.9014130434781435, + 1.2 ] }, "WT": { - "HLA-B*45:01": [ - 0.3784999999999997, - 21.51, - 9.1, - 2.8, - 1.8, - 4.4, - 14.0, - 13.0, - 0.274510869565205, - 0.82 + "HLA-A*29:02": [ + 0.99075, + 9.73, + 2.4, + 3.6, + 1.6, + 8.8, + 3.7, + 5.0, + 0.5419293478260414, + 0.93 ] } }, - "wt_peptide": "KEIDAKLRYL" - }, - "EEKEIYAK": { + "wt_peptide": "QMHAGISSF" + } + }, + "transcripts": [ + "ENST00000346085.10-ARID1B-G/A-910", + "ENST00000350026.10-ARID1B-G/A-814", + "ENST00000637810.1-ARID1B-G/A-64", + "ENST00000636930.2-ARID1B-G/A-897", + "ENST00000319584.11-ARID1B-G/A-235", + "ENST00000414678.7-ARID1B-G/A-283", + "ENST00000637904.1-ARID1B-G/A-64", + "ENST00000637003.1-ARID1B-G/A-64", + "ENST00000647938.1-ARID1B-G/A-827" + ], + "transcript_expr": [ + 0.097, + 0.0, + 0.51, + 0.479, + 0.797, + 5.811, + 3.524, + 0.976, + 1.723 + ], + "tsl": [ + 1, + 1, + 1, + 2, + 2, + 5, + 5, + 5, + "NA" + ], + "biotype": [ + "protein_coding", + "protein_coding", + "protein_coding", + "protein_coding", + "protein_coding", + "protein_coding", + "protein_coding", + "protein_coding", + "protein_coding" + ], + "transcript_length": [ + 2332, + 2236, + 1486, + 2372, + 727, + 1758, + 1539, + 97, + 2249 + ], + "transcript_count": 9, + "peptide_count": 1, + "total_expr": 13.917 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 9 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 13.917 + ], + "DNA VAF": 1.0, + "RNA VAF": 1.0, + "gene_expr": 39.757, + "best_peptide_mt": "QMHAAISSF", + "best_peptide_wt": "QMHAGISSF", + "best_hla_allele": "HLA-A*29:02" + }, + "chr7-27130623-27130624-C-T": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "GGPDGGPGY": { "ic50s_MT": [ - "X", - 3434.875 + 5038.81982421875, + "X" ], "percentiles_MT": [ - "X", - 2.6500000953674316 + 3.799999952316284, + "X" ], "ic50s_WT": [ - "X", - 4011.535 + 5061.965, + "X" ], "percentiles_WT": [ - "X", - 4.25 + 3.8, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "6", + "mutation_position": "4", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -149003,27 +167011,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 811.7195709046441, - 11256.81, - 17845.14, - 995.27, - 18603.6, - 1691.19, - 3100.63, - 3769.12 + "HLA-A*29:02": [ + 662.1541320591791, + 5615.52, + 4517.58, + 5560.06, + 12599.12, + 20368.33, + 983.47, + 1047.06 ] }, "WT": { - "HLA-B*45:01": [ - 1760.2768568503798, - 15022.15, - 28070.3, - 3491.59, - 25584.77, - 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"HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 1.5343206521738182, - 2.0, + 37.35904891304347, + 4.4, "NA", "NA" ] @@ -149325,58 +167377,102 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 2.1670000553131104, - 1.7799999713897705, - 4.900000095367432, - 1.2999999523162842, - 3.5999999046325684, - 2.4000000953674316, - 3.5, - 37.0, - 1.933858695652077, - 1.3 + "HLA-B*45:01": [ + 5.373499870300293, + 20.1299991607666, + 8.300000190734863, + 12.0, + 5.800000190734863, + 7.199999809265137, + 2.7, + 5.5, + 46.22467391304348, + 5.2 ] }, "WT": { - "HLA-A*29:02": [ - 1.58025, - 1.18, - 12.0, - 3.1, - 7.9, - 26.0, - 3.6, - 42.0, - 1.5343206521738182, - 2.0 + "HLA-B*45:01": [ + 4.531125, + 23.15, + 8.1, + 10.0, + 5.6, + 7.1, + 2.4, + 3.8, + 37.35904891304347, + 4.4 ] } }, - "wt_peptide": "EIDAKLRY" - }, - "LDEEEKEIYA": { + "wt_peptide": "STNQHPQPA" + } + }, + "transcripts": [ + "ENST00000518318.7-POU6F2-Q/H-232" + ], + "transcript_expr": [ + 0.001 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 720 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0.001 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0.001 + ], + "DNA VAF": 0.299, + "RNA VAF": 0.0, + "gene_expr": 0.273, + "best_peptide_mt": "STNHHPQPA", + "best_peptide_wt": "STNQHPQPA", + "best_hla_allele": "HLA-B*45:01" + }, + "chr7-47833094-47833095-G-A": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "SHCCPPHIQA": { "ic50s_MT": [ "X", - 4972.91015625 + 13887.087890625 ], "percentiles_MT": [ "X", - 5.0 + 8.199999809265137 ], "ic50s_WT": [ "X", - 9306.98 + 13677.09 ], "percentiles_WT": [ "X", - 6.0 + 8.665 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "9", + "mutation_position": "8", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -149392,26 +167488,26 @@ ], "MT": { "HLA-B*45:01": [ - 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0.2268771 + 0.2532601878046989, + 0.0126133652651051, + 0.00353, + 0.003119044, + 0.016178166 ] }, "WT": { "HLA-B*45:01": [ - 0.0019539631903171, - 0.01648849691117, - 0.0248, - 0.0063728984, - 0.06914559 + 0.0648184195160865, + 0.0063686459318618, + 0.00335, + 0.0011612015, + 0.0054995483 ] } }, @@ -149489,8 +167585,8 @@ "MT": { "HLA-B*45:01": [ "NA", - 10.655842391304333, - 0.9, + 18.61798913043478, + 5.6, "NA", "NA" ] @@ -149498,8 +167594,8 @@ "WT": { "HLA-B*45:01": [ "NA", - 14.277038043478257, - 2.3, + 37.35904891304347, + 5.8, "NA", "NA" ] @@ -149520,111 +167616,101 @@ ], "MT": { "HLA-B*45:01": [ - 2.1241250038146973, - 38.540000915527344, - 4.199999809265137, - 12.0, - 2.0999999046325684, - 24.0, - 5.7, - 4.3, - 10.655842391304333, - 0.9 + 5.671999931335449, + 6.599999904632568, + 19.0, + 13.0, + 9.800000190734863, + 13.0, + 5.1, + 6.1, + 18.61798913043478, + 5.6 ] }, "WT": { "HLA-B*45:01": [ - 2.34975, - 39.81, - 5.2, - 18.0, - 4.4, - 24.0, - 6.8, - 4.5, - 14.277038043478257, - 2.3 + 5.891375, + 7.53, + 19.0, + 16.0, + 9.8, + 10.0, + 4.9, + 6.4, + 37.35904891304347, + 5.8 ] } }, - "wt_peptide": "LDEEEKEIDA" + "wt_peptide": "SHCCPPHTQA" } }, "transcripts": [ - "ENST00000437081.1-PCLO-D/Y-515", - "ENST00000333891.14-PCLO-D/Y-3795", - "ENST00000423517.6-PCLO-D/Y-3795" + "ENST00000289672.7-PKD1L1-T/I-2111" ], "transcript_expr": [ - 0.832, - 0.037, - 2.087 + 0.007 ], "tsl": [ - 1, - 2, - 5 + 1 ], "biotype": [ - "protein_coding", - "protein_coding", "protein_coding" ], "transcript_length": [ - 1217, - 5142, - 4935 + 2849 ], - "transcript_count": 3, - "peptide_count": 11, - "total_expr": 2.9560000000000004 + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0.007 } }, "sets": [ "Transcript Set 1" ], "transcript_counts": [ - 3 + 1 ], "peptide_counts": [ - 11 + 1 ], "set_expr": [ - 2.9560000000000004 + 0.007 ], - "DNA VAF": 0.222, - "RNA VAF": 0.171, - "gene_expr": 4.482, - "best_peptide_mt": "EEEKEIYA", - "best_peptide_wt": "EEEKEIDA", + "DNA VAF": 0.322, + "RNA VAF": 0.0, + "gene_expr": 0.696, + "best_peptide_mt": "SHCCPPHIQA", + "best_peptide_wt": "SHCCPPHTQA", "best_hla_allele": "HLA-B*45:01" }, - "chr7-87424004-87424005-A-C": { + "chr7-75881385-75881386-G-A": { "good_binders": { "Transcript Set 1": { "peptides": { - "KLKKTEWPY": { + "MEGGVKITA": { "ic50s_MT": [ - 1107.7750244140625, - "X" + "X", + 61.46500015258789 ], "percentiles_MT": [ - 2.4000000953674316, - "X" + "X", + 0.15000000596046448 ], "ic50s_WT": [ - 459.77, - "X" + "X", + 53.445 ], "percentiles_WT": [ - 0.935, - "X" + "X", + 0.15 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "3", + "mutation_position": "6", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -149639,27 +167725,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 66.02103875187744, - 5223.41, - 2103.73, - 642.15, - 661.32, - 2781.92, - 999.45, - 1216.1 + "HLA-B*45:01": [ + 43.087156465526704, + 91.42, + 65.11, + 57.82, + 56.72, + 165.16, + 46.69, + 91.75 ] }, "WT": { - "HLA-A*29:02": [ - 44.131037697373685, - 2886.28, - 978.65, - 210.69, - 154.48, - 1362.11, - 404.35, - 515.19 + "HLA-B*45:01": [ + 44.04870151626124, + 52.99, + 69.33, + 53.9, + 41.96, + 174.34, + 52.75, + 107.06 ] } }, @@ -149675,27 +167761,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 0.2683750092983246, - 3.130000114440918, - 2.5, - 2.299999952316284, - 0.75, - 5.199999809265137, - 3.5, - 4.0 + "HLA-B*45:01": [ + 0.011500000022351742, + 0.4099999964237213, + 0.10000000149011612, + 0.20000000298023224, + 0.07999999821186066, + 0.30000001192092896, + 0.3, + 0.4 ] }, "WT": { - "HLA-A*29:02": [ - 0.138, - 0.47, - 1.7, - 1.4, + "HLA-B*45:01": [ + 0.014125, + 0.26, + 0.11, + 0.19, + 0.07, 0.3, - 1.5, - 1.9, - 2.4 + 0.3, + 0.4 ] } }, @@ -149708,21 +167794,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.1748526468873024, - 0.7052908171723923, - 0.254, - 0.07837617, - 0.53397125 + "HLA-B*45:01": [ + 0.7363156080245972, + 0.9635145255511188, + 0.87, + 0.94133085, + 0.11244655 ] }, "WT": { - "HLA-A*29:02": [ - 0.1974895521998405, - 0.7931444098859761, - 0.378, - 0.04944539, - 0.6616603 + "HLA-B*45:01": [ + 0.7228128388524055, + 0.9610017756888022, + 0.832, + 0.8328333, + 0.07014678 ] } }, @@ -149735,19 +167821,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 0.4295380434782458, - 0.44, + 0.0282065217391647, + 0.03, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 0.288179347826059, - 0.29, + 0.031548913043494, + 0.04, "NA", "NA" ] @@ -149767,58 +167853,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 0.2683750092983246, - 3.130000114440918, - 2.5, - 2.299999952316284, - 0.75, - 5.199999809265137, - 3.5, - 4.0, - 0.4295380434782458, - 0.44 + "HLA-B*45:01": [ + 0.011500000022351742, + 0.4099999964237213, + 0.10000000149011612, + 0.20000000298023224, + 0.07999999821186066, + 0.30000001192092896, + 0.3, + 0.4, + 0.0282065217391647, + 0.03 ] }, "WT": { - "HLA-A*29:02": [ - 0.138, - 0.47, - 1.7, - 1.4, + "HLA-B*45:01": [ + 0.014125, + 0.26, + 0.11, + 0.19, + 0.07, 0.3, - 1.5, - 1.9, - 2.4, - 0.288179347826059, - 0.29 + 0.3, + 0.4, + 0.031548913043494, + 0.04 ] } }, - "wt_peptide": "KLNKTEWPY" + "wt_peptide": "MEGGVRITA" }, - "LKLKKTEWPY": { + "MEGGVKITAE": { "ic50s_MT": [ - 2665.60498046875, - "X" + "X", + 1680.1650390625 ], "percentiles_MT": [ - 3.5, - "X" + "X", + 2.200000047683716 ], "ic50s_WT": [ - 1692.26, - "X" + "X", + 1632.045 ], "percentiles_WT": [ - 3.3, - "X" + "X", + 2.2 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "4", + "mutation_position": "6", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -149833,27 +167919,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 16165.990930439137, - 5667.38, - 3309.47, - 2021.74, - 2009.9, - 31060.99, - 376.08, - 770.07 + "HLA-B*45:01": [ + 3049.998123289672, + 6364.92, + 651.2, + 2111.16, + 3098.87, + 1249.17, + 1065.84, + 563.55 ] }, "WT": { - "HLA-A*29:02": [ - 9028.208537920678, - 5340.41, - 1808.18, - 1576.34, - 633.36, - 25564.3, - 405.77, - 766.53 + "HLA-B*45:01": [ + 3974.2174677671815, + 5597.18, + 690.9, + 2054.82, + 2175.86, + 1209.27, + 846.62, + 554.54 ] } }, @@ -149869,27 +167955,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 8.31712532043457, - 10.119999885559082, - 3.200000047683716, - 3.799999952316284, + "HLA-B*45:01": [ + 1.784999966621399, + 7.079999923706055, + 0.8899999856948853, + 2.299999952316284, + 1.5, 1.600000023841858, - 33.0, - 1.7, - 3.1 + 4.3, + 2.1 ] }, "WT": { - "HLA-A*29:02": [ - 4.786999999999998, - 3.93, + "HLA-B*45:01": [ + 2.002124999999999, + 6.38, + 0.94, 2.3, - 3.5, - 0.72, - 28.0, - 1.8, - 3.1 + 1.2, + 1.6, + 3.3, + 2.1 ] } }, @@ -149902,21 +167988,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.062829777598381, - 0.0076388141303446, - 0.0125, - 0.006910551, - 0.31094095 + "HLA-B*45:01": [ + 0.0996569022536277, + 0.0424295975551177, + 0.022, + 0.002890248, + 0.00029853877 ] }, "WT": { - 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"chr7-77600798-77600799-C-T": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "HEDVPICIYC": { "ic50s_MT": [ - 4916.26513671875, - "X" + "X", + 4446.5498046875 ], "percentiles_MT": [ - 4.599999904632568, - "X" + "X", + 3.8499999046325684 ], "ic50s_WT": [ - 5073.275, - "X" + "X", + 5566.405 ], "percentiles_WT": [ - 4.55, - "X" + "X", + 4.75 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "8", + "mutation_position": "9", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -150293,27 +168351,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 297.509634938359, - 5789.05, - 4043.48, - 3954.23, - 3424.06, - 8208.09, - 13175.28, - 10115.1 + "HLA-B*45:01": [ + 278.752774435432, + 17097.24, + 4895.86, + 3997.24, + 3702.63, + 6469.41, + 5684.47, + 3810.04 ] }, "WT": { - "HLA-A*29:02": [ - 358.49541442088105, - 5740.48, - 3437.13, - 4406.07, - 3019.24, - 6978.43, - 11528.16, - 9225.08 + "HLA-B*45:01": [ + 262.7008143715017, 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1.372880434782516, + 1.2 ] } }, - "wt_peptide": "SSKSAFMEF" + "wt_peptide": "HEDVPICIHC" } }, "transcripts": [ - "ENST00000518156.3-DLX6-E/Q-23" + "ENST00000248594.11-PTPN12-H/Y-230", + "ENST00000435495.6-PTPN12-H/Y-100", + "ENST00000415482.6-PTPN12-H/Y-111", + "ENST00000522115.6-PTPN12-H/Y-169", + "ENST00000447995.2-PTPN12-H/Y-111" ], "transcript_expr": [ - 2.233 + 14.21, + 35.285, + 46.053, + 0.28, + 1.021 ], "tsl": [ - 1 + 1, + 2, + 5, + 5, + 3 ], "biotype": [ - "protein_coding" + "protein_coding", + "protein_coding", + "protein_coding", + "protein_coding", + "nonsense_mediated_decay" ], "transcript_length": [ - 293 + 780, + 650, + 661, + 214, + 113 ], - "transcript_count": 1, - "peptide_count": 2, - "total_expr": 2.233 + "transcript_count": 5, + "peptide_count": 1, + "total_expr": 96.849 } }, "sets": [ "Transcript Set 1" ], "transcript_counts": [ - 1 + 5 ], "peptide_counts": [ - 2 + 1 ], "set_expr": [ - 2.233 + 96.849 ], - "DNA VAF": 0.411, - "RNA VAF": 0.424, - "gene_expr": 2.584, - "best_peptide_mt": "FMQFGQQQQ", - "best_peptide_wt": "FMEFGQQQQ", - "best_hla_allele": "HLA-A*29:02" - }, - "chr7-102317255-102317256-A-G": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 0.181, - "RNA VAF": 0.223, - "gene_expr": 6.055, - "best_peptide_mt": "ELSDYPWFR", - "best_peptide_wt": "ELSDYPWFH", - "best_hla_allele": "HLA-A*29:02" + "DNA VAF": 0.203, + "RNA VAF": 0.161, + "gene_expr": 128.676, + "best_peptide_mt": "HEDVPICIYC", + "best_peptide_wt": "HEDVPICIHC", + "best_hla_allele": "HLA-B*45:01" }, - "chr7-112342710-112342711-G-C": { + "chr7-82908982-82908983-C-G": { "good_binders": { "Transcript Set 1": { "peptides": { - "SSIFNQLLL": { + "EETDSFDKP": { "ic50s_MT": [ - 3085.7451171875, - "X" + "X", + 1687.1099853515625 ], "percentiles_MT": [ - 3.0329999923706055, - "X" + "X", + 3.75 ], "ic50s_WT": [ - 5117.275, - "X" + "X", + 1650.12 ], "percentiles_WT": [ - 5.25, - "X" + "X", + 3.6 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "4", + "mutation_position": "5", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -150544,27 +168609,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 3868.1827764666336, - 5063.83, - 2405.18, - 2180.81, - 3876.12, - 3766.31, - 1441.32, - 1134.93 + "HLA-B*45:01": [ + 75.21630326402004, + 12836.03, + 12298.36, + 2551.25, + 1336.14, + 2010.83, + 1230.86, + 1363.39 ] }, "WT": { - "HLA-A*29:02": [ - 5626.3803280678685, - 5377.84, - 4848.78, - 4856.71, - 7289.28, - 5441.03, - 2464.68, - 2529.12 + "HLA-B*45:01": [ + 76.95703778172935, + 13201.66, + 9383.57, + 1989.19, + 1190.11, + 2077.17, + 1230.86, + 1311.05 ] } }, @@ -150580,27 +168645,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 3.0063750743865967, - 2.4200000762939453, - 2.700000047683716, - 4.0, - 2.4000000953674316, - 8.199999809265137, - 4.5, - 3.9 + "HLA-B*45:01": [ + 0.14637500047683716, + 13.329999923706055, + 8.5, + 2.9000000953674316, 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"HLA-B*45:01" ], - "mutation_position": "10", + "mutation_position": "6", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -150738,27 +168803,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 8722.313432017447, - 5602.05, - 6783.6, - 2751.98, - 3613.54, - 17695.75, - 824.67, - 773.62 + "HLA-B*45:01": [ + 177.6312469302498, + 6187.2, + 17103.17, + 6539.79, + 2462.59, + 4830.5, + 2447.32, + 1002.14 ] }, "WT": { - "HLA-A*29:02": [ - 25632.388778379045, - 5814.12, - 20870.51, - 12315.54, - 17435.56, - 29425.27, - 6270.18, - 6173.48 + "HLA-B*45:01": [ + 336.9722349416143, + 5915.85, + 10088.75, + 5411.67, + 2686.18, + 5099.03, + 2391.61, + 839.32 ] } }, @@ -150774,27 +168839,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 4.682875156402588, - 7.940000057220459, - 5.400000095367432, - 4.199999809265137, - 2.299999952316284, - 20.0, - 3.3, - 3.1 + "HLA-B*45:01": [ + 0.4440000057220459, + 6.920000076293945, + 13.0, + 4.5, + 1.2999999523162842, + 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"NA", "NA" ] @@ -150866,60 +168931,60 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 4.682875156402588, - 7.940000057220459, - 5.400000095367432, - 4.199999809265137, - 2.299999952316284, - 20.0, - 3.3, - 3.1, - 17.305597826086952, - 2.4 + "HLA-B*45:01": [ + 0.4440000057220459, + 6.920000076293945, + 13.0, + 4.5, + 1.2999999523162842, + 6.599999904632568, + 9.0, + 4.0, + 0.5453532608695184, + 0.57 ] }, "WT": { - "HLA-A*29:02": [ - 20.251124999999995, - 21.53, - 19.0, - 14.0, - 12.0, - 32.0, - 16.0, - 15.0, - 62.74467391304348, - 13.0 + "HLA-B*45:01": [ + 0.6848749999999995, + 6.68, + 7.1, + 4.2, + 1.4, + 6.9, + 8.8, + 3.2, + 0.5181249999999551, + 1.2 ] } }, - "wt_peptide": "LYALKQSSIL" + "wt_peptide": "REETDWFDKP" } }, "transcripts": [ - "ENST00000361822.8-ZNF277-L/F-445", - "ENST00000421864.2-ZNF277-L/F-113" - ], + "ENST00000333891.14-PCLO-W/S-4444", + "ENST00000423517.6-PCLO-W/S-4444" + ], "transcript_expr": [ - 9.179, - 0.546 + 0.037, + 2.087 ], "tsl": [ - 1, - 3 + 2, + 5 ], 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-151320,19 +175045,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 7.558260869565203, - 2.6, + 12.187228260869546, + 3.8, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 16.15755434782608, - 4.5, + 5.788070652173886, + 2.0, "NA", "NA" ] @@ -151352,58 +175077,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 2.631999969482422, - 0.49000000953674316, - 1.2999999523162842, - 3.799999952316284, - 2.200000047683716, - 1.899999976158142, - 1.5, - 1.4, - 7.558260869565203, - 2.6 + "HLA-B*45:01": [ + 2.18387508392334, + 4.730000019073486, + 4.199999809265137, + 3.5, + 8.100000381469727, + 7.0, + 3.4, + 6.5, + 12.187228260869546, + 3.8 ] }, "WT": { - "HLA-A*29:02": [ - 3.976374999999999, - 0.5499999999999999, - 1.5, - 3.6, - 1.2, - 2.5, - 2.5, - 1.6, - 16.15755434782608, - 4.5 + "HLA-B*45:01": [ + 1.5227499999999985, + 4.51, + 4.3, + 4.2, + 5.7, + 4.3, + 4.6, + 9.6, + 5.788070652173886, + 2.0 ] } }, - "wt_peptide": "FFSNFSLLG" + "wt_peptide": "EEEDDADSS" }, - "LFFSNFSLLC": { + "EEEEDDADCS": { "ic50s_MT": [ - 2593.945068359375, - "X" + "X", + 4469.94677734375 ], "percentiles_MT": [ - 2.450000047683716, - "X" + "X", + 6.849999904632568 ], "ic50s_WT": [ - 2454.015, - "X" + "X", + 3057.095 ], "percentiles_WT": [ - 2.2, - "X" + "X", + 4.55 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "10", + "mutation_position": "9", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -151418,27 +175143,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 14672.701354991608, - 4169.64, - 1636.36, - 2664.09, - 4443.75, - 2523.8, - 430.8, - 340.82 + "HLA-B*45:01": [ + 4109.393935827379, + 3251.19, + 10842.46, + 5712.5, + 26769.03, + 4830.5, + 1843.7, + 1327.18 ] }, "WT": { - "HLA-A*29:02": [ - 20183.57297690686, - 4595.2, - 1928.66, - 2607.06, - 2300.97, - 2936.57, - 242.82, - 472.64 + "HLA-B*45:01": [ + 2041.26232014338, + 3014.38, + 11383.06, + 5530.06, + 21763.9, + 3099.81, + 1299.24, + 963.67 ] } }, @@ -151454,27 +175179,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 7.425749778747559, - 0.9800000190734863, - 2.200000047683716, - 4.099999904632568, - 2.700000047683716, - 1.0, - 1.9, - 1.5 + "HLA-B*45:01": [ + 2.0321249961853027, + 4.309999942779541, + 7.599999904632568, + 4.300000190734863, + 15.0, + 6.599999904632568, + 7.1, + 5.3 ] }, "WT": { - "HLA-A*29:02": [ - 11.606874999999995, - 1.39, - 2.4, - 4.1, - 1.7, - 1.3, - 1.1, - 2.0 + "HLA-B*45:01": [ + 1.5102499999999983, + 4.1000000000000005, + 7.9, + 4.2, + 9.4, + 4.5, + 5.2, + 3.9 ] } }, @@ -151487,21 +175212,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.0029647462069988, - 0.0067966169715762, - 0.00143, - 0.11539447, - 0.7188198 + "HLA-B*45:01": [ + 0.0002126852459696, + 0.0227986015068068, + 0.00134, + 4.7771704e-05, + 0.0001300363 ] }, "WT": { - "HLA-A*29:02": [ - 0.0028411336243152, - 0.0049930971707578, - 0.000692, - 0.084187604, - 0.5674923 + "HLA-B*45:01": [ + 0.0002121881834682, + 0.0440099180142696, + 0.0057, + 6.975066e-05, + 0.00010956572 ] } }, @@ -151514,19 +175239,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 37.35904891304347, - 8.0, + 10.655842391304333, + 8.5, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 62.74467391304348, - 12.0, + 5.788070652173886, + 4.6, "NA", "NA" ] @@ -151546,58 +175271,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 7.425749778747559, - 0.9800000190734863, - 2.200000047683716, - 4.099999904632568, - 2.700000047683716, - 1.0, - 1.9, - 1.5, - 37.35904891304347, - 8.0 + "HLA-B*45:01": [ + 2.0321249961853027, + 4.309999942779541, + 7.599999904632568, + 4.300000190734863, + 15.0, + 6.599999904632568, + 7.1, + 5.3, + 10.655842391304333, + 8.5 ] }, "WT": { - "HLA-A*29:02": [ - 11.606874999999995, - 1.39, - 2.4, - 4.1, - 1.7, - 1.3, - 1.1, - 2.0, - 62.74467391304348, - 12.0 + "HLA-B*45:01": [ + 1.5102499999999983, + 4.1000000000000005, + 7.9, + 4.2, + 9.4, + 4.5, + 5.2, + 3.9, + 5.788070652173886, + 4.6 ] } }, - "wt_peptide": "LFFSNFSLLG" + "wt_peptide": "EEEEDDADSS" }, - "FFSNFSLLCT": { + "EEEDDADCSL": { "ic50s_MT": [ - 4323.98486328125, - "X" + "X", + 4699.97021484375 ], "percentiles_MT": [ - 7.0, - "X" + "X", + 5.050000190734863 ], "ic50s_WT": [ - 4312.3, - "X" + "X", + 4023.365 ], "percentiles_WT": [ - 6.55, - "X" + "X", + 4.9 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "9", + "mutation_position": "8", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -151612,27 +175337,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 16784.061979335867, - 4664.41, - 3086.99, - 4883.05, - 3983.56, - 8853.9, - 900.08, - 3940.31 + "HLA-B*45:01": [ + 173.04182849126374, + 10718.7, + 12394.54, + 7733.88, + 15639.25, + 1235.73, + 1666.06, + 1291.01 ] }, "WT": { - "HLA-A*29:02": [ - 15015.62838727103, - 4983.08, - 3103.8, - 4676.23, - 3948.37, - 8032.38, - 783.93, - 3635.21 + "HLA-B*45:01": [ + 127.54874368583472, + 16603.05, + 11162.18, + 6365.26, + 15467.6, + 1133.26, + 1681.47, + 1358.09 ] } }, @@ -151648,27 +175373,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 8.788374900817871, - 1.4800000190734863, - 3.0999999046325684, + "HLA-B*45:01": [ + 0.4336250126361847, + 11.140000343322754, + 8.5, + 5.0, 6.0, - 2.5, - 8.0, - 3.5, - 9.9 + 1.600000023841858, + 6.4, + 5.1 ] }, "WT": { - "HLA-A*29:02": [ - 7.596999999999999, - 2.15, - 3.1, + "HLA-B*45:01": [ + 0.3257499999999998, + 17.71, + 7.8, + 4.4, 5.9, - 2.5, - 7.2, - 3.2, - 9.3 + 1.4, + 6.5, + 5.4 ] } }, @@ -151681,21 +175406,21 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ - 0.0254397615790367, - 0.0064604128050396, - 0.000514, - 0.03261264, - 0.36430383 + "HLA-B*45:01": [ + 0.0046487934887409, + 0.3394964280445082, + 0.0405, + 0.00053143786, + 0.00021460983 ] }, "WT": { - "HLA-A*29:02": [ - 0.0239849463105201, - 0.0071563061254493, - 0.000527, - 0.056664884, - 0.4179659 + "HLA-B*45:01": [ + 0.0042962208390235, + 0.4084226115491068, + 0.089, + 0.000425139, + 0.0001650358 ] } }, @@ -151708,19 +175433,19 @@ "BigMHC_IM" ], "MT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 37.35904891304347, - 13.0, + 1.230081521738995, + 1.8, "NA", "NA" ] }, "WT": { - "HLA-A*29:02": [ + "HLA-B*45:01": [ "NA", - 31.64317934782608, - 13.0, + 1.0341304347824831, + 1.1, "NA", "NA" ] @@ -151740,60 +175465,60 @@ "NetMHCpanEL" ], "MT": { - "HLA-A*29:02": [ - 8.788374900817871, - 1.4800000190734863, - 3.0999999046325684, + "HLA-B*45:01": [ + 0.4336250126361847, + 11.140000343322754, + 8.5, + 5.0, 6.0, - 2.5, - 8.0, - 3.5, - 9.9, - 37.35904891304347, - 13.0 + 1.600000023841858, + 6.4, + 5.1, + 1.230081521738995, + 1.8 ] }, "WT": { - "HLA-A*29:02": [ - 7.596999999999999, - 2.15, - 3.1, + "HLA-B*45:01": [ + 0.3257499999999998, + 17.71, + 7.8, + 4.4, 5.9, - 2.5, - 7.2, - 3.2, - 9.3, - 31.64317934782608, - 13.0 + 1.4, + 6.5, + 5.4, + 1.0341304347824831, + 1.1 ] } }, - "wt_peptide": "FFSNFSLLGT" + "wt_peptide": "EEEDDADSSL" } }, "transcripts": [ - "ENST00000003084.11-CFTR-G/C-437", - "ENST00000426809.5-CFTR-G/C-407" + "ENST00000297788.9-CCDC136-S/C-1103", + "ENST00000494552.5-CCDC136-S/C-980" ], "transcript_expr": [ - 0.0, - 0.0 + 0.018, + 0.905 ], "tsl": [ 1, - 5 + 1 ], "biotype": [ "protein_coding", "protein_coding" ], "transcript_length": [ - 1480, - 1438 + 1154, + 1034 ], "transcript_count": 2, - "peptide_count": 3, - "total_expr": 0.0 + "peptide_count": 5, + "total_expr": 0.923 } }, "sets": [ @@ -151803,44 +175528,44 @@ 2 ], "peptide_counts": [ - 3 + 5 ], "set_expr": [ - 0.0 + 0.923 ], - "DNA VAF": 0.116, - "RNA VAF": 0.0, - "gene_expr": 1.844, - "best_peptide_mt": "FFSNFSLLC", - "best_peptide_wt": "FFSNFSLLG", - "best_hla_allele": "HLA-A*29:02" + "DNA VAF": 0.2, + "RNA VAF": 0.25, + "gene_expr": 4.998, + "best_peptide_mt": "SEEEEDDADC", + "best_peptide_wt": "SEEEEDDADS", + "best_hla_allele": "HLA-B*45:01" }, - "chr7-122013415-122013416-A-G": { + "chr7-132508196-132508197-C-A": { "good_binders": { "Transcript Set 1": { "peptides": { - "RESQEKVMS": { + "NEIGSVFGV": { "ic50s_MT": [ "X", - 2005.1700439453125 + 315.68499755859375 ], "percentiles_MT": [ "X", - 3.450000047683716 + 0.42500001192092896 ], "ic50s_WT": [ "X", - 5467.29 + 319.74 ], "percentiles_WT": [ "X", - 7.7 + 0.613 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "9", + "mutation_position": "3", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -151856,26 +175581,26 @@ ], "MT": { "HLA-B*45:01": [ - 285.21683871124867, - 5414.97, - 5256.15, - 1904.94, - 1910.57, - 2099.77, - 1384.24, - 2236.76 + 74.84714226285972, + 255.5, + 392.45, + 49.16, + 181.59, + 375.87, + 399.22, + 420.36 ] }, "WT": { "HLA-B*45:01": [ - 4073.737705309377, - 12395.98, - 15088.25, - 4830.5, - 11899.9, - 2968.51, - 1706.91, - 6104.08 + 80.86307080557151, + 217.88, + 518.74, + 75.79, + 305.79, + 333.69, + 416.11, + 452.5 ] } }, @@ -151892,26 +175617,26 @@ ], "MT": { "HLA-B*45:01": [ - 0.6151250004768372, - 6.230000019073486, - 4.300000190734863, - 2.5999999046325684, - 0.949999988079071, - 6.599999904632568, - 5.3, - 8.4 + 0.14637500047683716, + 0.8500000238418579, + 0.5600000023841858, + 0.17000000178813934, + 0.17000000178813934, + 0.8999999761581421, + 1.4, + 1.5 ] }, "WT": { "HLA-B*45:01": [ - 2.022499999999999, - 12.89, - 12.0, - 3.9, - 4.4, - 8.9, - 6.5, - 17.0 + 0.172625, + 0.76, + 0.74, + 0.25, + 0.26, + 0.8, + 1.4, + 1.6 ] } }, @@ -151925,20 +175650,20 @@ ], "MT": { "HLA-B*45:01": [ - 0.0565602108836174, - 0.2754248004881812, - 0.29, - 0.0019465723, - 0.00024170734 + 0.5909419730305672, + 0.9022888508337276, + 0.379, + 0.18901427, + 0.012573305 ] }, "WT": { "HLA-B*45:01": [ - 0.023393977433443, - 0.0249039346955038, - 0.0201, - 0.0010593917, - 0.00014633664 + 0.1866937726736068, + 0.6720655036664591, + 0.358, + 0.029892454, + 0.003756786 ] } }, @@ -151953,8 +175678,8 @@ "MT": { "HLA-B*45:01": [ "NA", - 1.4566304347825252, - 0.4, + 0.1181521739130602, + 0.29, "NA", "NA" ] @@ -151962,8 +175687,8 @@ "WT": { "HLA-B*45:01": [ "NA", - 9.849456521739114, - 2.6, + 0.4865489130434355, + 0.31, "NA", "NA" ] @@ -151984,57 +175709,57 @@ ], "MT": { "HLA-B*45:01": [ - 0.6151250004768372, - 6.230000019073486, - 4.300000190734863, - 2.5999999046325684, - 0.949999988079071, - 6.599999904632568, - 5.3, - 8.4, - 1.4566304347825252, - 0.4 + 0.14637500047683716, + 0.8500000238418579, + 0.5600000023841858, + 0.17000000178813934, + 0.17000000178813934, + 0.8999999761581421, + 1.4, + 1.5, + 0.1181521739130602, + 0.29 ] }, "WT": { "HLA-B*45:01": [ - 2.022499999999999, - 12.89, - 12.0, - 3.9, - 4.4, - 8.9, - 6.5, - 17.0, - 9.849456521739114, - 2.6 + 0.172625, + 0.76, + 0.74, + 0.25, + 0.26, + 0.8, + 1.4, + 1.6, + 0.4865489130434355, + 0.31 ] } }, - "wt_peptide": "RESQEKVMN" + "wt_peptide": "NESGSVFGV" }, - "QEKVMSDSDT": { + "NEIGSVFGVI": { "ic50s_MT": [ "X", - 2311.22998046875 + 782.114990234375 ], "percentiles_MT": [ "X", - 3.299999952316284 + 1.2999999523162842 ], "ic50s_WT": [ "X", - 3239.96 + 900.805 ], "percentiles_WT": [ "X", - 3.75 + 1.3 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "6", + "mutation_position": "3", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -152050,26 +175775,26 @@ ], "MT": { "HLA-B*45:01": [ - 8412.5747661726, - 2262.36, - 1475.78, - 3705.68, - 4863.18, - 2240.61, - 1547.71, - 2360.1 + 197.7050035163417, + 703.38, + 1019.27, + 352.24, + 640.45, + 995.27, + 880.42, + 860.85 ] }, "WT": { "HLA-B*45:01": [ - 9013.328638273186, - 3763.92, - 2206.68, - 4625.9, - 6445.73, - 2551.25, - 2176.16, - 2716.0 + 199.76959645870824, + 586.62, + 1251.83, + 439.71, + 918.01, + 883.6, + 1326.45, + 1020.77 ] } }, @@ -152086,26 +175811,26 @@ ], "MT": { "HLA-B*45:01": [ - 2.7939999103546143, - 3.359999895095825, - 1.7999999523162842, - 3.299999952316284, - 2.0, - 3.299999952316284, - 6.0, - 8.7 + 0.48262500762939453, + 1.5800000429153442, + 1.399999976158142, + 0.49000000953674316, + 0.44999998807907104, + 1.2000000476837158, + 3.5, + 3.4 ] }, "WT": { "HLA-B*45:01": [ - 2.900625, - 4.78, - 2.3, - 3.8, - 2.5, - 3.7, - 8.1, - 10.0 + 0.4874999999999998, + 1.4200000000000002, + 1.6, + 0.62, + 0.59, + 0.9, + 5.3, + 4.1 ] } }, @@ -152119,20 +175844,20 @@ ], "MT": { "HLA-B*45:01": [ - 0.0083664990961551, - 0.0118316805537114, - 0.0141, - 7.62618e-05, - 6.319175e-05 + 0.2807587683200836, + 0.5453619275078575, + 0.0366, + 0.021850778, + 0.0030891465 ] }, "WT": { "HLA-B*45:01": [ - 0.0090522207319736, - 0.0111000116553197, - 0.00969, - 0.00013873704, - 0.00014033858 + 0.0645084977149963, + 0.35588618011666, + 0.0368, + 0.008079912, + 0.00080067 ] } }, @@ -152147,8 +175872,8 @@ "MT": { "HLA-B*45:01": [ "NA", - 20.2322554347826, - 3.0, + 0.726657608695561, + 1.9, "NA", "NA" ] @@ -152156,8 +175881,8 @@ "WT": { "HLA-B*45:01": [ "NA", - 20.2322554347826, - 3.6, + 1.1791847826086013, + 1.9, "NA", "NA" ] @@ -152178,57 +175903,57 @@ ], "MT": { "HLA-B*45:01": [ - 2.7939999103546143, - 3.359999895095825, - 1.7999999523162842, - 3.299999952316284, - 2.0, - 3.299999952316284, - 6.0, - 8.7, - 20.2322554347826, - 3.0 + 0.48262500762939453, + 1.5800000429153442, + 1.399999976158142, + 0.49000000953674316, + 0.44999998807907104, + 1.2000000476837158, + 3.5, + 3.4, + 0.726657608695561, + 1.9 ] }, "WT": { "HLA-B*45:01": [ - 2.900625, - 4.78, - 2.3, - 3.8, - 2.5, - 3.7, - 8.1, - 10.0, - 20.2322554347826, - 3.6 + 0.4874999999999998, + 1.4200000000000002, + 1.6, + 0.62, + 0.59, + 0.9, + 5.3, + 4.1, + 1.1791847826086013, + 1.9 ] } }, - "wt_peptide": "QEKVMNDSDT" + "wt_peptide": "NESGSVFGVI" }, - "RESQEKVMSD": { + "GVNEIGSVF": { "ic50s_MT": [ - "X", - 4000.195068359375 + 4164.71484375, + "X" ], "percentiles_MT": [ - "X", - 4.25 + 4.699999809265137, + "X" ], "ic50s_WT": [ - "X", - 5919.75 + 5832.995, + "X" ], "percentiles_WT": [ - "X", - 6.35 + 7.35, + "X" ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "9", + "mutation_position": "5", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -152243,27 +175968,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 856.7572109077255, - 7115.57, - 8044.03, - 5126.69, - 10391.53, - 2873.7, - 1457.77, - 1046.96 + "HLA-A*29:02": [ + 601.0312419871138, + 4563.12, + 8557.04, + 4830.5, + 5677.57, + 3766.31, + 3433.68, + 2773.13 ] }, "WT": { - "HLA-B*45:01": [ - 1859.3190828578088, - 10194.85, - 15127.65, - 6903.33, - 15547.3, + "HLA-A*29:02": [ + 2115.407389625376, + 5388.57, + 13131.19, + 8806.13, + 9337.29, 4936.17, - 1805.88, - 1293.99 + 6120.12, + 5545.87 ] } }, @@ -152279,27 +176004,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 1.0642499923706055, - 7.769999980926514, - 5.900000095367432, - 4.0, - 3.9000000953674316, - 4.300000190734863, - 5.7, - 4.2 + "HLA-A*29:02": [ + 1.3537499904632568, + 1.350000023841858, + 6.5, + 6.199999809265137, + 3.200000047683716, + 8.199999809265137, + 7.8, + 6.7 ] }, "WT": { - "HLA-B*45:01": [ - 1.4558749999999985, - 10.63, - 12.0, - 4.6, - 6.0, - 6.7, - 6.9, - 5.2 + "HLA-A*29:02": [ + 2.317375, + 4.37, + 9.7, + 10.0, + 5.0, + 13.0, + 13.0, + 12.0 ] } }, @@ -152312,21 +176037,21 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.0216093212366104, - 0.1034627846166771, - 0.00545, - 0.00043291174, - 2.0338974e-05 + "HLA-A*29:02": [ + 0.1728847622871399, + 0.2175938767943624, + 0.0822, + 0.08774917, + 0.118384585 ] }, "WT": { - "HLA-B*45:01": [ - 0.0209046564996242, - 0.0514445250586175, - 0.00116, - 0.00031777262, - 2.7903474e-05 + "HLA-A*29:02": [ + 0.0987394116818904, + 0.0592792295014058, + 0.0419, + 0.0052266456, + 0.111462064 ] } }, @@ -152339,19 +176064,19 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 2.851521739130362, - 4.6, + 1.731739130434704, + 1.1, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 4.968641304347784, - 9.0, + 4.391929347826036, + 1.6, "NA", "NA" ] @@ -152371,137 +176096,117 @@ "NetMHCpanEL" ], "MT": { - 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0.1181521739130602, - 0.29, + 0.7058152173912049, + 0.85, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.4865489130434355, - 0.31, + 0.1581249999999983, + 0.67, "NA", "NA" ] @@ -153663,58 +177417,58 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 0.14637500047683716, - 0.8500000238418579, - 0.5600000023841858, - 0.17000000178813934, - 0.17000000178813934, - 0.8999999761581421, - 1.4, - 1.5, - 0.1181521739130602, - 0.29 + "HLA-A*29:02": [ + 0.9238749742507935, + 1.9500000476837158, + 5.0, + 4.300000190734863, + 2.4000000953674316, + 22.0, + 5.8, + 5.3, + 0.7058152173912049, + 0.85 ] }, "WT": { - "HLA-B*45:01": [ - 0.172625, - 0.76, - 0.74, - 0.25, - 0.26, - 0.8, - 1.4, - 1.6, - 0.4865489130434355, - 0.31 + "HLA-A*29:02": [ + 0.7218749999999999, + 1.47, + 4.2, + 3.8, + 2.0, + 22.0, + 4.9, + 4.5, + 0.1581249999999983, + 0.67 ] } }, - "wt_peptide": "NESGSVFGV" + "wt_peptide": "KAEFQTNRY" }, - "NEIGSVFGVI": { + "LKAEFRTNRY": { "ic50s_MT": [ - "X", - 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"BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 0.726657608695561, - 1.9, + 2.7954347826086234, + 2.8, "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-A*29:02": [ "NA", - 1.1791847826086013, - 1.9, + 0.9356793478259532, + 2.1, "NA", "NA" ] @@ -153857,58 +177611,102 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 0.48262500762939453, - 1.5800000429153442, - 1.399999976158142, - 0.49000000953674316, - 0.44999998807907104, - 1.2000000476837158, + "HLA-A*29:02": [ + 3.100374937057495, + 2.619999885559082, + 5.099999904632568, + 3.799999952316284, 3.5, - 3.4, - 0.726657608695561, - 1.9 + 27.0, + 5.3, + 5.3, + 2.7954347826086234, + 2.8 ] }, "WT": { - "HLA-B*45:01": [ - 0.4874999999999998, - 1.4200000000000002, - 1.6, - 0.62, - 0.59, - 0.9, - 5.3, - 4.1, - 1.1791847826086013, - 1.9 + "HLA-A*29:02": [ + 2.0355, + 1.91, + 4.3, + 3.5, + 2.8, + 26.0, + 4.9, + 4.2, + 0.9356793478259532, + 2.1 ] } }, - "wt_peptide": "NESGSVFGVI" - }, - "GVNEIGSVF": { + "wt_peptide": "LKAEFQTNRY" + } + }, + "transcripts": [ + "ENST00000297375.4-EN2-Q/R-264" + ], + "transcript_expr": [ + 0.408 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 333 + ], + "transcript_count": 1, + "peptide_count": 4, + "total_expr": 0.408 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 4 + ], + "set_expr": [ + 0.408 + ], + "DNA VAF": 0.263, + "RNA VAF": 0.375, + "gene_expr": 0.408, + "best_peptide_mt": "AEFRTNRYLT", + "best_peptide_wt": "AEFQTNRYLT", + "best_hla_allele": "HLA-B*45:01" + }, + "chr7-157005551-157005552-G-A": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "SEDDSPPSRP": { "ic50s_MT": [ - 4164.71484375, - "X" + "X", + 2653.235107421875 ], "percentiles_MT": [ - 4.699999809265137, - "X" + "X", + 4.670000076293945 ], "ic50s_WT": [ - 5832.995, - "X" + "X", + 2299.625 ], "percentiles_WT": [ - 7.35, - "X" + "X", + 3.855 ], "hla_types": [ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "5", + "mutation_position": "8", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -153923,27 +177721,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 601.0312419871138, - 4563.12, - 8557.04, - 4830.5, - 5677.57, - 3766.31, - 3433.68, - 2773.13 + "HLA-B*45:01": [ + 76.30315827247688, + 2848.19, + 20932.47, + 8998.77, + 2458.28, + 3807.28, + 2397.12, + 1644.11 ] }, "WT": { - "HLA-A*29:02": [ - 2115.407389625376, - 5388.57, - 13131.19, - 8806.13, - 9337.29, - 4936.17, - 6120.12, - 5545.87 + "HLA-B*45:01": [ + 67.35760936565788, + 1646.43, + 21423.49, + 7609.38, + 2267.46, + 3646.02, + 2331.79, + 1674.67 ] } }, @@ -153959,27 +177757,27 @@ "SMMPMBEC" ], "MT": { - "HLA-A*29:02": [ - 1.3537499904632568, - 1.350000023841858, - 6.5, - 6.199999809265137, - 3.200000047683716, - 8.199999809265137, - 7.8, - 6.7 + "HLA-B*45:01": [ + 0.15449999272823334, + 3.940000057220459, + 15.0, + 5.5, + 1.2999999523162842, + 5.400000095367432, + 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"HLA-B*45:01": [ - 0.15449999272823334, - 3.940000057220459, + 2.443000078201294, + 42.91999816894531, + 5.800000190734863, + 3.299999952316284, + 2.5999999046325684, + 7.199999809265137, 15.0, - 5.5, - 1.2999999523162842, - 5.400000095367432, - 8.8, - 6.3 + 13.0 ] }, "WT": { "HLA-B*45:01": [ - 0.112625, - 2.71, - 16.0, - 5.0, - 1.2, - 5.1, - 8.6, - 6.4 + 1.8571249999999984, + 31.03, + 5.4, + 3.7, + 2.3, + 6.5, + 17.0, + 14.0 ] } }, @@ -155746,20 +179700,20 @@ ], "MT": { "HLA-B*45:01": [ - 0.0405037030577659, - 0.5638206542651836, - 0.601, - 0.019492762, - 0.012703958 + 0.0483118966221809, + 0.0177458653075608, + 0.0171, + 0.0009044382, + 0.000105876316 ] }, "WT": { "HLA-B*45:01": [ - 0.1756776794791221, - 0.701839325416416, - 0.516, - 0.13328491, - 0.033693288 + 0.0568480975925922, + 0.0334299018664143, + 0.0309, + 0.0014957244, + 0.00010227051 ] } }, @@ -155774,8 +179728,8 @@ "MT": { "HLA-B*45:01": [ "NA", - 0.6874999999999147, - 0.12, + 13.500896739130424, + 2.8, "NA", "NA" ] @@ 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- "best_peptide_wt": "NA", - "best_hla_allele": "HLA-A*29:02" - }, - "chr8-123220246-123220247-C-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 0.129, - "RNA VAF": 0.173, - "gene_expr": 45.915, - "best_peptide_mt": "DEVHPDVKCV", - "best_peptide_wt": "DEVHPEVKCV", - "best_hla_allele": "HLA-B*45:01" - }, - "chr8-125028638-125028639-T-C": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 0.139, - "RNA VAF": 0.212, - "gene_expr": 65.088, - "best_peptide_mt": "YVRCTKLPR", - "best_peptide_wt": "YVRYTKLPR", - "best_hla_allele": "HLA-A*29:02" - }, - "chr8-125102410-125102411-G-C": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], "DNA VAF": 0.262, "RNA VAF": 0.242, "gene_expr": 78.578, @@ -158032,11 +181877,236 @@ "best_hla_allele": "HLA-A*29:02" }, "chr8-132141242-132141243-C-G": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "KLFTPLNVH": { + "ic50s_MT": [ + 9498.3447265625, + "X" + ], + "percentiles_MT": [ + 5.814000129699707, + "X" + ], + "ic50s_WT": [ + 32680.61, + "X" + ], + "percentiles_WT": [ + 45.5, + "X" + ], + "hla_types": [ + "HLA-A*29:02", + "HLA-B*45:01" + ], + "mutation_position": "9", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 4952.951956591871, + 5277.56, + 16911.06, + 12790.86, + 10002.34, + 1989.19, + 10274.48, + 8994.35 + ] + }, + "WT": { + "HLA-A*29:02": [ + 30187.553213415747, + 5830.62, + 32216.9, + 33144.32, + 35772.65, + 5932.98, + 57777.67, + 53823.26 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 3.3903748989105225, + 3.4600000381469727, + 14.0, + 16.0, + 5.300000190734863, + 3.0999999046325684, + 19.0, + 17.0 + ] + }, + "WT": { + "HLA-A*29:02": [ + 41.302125, + 24.3, + 43.0, + 70.0, + 48.0, + 16.0, + 52.0, + 51.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "HLA-A*29:02": [ + 0.2093384489417076, + 0.0391868334336869, + 0.0333, + 0.001917784, + 0.071193576 + ] + }, + "WT": { + "HLA-A*29:02": [ + 0.0387754961848259, + 0.0038394418730003, + 4.6e-05, + 0.0012500475, + 0.034755886 + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "HLA-A*29:02": [ + 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"sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0.0 + ], "DNA VAF": 0.291, "RNA VAF": 1.0, "gene_expr": 0.019, @@ -158045,11 +182115,236 @@ "best_hla_allele": "HLA-A*29:02" }, "chr8-132948805-132948806-C-G": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "LLSSRSVLL": { + "ic50s_MT": [ + 7171.85009765625, + "X" + ], + "percentiles_MT": [ + 9.074999809265137, + "X" + ], + "ic50s_WT": [ + 5825.865, + "X" + ], + "percentiles_WT": [ + 7.3, + "X" + ], + "hla_types": [ + "HLA-A*29:02", + "HLA-B*45:01" + ], + "mutation_position": "5", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 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"best_hla_allele": "HLA-B*45:01" - }, - "chrX-135796713-135796714-C-T": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], "DNA VAF": 0.554, "RNA VAF": 0.0, "gene_expr": 0.102, @@ -172269,11 +200164,236 @@ "best_hla_allele": "HLA-B*45:01" }, "chrX-149548665-149548666-C-T": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "QSFRHSGMW": { + "ic50s_MT": [ + 9111.603515625, + "X" + ], + "percentiles_MT": [ + 15.0, + "X" + ], + "ic50s_WT": [ + 13005.065, + "X" + ], + "percentiles_WT": [ + 20.5, + "X" + ], + "hla_types": [ + "HLA-A*29:02", + "HLA-B*45:01" + ], + "mutation_position": "5", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 8673.608036781108, + 5985.1, + 16089.98, + 15044.73, + 9549.6, + 6829.04, + 9655.17, + 8336.24 + ] + }, + "WT": { + "HLA-A*29:02": [ + 13039.229430166588, + 5991.07, + 21894.27, + 19088.05, + 11997.51, + 7945.94, + 13955.97, + 12970.9 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 4.682875156402588, + 90.77999877929688, + 14.0, + 19.0, + 5.099999904632568, + 18.0, + 18.0, + 16.0 + ] + }, + "WT": { + "HLA-A*29:02": [ + 6.538374999999999, + 92.85, + 20.0, + 27.0, + 6.5, + 21.0, + 23.0, + 22.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "HLA-A*29:02": [ + 0.2880927622318268, + 0.0303232947266882, + 0.0107, + 0.0029545182, + 0.17802016 + ] + }, + "WT": { + "HLA-A*29:02": [ + 0.1548971123993396, + 0.0129668322175117, + 0.00439, + 0.0014310348, + 0.10597769 + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "HLA-A*29:02": [ + "NA", + 8.01565217391304, + 3.1, + "NA", + "NA" + ] + }, + "WT": { + "HLA-A*29:02": [ + "NA", + 18.61798913043478, + 4.7, + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "MHCflurryEL Presentation", + "NetMHCpanEL" + ], + "MT": { + "HLA-A*29:02": [ + 4.682875156402588, + 90.77999877929688, + 14.0, + 19.0, + 5.099999904632568, + 18.0, + 18.0, + 16.0, + 8.01565217391304, + 3.1 + ] + }, + "WT": { + "HLA-A*29:02": [ + 6.538374999999999, + 92.85, + 20.0, + 27.0, + 6.5, + 21.0, + 23.0, + 22.0, + 18.61798913043478, + 4.7 + ] + } + }, + "wt_peptide": "QSFRRSGMW" + } + }, + "transcripts": [ + "ENST00000431993.4-HSFX3-R/H-243" + ], + "transcript_expr": [ + 0.012 + ], + "tsl": [ + 3 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 333 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0.012 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0.012 + ], "DNA VAF": 0.61, "RNA VAF": 0.0, "gene_expr": 0.012, @@ -172282,11 +200402,236 @@ "best_hla_allele": "HLA-A*29:02" }, "chrX-149930830-149930831-G-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "QSFRHSGMW": { + "ic50s_MT": [ + 9111.603515625, + "X" + ], + "percentiles_MT": [ + 15.0, + "X" + ], + "ic50s_WT": [ + 13005.065, + "X" + ], + "percentiles_WT": [ + 20.5, + "X" + ], + "hla_types": [ + "HLA-A*29:02", + "HLA-B*45:01" + ], + "mutation_position": "5", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 8673.608036781108, + 5985.1, + 16089.98, + 15044.73, + 9549.6, + 6829.04, + 9655.17, + 8336.24 + ] + }, + "WT": { + "HLA-A*29:02": [ + 13039.229430166588, + 5991.07, + 21894.27, + 19088.05, + 11997.51, + 7945.94, + 13955.97, + 12970.9 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 4.682875156402588, + 90.77999877929688, + 14.0, + 19.0, + 5.099999904632568, + 18.0, + 18.0, + 16.0 + ] + }, + "WT": { + "HLA-A*29:02": [ + 6.538374999999999, + 92.85, + 20.0, + 27.0, + 6.5, + 21.0, + 23.0, + 22.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "HLA-A*29:02": [ + 0.2880927622318268, + 0.0303232947266882, + 0.0107, + 0.0029545182, + 0.17802016 + ] + }, + "WT": { + "HLA-A*29:02": [ + 0.1548971123993396, + 0.0129668322175117, + 0.00439, + 0.0014310348, + 0.10597769 + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "HLA-A*29:02": [ + "NA", + 8.01565217391304, + 3.1, + "NA", + "NA" + ] + }, + "WT": { + "HLA-A*29:02": [ + "NA", + 18.61798913043478, + 4.7, + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "MHCflurryEL Presentation", + "NetMHCpanEL" + ], + "MT": { + "HLA-A*29:02": [ + 4.682875156402588, + 90.77999877929688, + 14.0, + 19.0, + 5.099999904632568, + 18.0, + 18.0, + 16.0, + 8.01565217391304, + 3.1 + ] + }, + "WT": { + "HLA-A*29:02": [ + 6.538374999999999, + 92.85, + 20.0, + 27.0, + 6.5, + 21.0, + 23.0, + 22.0, + 18.61798913043478, + 4.7 + ] + } + }, + "wt_peptide": "QSFRRSGMW" + } + }, + "transcripts": [ + "ENST00000457775.3-HSFX4-R/H-243" + ], + "transcript_expr": [ + 0.012 + ], + "tsl": [ + 3 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 333 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0.012 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0.012 + ], "DNA VAF": 0.422, "RNA VAF": 0.286, "gene_expr": 0.012, @@ -172295,11 +200640,236 @@ "best_hla_allele": "HLA-A*29:02" }, "chrX-154349376-154349377-C-G": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "SSFTVHCSK": { + "ic50s_MT": [ + 12818.703125, + "X" + ], + "percentiles_MT": [ + 16.1200008392334, + "X" + ], + "ic50s_WT": [ + 17958.42, + "X" + ], + "percentiles_WT": [ + 21.99, + "X" + ], + "hla_types": [ + "HLA-A*29:02", + "HLA-B*45:01" + ], + "mutation_position": "6", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 11307.646298896185, + 5744.18, + 20962.61, + 14329.76, + 8386.37, + 1584.89, + 28038.84, + 22385.66 + ] + }, + "WT": { + "HLA-A*29:02": [ + 10978.843004205257, + 5798.66, + 25371.68, + 20040.43, + 15876.41, + 2314.53, + 31751.19, + 28971.43 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 5.732500076293945, + 14.239999771118164, + 19.0, + 18.0, + 4.5, + 2.0, + 36.0, + 31.0 + ] + }, + "WT": { + "HLA-A*29:02": [ + 5.632499999999998, + 19.4, + 26.0, + 29.0, + 9.1, + 3.9, + 39.0, + 37.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "HLA-A*29:02": [ + 0.0360010527074337, + 0.0098091998527903, + 0.00699, + 0.0017780643, + 0.04063127 + ] + }, + "WT": { + "HLA-A*29:02": [ + 0.0083137899637222, + 0.0091584806676021, + 0.00126, + 0.0037651488, + 0.047771256 + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "HLA-A*29:02": [ + "NA", + 24.57923913043477, + 3.8, + "NA", + "NA" + ] + }, + "WT": { + "HLA-A*29:02": [ + "NA", + 24.57923913043477, + 8.5, + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "MHCflurryEL Presentation", + "NetMHCpanEL" + ], + "MT": { + "HLA-A*29:02": [ + 5.732500076293945, + 14.239999771118164, + 19.0, + 18.0, + 4.5, + 2.0, + 36.0, + 31.0, + 24.57923913043477, + 3.8 + ] + }, + "WT": { + "HLA-A*29:02": [ + 5.632499999999998, + 19.4, + 26.0, + 29.0, + 9.1, + 3.9, + 39.0, + 37.0, + 24.57923913043477, + 8.5 + ] + } + }, + "wt_peptide": "SSFTVDCSK" + } + }, + "transcripts": [ + "ENST00000369850.10-FLNA-D/H-2581" + ], + "transcript_expr": [ + 21.322 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 2647 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 21.322 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 21.322 + ], "DNA VAF": 0.992, "RNA VAF": 0.998, "gene_expr": 706.463, diff --git a/pvactools/tools/pvacseq/example_data/results/MHC_Class_I/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv b/pvactools/tools/pvacseq/example_data/results/MHC_Class_I/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv index fc65be01..0533e87c 100644 --- a/pvactools/tools/pvacseq/example_data/results/MHC_Class_I/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv +++ b/pvactools/tools/pvacseq/example_data/results/MHC_Class_I/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv @@ -88,13 +88,13 @@ chr1-179109009-179109010-T-C 76.ABL2.ENST00000502732.6.missense.753T/A 1 ABL2 T chr19-35841840-35841841-C-A 1034.NPHS1.ENST00000378910.10.missense.897G/C 3 NPHS1 G897C 2 TEHTYHQCG ENST00000378910.10 1 HLA-B*45:01 8 None 3 0 685.930 1092.140 1.800 1.739 0.377 1.000 0.377 2.000 0.081 Poor Pending chr18-14106118-14106119-G-C 985.ZNF519.ENST00000590202.3.missense.141P/A 3 ZNF519 P141A 1 AMNKYQHKF ENST00000590202.3 1 HLA-A*29:02 1 None 3 0 1342.785 3172.260 1.650 4.277 8.050 0.350 2.817 20.000 0.453 Poor Pending chr15-74280668-74280669-G-T 890.CCDC33.ENST00000558659.5.missense.178M/I 1 CCDC33 M178I 2 LEYYSSTSI ENST00000558659.5 1 HLA-B*45:01 9 None 1 0 636.165 2295.485 1.002 2.350 0.158 1.000 0.158 1.000 0.585 Poor Pending -chr11-64320894-64320895-T-C 709.PRDX5.ENST00000265462.9.missense.157F/L PRDX5 F157L 0 LLADPTGAL ENST00000265462.9 1 HLA-A*29:02 9 None 0 0 6583.990 1039.870 7.920 1.685 580.692 0.439 254.924 6089.000 0.427 Poor Pending +chr11-64320894-64320895-T-C 709.PRDX5.ENST00000265462.9.missense.157F/L 1 PRDX5 F157L 1 LLADPTGAL ENST00000265462.9 1 HLA-A*29:02 9 None 1 0 6583.990 1039.870 7.920 1.685 580.692 0.439 254.924 6089.000 0.427 Poor Pending chr14-55180753-55180754-G-A 806.DLGAP5.ENST00000247191.7.missense.202S/L 1 DLGAP5 S202L 3 PVMPTLLRM ENST00000247191.7 1 HLA-A*29:02 6 None 1 0 2937.570 2712.850 3.700 3.450 53.642 0.224 12.016 825.000 0.240 Poor Pending -chr5-1331835-1331836-C-A 319.CLPTM1L.ENST00000320895.10.missense.313K/N CLPTM1L K313N 0 SFWNKKKSM ENST00000320895.10 1 HLA-A*29:02 4 None 0 0 5520.520 8286.575 7.090 9.880 169.373 0.325 55.046 1031.000 0.378 Poor Pending +chr5-1331835-1331836-C-A 319.CLPTM1L.ENST00000320895.10.missense.313K/N 1 CLPTM1L K313N 1 SFWNKKKSM ENST00000320895.10 1 HLA-A*29:02 4 None 1 0 5520.520 8286.575 7.090 9.880 169.373 0.325 55.046 1031.000 0.378 Poor Pending chr10-32567832-32567833-C-T 608.CCDC7.ENST00000277657.12.missense.454S/L 3 CCDC7 S454L 5 KETRKLLVS ENST00000277657.12 1 HLA-B*45:01 6 None 3 0 1996.650 1671.175 2.826 2.895 20.750 0.208 4.316 226.000 0.359 Poor Pending chr20-59944225-59944226-A-G 1083.FAM217B.ENST00000360816.8.missense.95S/G 1 FAM217B S95G 2 KENADEDSAG ENST00000360816.8 1 HLA-B*45:01 10 None 1 0 2469.290 2335.780 3.780 2.750 16.580 0.446 7.395 130.000 0.578 Poor Pending chr12-31697921-31697922-G-T 731.AMN1.ENST00000281471.11.missense.118H/N 1 2 AMN1 H118N 4 NEASLKRCC ENST00000281471.11 1 HLA-B*45:01 1 None 3 0 1539.545 1902.735 1.941 2.150 15.000 0.178 2.670 73.000 0.453 Poor Pending -chr20-41165771-41165772-C-G 1073.PLCG1.ENST00000373271.5.missense.582S/C PLCG1 S582C 0 CFLVRESETF ENST00000373271.5 1 HLA-A*29:02 1 None 0 0 5123.630 4236.635 5.527 3.879 67.838 0.444 30.120 392.000 0.429 Poor Pending +chr20-41165771-41165772-C-G 1073.PLCG1.ENST00000373271.5.missense.582S/C 1 PLCG1 S582C 1 CFLVRESETF ENST00000373271.5 1 HLA-A*29:02 1 None 1 0 5123.630 4236.635 5.527 3.879 67.838 0.444 30.120 392.000 0.429 Poor Pending chr7-77600798-77600799-C-T 425.PTPN12.ENST00000248594.11.missense.230H/Y 1 PTPN12 H230Y 5 HEDVPICIYC ENST00000248594.11 1 HLA-B*45:01 9 None 1 0 4446.550 5566.405 3.850 4.750 128.676 0.161 20.717 732.000 0.203 Poor Pending chr15-45133932-45133933-G-A 870.DUOX1.ENST00000321429.8.missense.43R/K 2 DUOX1 R43K 3 MEHKWGSKG ENST00000321429.8 1 HLA-B*45:01 4 None 2 0 1211.600 1253.160 1.550 1.906 0.947 1.000 0.947 2.000 1.000 Poor Pending chr7-82916602-82916603-C-A 434.PCLO.ENST00000437081.1.missense.515D/Y 3 8 PCLO D515Y 3 EEEKEIYA ENST00000437081.1 1 HLA-B*45:01 7 None 11 0 1183.510 1933.093 1.264 1.750 4.482 0.171 0.766 35.000 0.222 Poor Pending @@ -104,119 +104,119 @@ chr7-82908982-82908983-C-G 430.PCLO.ENST00000333891.14.missense.4444W/S 2 PCLO chr19-6755017-6755018-T-C 1005.SH2D3A.ENST00000245908.11.missense.265E/G 3 SH2D3A E265G 2 AEEDEGEEN ENST00000245908.11 1 HLA-B*45:01 6 None 3 0 2187.524 1879.948 4.253 5.173 3.820 1.000 3.820 5.000 0.985 Poor Pending chr6-29726902-29726904-AA-CT 370.HLA-F.ENST00000259951.12.missense.353N/L 3 HLA-F N353L 2 YSVVSGLLM ENST00000259951.12 NA HLA-A*29:02 7 None 3 0 688.260 3512.527 2.325 4.996 74.251 NA NA NA 0.648 Poor Pending chr16-25246937-25246938-C-T 910.ZKSCAN2.ENST00000328086.12.missense.420E/K 4 1 ZKSCAN2 E420K 1 FFKDMDALL ENST00000328086.12 1 HLA-A*29:02 3 None 5 0 1700.785 1864.320 1.949 1.947 4.925 0.441 2.172 68.000 0.454 Poor Pending -chr22-18606897-18606898-G-A 1089.RIMBP3.ENST00000619918.1.missense.1513R/C RIMBP3 R1513C 0 GNIPGCLVA ENST00000619918.1 NA HLA-B*45:01 6 None 0 0 8044.275 13925.957 6.600 11.558 207.888 1.000 207.888 2.000 0.504 Poor Pending +chr22-18606897-18606898-G-A 1089.RIMBP3.ENST00000619918.1.missense.1513R/C 1 RIMBP3 R1513C 1 GNIPGCLVA ENST00000619918.1 NA HLA-B*45:01 6 None 1 0 8044.275 13925.957 6.600 11.558 207.888 1.000 207.888 2.000 0.504 Poor Pending chrX-9967396-9967397-G-A 1131.CLDN34.ENST00000445307.4.missense.14V/I 3 3 CLDN34 V14I 1 ADCQFSIFA ENST00000445307.4 NA HLA-B*45:01 7 None 6 0 834.053 710.211 1.200 1.100 0.013 1.000 0.013 1.000 0.989 Poor Pending chr8-143795429-143795430-C-T 556.SCRIB.ENST00000320476.7.missense.1235G/D 1 SCRIB G1235D 5 RELSPEDPG ENST00000320476.7 1 HLA-B*45:01 7 None 1 0 3498.040 2819.815 3.900 3.750 61.627 0.141 8.689 687.000 0.162 Poor Pending chrX-78015862-78015863-G-C 1180.ATP7A.ENST00000341514.11.missense.870D/H 4 ATP7A D870H 13 VHESLITGEA ENST00000341514.11 1 HLA-B*45:01 2 None 4 1 2827.710 3554.718 5.375 2.096 5.153 0.951 4.901 41.000 0.982 Poor Pending -chr8-38428419-38428420-G-A 498.FGFR1.ENST00000356207.9.missense.36S/L FGFR1 S36L 0 PEQDALPSL ENST00000356207.9 1 HLA-B*45:01 9 None 0 0 9052.655 5989.315 5.900 6.100 143.964 0.999 143.820 1501.000 1.000 Poor Pending +chr8-38428419-38428420-G-A 498.FGFR1.ENST00000356207.9.missense.36S/L 1 FGFR1 S36L 1 PEQDALPSL ENST00000356207.9 1 HLA-B*45:01 9 None 1 0 9052.655 5989.315 5.900 6.100 143.964 0.999 143.820 1501.000 1.000 Poor Pending chr19-14049194-14049195-C-T 1014.IL27RA.ENST00000263379.4.missense.428A/V 1 IL27RA A428V 1 QDVPPGTPA ENST00000263379.4 1 HLA-B*45:01 3 None 1 0 2943.720 1800.660 4.350 2.300 13.617 0.305 4.153 197.000 0.262 Poor Pending chr8-143805313-143805314-A-C 561.SCRIB.ENST00000320476.7.missense.823V/G 1 SCRIB V823G 6 PENAGTITP ENST00000320476.7 1 HLA-B*45:01 5 None 1 0 2734.350 2170.995 4.800 3.200 61.627 0.055 3.389 402.000 0.164 Poor Pending chr16-74391670-74391671-C-T 929.NPIPB15.ENST00000429990.1.missense.308P/L 1 1 NPIPB15 P308L 2 KEYLLVPLPL ENST00000429990.1 5 HLA-B*45:01 10 None 2 0 1233.525 1038.220 1.709 2.130 10.432 0.015 0.156 68.000 0.409 Poor Pending -chr8-125102410-125102411-G-C 531.NSMCE2.ENST00000287437.8.missense.27L/F NSMCE2 L27F 0 VESALSSFK ENST00000287437.8 1 HLA-B*45:01 8 None 0 0 5585.211 5058.075 6.500 5.950 78.578 0.242 19.016 996.000 0.262 Poor Pending +chr8-125102410-125102411-G-C 531.NSMCE2.ENST00000287437.8.missense.27L/F 1 NSMCE2 L27F 1 VESALSSFK ENST00000287437.8 1 HLA-B*45:01 8 None 1 0 5585.211 5058.075 6.500 5.950 78.578 0.242 19.016 996.000 0.262 Poor Pending chr1-43432295-43432296-G-C 35.SZT2.ENST00000634258.3.missense.1767G/R 1 SZT2 G1767R 2 EEFRRLHLPR ENST00000634258.3 5 HLA-B*45:01 10 None 1 0 4278.255 1522.130 3.998 2.649 34.708 0.344 11.940 96.000 0.338 Poor Pending chr6-33723018-33723020-CA-TG 379.IP6K3.ENST00000293756.5.missense.311-312SV/SI 2 IP6K3 SV311-312SI 2 LSIIRSQSSY ENST00000293756.5 1 HLA-A*29:02 3 None 2 1 978.755 1520.150 1.950 2.450 0.009 NA NA NA 0.718 Poor Pending -chr2-61348284-61348285-C-G 137.USP34.ENST00000398571.7.missense.624D/H USP34 D624H 0 EEHEDDDHG ENST00000398571.7 5 HLA-B*45:01 3 None 0 0 5162.410 11829.615 7.196 14.999 47.363 0.355 16.814 591.000 0.284 Poor Pending +chr2-61348284-61348285-C-G 137.USP34.ENST00000398571.7.missense.624D/H 1 USP34 D624H 1 EEHEDDDHG ENST00000398571.7 5 HLA-B*45:01 3 None 1 0 5162.410 11829.615 7.196 14.999 47.363 0.355 16.814 591.000 0.284 Poor Pending chr6-43587456-43587457-G-A 384.POLH.ENST00000372236.9.missense.153G/D 1 POLH G153D 2 IEGLPQDPT ENST00000372236.9 1 HLA-B*45:01 7 None 1 0 2977.985 3031.475 2.900 2.898 12.570 0.291 3.658 237.000 0.230 Poor Pending chr11-6401000-6401001-C-T 677.APBB1.ENST00000311051.7.missense.552A/T 1 APBB1 A552T 11 YYLGNVPVTK ENST00000311051.7 1 HLA-A*29:02 9 None 1 0 3685.900 3431.630 2.399 2.672 6.678 1.000 6.678 85.000 0.990 Poor Pending -chr9-133354714-133354715-G-C 591.SURF1.ENST00000371974.8.missense.89N/K SURF1 N89K 0 RKWKLKLIA ENST00000371974.8 1 HLA-B*45:01 6 None 0 0 8318.575 5691.345 7.228 6.550 46.709 0.762 35.592 563.000 0.700 Poor Pending +chr9-133354714-133354715-G-C 591.SURF1.ENST00000371974.8.missense.89N/K 1 SURF1 N89K 1 RKWKLKLIA ENST00000371974.8 1 HLA-B*45:01 6 None 1 0 8318.575 5691.345 7.228 6.550 46.709 0.762 35.592 563.000 0.700 Poor Pending chr9-129102403-129102404-T-C 584.CRAT.ENST00000318080.7.missense.209Y/C 4 CRAT Y209C 6 TVVHNCQFF ENST00000318080.7 1 HLA-A*29:02 6 None 4 0 1355.020 1321.090 2.304 1.964 11.624 0.018 0.209 169.000 0.275 Poor Pending -chr2-669669-669670-C-T 124.TMEM18.ENST00000281017.8.missense.111M/I TMEM18 M111I 0 MIIVVIWVW ENST00000281017.8 1 HLA-A*29:02 6 None 0 0 5621.880 5872.155 8.750 6.900 55.263 0.306 16.910 980.000 0.262 Poor Pending +chr2-669669-669670-C-T 124.TMEM18.ENST00000281017.8.missense.111M/I 1 TMEM18 M111I 1 MIIVVIWVW ENST00000281017.8 1 HLA-A*29:02 6 None 1 0 5621.880 5872.155 8.750 6.900 55.263 0.306 16.910 980.000 0.262 Poor Pending chr11-6410863-6410864-C-T 688.APBB1.ENST00000311051.7.missense.162E/K 1 APBB1 E162K 4 GEAEEEEKD ENST00000311051.7 1 HLA-B*45:01 8 None 1 0 3743.880 2485.220 8.300 5.850 6.678 1.000 6.678 65.000 1.000 Poor Pending chr22-37374977-37374978-G-A 1094.ELFN2.ENST00000402918.7.missense.186P/L 3 3 ELFN2 P186L 1 CELAGNLFNC ENST00000402918.7 4 HLA-B*45:01 7 None 6 0 1464.895 1705.490 2.127 2.300 0.890 0.368 0.328 19.000 0.168 Poor Pending chr10-132163376-132163377-C-G 640.JAKMIP3.ENST00000298622.9.missense.795R/G 3 JAKMIP3 R795G 20 RERDAQILG ENST00000298622.9 5 HLA-B*45:01 9 None 3 1 2636.760 6524.485 3.300 5.150 3.848 0.625 2.405 24.000 0.462 Poor Pending -chr12-112043094-112043095-A-C 739.NAA25.ENST00000261745.9.missense.789S/R NAA25 S789R 0 YELDTRGLED ENST00000261745.9 1 HLA-B*45:01 6 None 0 0 7553.065 8834.680 5.350 5.516 23.927 1.000 23.927 192.000 1.000 Poor Pending +chr12-112043094-112043095-A-C 739.NAA25.ENST00000261745.9.missense.789S/R 1 NAA25 S789R 1 YELDTRGLED ENST00000261745.9 1 HLA-B*45:01 6 None 1 0 7553.065 8834.680 5.350 5.516 23.927 1.000 23.927 192.000 1.000 Poor Pending chr7-128815875-128815876-C-G 474.CCDC136.ENST00000297788.9.missense.1103S/C 5 CCDC136 S1103C 2 SEEEEDDADC ENST00000297788.9 1 HLA-B*45:01 10 None 5 0 2356.280 2591.060 4.350 5.425 4.998 0.250 1.250 32.000 0.200 Poor Pending chr15-30089755-30089756-C-G 845.GOLGA8J.ENST00000567927.2.missense.311L/V 3 GOLGA8J L311V 1 SEVELQHV ENST00000567927.2 5 HLA-B*45:01 8 None 3 0 1580.310 4878.700 0.955 2.200 0.354 1.000 0.354 10.000 0.119 Poor Pending -chr6-109451607-109451608-G-T 394.MICAL1.ENST00000358577.7.missense.309L/M MICAL1 L309M 0 VMRQPFWPL ENST00000358577.7 1 HLA-A*29:02 2 None 0 0 5082.780 10672.890 6.250 12.903 12.825 1.000 12.825 96.000 0.981 Poor Pending +chr6-109451607-109451608-G-T 394.MICAL1.ENST00000358577.7.missense.309L/M 1 MICAL1 L309M 1 VMRQPFWPL ENST00000358577.7 1 HLA-A*29:02 2 None 1 0 5082.780 10672.890 6.250 12.903 12.825 1.000 12.825 96.000 0.981 Poor Pending chr20-10054508-10054509-G-C 1060.ANKEF1.ENST00000378392.6.missense.694K/N 1 ANKEF1 K694N 2 SEGNKVQKG ENST00000378392.6 1 HLA-B*45:01 4 None 1 0 2509.040 2375.340 3.300 3.600 3.908 0.382 1.493 34.000 0.521 Poor Pending -chr12-49526214-49526215-G-A 736.SPATS2.ENST00000321898.10.missense.533R/H SPATS2 R533H 0 SFKKGLPQH ENST00000321898.10 1 HLA-A*29:02 9 None 0 0 7756.855 17144.170 7.135 14.080 23.424 1.000 23.424 334.000 0.968 Poor Pending +chr12-49526214-49526215-G-A 736.SPATS2.ENST00000321898.10.missense.533R/H 1 SPATS2 R533H 1 SFKKGLPQH ENST00000321898.10 1 HLA-A*29:02 9 None 1 0 7756.855 17144.170 7.135 14.080 23.424 1.000 23.424 334.000 0.968 Poor Pending chr7-112821984-112821985-G-T 462.BMT2.ENST00000297145.9.missense.326T/K 1 BMT2 T326K 2 KSDLVSRNY ENST00000297145.9 1 HLA-A*29:02 1 None 1 0 3962.365 2481.540 5.110 3.255 34.269 0.188 6.443 224.000 0.179 Poor Pending -chrX-154349376-154349377-C-G 1211.FLNA.ENST00000369850.10.missense.2581D/H FLNA D2581H 0 SSFTVHCSK ENST00000369850.10 1 HLA-A*29:02 6 None 0 0 12818.703 17958.420 16.120 21.990 706.463 0.998 705.050 5609.000 0.992 Poor Pending -chr1-39429921-39429922-G-C 30.MACF1.ENST00000567887.5.missense.5699E/Q MACF1 E5699Q 0 SKALRTLQQA ENST00000567887.5 5 HLA-B*45:01 8 None 0 0 10421.945 13712.205 10.300 12.500 126.838 0.372 47.184 819.000 0.333 Poor Pending +chrX-154349376-154349377-C-G 1211.FLNA.ENST00000369850.10.missense.2581D/H 1 FLNA D2581H 1 SSFTVHCSK ENST00000369850.10 1 HLA-A*29:02 6 None 1 0 12818.703 17958.420 16.120 21.990 706.463 0.998 705.050 5609.000 0.992 Poor Pending +chr1-39429921-39429922-G-C 30.MACF1.ENST00000567887.5.missense.5699E/Q 1 MACF1 E5699Q 1 SKALRTLQQA ENST00000567887.5 5 HLA-B*45:01 8 None 1 0 10421.945 13712.205 10.300 12.500 126.838 0.372 47.184 819.000 0.333 Poor Pending chr14-21403125-21403126-C-A 782.CHD8.ENST00000430710.8.missense.923R/L 1 CHD8 R923L 7 RFSKPDSDLF ENST00000430710.8 1 HLA-A*29:02 9 None 1 0 3112.380 5276.510 3.300 4.250 62.447 0.042 2.623 518.000 0.071 Poor Pending chr15-62819536-62819537-G-A 882.TLN2.ENST00000561311.5.missense.2265E/K 2 TLN2 E2265K 3 ILQKPTPKF ENST00000561311.5 5 HLA-A*29:02 8 None 2 0 4310.605 3185.955 3.950 2.850 20.006 0.351 7.022 154.000 0.452 Poor Pending -chr18-80138228-80138229-G-T 992.ADNP2.ENST00000262198.9.missense.939R/I ADNP2 R939I 0 AVHLVRCISA ENST00000262198.9 1 HLA-B*45:01 8 None 0 0 7262.155 10890.455 7.600 9.750 19.521 0.959 18.721 122.000 1.000 Poor Pending -chr15-50643416-50643417-T-G 879.TRPM7.ENST00000560955.5.missense.153K/T TRPM7 K153T 0 FELHPRIT ENST00000560955.5 1 HLA-B*45:01 8 None 0 0 5450.200 9255.799 4.600 8.400 28.628 0.450 12.883 416.000 0.500 Poor Pending +chr18-80138228-80138229-G-T 992.ADNP2.ENST00000262198.9.missense.939R/I 1 ADNP2 R939I 1 AVHLVRCISA ENST00000262198.9 1 HLA-B*45:01 8 None 1 0 7262.155 10890.455 7.600 9.750 19.521 0.959 18.721 122.000 1.000 Poor Pending +chr15-50643416-50643417-T-G 879.TRPM7.ENST00000560955.5.missense.153K/T 1 TRPM7 K153T 1 FELHPRIT ENST00000560955.5 1 HLA-B*45:01 8 None 1 0 5450.200 9255.799 4.600 8.400 28.628 0.450 12.883 416.000 0.500 Poor Pending chr6-46662451-46662452-C-G 385.SLC25A27.ENST00000371347.10.missense.154Q/E 1 SLC25A27 Q154E 3 VEMQMEGKR ENST00000371347.10 1 HLA-B*45:01 2 None 1 0 4717.186 35656.275 8.647 39.000 14.615 0.521 7.614 71.000 0.484 Poor Pending chr17-82961144-82961145-G-C 982.B3GNTL1.ENST00000320865.4.missense.198L/V 2 1 B3GNTL1 L198V 3 LFFYEHVRK ENST00000320865.4 1 HLA-A*29:02 7 None 3 0 3140.125 974.350 4.550 2.250 10.001 0.235 2.350 81.000 0.221 Poor Pending chr14-91783159-91783160-T-A 818.TC2N.ENST00000340892.9.missense.471K/N 3 TC2N K471N 5 IEAVNQWNET ENST00000340892.9 1 HLA-B*45:01 8 None 3 0 1901.265 3255.500 2.750 3.450 1.985 0.125 0.248 16.000 0.151 Poor Pending chr19-17052841-17052842-C-G 1028.HAUS8.ENST00000253669.10.missense.304K/N 1 HAUS8 K304N 3 SELKDVTAKN ENST00000253669.10 1 HLA-B*45:01 10 None 1 0 4520.046 7503.075 5.050 3.950 10.348 0.602 6.229 98.000 0.548 Poor Pending -chr2-175093191-175093192-C-G 176.ATF2.ENST00000264110.7.missense.352D/H ATF2 D352H 0 HEKRRKFLE ENST00000264110.7 1 HLA-B*45:01 1 None 0 0 11919.840 19454.849 10.350 17.500 100.906 0.445 44.903 878.000 0.461 Poor Pending -chr2-219471924-219471925-A-G 212.SPEG.ENST00000312358.12.missense.1258Y/C SPEG Y1258C 0 AGVCKSVIA ENST00000312358.12 5 HLA-B*45:01 4 None 0 0 9580.850 8433.635 9.700 9.285 66.211 0.397 26.286 126.000 0.333 Poor Pending -chr8-125028638-125028639-T-C 529.WASHC5.ENST00000318410.12.missense.1135Y/C WASHC5 Y1135C 0 YVRCTKLPR ENST00000318410.12 1 HLA-A*29:02 4 None 0 0 6455.970 5628.810 8.650 7.681 65.088 0.212 13.799 448.000 0.139 Poor Pending -chr9-37784015-37784016-T-A 574.EXOSC3.ENST00000327304.10.missense.124K/N EXOSC3 K124N 0 VTANSGDIF ENST00000327304.10 1 HLA-A*29:02 4 None 0 0 6920.210 9886.520 9.825 15.235 28.784 0.533 15.342 255.000 0.480 Poor Pending -chr4-48420360-48420361-A-G 295.SLAIN2.ENST00000264313.11.missense.533R/G SLAIN2 R533G 0 TAMGSGLPR ENST00000264313.11 1 HLA-A*29:02 4 None 0 0 7947.620 10844.016 6.500 12.594 58.280 0.312 18.183 365.000 0.290 Poor Pending +chr2-175093191-175093192-C-G 176.ATF2.ENST00000264110.7.missense.352D/H 1 ATF2 D352H 1 HEKRRKFLE ENST00000264110.7 1 HLA-B*45:01 1 None 1 0 11919.840 19454.849 10.350 17.500 100.906 0.445 44.903 878.000 0.461 Poor Pending +chr2-219471924-219471925-A-G 212.SPEG.ENST00000312358.12.missense.1258Y/C 1 SPEG Y1258C 1 AGVCKSVIA ENST00000312358.12 5 HLA-B*45:01 4 None 1 0 9580.850 8433.635 9.700 9.285 66.211 0.397 26.286 126.000 0.333 Poor Pending +chr8-125028638-125028639-T-C 529.WASHC5.ENST00000318410.12.missense.1135Y/C 1 WASHC5 Y1135C 1 YVRCTKLPR ENST00000318410.12 1 HLA-A*29:02 4 None 1 0 6455.970 5628.810 8.650 7.681 65.088 0.212 13.799 448.000 0.139 Poor Pending +chr9-37784015-37784016-T-A 574.EXOSC3.ENST00000327304.10.missense.124K/N 1 EXOSC3 K124N 1 VTANSGDIF ENST00000327304.10 1 HLA-A*29:02 4 None 1 0 6920.210 9886.520 9.825 15.235 28.784 0.533 15.342 255.000 0.480 Poor Pending +chr4-48420360-48420361-A-G 295.SLAIN2.ENST00000264313.11.missense.533R/G 1 SLAIN2 R533G 1 TAMGSGLPR ENST00000264313.11 1 HLA-A*29:02 4 None 1 0 7947.620 10844.016 6.500 12.594 58.280 0.312 18.183 365.000 0.290 Poor Pending chr7-157005551-157005552-G-A 485.MNX1.ENST00000252971.11.missense.392P/S 1 MNX1 P392S 2 SEDDSPPSRP ENST00000252971.11 1 HLA-B*45:01 8 None 1 0 2653.235 2299.625 4.670 3.855 18.982 0.040 0.759 101.000 0.054 Poor Pending chr5-141332647-141332648-C-T 342.PCDHGA1.ENST00000517417.3.missense.655S/F 1 PCDHGA1 S655F 2 LFATVTLTV ENST00000517417.3 1 HLA-A*29:02 2 None 1 0 2028.966 8022.440 3.200 12.650 0.326 0.571 0.186 7.000 0.681 Poor Pending -chr20-17659330-17659331-C-T 1061.RRBP1.ENST00000246043.8.missense.393E/K RRBP1 E393K 0 NQGKKVKGA ENST00000246043.8 1 HLA-B*45:01 7 None 0 0 15310.575 12423.338 8.700 7.800 153.904 0.493 75.875 676.000 0.574 Poor Pending +chr20-17659330-17659331-C-T 1061.RRBP1.ENST00000246043.8.missense.393E/K 1 RRBP1 E393K 1 NQGKKVKGA ENST00000246043.8 1 HLA-B*45:01 7 None 1 0 15310.575 12423.338 8.700 7.800 153.904 0.493 75.875 676.000 0.574 Poor Pending chr1-86453473-86453474-G-A 49.CLCA2.ENST00000370565.5.missense.754G/E 2 CLCA2 G754E 1 LEVPAGPHP ENST00000370565.5 1 HLA-B*45:01 2 None 2 0 2487.725 36247.860 5.200 52.612 0.509 1.000 0.509 2.000 0.575 Poor Pending chr19-13765994-13765995-G-C 1011.MRI1.ENST00000040663.8.missense.138R/T 1 MRI1 R138T 1 TEDMLEKDLT ENST00000040663.8 1 HLA-B*45:01 10 None 1 0 4861.945 18342.410 4.750 9.100 24.532 0.201 4.931 389.000 0.224 Poor Pending -chr11-63544840-63544860-GTGAGCACTTTGTCACCCAGC-G 706.PLAAT4.ENST00000255688.8.FS.113-120GTGAGCACTTTGTCACCCAGC/G PLAAT4 FS113-120 0 CEIWQVPL ENST00000255688.8 1 HLA-B*45:01 3-8 None 0 0 5039.270 NA 3.153 NA 43.703 0.115 5.026 426.000 0.071 Poor Pending -chr1-52961569-52961570-C-A 39.SCP2.ENST00000371514.8.missense.155A/D SCP2 A155D 0 SDHPVAPQMF ENST00000371514.8 1 HLA-A*29:02 2 None 0 0 11822.961 6381.940 13.403 7.700 51.669 0.534 27.591 219.000 0.482 Poor Pending +chr11-63544840-63544860-GTGAGCACTTTGTCACCCAGC-G 706.PLAAT4.ENST00000255688.8.FS.113-120GTGAGCACTTTGTCACCCAGC/G 1 PLAAT4 FS113-120 1 CEIWQVPL ENST00000255688.8 1 HLA-B*45:01 3-8 None 1 0 5039.270 NA 3.153 NA 43.703 0.115 5.026 426.000 0.071 Poor Pending +chr1-52961569-52961570-C-A 39.SCP2.ENST00000371514.8.missense.155A/D 1 SCP2 A155D 1 SDHPVAPQMF ENST00000371514.8 1 HLA-A*29:02 2 None 1 0 11822.961 6381.940 13.403 7.700 51.669 0.534 27.591 219.000 0.482 Poor Pending chr1-36179726-36179728-GG-AA 17.MAP7D1.ENST00000373151.6.missense.764-765EE/EK 3 MAP7D1 EE764-765EK 4 KEKPIPQEP ENST00000373151.6 1 HLA-B*45:01 3 None 3 0 1880.870 1720.405 3.850 3.210 93.193 NA NA NA 0.361 Poor Pending chrX-43656385-43656386-C-A 1164.MAOA.ENST00000338702.4.missense.15D/E 1 2 MAOA D15E 2 SIAGHMFEV ENST00000338702.4 1 HLA-A*29:02 8 None 3 0 3238.095 4035.900 3.551 6.650 0.784 1.000 0.784 2.000 1.000 Poor Pending -chr3-33053544-33053545-G-T 222.GLB1.ENST00000307363.10.missense.246S/R GLB1 S246R 0 RNITDAFLS ENST00000307363.10 1 HLA-A*29:02 1 None 0 0 10770.730 8498.385 17.500 15.000 77.589 0.253 19.630 782.000 0.314 Poor Pending +chr3-33053544-33053545-G-T 222.GLB1.ENST00000307363.10.missense.246S/R 1 GLB1 S246R 1 RNITDAFLS ENST00000307363.10 1 HLA-A*29:02 1 None 1 0 10770.730 8498.385 17.500 15.000 77.589 0.253 19.630 782.000 0.314 Poor Pending chr15-43149136-43149137-G-C 852.TMEM62.ENST00000260403.7.missense.284W/C 1 TMEM62 W284C 2 LELEVGDCK ENST00000260403.7 1 HLA-B*45:01 8 None 1 0 4702.850 5491.988 6.810 12.094 3.179 1.000 3.179 39.000 0.960 Poor Pending chr4-40808808-40808809-A-G 294.NSUN7.ENST00000381782.7.missense.676Y/C 2 NSUN7 Y676C 1 TQHLCCRWVA ENST00000381782.7 1 HLA-B*45:01 5 None 2 0 2476.125 2010.980 5.650 4.800 0.405 0.333 0.135 6.000 0.471 Poor Pending -chr8-22566400-22566401-G-C 487.SORBS3.ENST00000240123.12.missense.336R/P SORBS3 R336P 0 YLGSAPSLS ENST00000240123.12 1 HLA-A*29:02 6 None 0 0 6955.165 9245.345 13.000 18.000 23.107 0.374 8.642 195.000 0.464 Poor Pending -chr1-168179177-168179178-A-T 74.TIPRL.ENST00000367833.7.missense.34E/V TIPRL E34V 0 VVKLADELH ENST00000367833.7 1 HLA-A*29:02 2 None 0 0 10081.885 31690.325 15.000 47.500 55.746 0.332 18.508 927.000 0.273 Poor Pending -chr2-31366060-31366061-G-C 129.XDH.ENST00000379416.4.missense.791R/G XDH R791G 0 GVKRMGGGF ENST00000379416.4 1 HLA-A*29:02 1 None 0 0 8019.631 8489.545 13.000 11.850 9.677 1.000 9.677 83.000 1.000 Poor Pending -chr6-43340177-43340178-C-G 382.ZNF318.ENST00000361428.3.missense.1274G/R ZNF318 G1274R 0 SSFRKFSWKK ENST00000361428.3 1 HLA-A*29:02 4 None 0 0 6805.415 5353.035 13.000 9.020 12.831 0.377 4.837 106.000 0.347 Poor Pending -chr22-26540809-26540810-G-T 1090.TPST2.ENST00000338754.9.missense.274P/H TPST2 P274H 0 HEDLIGKHGG ENST00000338754.9 1 HLA-B*45:01 8 None 0 0 7433.355 7272.905 9.500 9.050 28.333 0.210 5.950 371.000 0.203 Poor Pending +chr8-22566400-22566401-G-C 487.SORBS3.ENST00000240123.12.missense.336R/P 1 SORBS3 R336P 1 YLGSAPSLS ENST00000240123.12 1 HLA-A*29:02 6 None 1 0 6955.165 9245.345 13.000 18.000 23.107 0.374 8.642 195.000 0.464 Poor Pending +chr1-168179177-168179178-A-T 74.TIPRL.ENST00000367833.7.missense.34E/V 1 TIPRL E34V 1 VVKLADELH ENST00000367833.7 1 HLA-A*29:02 2 None 1 0 10081.885 31690.325 15.000 47.500 55.746 0.332 18.508 927.000 0.273 Poor Pending +chr2-31366060-31366061-G-C 129.XDH.ENST00000379416.4.missense.791R/G 1 XDH R791G 1 GVKRMGGGF ENST00000379416.4 1 HLA-A*29:02 1 None 1 0 8019.631 8489.545 13.000 11.850 9.677 1.000 9.677 83.000 1.000 Poor Pending +chr6-43340177-43340178-C-G 382.ZNF318.ENST00000361428.3.missense.1274G/R 1 ZNF318 G1274R 1 SSFRKFSWKK ENST00000361428.3 1 HLA-A*29:02 4 None 1 0 6805.415 5353.035 13.000 9.020 12.831 0.377 4.837 106.000 0.347 Poor Pending +chr22-26540809-26540810-G-T 1090.TPST2.ENST00000338754.9.missense.274P/H 1 TPST2 P274H 1 HEDLIGKHGG ENST00000338754.9 1 HLA-B*45:01 8 None 1 0 7433.355 7272.905 9.500 9.050 28.333 0.210 5.950 371.000 0.203 Poor Pending chr7-97006043-97006044-G-C 457.DLX6.ENST00000518156.3.missense.23E/Q 2 DLX6 E23Q 1 FMQFGQQQQ ENST00000518156.3 1 HLA-A*29:02 3 None 2 0 4505.550 6295.350 5.950 10.433 2.584 0.424 1.096 33.000 0.411 Poor Pending -chr1-223264671-223264672-G-C 97.SUSD4.ENST00000366878.9.missense.228L/V SUSD4 L228V 0 LECLQNVIWS ENST00000366878.9 1 HLA-B*45:01 7 None 0 0 7615.945 8447.660 7.365 8.800 24.362 0.203 4.945 236.000 0.374 Poor Pending +chr1-223264671-223264672-G-C 97.SUSD4.ENST00000366878.9.missense.228L/V 1 SUSD4 L228V 1 LECLQNVIWS ENST00000366878.9 1 HLA-B*45:01 7 None 1 0 7615.945 8447.660 7.365 8.800 24.362 0.203 4.945 236.000 0.374 Poor Pending chr19-14049194-14049196-CC-TT 1015.IL27RA.ENST00000263379.4.missense.428A/V 1 IL27RA A428V 1 QDVPPGTPA ENST00000263379.4 1 HLA-B*45:01 3 None 1 0 2943.720 1800.660 4.350 2.300 13.617 NA NA NA 0.268 Poor Pending -chr8-123220246-123220247-C-A 528.C8orf76.ENST00000276704.6.missense.333E/D C8orf76 E333D 0 DEVHPDVKCV ENST00000276704.6 1 HLA-B*45:01 6 None 0 0 8863.500 7758.295 4.650 4.600 45.915 0.173 7.943 352.000 0.129 Poor Pending -chr22-37631020-37631021-C-G 1098.GGA1.ENST00000381756.9.missense.501P/A GGA1 P501A 0 LHTVSPEPA ENST00000381756.9 1 HLA-B*45:01 9 None 0 0 19041.283 38381.280 17.500 60.500 51.482 0.435 22.395 386.000 0.436 Poor Pending -chr3-56617278-56617279-G-C 236.CCDC66.ENST00000394672.8.missense.671E/Q CCDC66 E671Q 0 QKENNRCNDQ ENST00000394672.8 1 HLA-B*45:01 1 None 0 0 26644.627 27135.480 39.500 46.000 24.974 1.000 24.974 133.000 1.000 Poor Pending -chr13-45399008-45399009-C-T 770.SLC25A30.ENST00000519676.6.missense.228M/I SLC25A30 M228I 0 RIMNQRVLR ENST00000519676.6 1 HLA-A*29:02 2 None 0 0 10953.560 4801.523 5.861 5.272 20.311 0.520 10.562 223.000 0.451 Poor Pending -chr9-137199427-137199428-T-A 593.TPRN.ENST00000409012.6.missense.428E/D TPRN E428D 0 DEAEPAEGL ENST00000409012.6 1 HLA-B*45:01 1 None 0 0 7302.025 2372.690 4.900 2.300 10.805 0.333 3.598 93.000 0.296 Poor Pending -chr18-80136551-80136552-C-T 991.ADNP2.ENST00000262198.9.missense.380P/L ADNP2 P380L 0 PLSQPVGLV ENST00000262198.9 1 HLA-A*29:02 8 None 0 0 19743.070 27068.148 26.000 41.000 19.521 1.000 19.521 143.000 0.932 Poor Pending -chr9-35750917-35750918-C-T 573.RGP1.ENST00000378078.5.missense.139T/I RGP1 T139I 0 YVYKLIIGC ENST00000378078.5 1 HLA-A*29:02 6 None 0 0 12007.495 8961.610 11.209 7.463 12.548 0.995 12.485 194.000 0.979 Poor Pending +chr8-123220246-123220247-C-A 528.C8orf76.ENST00000276704.6.missense.333E/D 1 C8orf76 E333D 1 DEVHPDVKCV ENST00000276704.6 1 HLA-B*45:01 6 None 1 0 8863.500 7758.295 4.650 4.600 45.915 0.173 7.943 352.000 0.129 Poor Pending +chr22-37631020-37631021-C-G 1098.GGA1.ENST00000381756.9.missense.501P/A 1 GGA1 P501A 1 LHTVSPEPA ENST00000381756.9 1 HLA-B*45:01 9 None 1 0 19041.283 38381.280 17.500 60.500 51.482 0.435 22.395 386.000 0.436 Poor Pending +chr3-56617278-56617279-G-C 236.CCDC66.ENST00000394672.8.missense.671E/Q 1 CCDC66 E671Q 1 QKENNRCNDQ ENST00000394672.8 1 HLA-B*45:01 1 None 1 0 26644.627 27135.480 39.500 46.000 24.974 1.000 24.974 133.000 1.000 Poor Pending +chr13-45399008-45399009-C-T 770.SLC25A30.ENST00000519676.6.missense.228M/I 1 SLC25A30 M228I 1 RIMNQRVLR ENST00000519676.6 1 HLA-A*29:02 2 None 1 0 10953.560 4801.523 5.861 5.272 20.311 0.520 10.562 223.000 0.451 Poor Pending +chr9-137199427-137199428-T-A 593.TPRN.ENST00000409012.6.missense.428E/D 1 TPRN E428D 1 DEAEPAEGL ENST00000409012.6 1 HLA-B*45:01 1 None 1 0 7302.025 2372.690 4.900 2.300 10.805 0.333 3.598 93.000 0.296 Poor Pending +chr18-80136551-80136552-C-T 991.ADNP2.ENST00000262198.9.missense.380P/L 1 ADNP2 P380L 1 PLSQPVGLV ENST00000262198.9 1 HLA-A*29:02 8 None 1 0 19743.070 27068.148 26.000 41.000 19.521 1.000 19.521 143.000 0.932 Poor Pending +chr9-35750917-35750918-C-T 573.RGP1.ENST00000378078.5.missense.139T/I 1 RGP1 T139I 1 YVYKLIIGC ENST00000378078.5 1 HLA-A*29:02 6 None 1 0 12007.495 8961.610 11.209 7.463 12.548 0.995 12.485 194.000 0.979 Poor Pending chr2-71611503-71611504-C-G 148.DYSF.ENST00000410020.8.missense.1367L/V 1 DYSF L1367V 11 RNMKSYQVA ENST00000410020.8 1 HLA-B*45:01 8 None 1 0 3710.915 5311.435 3.650 5.100 0.119 1.000 0.119 2.000 1.000 Poor Pending -chrX-71378281-71378287-GAGATAT-G 1170.TAF1.ENST00000373790.9.inframe_del.306-308GDI/G TAF1 GDI306-308G 0 KFSQSTGDK ENST00000373790.9 1 HLA-A*29:02 8-9 None 0 0 13926.875 8908.985 17.000 16.000 18.137 0.745 13.512 153.000 0.894 Poor Pending -chr6-1930220-1930221-A-T 356.GMDS.ENST00000380815.5.missense.218F/Y GMDS F218Y 0 HESPRRGANY ENST00000380815.5 1 HLA-A*29:02 10 None 0 0 5513.520 22086.255 7.100 27.500 52.423 0.020 1.048 498.000 0.212 Poor Pending -chr7-27130623-27130624-C-T 416.HOXA4.ENST00000360046.10.missense.37G/D HOXA4 G37D 0 GGPDGGPGY ENST00000360046.10 1 HLA-A*29:02 4 None 0 0 5038.820 5061.965 3.800 3.800 1.689 0.375 0.633 16.000 0.375 Poor Pending -chr7-102317255-102317256-A-G 459.SH2B2.ENST00000536178.3.missense.462H/R SH2B2 H462R 0 ELSDYPWFR ENST00000536178.3 1 HLA-A*29:02 9 None 0 0 5981.995 3205.479 4.365 3.048 6.055 0.223 1.350 94.000 0.181 Poor Pending +chrX-71378281-71378287-GAGATAT-G 1170.TAF1.ENST00000373790.9.inframe_del.306-308GDI/G 1 TAF1 GDI306-308G 1 KFSQSTGDK ENST00000373790.9 1 HLA-A*29:02 8-9 None 1 0 13926.875 8908.985 17.000 16.000 18.137 0.745 13.512 153.000 0.894 Poor Pending +chr6-1930220-1930221-A-T 356.GMDS.ENST00000380815.5.missense.218F/Y 1 GMDS F218Y 1 HESPRRGANY ENST00000380815.5 1 HLA-A*29:02 10 None 1 0 5513.520 22086.255 7.100 27.500 52.423 0.020 1.048 498.000 0.212 Poor Pending +chr7-27130623-27130624-C-T 416.HOXA4.ENST00000360046.10.missense.37G/D 1 HOXA4 G37D 1 GGPDGGPGY ENST00000360046.10 1 HLA-A*29:02 4 None 1 0 5038.820 5061.965 3.800 3.800 1.689 0.375 0.633 16.000 0.375 Poor Pending +chr7-102317255-102317256-A-G 459.SH2B2.ENST00000536178.3.missense.462H/R 1 SH2B2 H462R 1 ELSDYPWFR ENST00000536178.3 1 HLA-A*29:02 9 None 1 0 5981.995 3205.479 4.365 3.048 6.055 0.223 1.350 94.000 0.181 Poor Pending chr13-25541936-25541938-GA-CT 751.ATP8A2.ENST00000381655.7.missense.224D/L 1 ATP8A2 D224L 6 LMQTREVLM ENST00000381655.7 1 HLA-A*29:02 1 None 1 0 3537.465 7111.135 4.100 7.700 0.145 NA NA NA 0.319 Poor Pending chr2-102015965-102015966-C-T 153.IL1R2.ENST00000332549.8.missense.143T/I 1 IL1R2 T143I 4 FISYPQILI ENST00000332549.8 1 HLA-A*29:02 9 None 1 0 4213.895 8236.105 6.280 12.790 0.517 0.300 0.155 10.000 0.200 Poor Pending -chr19-6044262-6044263-G-C 999.RFX2.ENST00000303657.10.missense.37A/G RFX2 A37G 0 AGSSNPKGA ENST00000303657.10 1 HLA-B*45:01 2 None 0 0 18548.789 21160.564 17.170 14.500 15.809 1.000 15.809 45.000 0.989 Poor Pending +chr19-6044262-6044263-G-C 999.RFX2.ENST00000303657.10.missense.37A/G 1 RFX2 A37G 1 AGSSNPKGA ENST00000303657.10 1 HLA-B*45:01 2 None 1 0 18548.789 21160.564 17.170 14.500 15.809 1.000 15.809 45.000 0.989 Poor Pending chr9-4286160-4286161-G-T 568.GLIS3.ENST00000477901.5.missense.89Q/K 1 GLIS3 Q89K 4 KMLTNGKPRF ENST00000477901.5 1 HLA-A*29:02 1 None 1 0 4069.043 3901.198 3.979 3.750 2.761 0.043 0.119 23.000 0.153 Poor Pending -chr1-16972417-16972418-C-G 5.CROCC.ENST00000375541.10.missense.2009S/C CROCC S2009C 0 SSAPFCPPS ENST00000375541.10 5 HLA-B*45:01 6 None 0 0 13779.645 13580.410 15.500 12.040 11.754 1.000 11.754 56.000 0.988 Poor Pending -chr20-35384131-35384132-C-G 1067.UQCC1.ENST00000374385.10.missense.44W/S 3 UQCC1 W44S 1 SPQMSQSRA ENST00000374385.10 1 HLA-B*45:01 1 None 3 0 18964.744 26118.567 14.500 24.500 47.722 0.327 15.605 581.000 0.434 Poor Pending -chr15-40622779-40622780-C-T 850.KNL1.ENST00000346991.9.missense.865P/L KNL1 P865L 0 SVQKPKFLK ENST00000346991.9 1 HLA-A*29:02 8 None 0 0 11386.921 15028.915 6.335 11.955 13.527 0.492 6.655 128.000 0.444 Poor Pending -chr16-49281350-49281351-C-T 916.CBLN1.ENST00000219197.11.missense.39D/N CBLN1 D39N 0 LEGKCLVVCN ENST00000219197.11 1 HLA-B*45:01 10 None 0 0 5071.920 5329.090 10.740 9.900 0.713 0.400 0.285 5.000 0.215 Poor Pending -chr7-92077866-92077867-G-C 439.AKAP9.ENST00000356239.8.missense.2313D/H AKAP9 D2313H 0 QLKITTHNK ENST00000356239.8 1 HLA-A*29:02 7 None 0 0 20518.145 27778.605 20.500 34.000 36.250 0.408 14.790 238.000 0.412 Poor Pending -chr1-27359862-27359863-T-G 11.MAP3K6.ENST00000357582.3.missense.772I/L MAP3K6 I772L 0 RDLKGDNVLI ENST00000357582.3 1 HLA-B*45:01 3 None 0 0 17128.240 17712.325 18.000 11.350 32.590 0.315 10.266 295.000 0.260 Poor Pending -chr4-154491218-154491219-G-C 310.DCHS2.ENST00000357232.10.missense.46S/C DCHS2 S46C 0 TQRCLLWLLV ENST00000357232.10 1 HLA-B*45:01 4 None 0 0 8861.125 9012.520 12.670 13.165 2.425 1.000 2.425 17.000 0.963 Poor Pending -chr19-422192-422193-G-C 993.SHC2.ENST00000264554.11.missense.525H/D SHC2 H525D 0 GMDAGQPKH ENST00000264554.11 1 HLA-A*29:02 3 None 0 0 6285.960 4157.485 5.800 5.158 8.139 0.070 0.570 115.000 0.110 Poor Pending -chr3-186164997-186164998-C-T 288.DGKG.ENST00000265022.8.missense.706E/K DGKG E706K 0 KVVGLEGAM ENST00000265022.8 1 HLA-A*29:02 1 None 0 0 6852.753 11717.510 12.000 15.500 0.612 1.000 0.612 2.000 0.518 Poor Pending -chr15-40622778-40622779-C-T 846.KNL1.ENST00000346991.9.missense.865P/S KNL1 P865S 0 DESVQKPKFS ENST00000346991.9 1 HLA-B*45:01 10 None 0 0 15822.606 11643.015 19.000 15.500 13.527 0.492 6.655 128.000 0.444 Poor Pending -chr6-1930219-1930220-G-T 354.GMDS.ENST00000380815.5.missense.218F/L GMDS F218L 0 HESPRRGANL ENST00000380815.5 1 HLA-B*45:01 10 None 0 0 8055.225 7388.880 5.450 6.150 52.423 0.020 1.048 505.000 0.211 Poor Pending -chr10-104021651-104021652-G-T 618.SLK.ENST00000369755.4.missense.1160E/D SLK E1160D 0 VEHDTQKLKE ENST00000369755.4 1 HLA-B*45:01 4 None 0 0 8577.985 7910.925 9.050 10.747 21.369 0.057 1.218 418.000 0.068 Poor Pending -chr1-183880710-183880711-A-C 78.RGL1.ENST00000304685.8.missense.209Y/S RGL1 Y209S 0 KLLDSLTRM ENST00000304685.8 1 HLA-A*29:02 5 None 0 0 5795.190 3727.115 4.750 2.700 0.461 0.286 0.132 7.000 0.300 Poor Pending -chr9-137436071-137436072-C-T 595.ENTPD8.ENST00000344119.6.missense.331G/S ENTPD8 G331S 0 SQEDCAFDGV ENST00000344119.6 1 HLA-B*45:01 1 None 0 0 6325.619 12107.929 6.550 10.400 0.236 0.500 0.118 4.000 0.346 Poor Pending -chr1-150261628-150261629-G-A 55.CA14.ENST00000369111.9.missense.83G/S CA14 G83S 0 TEPLDLHNNS ENST00000369111.9 1 HLA-B*45:01 10 None 0 0 6752.005 10119.155 6.735 7.965 0.137 0.500 0.069 4.000 0.321 Poor Pending -chr1-232805681-232805682-C-T 119.MAP10.ENST00000418460.4.missense.78P/L MAP10 P78L 0 VYPPDGPGAL ENST00000418460.4 NA HLA-A*29:02 10 None 0 0 10383.320 32128.380 12.500 44.500 1.996 0.469 0.936 32.000 0.233 Poor Pending -chr16-87417563-87417564-G-C 931.ZCCHC14.ENST00000268616.9.missense.290L/V ZCCHC14 L290V 0 ILMPSSVQT ENST00000268616.9 1 HLA-A*29:02 7 None 0 0 17165.590 6940.345 17.500 8.000 12.705 0.248 3.151 153.000 0.277 Poor Pending -chrX-9937278-9937279-G-C 1128.SHROOM2.ENST00000380913.8.missense.1245D/H SHROOM2 D1245H 0 LEKHQIKTLS ENST00000380913.8 1 HLA-B*45:01 4 None 0 0 9323.535 9436.910 6.600 5.957 0.608 1.000 0.608 4.000 1.000 Poor Pending -chr6-152325133-152325134-C-T 405.SYNE1.ENST00000367255.10.missense.5203E/K SYNE1 E5203K 0 DQKKILEDA ENST00000367255.10 1 HLA-B*45:01 3 None 0 0 12351.545 9854.275 13.500 12.895 5.739 0.286 1.641 7.000 0.323 Poor Pending -chr12-116009024-116009025-G-C 740.MED13L.ENST00000281928.9.missense.463A/G MED13L A463G 0 SLPPPGSSK ENST00000281928.9 1 HLA-A*29:02 6 None 0 0 18804.715 17050.555 14.710 13.635 77.827 0.038 2.957 586.000 0.050 Poor Pending -chrX-107601385-107601386-G-T 1197.FRMPD3.ENST00000276185.9.missense.1116S/I FRMPD3 S1116I 0 LESTPKRIKL ENST00000276185.9 5 HLA-B*45:01 8 None 0 0 8012.715 9166.905 5.700 6.450 0.100 0.500 0.050 4.000 0.391 Poor Pending -chr22-37570267-37570268-C-G 1095.LGALS2.ENST00000215886.6.missense.132E/Q LGALS2 E132Q 0 NMSSFKLKQ ENST00000215886.6 1 HLA-A*29:02 9 None 0 0 8035.340 10549.745 8.000 13.000 0.067 0.222 0.015 9.000 0.484 Poor Pending -chr14-32773880-32773881-G-T 800.AKAP6.ENST00000280979.9.missense.1192M/I AKAP6 M1192I 0 IGKESETLNV ENST00000280979.9 1 HLA-B*45:01 1 None 0 0 26663.055 19120.189 53.000 31.500 2.905 1.000 2.905 6.000 0.607 Poor Pending -chrX-68717715-68717716-G-A 1168.STARD8.ENST00000374599.8.missense.268G/S STARD8 G268S 0 AKNWAATSAS ENST00000374599.8 1 HLA-B*45:01 10 None 0 0 13320.040 13900.995 17.000 15.500 0.753 1.000 0.753 3.000 1.000 Poor Pending -chr4-176120050-176120052-AG-GA 311.WDR17.ENST00000280190.8.missense.188-189KV/KI WDR17 KV188-189KI 0 HTHQKGKIVF ENST00000280190.8 1 HLA-A*29:02 8 None 0 0 8364.835 9623.640 10.400 13.135 0.514 NA NA NA 0.508 Poor Pending -chr1-227091906-227091907-GC-G 111.CDC42BPA.ENST00000366769.7.FS.778GC/G CDC42BPA FS778 0 VLLTEENKN ENST00000366769.7 1 HLA-A*29:02 9 None 0 0 37126.609 26137.435 57.500 29.822 40.050 0.061 2.443 312.000 0.236 Poor Pending -chrX-149930830-149930831-G-A 1209.HSFX4.ENST00000457775.3.missense.243R/H HSFX4 R243H 0 QSFRHSGMW ENST00000457775.3 3 HLA-A*29:02 5 None 0 0 9111.604 13005.065 15.000 20.500 0.012 0.286 0.003 7.000 0.422 Poor Pending -chr8-132141242-132141243-C-G 546.KCNQ3.ENST00000388996.10.missense.451D/H KCNQ3 D451H 0 KLFTPLNVH ENST00000388996.10 1 HLA-A*29:02 9 None 0 0 9498.345 32680.610 5.814 45.500 0.019 1.000 0.019 2.000 0.291 Poor Pending -chr8-66813873-66813874-C-T 517.SGK3.ENST00000345714.8.missense.92A/V SGK3 A92V 0 KQRRVGLNEF ENST00000345714.8 1 HLA-A*29:02 5 None 0 0 20174.055 20565.870 21.000 21.000 2.109 0.571 1.204 7.000 0.230 Poor Pending -chrX-15355261-15355262-C-T 1132.VEGFD.ENST00000297904.4.missense.177E/K VEGFD E177K 0 SVPLTSVPK ENST00000297904.4 1 HLA-A*29:02 9 None 0 0 17753.369 29272.610 11.175 39.000 0.674 1.000 0.674 5.000 0.987 Poor Pending -chr2-219514658-219514659-C-A 213.ASIC4.ENST00000693692.1.missense.106P/T ASIC4 P106T 0 GRATGLLA ENST00000693692.1 NA HLA-B*45:01 4 None 0 0 17753.904 18582.665 14.500 14.000 0.692 0.667 0.462 6.000 0.238 Poor Pending -chr15-40622778-40622780-CC-TT 848.KNL1.ENST00000346991.9.missense.865P/L KNL1 P865L 0 SVQKPKFLK ENST00000346991.9 1 HLA-A*29:02 8 None 0 0 11386.921 15028.915 6.335 11.955 13.527 NA NA NA 0.450 Poor Pending -chr17-7588499-7588500-G-C 943.SOX15.ENST00000250055.3.missense.194Q/E SOX15 Q194E 0 PESDPRLQG ENST00000250055.3 1 HLA-B*45:01 2 None 0 0 18764.080 40942.520 13.750 66.872 0.580 0.692 0.401 13.000 0.722 Poor Pending -chr3-184239802-184239803-C-T 286.VWA5B2.ENST00000426955.6.missense.836A/V VWA5B2 A836V 0 PQVPRCHVV ENST00000426955.6 1 HLA-B*45:01 3 None 0 0 21460.449 20771.976 27.610 20.500 0.083 1.000 0.083 2.000 0.429 Poor Pending -chr2-106425181-106425182-C-T 158.RGPD3.ENST00000409886.4.missense.929E/K RGPD3 E929K 0 GFKFGISK ENST00000409886.4 1 HLA-A*29:02 8 None 0 0 21312.447 31539.423 20.096 45.500 0.014 0.364 0.005 22.000 0.139 Poor Pending +chr1-16972417-16972418-C-G 5.CROCC.ENST00000375541.10.missense.2009S/C 1 CROCC S2009C 1 SSAPFCPPS ENST00000375541.10 5 HLA-B*45:01 6 None 1 0 13779.645 13580.410 15.500 12.040 11.754 1.000 11.754 56.000 0.988 Poor Pending +chr20-35384131-35384132-C-G 1067.UQCC1.ENST00000374385.10.missense.44W/S 4 UQCC1 W44S 2 SPQMSQSRA ENST00000374385.10 1 HLA-B*45:01 1 None 4 0 18964.744 26118.567 14.500 24.500 47.722 0.327 15.605 581.000 0.434 Poor Pending +chr15-40622779-40622780-C-T 850.KNL1.ENST00000346991.9.missense.865P/L 1 KNL1 P865L 1 SVQKPKFLK ENST00000346991.9 1 HLA-A*29:02 8 None 1 0 11386.921 15028.915 6.335 11.955 13.527 0.492 6.655 128.000 0.444 Poor Pending +chr16-49281350-49281351-C-T 916.CBLN1.ENST00000219197.11.missense.39D/N 1 CBLN1 D39N 1 LEGKCLVVCN ENST00000219197.11 1 HLA-B*45:01 10 None 1 0 5071.920 5329.090 10.740 9.900 0.713 0.400 0.285 5.000 0.215 Poor Pending +chr7-92077866-92077867-G-C 439.AKAP9.ENST00000356239.8.missense.2313D/H 1 AKAP9 D2313H 1 QLKITTHNK ENST00000356239.8 1 HLA-A*29:02 7 None 1 0 20518.145 27778.605 20.500 34.000 36.250 0.408 14.790 238.000 0.412 Poor Pending +chr1-27359862-27359863-T-G 11.MAP3K6.ENST00000357582.3.missense.772I/L 1 MAP3K6 I772L 1 RDLKGDNVLI ENST00000357582.3 1 HLA-B*45:01 3 None 1 0 17128.240 17712.325 18.000 11.350 32.590 0.315 10.266 295.000 0.260 Poor Pending +chr4-154491218-154491219-G-C 310.DCHS2.ENST00000357232.10.missense.46S/C 1 DCHS2 S46C 1 TQRCLLWLLV ENST00000357232.10 1 HLA-B*45:01 4 None 1 0 8861.125 9012.520 12.670 13.165 2.425 1.000 2.425 17.000 0.963 Poor Pending +chr19-422192-422193-G-C 993.SHC2.ENST00000264554.11.missense.525H/D 1 SHC2 H525D 1 GMDAGQPKH ENST00000264554.11 1 HLA-A*29:02 3 None 1 0 6285.960 4157.485 5.800 5.158 8.139 0.070 0.570 115.000 0.110 Poor Pending +chr3-186164997-186164998-C-T 288.DGKG.ENST00000265022.8.missense.706E/K 1 DGKG E706K 1 KVVGLEGAM ENST00000265022.8 1 HLA-A*29:02 1 None 1 0 6852.753 11717.510 12.000 15.500 0.612 1.000 0.612 2.000 0.518 Poor Pending +chr15-40622778-40622779-C-T 846.KNL1.ENST00000346991.9.missense.865P/S 1 KNL1 P865S 1 DESVQKPKFS ENST00000346991.9 1 HLA-B*45:01 10 None 1 0 15822.606 11643.015 19.000 15.500 13.527 0.492 6.655 128.000 0.444 Poor Pending +chr6-1930219-1930220-G-T 354.GMDS.ENST00000380815.5.missense.218F/L 1 GMDS F218L 1 HESPRRGANL ENST00000380815.5 1 HLA-B*45:01 10 None 1 0 8055.225 7388.880 5.450 6.150 52.423 0.020 1.048 505.000 0.211 Poor Pending +chr10-104021651-104021652-G-T 618.SLK.ENST00000369755.4.missense.1160E/D 1 SLK E1160D 1 VEHDTQKLKE ENST00000369755.4 1 HLA-B*45:01 4 None 1 0 8577.985 7910.925 9.050 10.747 21.369 0.057 1.218 418.000 0.068 Poor Pending +chr1-183880710-183880711-A-C 78.RGL1.ENST00000304685.8.missense.209Y/S 1 RGL1 Y209S 1 KLLDSLTRM ENST00000304685.8 1 HLA-A*29:02 5 None 1 0 5795.190 3727.115 4.750 2.700 0.461 0.286 0.132 7.000 0.300 Poor Pending +chr9-137436071-137436072-C-T 595.ENTPD8.ENST00000344119.6.missense.331G/S 1 ENTPD8 G331S 1 SQEDCAFDGV ENST00000344119.6 1 HLA-B*45:01 1 None 1 0 6325.619 12107.929 6.550 10.400 0.236 0.500 0.118 4.000 0.346 Poor Pending +chr1-150261628-150261629-G-A 55.CA14.ENST00000369111.9.missense.83G/S 1 CA14 G83S 1 TEPLDLHNNS ENST00000369111.9 1 HLA-B*45:01 10 None 1 0 6752.005 10119.155 6.735 7.965 0.137 0.500 0.069 4.000 0.321 Poor Pending +chr1-232805681-232805682-C-T 119.MAP10.ENST00000418460.4.missense.78P/L 1 MAP10 P78L 1 VYPPDGPGAL ENST00000418460.4 NA HLA-A*29:02 10 None 1 0 10383.320 32128.380 12.500 44.500 1.996 0.469 0.936 32.000 0.233 Poor Pending +chr16-87417563-87417564-G-C 931.ZCCHC14.ENST00000268616.9.missense.290L/V 1 ZCCHC14 L290V 1 ILMPSSVQT ENST00000268616.9 1 HLA-A*29:02 7 None 1 0 17165.590 6940.345 17.500 8.000 12.705 0.248 3.151 153.000 0.277 Poor Pending +chrX-9937278-9937279-G-C 1128.SHROOM2.ENST00000380913.8.missense.1245D/H 1 SHROOM2 D1245H 1 LEKHQIKTLS ENST00000380913.8 1 HLA-B*45:01 4 None 1 0 9323.535 9436.910 6.600 5.957 0.608 1.000 0.608 4.000 1.000 Poor Pending +chr6-152325133-152325134-C-T 405.SYNE1.ENST00000367255.10.missense.5203E/K 1 SYNE1 E5203K 1 DQKKILEDA ENST00000367255.10 1 HLA-B*45:01 3 None 1 0 12351.545 9854.275 13.500 12.895 5.739 0.286 1.641 7.000 0.323 Poor Pending +chr12-116009024-116009025-G-C 740.MED13L.ENST00000281928.9.missense.463A/G 1 MED13L A463G 1 SLPPPGSSK ENST00000281928.9 1 HLA-A*29:02 6 None 1 0 18804.715 17050.555 14.710 13.635 77.827 0.038 2.957 586.000 0.050 Poor Pending +chrX-107601385-107601386-G-T 1197.FRMPD3.ENST00000276185.9.missense.1116S/I 1 FRMPD3 S1116I 1 LESTPKRIKL ENST00000276185.9 5 HLA-B*45:01 8 None 1 0 8012.715 9166.905 5.700 6.450 0.100 0.500 0.050 4.000 0.391 Poor Pending +chr22-37570267-37570268-C-G 1095.LGALS2.ENST00000215886.6.missense.132E/Q 1 LGALS2 E132Q 1 NMSSFKLKQ ENST00000215886.6 1 HLA-A*29:02 9 None 1 0 8035.340 10549.745 8.000 13.000 0.067 0.222 0.015 9.000 0.484 Poor Pending +chr14-32773880-32773881-G-T 800.AKAP6.ENST00000280979.9.missense.1192M/I 1 AKAP6 M1192I 1 IGKESETLNV ENST00000280979.9 1 HLA-B*45:01 1 None 1 0 26663.055 19120.189 53.000 31.500 2.905 1.000 2.905 6.000 0.607 Poor Pending +chrX-68717715-68717716-G-A 1168.STARD8.ENST00000374599.8.missense.268G/S 1 STARD8 G268S 1 AKNWAATSAS ENST00000374599.8 1 HLA-B*45:01 10 None 1 0 13320.040 13900.995 17.000 15.500 0.753 1.000 0.753 3.000 1.000 Poor Pending +chr4-176120050-176120052-AG-GA 311.WDR17.ENST00000280190.8.missense.188-189KV/KI 1 WDR17 KV188-189KI 1 HTHQKGKIVF ENST00000280190.8 1 HLA-A*29:02 8 None 1 0 8364.835 9623.640 10.400 13.135 0.514 NA NA NA 0.508 Poor Pending +chr1-227091906-227091907-GC-G 111.CDC42BPA.ENST00000366769.7.FS.778GC/G 1 CDC42BPA FS778 1 VLLTEENKN ENST00000366769.7 1 HLA-A*29:02 9 None 1 0 37126.609 26137.435 57.500 29.822 40.050 0.061 2.443 312.000 0.236 Poor Pending +chrX-149930830-149930831-G-A 1209.HSFX4.ENST00000457775.3.missense.243R/H 1 HSFX4 R243H 1 QSFRHSGMW ENST00000457775.3 3 HLA-A*29:02 5 None 1 0 9111.604 13005.065 15.000 20.500 0.012 0.286 0.003 7.000 0.422 Poor Pending +chr8-132141242-132141243-C-G 546.KCNQ3.ENST00000388996.10.missense.451D/H 1 KCNQ3 D451H 1 KLFTPLNVH ENST00000388996.10 1 HLA-A*29:02 9 None 1 0 9498.345 32680.610 5.814 45.500 0.019 1.000 0.019 2.000 0.291 Poor Pending +chr8-66813873-66813874-C-T 517.SGK3.ENST00000345714.8.missense.92A/V 1 SGK3 A92V 1 KQRRVGLNEF ENST00000345714.8 1 HLA-A*29:02 5 None 1 0 20174.055 20565.870 21.000 21.000 2.109 0.571 1.204 7.000 0.230 Poor Pending +chrX-15355261-15355262-C-T 1132.VEGFD.ENST00000297904.4.missense.177E/K 1 VEGFD E177K 1 SVPLTSVPK ENST00000297904.4 1 HLA-A*29:02 9 None 1 0 17753.369 29272.610 11.175 39.000 0.674 1.000 0.674 5.000 0.987 Poor Pending +chr2-219514658-219514659-C-A 213.ASIC4.ENST00000693692.1.missense.106P/T 1 ASIC4 P106T 1 GRATGLLA ENST00000693692.1 NA HLA-B*45:01 4 None 1 0 17753.904 18582.665 14.500 14.000 0.692 0.667 0.462 6.000 0.238 Poor Pending +chr15-40622778-40622780-CC-TT 848.KNL1.ENST00000346991.9.missense.865P/L 1 KNL1 P865L 1 SVQKPKFLK ENST00000346991.9 1 HLA-A*29:02 8 None 1 0 11386.921 15028.915 6.335 11.955 13.527 NA NA NA 0.450 Poor Pending +chr17-7588499-7588500-G-C 943.SOX15.ENST00000250055.3.missense.194Q/E 1 SOX15 Q194E 1 PESDPRLQG ENST00000250055.3 1 HLA-B*45:01 2 None 1 0 18764.080 40942.520 13.750 66.872 0.580 0.692 0.401 13.000 0.722 Poor Pending +chr3-184239802-184239803-C-T 286.VWA5B2.ENST00000426955.6.missense.836A/V 1 VWA5B2 A836V 1 PQVPRCHVV ENST00000426955.6 1 HLA-B*45:01 3 None 1 0 21460.449 20771.976 27.610 20.500 0.083 1.000 0.083 2.000 0.429 Poor Pending +chr2-106425181-106425182-C-T 158.RGPD3.ENST00000409886.4.missense.929E/K 1 RGPD3 E929K 1 GFKFGISK ENST00000409886.4 1 HLA-A*29:02 8 None 1 0 21312.447 31539.423 20.096 45.500 0.014 0.364 0.005 22.000 0.139 Poor Pending chr11-20638483-20638484-T-A 691.SLC6A5.ENST00000525748.6.missense.632V/E 6 4 SLC6A5 V632E 1 YMFQLEDTY ENST00000525748.6 1 HLA-A*29:02 6 None 10 2 11.735 9.050 0.107 0.065 0.006 0.000 0.000 1.000 0.452 NoExpr Pending chr20-59301546-59301547-G-T 1076.EDN3.ENST00000337938.7.missense.64G/W 3 EDN3 G64W 7 GEWTVAPTA ENST00000337938.7 1 HLA-B*45:01 3 None 3 1 42.900 80.960 0.050 0.095 0.019 0.000 0.000 0.000 0.220 NoExpr Pending chr11-59364558-59364559-T-A 697.OR5AN1.ENST00000313940.2.missense.34V/E 6 2 OR5AN1 V34E 3 VLFTIFLEIY ENST00000313940.2 NA HLA-A*29:02 8 None 8 3 53.390 63.505 0.290 0.240 0.154 0.000 0.000 0.000 0.116 NoExpr Pending @@ -314,52 +314,52 @@ chr21-43172070-43172071-G-C 1085.CRYAA.ENST00000291554.6.missense.105D/H 1 CRYA chr6-55351464-55351465-G-C 390.GFRAL.ENST00000340465.2.missense.195D/H 1 GFRAL D195H 1 AFCDCAQSH ENST00000340465.2 1 HLA-A*29:02 9 None 1 0 4713.925 22449.227 6.300 32.000 0.013 0.000 0.000 0.000 0.511 NoExpr Pending chr5-136274698-136274699-C-T 339.TRPC7.ENST00000513104.6.missense.368A/T 3 TRPC7 A368T 3 PFLAITYWI ENST00000513104.6 5 HLA-A*29:02 6 None 3 1 4831.515 5173.105 5.850 6.350 0.005 0.000 0.000 0.000 0.366 NoExpr Pending chr16-67239382-67239411-GCTGCTCTTCCAGGGACAGCTCGGTGTCCA-G 923.FHOD1.ENST00000258201.9.FS.82-91GCTGCTCTTCCAGGGACAGCTCGGTGTCCA/G 1 FHOD1 FS82-91 2 YYPGDAGGLL ENST00000258201.9 1 HLA-A*29:02 3-10 None 1 0 4914.115 NA 4.179 NA 20.928 0.000 0.000 131.000 0.133 NoExpr Pending -chr1-160876800-160876801-C-T 72.ITLN1.ENST00000326245.4.missense.269G/R ITLN1 G269R 0 TEHHCIGGRG ENST00000326245.4 1 HLA-B*45:01 9 None 0 0 5135.530 3227.243 6.690 5.500 0.000 0.000 0.000 0.000 0.250 NoExpr Pending -chr4-5988666-5988667-T-A 292.C4orf50.ENST00000531445.3.missense.1127M/L C4orf50 M1127L 0 REHLQGKAKL ENST00000531445.3 5 HLA-B*45:01 10 None 0 0 5147.705 7818.115 3.000 3.200 0.025 0.000 0.000 0.000 0.946 NoExpr Pending -chr19-13931970-13931971-A-G 1013.PODNL1.ENST00000588872.3.missense.523F/L PODNL1 F523L 0 LLRANRLHM ENST00000588872.3 3 HLA-A*29:02 1 None 0 0 5278.495 2834.438 6.200 4.000 7.123 0.000 0.000 12.000 0.142 NoExpr Pending -chr5-141123692-141123693-G-C 340.PCDHB4.ENST00000194152.4.missense.565Q/H PCDHB4 Q565H 0 SPFVLYPLH ENST00000194152.4 NA HLA-A*29:02 9 None 0 0 5358.045 12281.800 5.700 20.876 1.436 0.000 0.000 20.000 0.307 NoExpr Pending -chr3-58210851-58210852-G-C 238.DNASE1L3.ENST00000394549.7.missense.19L/V DNASE1L3 L19V 0 AVAMRICSF ENST00000394549.7 1 HLA-A*29:02 2 None 0 0 5422.830 6990.685 6.285 6.880 0.181 0.000 0.000 0.000 1.000 NoExpr Pending -chrX-135721216-135721217-G-A 1201.CT45A1.ENST00000594117.4.missense.120R/Q CT45A1 R120Q 0 QEINADIKR ENST00000594117.4 1 HLA-B*45:01 1 None 0 0 5632.290 6664.705 7.330 6.980 0.000 0.000 0.000 0.000 0.582 NoExpr Pending -chrX-135779451-135779452-C-T 1204.CT45A5.ENST00000617203.1.missense.120R/Q CT45A5 R120Q 0 QEINADIKR ENST00000617203.1 1 HLA-B*45:01 1 None 0 0 5632.290 6664.705 7.330 6.980 0.000 0.000 0.000 0.000 0.577 NoExpr Pending -chrX-135796713-135796714-C-T 1205.CT45A6.ENST00000612878.4.missense.120R/Q CT45A6 R120Q 0 QEINADIKR ENST00000612878.4 1 HLA-B*45:01 1 None 0 0 5632.290 6664.705 7.330 6.980 0.102 0.000 0.000 0.000 0.554 NoExpr Pending -chr4-110559663-110559664-G-C 303.ENPEP.ENST00000265162.10.missense.887R/T ENPEP R887T 0 YTLNNTNLGR ENST00000265162.10 1 HLA-A*29:02 6 None 0 0 5968.100 7481.305 5.750 8.500 0.032 0.000 0.000 0.000 0.239 NoExpr Pending -chr1-111727105-111727106-G-T 50.INKA2.ENST00000357260.6.missense.252S/R INKA2 S252R 0 RLSKGSGHF ENST00000357260.6 1 HLA-A*29:02 1 None 0 0 6086.820 3915.305 4.800 3.055 2.143 0.000 0.000 29.000 0.063 NoExpr Pending -chrX-32389609-32389610-C-T 1133.DMD.ENST00000357033.9.missense.1470R/H DMD R1470H 0 FEQHLQESKM ENST00000357033.9 1 HLA-B*45:01 4 None 0 0 6165.655 5931.815 4.450 4.600 3.178 0.000 0.000 0.000 1.000 NoExpr Pending -chr1-22660990-22660991-G-A 9.C1QB.ENST00000509305.6.missense.121A/T C1QB A121T 0 ATQKITFSA ENST00000509305.6 1 HLA-B*45:01 6 None 0 0 6294.760 5577.395 4.772 5.010 0.000 0.000 0.000 0.000 0.984 NoExpr Pending -chr4-121932625-121932626-C-A 306.TRPC3.ENST00000379645.8.missense.211C/F TRPC3 C211F 0 FEQELQDDDF ENST00000379645.8 1 HLA-B*45:01 1 None 0 0 6835.385 4604.125 7.350 4.500 0.068 0.000 0.000 0.000 0.300 NoExpr Pending -chr8-132948805-132948806-C-G 551.TG.ENST00000220616.9.missense.1755P/R TG P1755R 0 LLSSRSVLL ENST00000220616.9 1 HLA-A*29:02 5 None 0 0 7171.850 5825.865 9.075 7.300 0.721 0.000 0.000 0.000 0.992 NoExpr Pending -chr9-138120681-138120682-G-A 600.CACNA1B.ENST00000371372.6.missense.2097G/D CACNA1B G2097D 0 GEGPTDCRR ENST00000371372.6 5 HLA-B*45:01 6 None 0 0 7694.035 7362.530 11.815 9.460 0.154 0.000 0.000 0.000 0.276 NoExpr Pending -chr11-46876561-46876562-C-T 694.LRP4.ENST00000378623.6.missense.1147R/Q LRP4 R1147Q 0 YWTDTGTNQI ENST00000378623.6 1 HLA-A*29:02 9 None 0 0 8002.015 8532.020 7.700 7.800 0.268 0.000 0.000 2.000 0.421 NoExpr Pending -chr1-16006133-16006134-G-T 4.SRARP.ENST00000329454.2.missense.100G/W SRARP G100W 0 PMGWGCLAQ ENST00000329454.2 1 HLA-A*29:02 4 None 0 0 8033.180 10860.410 17.445 16.060 0.082 0.000 0.000 0.000 1.000 NoExpr Pending -chr14-94382907-94382908-C-G 823.SERPINA1.ENST00000355814.8.missense.110E/D SERPINA1 E110D 0 LEGLNFNLTD ENST00000355814.8 1 HLA-B*45:01 10 None 0 0 8280.080 8248.135 10.800 10.250 4.892 0.000 0.000 0.000 0.180 NoExpr Pending -chr4-176120051-176120052-G-A 315.WDR17.ENST00000280190.8.missense.189V/I WDR17 V189I 0 HTHQKGKIVF ENST00000280190.8 1 HLA-A*29:02 8 None 0 0 8364.835 9623.640 10.400 13.135 0.514 0.000 0.000 2.000 0.489 NoExpr Pending -chr20-2312957-2312958-C-T 1051.TGM3.ENST00000381458.6.missense.201R/C TGM3 R201C 0 CDAATDVA ENST00000381458.6 1 HLA-B*45:01 1 None 0 0 8704.815 9939.463 7.043 6.050 0.000 0.000 0.000 0.000 0.650 NoExpr Pending -chrX-149548665-149548666-C-T 1208.HSFX3.ENST00000431993.4.missense.243R/H HSFX3 R243H 0 QSFRHSGMW ENST00000431993.4 3 HLA-A*29:02 5 None 0 0 9111.604 13005.065 15.000 20.500 0.012 0.000 0.000 0.000 0.610 NoExpr Pending -chr2-106830076-106830077-G-C 159.ST6GAL2.ENST00000361686.8.missense.436S/C ST6GAL2 S436C 0 CGFIGILIM ENST00000361686.8 1 HLA-A*29:02 1 None 0 0 9240.814 7222.511 13.500 7.442 0.080 0.000 0.000 1.000 0.694 NoExpr Pending -chr11-1078020-1078022-CTA-C 674.MUC2.ENST00000675028.1.FS.178CTA/C MUC2 FS178 0 DYNGLQSFRI ENST00000675028.1 NA HLA-A*29:02 8-10 None 0 0 9494.880 21985.295 9.462 27.295 0.001 0.000 0.000 0.000 0.918 NoExpr Pending -chr2-113482183-113482183-G-GA 169.CBWD2.ENST00000259199.9.FS.257-258G/GA CBWD2 FS257-258 0 LQKKTSACA ENST00000259199.9 1 HLA-B*45:01 5-9 None 0 0 9542.735 NA 5.100 NA 3.384 0.000 0.000 62.000 0.113 NoExpr Pending -chr19-38802098-38802099-G-A 1035.LGALS4.ENST00000307751.9.missense.240R/C LGALS4 R240C 0 IALHINPCM ENST00000307751.9 1 HLA-A*29:02 8 None 0 0 9632.405 8072.775 7.900 6.800 0.232 0.000 0.000 0.000 1.000 NoExpr Pending -chr16-16387708-16387709-G-A 904.NPIPA7.ENST00000530217.2.missense.114E/K NPIPA7 E114K 0 RQVKTKVRA ENST00000530217.2 5 HLA-B*45:01 4 None 0 0 9667.445 5838.793 7.000 5.500 8.705 0.000 0.000 238.000 0.254 NoExpr Pending -chr16-18324187-18324188-C-T 905.NPIPA8.ENST00000525596.5.missense.114E/K NPIPA8 E114K 0 RQVKTKVRA ENST00000525596.5 1 HLA-B*45:01 4 None 0 0 9667.445 5838.793 7.000 5.500 2.994 0.000 0.000 177.000 0.216 NoExpr Pending -chr2-94874875-94874876-T-A 152.TEKT4.ENST00000295201.5.missense.272C/S TEKT4 C272S 0 RVLVDSILR ENST00000295201.5 1 HLA-A*29:02 6 None 0 0 10401.293 9015.341 9.247 11.500 0.614 0.000 0.000 0.000 0.446 NoExpr Pending -chr1-13318693-13318694-G-A 3.PRAMEF15.ENST00000376152.2.missense.96R/H PRAMEF15 R96H 0 LLTQGVHPR ENST00000376152.2 1 HLA-A*29:02 7 None 0 0 11195.120 22722.072 10.630 20.500 0.000 0.000 0.000 0.000 0.098 NoExpr Pending -chr16-72128664-72128665-T-G 925.PMFBP1.ENST00000237353.15.missense.694N/H PMFBP1 N694H 0 IQDLHKEIA ENST00000237353.15 1 HLA-B*45:01 5 None 0 0 11322.405 12593.730 12.000 14.000 0.380 0.000 0.000 0.000 0.065 NoExpr Pending -chr8-123220221-123220221-A-AGGGCTAC 527.C8orf76.ENST00000276704.6.FS.342A/AGGGCTAC C8orf76 FS342 0 CLGDCILRR ENST00000276704.6 1 HLA-A*29:02 1-9 None 0 0 11428.675 NA 12.000 NA 45.915 0.000 0.000 344.000 0.724 NoExpr Pending -chr3-156291991-156291992-G-T 269.KCNAB1.ENST00000302490.12.missense.29A/S KCNAB1 A29S 0 TSPNVVNAA ENST00000302490.12 1 HLA-B*45:01 2 None 0 0 11515.824 11127.270 15.104 13.905 0.000 0.000 0.000 0.000 0.064 NoExpr Pending -chr8-23368189-23368210-TGGCCACGTTGGCGGGGGCCTG-T 488.LOXL2.ENST00000389131.8.inframe_del.48-54QAPANVA/- LOXL2 QAPANVA48-54- 0 YHQPKIQLRL ENST00000389131.8 1 HLA-A*29:02 4-5 None 0 0 11628.085 23517.365 12.116 22.293 102.877 0.000 0.000 110.000 0.706 NoExpr Pending -chr3-39188114-39188115-A-T 229.XIRP1.ENST00000340369.4.missense.444L/H XIRP1 L444H 0 KTFKNHFET ENST00000340369.4 1 HLA-A*29:02 6 None 0 0 11756.050 14047.080 11.040 12.200 0.042 0.000 0.000 0.000 0.661 NoExpr Pending -chr5-134703847-134703848-G-T 333.SEC24A.ENST00000398844.7.missense.786A/S SEC24A A786S 0 AGYSVQMSV ENST00000398844.7 2 HLA-B*45:01 4 None 0 0 11899.845 10023.730 11.400 9.700 10.713 0.000 0.000 133.000 0.053 NoExpr Pending -chr6-47000271-47000272-C-T 389.ADGRF1.ENST00000371253.7.missense.895G/R ADGRF1 G895R 0 GHYAFSHTR ENST00000371253.7 1 HLA-A*29:02 9 None 0 0 12229.660 20282.765 10.690 30.500 0.655 0.000 0.000 0.000 0.491 NoExpr Pending -chr21-44330789-44330813-AGGCAGCCGCGGCCCCTAGCGGCCC-A 1088.CFAP410.ENST00000397956.7.inframe_del.217-224GPLGAAAA/- CFAP410 GPLGAAAA217-224- 0 SHRGRVSGSA ENST00000397956.7 1 HLA-B*45:01 8-9 None 0 0 12678.690 32162.840 12.000 44.000 6.570 0.000 0.000 18.000 0.376 NoExpr Pending -chr15-94399982-94399983-G-T 893.MCTP2.ENST00000357742.10.missense.651K/N MCTP2 K651N 0 VEDSRNLS ENST00000357742.10 1 HLA-B*45:01 6 None 0 0 13471.106 14118.362 7.850 12.500 0.138 0.000 0.000 0.000 0.203 NoExpr Pending -chr7-39339738-39339739-G-C 420.POU6F2.ENST00000518318.7.missense.232Q/H POU6F2 Q232H 0 STNHHPQPA ENST00000518318.7 1 HLA-B*45:01 4 None 0 0 13649.930 13332.405 6.500 6.350 0.273 0.000 0.000 0.000 0.299 NoExpr Pending -chr7-47833094-47833095-G-A 421.PKD1L1.ENST00000289672.7.missense.2111T/I PKD1L1 T2111I 0 SHCCPPHIQA ENST00000289672.7 1 HLA-B*45:01 8 None 0 0 13887.088 13677.090 8.200 8.665 0.696 0.000 0.000 0.000 0.322 NoExpr Pending -chr15-84036950-84036951-A-T 891.ADAMTSL3.ENST00000286744.10.missense.1645I/F ADAMTSL3 I1645F 0 PFSWRHCLG ENST00000286744.10 1 HLA-A*29:02 2 None 0 0 14164.925 28748.631 27.315 51.500 2.043 0.000 0.000 0.000 0.366 NoExpr Pending -chr3-52517959-52517960-A-C 234.STAB1.ENST00000321725.10.missense.1573H/P STAB1 H1573P 0 CTCDTAPTV ENST00000321725.10 1 HLA-A*29:02 7 None 0 0 14724.066 10839.774 21.000 17.000 0.090 0.000 0.000 0.000 1.000 NoExpr Pending -chr8-138737576-138737577-C-A 554.COL22A1.ENST00000303045.11.missense.696G/W COL22A1 G696W 0 GLQGLRWKK ENST00000303045.11 1 HLA-A*29:02 7 None 0 0 14844.085 22610.353 15.630 29.000 0.308 0.000 0.000 2.000 0.200 NoExpr Pending -chr16-28652309-28652310-C-T 911.NPIPB8.ENST00000526428.1.missense.26T/M NPIPB8 T26M 0 TMKINRHDK ENST00000526428.1 3 HLA-A*29:02 2 None 0 0 15526.305 26727.390 20.000 40.500 0.703 0.000 0.000 5.000 0.107 NoExpr Pending -chr16-28766434-28766435-C-T 915.NPIPB9.ENST00000550983.1.missense.179T/M NPIPB9 T179M 0 TMKINRHDK ENST00000550983.1 1 HLA-A*29:02 2 None 0 0 15526.305 26727.390 20.000 40.500 1.874 0.000 0.000 10.000 0.117 NoExpr Pending -chr3-44242057-44242058-G-A 231.TOPAZ1.ENST00000309765.4.missense.2R/Q TOPAZ1 R2Q 0 MQRPPPLGPT ENST00000309765.4 5 HLA-B*45:01 2 None 0 0 18453.590 24155.798 18.500 30.500 0.005 0.000 0.000 0.000 0.307 NoExpr Pending -chr14-26448937-26448938-G-C 794.NOVA1.ENST00000539517.7.missense.182T/R NOVA1 T182R 0 IIVPNSRAGL ENST00000539517.7 1 HLA-A*29:02 7 None 0 0 19554.959 15264.273 23.096 18.500 0.694 0.000 0.000 2.000 0.462 NoExpr Pending -chr6-10801907-10801908-C-G 362.MAK.ENST00000474039.5.missense.272R/P MAK R272P 0 NWDPKKPPTA ENST00000474039.5 1 HLA-B*45:01 7 None 0 0 22818.242 29208.615 25.500 33.000 0.038 0.000 0.000 1.000 0.323 NoExpr Pending -chr1-196995755-196995756-A-G 80.CFHR5.ENST00000256785.5.missense.216N/S CFHR5 N216S 0 QLSSGEVK ENST00000256785.5 1 HLA-A*29:02 4 None 0 0 26128.002 26691.050 32.500 34.000 0.000 0.000 0.000 0.000 0.287 NoExpr Pending +chr1-160876800-160876801-C-T 72.ITLN1.ENST00000326245.4.missense.269G/R 1 ITLN1 G269R 1 TEHHCIGGRG ENST00000326245.4 1 HLA-B*45:01 9 None 1 0 5135.530 3227.243 6.690 5.500 0.000 0.000 0.000 0.000 0.250 NoExpr Pending +chr4-5988666-5988667-T-A 292.C4orf50.ENST00000531445.3.missense.1127M/L 1 C4orf50 M1127L 1 REHLQGKAKL ENST00000531445.3 5 HLA-B*45:01 10 None 1 0 5147.705 7818.115 3.000 3.200 0.025 0.000 0.000 0.000 0.946 NoExpr Pending +chr19-13931970-13931971-A-G 1013.PODNL1.ENST00000588872.3.missense.523F/L 1 PODNL1 F523L 1 LLRANRLHM ENST00000588872.3 3 HLA-A*29:02 1 None 1 0 5278.495 2834.438 6.200 4.000 7.123 0.000 0.000 12.000 0.142 NoExpr Pending +chr5-141123692-141123693-G-C 340.PCDHB4.ENST00000194152.4.missense.565Q/H 1 PCDHB4 Q565H 1 SPFVLYPLH ENST00000194152.4 NA HLA-A*29:02 9 None 1 0 5358.045 12281.800 5.700 20.876 1.436 0.000 0.000 20.000 0.307 NoExpr Pending +chr3-58210851-58210852-G-C 238.DNASE1L3.ENST00000394549.7.missense.19L/V 1 DNASE1L3 L19V 1 AVAMRICSF ENST00000394549.7 1 HLA-A*29:02 2 None 1 0 5422.830 6990.685 6.285 6.880 0.181 0.000 0.000 0.000 1.000 NoExpr Pending +chrX-135721216-135721217-G-A 1201.CT45A1.ENST00000594117.4.missense.120R/Q 1 CT45A1 R120Q 1 QEINADIKR ENST00000594117.4 1 HLA-B*45:01 1 None 1 0 5632.290 6664.705 7.330 6.980 0.000 0.000 0.000 0.000 0.582 NoExpr Pending +chrX-135779451-135779452-C-T 1204.CT45A5.ENST00000617203.1.missense.120R/Q 1 CT45A5 R120Q 1 QEINADIKR ENST00000617203.1 1 HLA-B*45:01 1 None 1 0 5632.290 6664.705 7.330 6.980 0.000 0.000 0.000 0.000 0.577 NoExpr Pending +chrX-135796713-135796714-C-T 1205.CT45A6.ENST00000612878.4.missense.120R/Q 1 CT45A6 R120Q 1 QEINADIKR ENST00000612878.4 1 HLA-B*45:01 1 None 1 0 5632.290 6664.705 7.330 6.980 0.102 0.000 0.000 0.000 0.554 NoExpr Pending +chr4-110559663-110559664-G-C 303.ENPEP.ENST00000265162.10.missense.887R/T 1 ENPEP R887T 1 YTLNNTNLGR ENST00000265162.10 1 HLA-A*29:02 6 None 1 0 5968.100 7481.305 5.750 8.500 0.032 0.000 0.000 0.000 0.239 NoExpr Pending +chr1-111727105-111727106-G-T 50.INKA2.ENST00000357260.6.missense.252S/R 1 INKA2 S252R 1 RLSKGSGHF ENST00000357260.6 1 HLA-A*29:02 1 None 1 0 6086.820 3915.305 4.800 3.055 2.143 0.000 0.000 29.000 0.063 NoExpr Pending +chrX-32389609-32389610-C-T 1133.DMD.ENST00000357033.9.missense.1470R/H 1 DMD R1470H 1 FEQHLQESKM ENST00000357033.9 1 HLA-B*45:01 4 None 1 0 6165.655 5931.815 4.450 4.600 3.178 0.000 0.000 0.000 1.000 NoExpr Pending +chr1-22660990-22660991-G-A 9.C1QB.ENST00000509305.6.missense.121A/T 1 C1QB A121T 1 ATQKITFSA ENST00000509305.6 1 HLA-B*45:01 6 None 1 0 6294.760 5577.395 4.772 5.010 0.000 0.000 0.000 0.000 0.984 NoExpr Pending +chr4-121932625-121932626-C-A 306.TRPC3.ENST00000379645.8.missense.211C/F 1 TRPC3 C211F 1 FEQELQDDDF ENST00000379645.8 1 HLA-B*45:01 1 None 1 0 6835.385 4604.125 7.350 4.500 0.068 0.000 0.000 0.000 0.300 NoExpr Pending +chr8-132948805-132948806-C-G 551.TG.ENST00000220616.9.missense.1755P/R 1 TG P1755R 1 LLSSRSVLL ENST00000220616.9 1 HLA-A*29:02 5 None 1 0 7171.850 5825.865 9.075 7.300 0.721 0.000 0.000 0.000 0.992 NoExpr Pending +chr9-138120681-138120682-G-A 600.CACNA1B.ENST00000371372.6.missense.2097G/D 1 CACNA1B G2097D 1 GEGPTDCRR ENST00000371372.6 5 HLA-B*45:01 6 None 1 0 7694.035 7362.530 11.815 9.460 0.154 0.000 0.000 0.000 0.276 NoExpr Pending +chr11-46876561-46876562-C-T 694.LRP4.ENST00000378623.6.missense.1147R/Q 1 LRP4 R1147Q 1 YWTDTGTNQI ENST00000378623.6 1 HLA-A*29:02 9 None 1 0 8002.015 8532.020 7.700 7.800 0.268 0.000 0.000 2.000 0.421 NoExpr Pending +chr1-16006133-16006134-G-T 4.SRARP.ENST00000329454.2.missense.100G/W 1 SRARP G100W 1 PMGWGCLAQ ENST00000329454.2 1 HLA-A*29:02 4 None 1 0 8033.180 10860.410 17.445 16.060 0.082 0.000 0.000 0.000 1.000 NoExpr Pending +chr14-94382907-94382908-C-G 823.SERPINA1.ENST00000355814.8.missense.110E/D 1 SERPINA1 E110D 1 LEGLNFNLTD ENST00000355814.8 1 HLA-B*45:01 10 None 1 0 8280.080 8248.135 10.800 10.250 4.892 0.000 0.000 0.000 0.180 NoExpr Pending +chr4-176120051-176120052-G-A 315.WDR17.ENST00000280190.8.missense.189V/I 1 WDR17 V189I 1 HTHQKGKIVF ENST00000280190.8 1 HLA-A*29:02 8 None 1 0 8364.835 9623.640 10.400 13.135 0.514 0.000 0.000 2.000 0.489 NoExpr Pending +chr20-2312957-2312958-C-T 1051.TGM3.ENST00000381458.6.missense.201R/C 1 TGM3 R201C 1 CDAATDVA ENST00000381458.6 1 HLA-B*45:01 1 None 1 0 8704.815 9939.463 7.043 6.050 0.000 0.000 0.000 0.000 0.650 NoExpr Pending +chrX-149548665-149548666-C-T 1208.HSFX3.ENST00000431993.4.missense.243R/H 1 HSFX3 R243H 1 QSFRHSGMW ENST00000431993.4 3 HLA-A*29:02 5 None 1 0 9111.604 13005.065 15.000 20.500 0.012 0.000 0.000 0.000 0.610 NoExpr Pending +chr2-106830076-106830077-G-C 159.ST6GAL2.ENST00000361686.8.missense.436S/C 1 ST6GAL2 S436C 1 CGFIGILIM ENST00000361686.8 1 HLA-A*29:02 1 None 1 0 9240.814 7222.511 13.500 7.442 0.080 0.000 0.000 1.000 0.694 NoExpr Pending +chr11-1078020-1078022-CTA-C 674.MUC2.ENST00000675028.1.FS.178CTA/C 1 MUC2 FS178 1 DYNGLQSFRI ENST00000675028.1 NA HLA-A*29:02 8-10 None 1 0 9494.880 21985.295 9.462 27.295 0.001 0.000 0.000 0.000 0.918 NoExpr Pending +chr2-113482183-113482183-G-GA 169.CBWD2.ENST00000259199.9.FS.257-258G/GA 1 CBWD2 FS257-258 1 LQKKTSACA ENST00000259199.9 1 HLA-B*45:01 5-9 None 1 0 9542.735 NA 5.100 NA 3.384 0.000 0.000 62.000 0.113 NoExpr Pending +chr19-38802098-38802099-G-A 1035.LGALS4.ENST00000307751.9.missense.240R/C 1 LGALS4 R240C 1 IALHINPCM ENST00000307751.9 1 HLA-A*29:02 8 None 1 0 9632.405 8072.775 7.900 6.800 0.232 0.000 0.000 0.000 1.000 NoExpr Pending +chr16-16387708-16387709-G-A 904.NPIPA7.ENST00000530217.2.missense.114E/K 1 NPIPA7 E114K 1 RQVKTKVRA ENST00000530217.2 5 HLA-B*45:01 4 None 1 0 9667.445 5838.793 7.000 5.500 8.705 0.000 0.000 238.000 0.254 NoExpr Pending +chr16-18324187-18324188-C-T 905.NPIPA8.ENST00000525596.5.missense.114E/K 1 NPIPA8 E114K 1 RQVKTKVRA ENST00000525596.5 1 HLA-B*45:01 4 None 1 0 9667.445 5838.793 7.000 5.500 2.994 0.000 0.000 177.000 0.216 NoExpr Pending +chr2-94874875-94874876-T-A 152.TEKT4.ENST00000295201.5.missense.272C/S 1 TEKT4 C272S 1 RVLVDSILR ENST00000295201.5 1 HLA-A*29:02 6 None 1 0 10401.293 9015.341 9.247 11.500 0.614 0.000 0.000 0.000 0.446 NoExpr Pending +chr1-13318693-13318694-G-A 3.PRAMEF15.ENST00000376152.2.missense.96R/H 1 PRAMEF15 R96H 1 LLTQGVHPR ENST00000376152.2 1 HLA-A*29:02 7 None 1 0 11195.120 22722.072 10.630 20.500 0.000 0.000 0.000 0.000 0.098 NoExpr Pending +chr16-72128664-72128665-T-G 925.PMFBP1.ENST00000237353.15.missense.694N/H 1 PMFBP1 N694H 1 IQDLHKEIA ENST00000237353.15 1 HLA-B*45:01 5 None 1 0 11322.405 12593.730 12.000 14.000 0.380 0.000 0.000 0.000 0.065 NoExpr Pending +chr8-123220221-123220221-A-AGGGCTAC 527.C8orf76.ENST00000276704.6.FS.342A/AGGGCTAC 1 C8orf76 FS342 1 CLGDCILRR ENST00000276704.6 1 HLA-A*29:02 1-9 None 1 0 11428.675 NA 12.000 NA 45.915 0.000 0.000 344.000 0.724 NoExpr Pending +chr3-156291991-156291992-G-T 269.KCNAB1.ENST00000302490.12.missense.29A/S 1 KCNAB1 A29S 1 TSPNVVNAA ENST00000302490.12 1 HLA-B*45:01 2 None 1 0 11515.824 11127.270 15.104 13.905 0.000 0.000 0.000 0.000 0.064 NoExpr Pending +chr8-23368189-23368210-TGGCCACGTTGGCGGGGGCCTG-T 488.LOXL2.ENST00000389131.8.inframe_del.48-54QAPANVA/- 1 LOXL2 QAPANVA48-54- 1 YHQPKIQLRL ENST00000389131.8 1 HLA-A*29:02 4-5 None 1 0 11628.085 23517.365 12.116 22.293 102.877 0.000 0.000 110.000 0.706 NoExpr Pending +chr3-39188114-39188115-A-T 229.XIRP1.ENST00000340369.4.missense.444L/H 1 XIRP1 L444H 1 KTFKNHFET ENST00000340369.4 1 HLA-A*29:02 6 None 1 0 11756.050 14047.080 11.040 12.200 0.042 0.000 0.000 0.000 0.661 NoExpr Pending +chr5-134703847-134703848-G-T 333.SEC24A.ENST00000398844.7.missense.786A/S 1 SEC24A A786S 1 AGYSVQMSV ENST00000398844.7 2 HLA-B*45:01 4 None 1 0 11899.845 10023.730 11.400 9.700 10.713 0.000 0.000 133.000 0.053 NoExpr Pending +chr6-47000271-47000272-C-T 389.ADGRF1.ENST00000371253.7.missense.895G/R 1 ADGRF1 G895R 1 GHYAFSHTR ENST00000371253.7 1 HLA-A*29:02 9 None 1 0 12229.660 20282.765 10.690 30.500 0.655 0.000 0.000 0.000 0.491 NoExpr Pending +chr21-44330789-44330813-AGGCAGCCGCGGCCCCTAGCGGCCC-A 1088.CFAP410.ENST00000397956.7.inframe_del.217-224GPLGAAAA/- 1 CFAP410 GPLGAAAA217-224- 1 SHRGRVSGSA ENST00000397956.7 1 HLA-B*45:01 8-9 None 1 0 12678.690 32162.840 12.000 44.000 6.570 0.000 0.000 18.000 0.376 NoExpr Pending +chr15-94399982-94399983-G-T 893.MCTP2.ENST00000357742.10.missense.651K/N 1 MCTP2 K651N 1 VEDSRNLS ENST00000357742.10 1 HLA-B*45:01 6 None 1 0 13471.106 14118.362 7.850 12.500 0.138 0.000 0.000 0.000 0.203 NoExpr Pending +chr7-39339738-39339739-G-C 420.POU6F2.ENST00000518318.7.missense.232Q/H 1 POU6F2 Q232H 1 STNHHPQPA ENST00000518318.7 1 HLA-B*45:01 4 None 1 0 13649.930 13332.405 6.500 6.350 0.273 0.000 0.000 0.000 0.299 NoExpr Pending +chr7-47833094-47833095-G-A 421.PKD1L1.ENST00000289672.7.missense.2111T/I 1 PKD1L1 T2111I 1 SHCCPPHIQA ENST00000289672.7 1 HLA-B*45:01 8 None 1 0 13887.088 13677.090 8.200 8.665 0.696 0.000 0.000 0.000 0.322 NoExpr Pending +chr15-84036950-84036951-A-T 891.ADAMTSL3.ENST00000286744.10.missense.1645I/F 1 ADAMTSL3 I1645F 1 PFSWRHCLG ENST00000286744.10 1 HLA-A*29:02 2 None 1 0 14164.925 28748.631 27.315 51.500 2.043 0.000 0.000 0.000 0.366 NoExpr Pending +chr3-52517959-52517960-A-C 234.STAB1.ENST00000321725.10.missense.1573H/P 1 STAB1 H1573P 1 CTCDTAPTV ENST00000321725.10 1 HLA-A*29:02 7 None 1 0 14724.066 10839.774 21.000 17.000 0.090 0.000 0.000 0.000 1.000 NoExpr Pending +chr8-138737576-138737577-C-A 554.COL22A1.ENST00000303045.11.missense.696G/W 1 COL22A1 G696W 1 GLQGLRWKK ENST00000303045.11 1 HLA-A*29:02 7 None 1 0 14844.085 22610.353 15.630 29.000 0.308 0.000 0.000 2.000 0.200 NoExpr Pending +chr16-28652309-28652310-C-T 911.NPIPB8.ENST00000526428.1.missense.26T/M 1 NPIPB8 T26M 1 TMKINRHDK ENST00000526428.1 3 HLA-A*29:02 2 None 1 0 15526.305 26727.390 20.000 40.500 0.703 0.000 0.000 5.000 0.107 NoExpr Pending +chr16-28766434-28766435-C-T 915.NPIPB9.ENST00000550983.1.missense.179T/M 1 NPIPB9 T179M 1 TMKINRHDK ENST00000550983.1 1 HLA-A*29:02 2 None 1 0 15526.305 26727.390 20.000 40.500 1.874 0.000 0.000 10.000 0.117 NoExpr Pending +chr3-44242057-44242058-G-A 231.TOPAZ1.ENST00000309765.4.missense.2R/Q 1 TOPAZ1 R2Q 1 MQRPPPLGPT ENST00000309765.4 5 HLA-B*45:01 2 None 1 0 18453.590 24155.798 18.500 30.500 0.005 0.000 0.000 0.000 0.307 NoExpr Pending +chr14-26448937-26448938-G-C 794.NOVA1.ENST00000539517.7.missense.182T/R 1 NOVA1 T182R 1 IIVPNSRAGL ENST00000539517.7 1 HLA-A*29:02 7 None 1 0 19554.959 15264.273 23.096 18.500 0.694 0.000 0.000 2.000 0.462 NoExpr Pending +chr6-10801907-10801908-C-G 362.MAK.ENST00000474039.5.missense.272R/P 1 MAK R272P 1 NWDPKKPPTA ENST00000474039.5 1 HLA-B*45:01 7 None 1 0 22818.242 29208.615 25.500 33.000 0.038 0.000 0.000 1.000 0.323 NoExpr Pending +chr1-196995755-196995756-A-G 80.CFHR5.ENST00000256785.5.missense.216N/S 1 CFHR5 N216S 1 QLSSGEVK ENST00000256785.5 1 HLA-A*29:02 4 None 1 0 26128.002 26691.050 32.500 34.000 0.000 0.000 0.000 0.000 0.287 NoExpr Pending diff --git a/pvactools/tools/pvacseq/example_data/results/MHC_Class_I/server.R b/pvactools/tools/pvacseq/example_data/results/MHC_Class_I/server.R index 7a02784f..ae51ad03 100644 --- a/pvactools/tools/pvacseq/example_data/results/MHC_Class_I/server.R +++ b/pvactools/tools/pvacseq/example_data/results/MHC_Class_I/server.R @@ -24,7 +24,7 @@ options(shiny.port = 3333) server <- shinyServer(function(input, output, session) { ## pVACtools version - output$version <- renderText({"pVACtools version 4.4.0"}) + output$version <- renderText({"pVACtools version 5.0.1"}) ##############################DATA UPLOAD TAB################################### ## helper function defined for generating shinyInputs in mainTable (Evaluation dropdown menus) @@ -36,10 +36,10 @@ server <- shinyServer(function(input, output, session) { inputs } ## helper function defined for generating shinyInputs in mainTable (Investigate button) - shinyInputSelect <- function(FUN, len, id, ...) { - inputs <- character(len) - for (i in seq_len(len)) { - inputs[i] <- as.character(FUN(paste0(id, i), ...)) + shinyInputSelect <- function(FUN, row_ids, button_label, ...) { + inputs <- character(nrow(row_ids)) + for (i in 1:nrow(row_ids)) { + inputs[i] <- as.character(FUN(paste0(button_label, row_ids[i, "ID"]), ...)) } inputs } @@ -55,28 +55,29 @@ server <- shinyServer(function(input, output, session) { })) } #set button styling based on values in Evaluation column - setButtonStyling <- function(evaluations) { + setButtonStyling <- function(evaluations, ids) { for (i in 1:length(evaluations)){ evaluation <- evaluations[i] + id <- ids[i] if (evaluation == 'Accept') { - html <- paste0("#button-acpt_", i ," { color: red !important; }") + html <- paste0("#button-acpt_", id ," { color: green !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-rej_", i, ')')) - removeUI(selector = paste0("style:contains(#button-rev_", i, ')')) + removeUI(selector = paste0("style:contains(#button-rej_", id, ')')) + removeUI(selector = paste0("style:contains(#button-rev_", id, ')')) } else if (evaluation == 'Reject') { - html <- paste0("#button-rej_", i ," { color: red !important; }") + html <- paste0("#button-rej_", id ," { color: red !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-acpt_", i, ')')) - removeUI(selector = paste0("style:contains(#button-rev_", i, ')')) + removeUI(selector = paste0("style:contains(#button-acpt_", id, ')')) + removeUI(selector = paste0("style:contains(#button-rev_", id, ')')) } else if (evaluation == 'Review') { - html <- paste0("#button-rev_", i ," { color: red !important; }") + html <- paste0("#button-rev_", id ," { color: orange !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-acpt_", i, ')')) - removeUI(selector = paste0("style:contains(#button-rej_", i, ')')) + removeUI(selector = paste0("style:contains(#button-acpt_", id, ')')) + removeUI(selector = paste0("style:contains(#button-rej_", id, ')')) } else if (evaluation == 'Pending') { - removeUI(selector = paste0("style:contains(#button-acpt_", i, ')')) - removeUI(selector = paste0("style:contains(#button-rej_", i, ')')) - removeUI(selector = paste0("style:contains(#button-rev_", i, ')')) + removeUI(selector = paste0("style:contains(#button-acpt_", id, ')')) + removeUI(selector = paste0("style:contains(#button-rej_", id, ')')) + removeUI(selector = paste0("style:contains(#button-rev_", id, ')')) } } } @@ -106,15 +107,15 @@ server <- shinyServer(function(input, output, session) { colnames(mainData) <- mainData[1, ] mainData <- mainData[-1, ] row.names(mainData) <- NULL - setButtonStyling(mainData$Evaluation) - mainData$Acpt <- shinyInputSelect(actionButton, nrow(mainData), "button-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - mainData$Rej <- shinyInputSelect(actionButton, nrow(mainData), "button-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - mainData$Rev <- shinyInputSelect(actionButton, nrow(mainData), "button-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + setButtonStyling(mainData$Evaluation, mainData$ID) + mainData$Acpt <- shinyInputSelect(actionButton, mainData["ID"], "button-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + mainData$Rej <- shinyInputSelect(actionButton, mainData["ID"], "button-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + mainData$Rev <- shinyInputSelect(actionButton, mainData["ID"], "button-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") mainData$`IC50 MT` <- as.numeric(mainData$`IC50 MT`) mainData$`%ile MT` <- as.numeric(mainData$`%ile MT`) mainData$`RNA Depth` <- as.character(as.integer(mainData$`RNA Depth`)) mainData$`TSL`[is.na(mainData$`TSL`)] <- "NA" - df$evaluations <- mainData[c("ID", "Evaluation")] + df$evaluations <- data.frame(data = mainData$Evaluation, row.names = mainData$ID) df$mainTable <- mainData df$metricsData <- NULL df$lastSelectedRow <- 1 @@ -190,22 +191,22 @@ server <- shinyServer(function(input, output, session) { ## Class I demo aggregate report #session$sendCustomMessage("unbind-DT", "mainTable") withProgress(message = "Loading Demo Data", value = 0, { - load(url("https://github.com/griffithlab/pVACtools/raw/489a68cdd9e84e38b1bacc661aba15d78410282f/pvactools/tools/pvacview/data/HCC1395_demo_data.rda")) + load(url("https://github.com/griffithlab/pVACtools/raw/a3cc6d2b190a344d846438c1f0e5073e748dbd52/pvactools/tools/pvacview/data/HCC1395_demo_data.rda")) incProgress(0.3) #data <- getURL("https://raw.githubusercontent.com/griffithlab/pVACtools/c5a4f4c5b0bfa9c2832fc752e98dddea4c1c9eda/pvactools/tools/pvacview/data/H_NJ-HCC1395-HCC1395.Class_I.all_epitopes.aggregated.tsv") #mainData <- read.table(text = data, sep = "\t", header = FALSE, stringsAsFactors = FALSE, check.names = FALSE) colnames(mainData) <- mainData[1, ] mainData <- mainData[-1, ] row.names(mainData) <- NULL - setButtonStyling(mainData$Evaluation) - mainData$Acpt <- shinyInputSelect(actionButton, nrow(mainData), "button-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - mainData$Rej <- shinyInputSelect(actionButton, nrow(mainData), "button-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - mainData$Rev <- shinyInputSelect(actionButton, nrow(mainData), "button-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + setButtonStyling(mainData$Evaluation, mainData$ID) + mainData$Acpt <- shinyInputSelect(actionButton, mainData["ID"], "button-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + mainData$Rej <- shinyInputSelect(actionButton, mainData["ID"], "button-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + mainData$Rev <- shinyInputSelect(actionButton, mainData["ID"], "button-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") mainData$`IC50 MT` <- as.numeric(mainData$`IC50 MT`) mainData$`%ile MT` <- as.numeric(mainData$`%ile MT`) mainData$`RNA Depth` <- as.character(as.integer(mainData$`RNA Depth`)) mainData$`TSL`[is.na(mainData$`TSL`)] <- "NA" - df$evaluations <- mainData[c("ID", "Evaluation")] + df$evaluations <- data.frame(data = mainData$Evaluation, row.names = mainData$ID) df$mainTable <- mainData incProgress(0.1) ## Class I demo metrics file @@ -254,7 +255,7 @@ server <- shinyServer(function(input, output, session) { rownames(df$comments) <- df$mainTable$ID incProgress(0.2) ## Class II additional demo aggregate report - add_data <- getURL("https://raw.githubusercontent.com/griffithlab/pVACtools/489a68cdd9e84e38b1bacc661aba15d78410282f/pvactools/tools/pvacview/data/H_NJ-HCC1395-HCC1395.Class_II.all_epitopes.aggregated.tsv") + add_data <- getURL("https://raw.githubusercontent.com/griffithlab/pVACtools/a3cc6d2b190a344d846438c1f0e5073e748dbd52/pvactools/tools/pvacview/data/H_NJ-HCC1395-HCC1395.Class_II.all_epitopes.aggregated.tsv") addData <- read.table(text = add_data, sep = "\t", header = FALSE, stringsAsFactors = FALSE, check.names = FALSE) colnames(addData) <- addData[1, ] addData <- addData[-1, ] @@ -643,37 +644,34 @@ server <- shinyServer(function(input, output, session) { if (is.null(df$mainTable)) { return() } - selectedRow <- as.numeric(strsplit(input$accept_eval, "_")[[1]][2]) - selectedID <- df$mainTable$ID[selectedRow] - df$evaluations[df$evaluations$ID == selectedID, "Evaluation"] <- "Accept" - html <- paste0("#button-acpt_", selectedRow ," { color: red !important; }") + selectedID <- strsplit(input$accept_eval, "_")[[1]][2] + df$evaluations[selectedID, 1] <- "Accept" + html <- paste0("#button-acpt_", selectedID ," { color: green !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-rej_", selectedRow, ')'), multiple = TRUE) - removeUI(selector = paste0("style:contains(#button-rev_", selectedRow, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-rej_", selectedID, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-rev_", selectedID, ')'), multiple = TRUE) }) observeEvent(input$reject_eval, { if (is.null(df$mainTable)) { return() } - selectedRow <- as.numeric(strsplit(input$reject_eval, "_")[[1]][2]) - selectedID <- df$mainTable$ID[selectedRow] - df$evaluations[df$evaluations$ID == selectedID, "Evaluation"] <- "Reject" - html <- paste0("#button-rej_", selectedRow ," { color: red !important; }") + selectedID <- strsplit(input$reject_eval, "_")[[1]][2] + df$evaluations[selectedID, 1] <- "Reject" + html <- paste0("#button-rej_", selectedID ," { color: red !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-acpt_", selectedRow, ')'), multiple = TRUE) - removeUI(selector = paste0("style:contains(#button-rev_", selectedRow, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-acpt_", selectedID, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-rev_", selectedID, ')'), multiple = TRUE) }) observeEvent(input$review_eval, { if (is.null(df$mainTable)) { return() } - selectedRow <- as.numeric(strsplit(input$review_eval, "_")[[1]][2]) - selectedID <- df$mainTable$ID[selectedRow] - df$evaluations[df$evaluations$ID == selectedID, "Evaluation"] <- "Review" - html <- paste0("#button-rev_", selectedRow ," { color: red !important; }") + selectedID <- strsplit(input$review_eval, "_")[[1]][2] + df$evaluations[selectedID, 1] <- "Review" + html <- paste0("#button-rev_", selectedID ," { color: orange !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-acpt_", selectedRow, ')'), multiple = TRUE) - removeUI(selector = paste0("style:contains(#button-rej_", selectedRow, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-acpt_", selectedID, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-rej_", selectedID, ')'), multiple = TRUE) }) ##selected row text box output$selected <- renderText({ @@ -950,7 +948,10 @@ server <- shinyServer(function(input, output, session) { ##Anchor Heatmap overlayed on selected peptide sequences anchorPlotHeight <- reactive({ if (is.null(df$metricsData)) { - return(0) + return(100) + } + if (length(df$metricsData[[selectedID()]]$good_binders) == 0) { + return(100) } peptide_data <- df$metricsData[[selectedID()]]$good_binders[[selectedTranscriptSet()]]$`peptides` peptide_names <- names(peptide_data) @@ -1097,12 +1098,12 @@ server <- shinyServer(function(input, output, session) { hla_allele_count <- length(unique(bindingScoreDataIC50()$HLA_allele)) incProgress(0.5) p <- ggplot(data = bindingScoreDataIC50(), aes(x = Mutant, y = Score, color = Mutant), trim = FALSE) + geom_violin() + facet_grid(cols = vars(HLA_allele)) + scale_y_continuous(trans = "log10") + #coord_trans(y = "log10") + - stat_summary(fun.y = mean, fun.ymin = mean, fun.ymax = mean, geom = "crossbar", width = 0.25, position = position_dodge(width = .25)) + - geom_jitter(data = bindingScoreDataIC50(), aes(shape = algorithms), sizes = 5, stroke = 1, position = position_jitter(0.3)) + + stat_summary(fun = mean, fun.min = mean, fun.max = mean, geom = "crossbar", width = 0.25, position = position_dodge(width = .25)) + + geom_jitter(data = bindingScoreDataIC50(), aes(shape = algorithms), size = 5, stroke = 1, position = position_jitter(0.3)) + scale_shape_manual(values = 0:8) + geom_hline(aes(yintercept = yintercept, linetype = Cutoffs), line.data, color = rep(line.data$color, hla_allele_count)) + scale_color_manual(values = rep(c("MT" = "#D2B4DE", "WT" = "#F7DC6F"), hla_allele_count)) + - theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 15), axis.ticks = element_line(size = 3), legend.text = element_text(size = 15), legend.title = element_text(size = 15)) + theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 15), axis.ticks = element_line(linewidth = 3), legend.text = element_text(size = 15), legend.title = element_text(size = 15)) incProgress(0.5) print(p) }else { @@ -1155,12 +1156,12 @@ server <- shinyServer(function(input, output, session) { hla_allele_count <- length(unique(combinedBindingElutionDataPercentile()$HLA_allele)) incProgress(0.5) p <- ggplot(data = combinedBindingElutionDataPercentile(), aes(x = Mutant, y = Score, color = Mutant), trim = FALSE) + geom_violin() + facet_grid(cols = vars(HLA_allele)) + scale_y_continuous(trans = "log10") + #coord_trans(y = "log10") + - stat_summary(fun.y = mean, fun.ymin = mean, fun.ymax = mean, geom = "crossbar", width = 0.25, position = position_dodge(width = .25)) + + stat_summary(fun = mean, fun.min = mean, fun.max = mean, geom = "crossbar", width = 0.25, position = position_dodge(width = .25)) + geom_jitter(data = combinedBindingElutionDataPercentile(), aes(shape = algorithms), size = 5, stroke = 1, position = position_jitter(0.3)) + scale_shape_manual(values = 0:10) + geom_hline(aes(yintercept = yintercept, linetype = Cutoffs), line.data, color = rep(line.data$color, hla_allele_count)) + scale_color_manual(values = rep(c("MT" = "#D2B4DE", "WT" = "#F7DC6F"), hla_allele_count)) + - theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 15), axis.ticks = element_line(size = 3), legend.text = element_text(size = 15), legend.title = element_text(size = 15)) + theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 15), axis.ticks = element_line(linewidth = 3), legend.text = element_text(size = 15), legend.title = element_text(size = 15)) incProgress(0.5) print(p) }else { @@ -1432,16 +1433,16 @@ server <- shinyServer(function(input, output, session) { return(nchar(df$metricsData[[selectedID()]]$reference_matches$query_peptide) * 20) } } ) - ##############################EXPORT TAB############################################## #evalutation overview table output$checked <- renderTable({ if (is.null(df$evaluations)) { return() } - data <- as.data.frame(table(df$evaluations$Evaluation)) + data <- as.data.frame(table(df$evaluations)) colnames(data) <- c("Evaluation","Count") data }) + ##############################EXPORT TAB############################################## #export table display with options to download output$ExportTable <- renderDataTable({ if (is.null(df$mainTable)) { @@ -1452,8 +1453,8 @@ server <- shinyServer(function(input, output, session) { "Col RNA Depth", "Col DNA VAF", "Percentile Fail", "Has Prob Pos", "Acpt", "Rej", "Rev") data <- df$mainTable[, !(colsToDrop)] col_names <- colnames(data) - data <- plyr::join(data, df$evaluations, by='ID') - colnames(data) <- c(col_names, "Evaluation") + evaluations <- data.frame("ID" = row.names(df$evaluations), Evaluation = df$evaluations[, 1]) + data <- join(data, evaluations) comments <- data.frame("ID" = row.names(df$comments), Comments = df$comments[, 1]) data <- join(data, comments) data[is.na(data)] <- "NA" @@ -1551,16 +1552,16 @@ server <- shinyServer(function(input, output, session) { len <- nrow(df_neofox$mainTable_neofox) if ('Evaluation' %in% colnames(df_neofox$mainTable_neofox)) { - setButtonStyling(df_neofox$mainTable_neofox$Evaluation) + setButtonStyling(df_neofox$mainTable_neofox$Evaluation, df_neofox$mainTable_neofox$ID) } else { df_neofox$mainTable_neofox["Evaluation"] = "Pending" } df_neofox$mainTable_neofox <- cbind(ID = rownames(df_neofox$mainTable_neofox), df_neofox$mainTable_neofox) df_neofox$evaluations <- df_neofox$mainTable_neofox[c("ID", "Evaluation")] df_neofox$mainTable_neofox$Evaluation <- NULL - df_neofox$mainTable_neofox$Acpt <- shinyInputSelect(actionButton, nrow(mainData_neofox), "button-neofox-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - df_neofox$mainTable_neofox$Rej <- shinyInputSelect(actionButton, nrow(mainData_neofox), "button-neofox-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - df_neofox$mainTable_neofox$Rev <- shinyInputSelect(actionButton, nrow(mainData_neofox), "button-neofox-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + df_neofox$mainTable_neofox$Acpt <- shinyInputSelect(actionButton, df_neofox$mainTable_neofox["ID"], "button-neofox-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + df_neofox$mainTable_neofox$Rej <- shinyInputSelect(actionButton, df_neofox$mainTable_neofox["ID"], "button-neofox-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + df_neofox$mainTable_neofox$Rev <- shinyInputSelect(actionButton, df_neofox$mainTable_neofox["ID"], "button-neofox-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") if ("Comments" %in% colnames(df_neofox$mainTable_neofox)) { df_neofox$comments <- data.frame(data = df_neofox$mainTable_neofox$`Comments`, nrow = nrow(df_neofox$mainTable_neofox), ncol = 1) @@ -1633,16 +1634,16 @@ server <- shinyServer(function(input, output, session) { len <- nrow(df_neofox$mainTable_neofox) if ('Evaluation' %in% colnames(df_neofox$mainTable_neofox)) { - setButtonStyling(df_neofox$mainTable_neofox$Evaluation) + setButtonStyling(df_neofox$mainTable_neofox$Evaluation, df_neofox$mainTable_neofox$ID) } else { df_neofox$mainTable_neofox["Evaluation"] = "Pending" } df_neofox$mainTable_neofox <- cbind(ID = rownames(df_neofox$mainTable_neofox), df_neofox$mainTable_neofox) df_neofox$evaluations <- df_neofox$mainTable_neofox[c("ID", "Evaluation")] df_neofox$mainTable_neofox$Evaluation <- NULL - df_neofox$mainTable_neofox$Acpt <- shinyInputSelect(actionButton, nrow(mainData_neofox), "button-neofox-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - df_neofox$mainTable_neofox$Rej <- shinyInputSelect(actionButton, nrow(mainData_neofox), "button-neofox-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - df_neofox$mainTable_neofox$Rev <- shinyInputSelect(actionButton, nrow(mainData_neofox), "button-neofox-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + df_neofox$mainTable_neofox$Acpt <- shinyInputSelect(actionButton, df_neofox$mainTable_neofox["ID"], "button-neofox-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + df_neofox$mainTable_neofox$Rej <- shinyInputSelect(actionButton, df_neofox$mainTable_neofox["ID"], "button-neofox-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + df_neofox$mainTable_neofox$Rev <- shinyInputSelect(actionButton, df_neofox$mainTable_neofox["ID"], "button-neofox-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") if ("Comments" %in% colnames(df_neofox$mainTable_neofox)) { df_neofox$comments <- data.frame(data = df_neofox$mainTable_neofox$`Comments`, nrow = nrow(df_neofox$mainTable_neofox), ncol = 1) @@ -1747,34 +1748,34 @@ server <- shinyServer(function(input, output, session) { if (is.null(df_neofox$mainTable_neofox)) { return() } - selectedRow <- as.numeric(strsplit(input$accept_neofox_eval, "_")[[1]][2]) - df_neofox$evaluations[df_neofox$evaluations$ID == selectedRow, "Evaluation"] <- "Accept" - html <- paste0("#button-neofox-acpt_", selectedRow ," { color: red !important; }") + selectedID <- strsplit(input$accept_neofox_eval, "_")[[1]][2] + df_neofox$evaluations[df_neofox$evaluations$ID == selectedID, "Evaluation"] <- "Accept" + html <- paste0("#button-neofox-acpt_", selectedID ," { color: red !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-neofox-rej_", selectedRow, ')'), multiple = TRUE) - removeUI(selector = paste0("style:contains(#button-neofox-rev_", selectedRow, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-neofox-rej_", selectedID, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-neofox-rev_", selectedID, ')'), multiple = TRUE) }) observeEvent(input$reject_neofox_eval, { if (is.null(df_neofox$mainTable_neofox)) { return() } - selectedRow <- as.numeric(strsplit(input$reject_neofox_eval, "_")[[1]][2]) - df_neofox$evaluations[df_neofox$evaluations$ID == selectedRow, "Evaluation"] <- "Reject" - html <- paste0("#button-neofox-rej_", selectedRow ," { color: red !important; }") + selectedID <- as.numeric(strsplit(input$reject_neofox_eval, "_")[[1]][2]) + df_neofox$evaluations[df_neofox$evaluations$ID == selectedID, "Evaluation"] <- "Reject" + html <- paste0("#button-neofox-rej_", selectedID ," { color: red !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-neofox-acpt_", selectedRow, ')'), multiple = TRUE) - removeUI(selector = paste0("style:contains(#button-neofox-rev_", selectedRow, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-neofox-acpt_", selectedID, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-neofox-rev_", selectedID, ')'), multiple = TRUE) }) observeEvent(input$review_neofox_eval, { if (is.null(df_neofox$mainTable_neofox)) { return() } - selectedRow <- as.numeric(strsplit(input$review_neofox_eval, "_")[[1]][2]) - df_neofox$evaluations[df_neofox$evaluations$ID == selectedRow, "Evaluation"] <- "Review" - html <- paste0("#button-neofox-rev_", selectedRow ," { color: red !important; }") + selectedID <- as.numeric(strsplit(input$review_neofox_eval, "_")[[1]][2]) + df_neofox$evaluations[df_neofox$evaluations$ID == selectedID, "Evaluation"] <- "Review" + html <- paste0("#button-neofox-rev_", selectedID ," { color: red !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-neofox-acpt_", selectedRow, ')'), multiple = TRUE) - removeUI(selector = paste0("style:contains(#button-neofox-rej_", selectedRow, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-neofox-acpt_", selectedID, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-neofox-rej_", selectedID, ')'), multiple = TRUE) }) # NeoFox evalutation overview table @@ -1852,7 +1853,7 @@ server <- shinyServer(function(input, output, session) { scale_color_manual(values = c("No" = "#939094", "Yes" = "#f42409")) + labs(x = NULL) + facet_wrap(~Feature, scales="free", ncol=6) + - theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 10), axis.ticks = element_line(size = 3), legend.text = element_text(size = 10), legend.title = element_text(size = 10)) + theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 10), axis.ticks = element_line(linewidth = 3), legend.text = element_text(size = 10), legend.title = element_text(size = 10)) incProgress(0.5) print(p_neofox) @@ -2111,7 +2112,7 @@ server <- shinyServer(function(input, output, session) { "Gene:", .data[["gene"]]))) + geom_point(aes(color = .data[[input$color_scatter]], size = .data[[input$size_scatter]])) + # Correct placement of aes() here scale_color_gradient(low = input$min_col, high = input$max_col) + - theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 15), axis.ticks = element_line(size = 3), legend.text = element_text(size = 15), legend.title = element_text(size = 15)) + theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 15), axis.ticks = element_line(linewidth = 3), legend.text = element_text(size = 15), legend.title = element_text(size = 15)) scatter_plot <- ggplotly(scatter_plot) @@ -2309,7 +2310,8 @@ server <- shinyServer(function(input, output, session) { df_custom$group_inds <- row_ind_df row_ind_top <- apply(row_ind_df, 1, function(x) {unlist(x[1])[1]}) df_custom$mainTable_custom <- as.data.frame(reformat_data[row_ind_top, ]) - df_custom$mainTable_custom <- cbind(Select = shinyInputSelect(actionButton, nrow(df_custom$mainTable_custom), "button_", label = "Investigate", onclick = 'Shiny.onInputChange(\"custom_select_button\", this.id)'), df_custom$mainTable_custom) + df_custom$mainTable_custom["ID"] <- 1:nrow(df_custom$mainTable_custom) + df_custom$mainTable_custom <- cbind(Select = shinyInputSelect(actionButton, df_custom$mainTable_custom["ID"], "button_", label = "Investigate", onclick = 'Shiny.onInputChange(\"custom_select_button\", this.id)'), df_custom$mainTable_custom) df_custom$metricsData <- get_group_inds(df_custom$fullData, df_custom$group_inds) df_custom$peptide_features <- input$peptide_features updateTabItems(session, "custom_tabs", "custom_explore") @@ -2610,7 +2612,7 @@ server <- shinyServer(function(input, output, session) { strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 15), - axis.ticks = element_line(size = 3), + axis.ticks = element_line(linewidth = 3), legend.text = element_text(size = 15), legend.title = element_text(size = 15) ) diff --git a/pvactools/tools/pvacseq/example_data/results/MHC_Class_I/ui.R b/pvactools/tools/pvacseq/example_data/results/MHC_Class_I/ui.R index 45154935..e2730359 100644 --- a/pvactools/tools/pvacseq/example_data/results/MHC_Class_I/ui.R +++ b/pvactools/tools/pvacseq/example_data/results/MHC_Class_I/ui.R @@ -275,7 +275,7 @@ explore_tab <- tabItem( DTOutput(outputId = "bindingDatatable"), style = "overflow-x: scroll;" ), tabPanel("Elution and Immunogenicity Data", - h4("Prediction score table showing exact MHC scpres for elution, immunogenicity, and percentile calculations."), + h4("Prediction score table showing exact MHC scores for elution, immunogenicity, and percentile calculations."), DTOutput(outputId = "elutionDatatable"), br(), strong("BigMHC_EL / BigMHC_IM"), span(": A deep learning tool for predicting MHC-I (neo)epitope presentation and immunogenicity. ("), diff --git a/pvactools/tools/pvacseq/example_data/results/MHC_Class_II/HCC1395_TUMOR_DNA.all_epitopes.aggregated.metrics.json b/pvactools/tools/pvacseq/example_data/results/MHC_Class_II/HCC1395_TUMOR_DNA.all_epitopes.aggregated.metrics.json index b50f8512..f5f90cfb 100644 --- a/pvactools/tools/pvacseq/example_data/results/MHC_Class_II/HCC1395_TUMOR_DNA.all_epitopes.aggregated.metrics.json +++ b/pvactools/tools/pvacseq/example_data/results/MHC_Class_II/HCC1395_TUMOR_DNA.all_epitopes.aggregated.metrics.json @@ -28976,11 +28976,168 @@ "best_hla_allele": "DRB1*04:05" }, "chr1-111727105-111727106-G-T": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "VKKRRLSKGSGHFPF": { + "ic50s_MT": [ + 6449.03515625 + ], + "percentiles_MT": [ + 80.0 + ], + "ic50s_WT": [ + 7542.075 + ], + "percentiles_WT": [ + 85.0 + ], + "hla_types": [ + "DRB1*04:05" + ], + "mutation_position": "5", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCnuggetsII", + "NNalign", + "NetMHCIIpan", + "SMMalign" + ], + "MT": { + "DRB1*04:05": [ + 6515.37, + 6382.7, + 4696.41, + 7806.0 + ] + }, + "WT": { + "DRB1*04:05": [ + 8897.15, + 9200.2, + 6047.24, + 6187.0 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCnuggetsII", + "NNalign", + "NetMHCIIpan", + "SMMalign" + ], + "MT": { + "DRB1*04:05": [ + 52.70000076293945, + 80.0, + 80.0, + 84.0 + ] + }, + "WT": { + "DRB1*04:05": [ + 59.4, + 88.0, + 85.0, + 79.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "NetMHCIIpanEL" + ], + "MT": { + "DRB1*04:05": [ + 0.0014 + ] + }, + "WT": { + "DRB1*04:05": [ + 0.0005 + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "NetMHCIIpanEL" + ], + "MT": { + "DRB1*04:05": [ + 85.0 + ] + }, + "WT": { + "DRB1*04:05": [ + 95.0 + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCnuggetsII", + "NNalign", + "NetMHCIIpan", + "SMMalign", + "NetMHCIIpanEL" + ], + "MT": { + "DRB1*04:05": [ + 52.70000076293945, + 80.0, + 80.0, + 84.0, + 85.0 + ] + }, + "WT": { + "DRB1*04:05": [ + 59.4, + 88.0, + 85.0, + 79.0, + 95.0 + ] + } + }, + "wt_peptide": "VKKRSLSKGSGHFPF" + } + }, + "transcripts": [ + "ENST00000357260.6-INKA2-S/R-252" + ], + "transcript_expr": [ + 1.081 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 297 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 1.081 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 1.081 + ], "DNA VAF": 0.063, "RNA VAF": 0.0, "gene_expr": 2.143, @@ -76566,11 +76723,168 @@ "best_hla_allele": "DRB1*04:05" }, "chr11-6410863-6410864-C-T": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "EEKAAGEAEEEEKDD": { + "ic50s_MT": [ + 19063.03515625 + ], + "percentiles_MT": [ + 99.0 + ], + "ic50s_WT": [ + 19847.97 + ], + "percentiles_WT": [ + 99.0 + ], + "hla_types": [ + "DRB1*04:05" + ], + "mutation_position": "13", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCnuggetsII", + "NNalign", + "NetMHCIIpan", + "SMMalign" + ], + "MT": { + "DRB1*04:05": [ + 11146.25, + 20922.5, + 17203.57, + 46443.0 + ] + }, + "WT": { + "DRB1*04:05": [ + 13572.73, + 21740.6, + 17955.34, + 42832.0 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCnuggetsII", + "NNalign", + "NetMHCIIpan", + "SMMalign" + ], + "MT": { + "DRB1*04:05": [ + 64.62000274658203, + 99.0, + 99.0, + 99.0 + ] + }, + "WT": { + "DRB1*04:05": [ + 69.36, + 99.0, + 99.0, + 99.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "NetMHCIIpanEL" + ], + "MT": { + "DRB1*04:05": [ + 0.006 + ] + }, + "WT": { + "DRB1*04:05": [ + 0.0051 + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "NetMHCIIpanEL" + ], + "MT": { + "DRB1*04:05": [ + 60.0 + ] + }, + "WT": { + "DRB1*04:05": [ + 63.0 + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCnuggetsII", + "NNalign", + "NetMHCIIpan", + "SMMalign", + "NetMHCIIpanEL" + ], + "MT": { + "DRB1*04:05": [ + 64.62000274658203, + 99.0, + 99.0, + 99.0, + 60.0 + ] + }, + "WT": { + "DRB1*04:05": [ + 69.36, + 99.0, + 99.0, + 99.0, + 63.0 + ] + } + }, + "wt_peptide": "EEKAAGEAEEEEEDD" + } + }, + "transcripts": [ + "ENST00000311051.7-APBB1-E/K-162" + ], + "transcript_expr": [ + 2.24 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 708 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 2.24 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 2.24 + ], "DNA VAF": 1.0, "RNA VAF": 1.0, "gene_expr": 6.678, @@ -113406,11 +113720,168 @@ "best_hla_allele": "DRB1*04:05" }, "chr12-116009024-116009025-G-C": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "FSAGPSSSSSLPPPG": { + "ic50s_MT": [ + 6508.23486328125 + ], + "percentiles_MT": [ + 89.0 + ], + "ic50s_WT": [ + 6703.74 + ], + "percentiles_WT": [ + 88.0 + ], + "hla_types": [ + "DRB1*04:05" + ], + "mutation_position": "15", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCnuggetsII", + "NNalign", + "NetMHCIIpan", + "SMMalign" + ], + "MT": { + "DRB1*04:05": [ + 3859.27, + 10351.0, + 9157.2, + 1117.0 + ] + }, + "WT": { + "DRB1*04:05": [ + 4934.64, + 9468.1, + 8472.84, + 968.0 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCnuggetsII", + "NNalign", + "NetMHCIIpan", + "SMMalign" + ], + "MT": { + "DRB1*04:05": [ + 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"transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0.0 + ], "DNA VAF": 0.554, "RNA VAF": 0.0, "gene_expr": 0.102, diff --git a/pvactools/tools/pvacseq/example_data/results/MHC_Class_II/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv b/pvactools/tools/pvacseq/example_data/results/MHC_Class_II/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv index dcacba65..098a4200 100644 --- a/pvactools/tools/pvacseq/example_data/results/MHC_Class_II/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv +++ b/pvactools/tools/pvacseq/example_data/results/MHC_Class_II/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv @@ -175,7 +175,7 @@ chr17-80086142-80086143-G-C 981.CCDC40.ENST00000397545.9.missense.792E/D 14 CCDC chr19-12580947-12580948-G-A 1009.ZNF490.ENST00000311437.11.missense.376S/F 11 ZNF490 S376F 1 CGEAFKSSSFCEVHE ENST00000311437.11 1 DRB1*04:05 10 None 11 0 1407.650 698.550 48.000 26.000 15.981 0.257 4.107 167.000 0.351 Poor Pending chr7-155462475-155462476-A-G 484.EN2.ENST00000297375.4.missense.264Q/R 15 EN2 Q264R 1 KAEFRTNRYLTEQRR ENST00000297375.4 1 DRB1*04:05 5 None 15 0 659.950 848.500 23.000 27.000 0.408 0.375 0.153 16.000 0.263 Poor Pending chr19-422192-422193-G-C 993.SHC2.ENST00000264554.11.missense.525H/D 11 SHC2 H525D 1 PGQYVLTGMDAGQPK ENST00000264554.11 1 DRB1*04:05 10 None 11 0 808.575 988.595 27.000 35.000 8.139 0.070 0.570 115.000 0.110 Poor Pending -chr4-48420360-48420361-A-G 295.SLAIN2.ENST00000264313.11.missense.533R/G SLAIN2 R533G 0 TTAMGSGLPRPSAPS ENST00000264313.11 1 DRB1*04:05 5 None 0 0 6773.235 3940.110 86.000 67.000 58.280 0.312 18.183 365.000 0.290 Poor Pending +chr4-48420360-48420361-A-G 295.SLAIN2.ENST00000264313.11.missense.533R/G 1 SLAIN2 R533G 1 TTAMGSGLPRPSAPS ENST00000264313.11 1 DRB1*04:05 5 None 1 0 6773.235 3940.110 86.000 67.000 58.280 0.312 18.183 365.000 0.290 Poor Pending chr8-143805313-143805314-A-C 561.SCRIB.ENST00000320476.7.missense.823V/G 10 SCRIB V823G 6 ENAGTITPLRPEDDY ENST00000320476.7 1 DRB1*04:05 4 None 10 0 1418.095 966.460 42.000 26.000 61.627 0.055 3.389 402.000 0.164 Poor Pending chr13-113425167-113425168-G-T 779.ADPRHL1.ENST00000375418.8.missense.220H/N 14 ADPRHL1 H220N 4 QENWFYFEAKWQFYL ENST00000375418.8 1 DRB1*04:05 3 None 14 0 1216.555 714.000 28.000 22.000 2.743 0.917 2.515 24.000 0.517 Poor Pending chr6-3723707-3723708-C-G 359.PXDC1.ENST00000380283.5.missense.203E/Q 6 PXDC1 E203Q 2 ENGSEFPSQLEDGDD ENST00000380283.5 1 DRB1*04:05 9 None 6 0 3432.875 6084.160 61.000 65.000 22.483 0.539 12.118 406.000 0.418 Poor Pending @@ -191,16 +191,16 @@ chr14-32773880-32773881-G-T 800.AKAP6.ENST00000280979.9.missense.1192M/I 15 AKAP chr13-25541936-25541938-GA-CT 751.ATP8A2.ENST00000381655.7.missense.224D/L 15 ATP8A2 D224L 6 LSHTALMQTREVLMK ENST00000381655.7 1 DRB1*04:05 6 None 15 0 785.420 3555.080 33.000 75.000 0.145 NA NA NA 0.319 Poor Pending chr6-33211510-33211511-C-A 378.RING1.ENST00000374656.5.missense.270P/H 13 RING1 P270H 1 EIELVFRPHHLLVEK ENST00000374656.5 1 DRB1*04:05 10 None 13 0 1185.450 917.335 30.000 20.000 27.953 0.022 0.615 276.000 0.060 Poor Pending chr19-6755017-6755018-T-C 1005.SH2D3A.ENST00000245908.11.missense.265E/G 4 SH2D3A E265G 2 APWWEAEEDEGEENR ENST00000245908.11 1 DRB1*04:05 11 None 4 0 2890.185 1924.415 63.000 51.000 3.820 1.000 3.820 5.000 0.985 Poor Pending -chr15-40622778-40622779-C-T 846.KNL1.ENST00000346991.9.missense.865P/S KNL1 P865S 0 MDVLEDESVQKPKFS ENST00000346991.9 1 DRB1*04:05 15 None 0 0 5009.045 6869.240 70.000 73.480 13.527 0.492 6.655 128.000 0.444 Poor Pending +chr15-40622778-40622779-C-T 846.KNL1.ENST00000346991.9.missense.865P/S 1 KNL1 P865S 1 MDVLEDESVQKPKFS ENST00000346991.9 1 DRB1*04:05 15 None 1 0 5009.045 6869.240 70.000 73.480 13.527 0.492 6.655 128.000 0.444 Poor Pending chr5-177460554-177460555-C-T 349.DBN1.ENST00000292385.9.missense.280E/K 13 DBN1 E280K 5 SEVEKAAAIIAQRPD ENST00000292385.9 1 DRB1*04:05 5 None 13 0 1604.875 2832.850 39.000 55.000 109.087 0.009 0.982 1076.000 0.285 Poor Pending chr10-104021651-104021652-G-T 618.SLK.ENST00000369755.4.missense.1160E/D 10 SLK E1160D 2 QLQNEKCHLLVEHDT ENST00000369755.4 1 DRB1*04:05 14 None 10 0 1775.345 1915.105 62.000 66.000 21.369 0.057 1.218 418.000 0.068 Poor Pending chrX-149930830-149930831-G-A 1209.HSFX4.ENST00000457775.3.missense.243R/H 9 HSFX4 R243H 1 TQSFRHSGMWSKKSA ENST00000457775.3 3 DRB1*04:05 6 None 9 0 993.555 870.825 46.000 45.000 0.012 0.286 0.003 7.000 0.422 Poor Pending -chr11-6410863-6410864-C-T 688.APBB1.ENST00000311051.7.missense.162E/K APBB1 E162K 0 EEKAAGEAEEEEKDD ENST00000311051.7 1 DRB1*04:05 13 None 0 0 19063.035 19847.970 99.000 99.000 6.678 1.000 6.678 65.000 1.000 Poor Pending +chr11-6410863-6410864-C-T 688.APBB1.ENST00000311051.7.missense.162E/K 1 APBB1 E162K 1 EEKAAGEAEEEEKDD ENST00000311051.7 1 DRB1*04:05 13 None 1 0 19063.035 19847.970 99.000 99.000 6.678 1.000 6.678 65.000 1.000 Poor Pending chr22-37374977-37374978-G-A 1094.ELFN2.ENST00000402918.7.missense.186P/L 15 ELFN2 P186L 1 SLMVCELAGNLFNCE ENST00000402918.7 4 DRB1*04:05 11 None 15 0 1438.450 1998.055 46.000 55.000 0.890 0.368 0.328 19.000 0.168 Poor Pending chrX-43656385-43656386-C-A 1164.MAOA.ENST00000338702.4.missense.15D/E 8 MAOA D15E 2 SIAGHMFEVVVIGGG ENST00000338702.4 1 DRB1*04:05 8 None 8 0 2394.765 2643.590 45.000 48.000 0.784 1.000 0.784 2.000 1.000 Poor Pending chr4-40808808-40808809-A-G 294.NSUN7.ENST00000381782.7.missense.676Y/C 12 NSUN7 Y676C 1 SPQGIRSRMPTQHLC ENST00000381782.7 1 DRB1*04:05 15 None 12 0 1381.750 1314.200 43.000 42.000 0.405 0.333 0.135 6.000 0.471 Poor Pending chr1-232805681-232805682-C-T 119.MAP10.ENST00000418460.4.missense.78P/L 2 MAP10 P78L 1 FPTLLVYPPDGPGAL ENST00000418460.4 NA DRB1*04:05 15 None 2 0 2565.660 2793.625 56.000 56.000 1.996 0.469 0.936 32.000 0.233 Poor Pending -chr12-116009024-116009025-G-C 740.MED13L.ENST00000281928.9.missense.463A/G MED13L A463G 0 FSAGPSSSSSLPPPG ENST00000281928.9 1 DRB1*04:05 15 None 0 0 6508.235 6703.740 89.000 88.000 77.827 0.038 2.957 586.000 0.050 Poor Pending +chr12-116009024-116009025-G-C 740.MED13L.ENST00000281928.9.missense.463A/G 1 MED13L A463G 1 FSAGPSSSSSLPPPG ENST00000281928.9 1 DRB1*04:05 15 None 1 0 6508.235 6703.740 89.000 88.000 77.827 0.038 2.957 586.000 0.050 Poor Pending chr2-106425181-106425182-C-T 158.RGPD3.ENST00000409886.4.missense.929E/K 7 RGPD3 E929K 2 ADGFKFGISKPGNQE ENST00000409886.4 1 DRB1*04:05 10 None 7 0 1230.900 718.340 37.000 21.000 0.014 0.364 0.005 22.000 0.139 Poor Pending chr22-37570267-37570268-C-G 1095.LGALS2.ENST00000215886.6.missense.132E/Q 1 LGALS2 E132Q 1 SVRGGFNMSSFKLKQ ENST00000215886.6 1 DRB1*04:05 15 None 1 0 1299.075 737.795 38.000 33.000 0.067 0.222 0.015 9.000 0.484 Poor Pending chr15-30089755-30089756-C-G 845.GOLGA8J.ENST00000567927.2.missense.311L/V 10 GOLGA8J L311V 1 VRKELERVAGELQAQ ENST00000567927.2 5 DRB1*04:05 1 None 10 0 1921.600 1927.550 49.000 49.000 0.354 1.000 0.354 10.000 0.119 Poor Pending @@ -210,10 +210,10 @@ chr7-128815875-128815876-C-G 474.CCDC136.ENST00000297788.9.missense.1103S/C 2 CC chr19-52384796-52384797-A-G 1041.ZNF880.ENST00000422689.3.missense.406Q/R 1 ZNF880 Q406R 1 KFCLTNHHRMHTGER ENST00000422689.3 2 DRB1*04:05 15 None 1 0 2720.390 3261.545 66.000 66.000 31.855 0.012 0.382 82.000 0.647 Poor Pending chr14-32600790-32600791-A-T 797.AKAP6.ENST00000280979.9.missense.910K/M 4 AKAP6 K910M 3 SPMAEVQLCYLEAQR ENST00000280979.9 1 DRB1*04:05 3 None 4 2 3380.585 3337.265 53.000 56.000 2.905 0.250 0.726 8.000 0.708 Poor Pending chr19-52384795-52384796-C-A 1040.ZNF880.ENST00000422689.3.missense.406Q/K 1 ZNF880 Q406K 1 KFCLTNHHRMHTGEK ENST00000422689.3 2 DRB1*04:05 15 None 1 0 2771.570 3261.545 67.000 66.000 31.855 0.012 0.382 85.000 0.588 Poor Pending -chr6-32181195-32181196-G-T 374.AGER.ENST00000375069.7.missense.404L/M AGER L404M 0 EEERAEMNQSEEPEA ENST00000375069.7 1 DRB1*04:05 7 None 0 0 7333.920 6507.265 71.000 69.000 2.211 0.462 1.021 26.000 0.510 Poor Pending +chr6-32181195-32181196-G-T 374.AGER.ENST00000375069.7.missense.404L/M 1 AGER L404M 1 EEERAEMNQSEEPEA ENST00000375069.7 1 DRB1*04:05 7 None 1 0 7333.920 6507.265 71.000 69.000 2.211 0.462 1.021 26.000 0.510 Poor Pending chr17-7588499-7588500-G-C 943.SOX15.ENST00000250055.3.missense.194Q/E 2 SOX15 Q194E 2 ESDPRLQGELLPTYT ENST00000250055.3 1 DRB1*04:05 1 None 2 0 3658.650 3642.200 74.000 75.000 0.580 0.692 0.401 13.000 0.722 Poor Pending -chr7-157005551-157005552-G-A 485.MNX1.ENST00000252971.11.missense.392P/S MNX1 P392S 0 AASSDCSSEDDSPPS ENST00000252971.11 1 DRB1*04:05 15 None 0 0 8254.215 10750.800 83.000 83.000 18.982 0.040 0.759 101.000 0.054 Poor Pending -chr7-27130623-27130624-C-T 416.HOXA4.ENST00000360046.10.missense.37G/D HOXA4 G37D 0 DGGPGYQQPPAPPTQ ENST00000360046.10 1 DRB1*04:05 1 None 0 0 7034.550 7503.190 67.000 67.000 1.689 0.375 0.633 16.000 0.375 Poor Pending +chr7-157005551-157005552-G-A 485.MNX1.ENST00000252971.11.missense.392P/S 1 MNX1 P392S 1 AASSDCSSEDDSPPS ENST00000252971.11 1 DRB1*04:05 15 None 1 0 8254.215 10750.800 83.000 83.000 18.982 0.040 0.759 101.000 0.054 Poor Pending +chr7-27130623-27130624-C-T 416.HOXA4.ENST00000360046.10.missense.37G/D 1 HOXA4 G37D 1 DGGPGYQQPPAPPTQ ENST00000360046.10 1 DRB1*04:05 1 None 1 0 7034.550 7503.190 67.000 67.000 1.689 0.375 0.633 16.000 0.375 Poor Pending chr3-184239802-184239803-C-T 286.VWA5B2.ENST00000426955.6.missense.836A/V 4 VWA5B2 A836V 3 PQVPRCHVVIRGLCG ENST00000426955.6 1 DRB1*04:05 3 None 4 0 3031.620 3623.450 66.000 66.000 0.083 1.000 0.083 2.000 0.429 Poor Pending chr15-40622778-40622780-CC-TT 848.KNL1.ENST00000346991.9.missense.865P/L 7 KNL1 P865L 2 QKPKFLKEKQNVKIW ENST00000346991.9 1 DRB1*04:05 6 None 7 0 2983.000 13258.140 63.000 96.000 13.527 NA NA NA 0.450 Poor Pending chr1-36179726-36179728-GG-AA 17.MAP7D1.ENST00000373151.6.missense.764-765EE/EK 3 MAP7D1 EE764-765EK 4 SPGLQKEAVQKEKPI ENST00000373151.6 1 DRB1*04:05 13 None 3 0 3203.665 2372.740 41.000 46.000 93.193 NA NA NA 0.361 Poor Pending @@ -348,18 +348,18 @@ chr21-30755335-30755336-C-T 1084.KRTAP21-1.ENST00000335093.5.missense.15G/S 2 KR chr7-47833094-47833095-G-A 421.PKD1L1.ENST00000289672.7.missense.2111T/I 1 PKD1L1 T2111I 3 CPPHIQAPSSGLEGL ENST00000289672.7 1 DRB1*04:05 5 None 1 0 4493.790 13006.655 66.000 89.000 0.696 0.000 0.000 0.000 0.322 NoExpr Pending chr6-32223881-32223881-T-TAGCAGC 377.NOTCH4.ENST00000375023.3.inframe_ins.16L/LLL 1 NOTCH4 L16LLL 1 LLLLLLLLLLLLCVS ENST00000375023.3 1 DRB1*04:05 11-12 None 1 0 4677.225 4716.005 91.000 91.000 1.260 0.000 0.000 0.000 0.187 NoExpr Pending chr10-122601958-122601959-T-C 622.DMBT1.ENST00000338354.10.missense.1169M/T 1 DMBT1 M1169T 12 LGCGWATSAPGNARF ENST00000338354.10 1 DRB1*04:05 7 None 1 0 4683.905 2739.600 74.000 51.000 0.052 0.000 0.000 0.000 0.923 NoExpr Pending -chrX-135721216-135721217-G-A 1201.CT45A1.ENST00000594117.4.missense.120R/Q CT45A1 R120Q 0 QEINADIKRKLVKEL ENST00000594117.4 1 DRB1*04:05 1 None 0 0 5009.080 4775.770 77.000 78.000 0.000 0.000 0.000 0.000 0.582 NoExpr Pending -chrX-135779451-135779452-C-T 1204.CT45A5.ENST00000617203.1.missense.120R/Q CT45A5 R120Q 0 QEINADIKRKLVKEL ENST00000617203.1 1 DRB1*04:05 1 None 0 0 5009.080 4775.770 77.000 78.000 0.000 0.000 0.000 0.000 0.577 NoExpr Pending -chrX-135796713-135796714-C-T 1205.CT45A6.ENST00000612878.4.missense.120R/Q CT45A6 R120Q 0 QEINADIKRKLVKEL ENST00000612878.4 1 DRB1*04:05 1 None 0 0 5009.080 4775.770 77.000 78.000 0.102 0.000 0.000 0.000 0.554 NoExpr Pending -chrX-7843975-7843976-C-T 1124.VCX.ENST00000381059.7.missense.194P/L VCX P194L 0 EEPLSQESQVEEPLS ENST00000381059.7 1 DRB1*04:05 14 None 0 0 5398.050 6271.600 72.000 72.000 0.000 0.000 0.000 0.000 1.000 NoExpr Pending -chrX-8466116-8466117-G-C 1127.VCX3B.ENST00000381032.6.missense.159E/Q VCX3B E159Q 0 EEPLSQESQVEEPLS ENST00000381032.6 5 DRB1*04:05 9 None 0 0 5398.050 7919.310 72.000 84.000 0.048 0.000 0.000 3.000 0.110 NoExpr Pending -chr1-111727105-111727106-G-T 50.INKA2.ENST00000357260.6.missense.252S/R INKA2 S252R 0 VKKRRLSKGSGHFPF ENST00000357260.6 1 DRB1*04:05 5 None 0 0 6449.035 7542.075 80.000 85.000 2.143 0.000 0.000 29.000 0.063 NoExpr Pending -chr14-24068642-24068643-G-A 790.CARMIL3.ENST00000342740.6.missense.1248E/K CARMIL3 E1248K 0 GKEEKEGTLFPERTL ENST00000342740.6 5 DRB1*04:05 2 None 0 0 7615.750 7815.315 86.000 87.000 1.601 0.000 0.000 25.000 0.185 NoExpr Pending -chr8-138737576-138737577-C-A 554.COL22A1.ENST00000303045.11.missense.696G/W COL22A1 G696W 0 PPGLQGLRWKKGDMG ENST00000303045.11 1 DRB1*04:05 9 None 0 0 8119.750 9664.005 86.000 86.000 0.308 0.000 0.000 2.000 0.200 NoExpr Pending -chr21-44330789-44330813-AGGCAGCCGCGGCCCCTAGCGGCCC-A 1088.CFAP410.ENST00000397956.7.inframe_del.217-224GPLGAAAA/- CFAP410 GPLGAAAA217-224- 0 SSHRGRVSGSAHCTH ENST00000397956.7 1 DRB1*04:05 9-10 None 0 0 9193.345 17908.385 87.000 96.000 6.570 0.000 0.000 18.000 0.376 NoExpr Pending -chr3-52517959-52517960-A-C 234.STAB1.ENST00000321725.10.missense.1573H/P STAB1 H1573P 0 GQRTCTCDTAPTVGD ENST00000321725.10 1 DRB1*04:05 11 None 0 0 10740.270 13563.605 80.000 88.000 0.090 0.000 0.000 0.000 1.000 NoExpr Pending -chr7-39339738-39339739-G-C 420.POU6F2.ENST00000518318.7.missense.232Q/H POU6F2 Q232H 0 PSTNHHPQPAPQAPS ENST00000518318.7 1 DRB1*04:05 5 None 0 0 13358.615 15114.250 93.000 94.000 0.273 0.000 0.000 0.000 0.299 NoExpr Pending -chr3-130409352-130409353-G-T 256.COL6A5.ENST00000312481.11.missense.1503G/W COL6A5 G1503W 0 APWQYGEKGFPGDPG ENST00000312481.11 1 DRB1*04:05 3 None 0 0 14454.785 18429.165 86.000 90.000 0.001 0.000 0.000 0.000 0.306 NoExpr Pending -chr9-138120681-138120682-G-A 600.CACNA1B.ENST00000371372.6.missense.2097G/D CACNA1B G2097D 0 GPTDCRRERERRQER ENST00000371372.6 5 DRB1*04:05 4 None 0 0 15249.780 15376.540 96.000 96.000 0.154 0.000 0.000 0.000 0.276 NoExpr Pending -chr3-44242057-44242058-G-A 231.TOPAZ1.ENST00000309765.4.missense.2R/Q TOPAZ1 R2Q 0 QRPPPLGPTTASGPE ENST00000309765.4 5 DRB1*04:05 1 None 0 0 19740.006 19466.445 92.000 92.000 0.005 0.000 0.000 0.000 0.307 NoExpr Pending -chr22-37723212-37723213-GA-G 1100.TRIOBP.ENST00000644935.1.FS.219GA/G TRIOBP FS219 0 GGGRSAGSTGQGSGE ENST00000644935.1 NA DRB1*04:05 8-15 None 0 0 21387.385 NA 95.000 NA 35.473 0.000 0.000 5.000 0.289 NoExpr Pending +chrX-135721216-135721217-G-A 1201.CT45A1.ENST00000594117.4.missense.120R/Q 1 CT45A1 R120Q 1 QEINADIKRKLVKEL ENST00000594117.4 1 DRB1*04:05 1 None 1 0 5009.080 4775.770 77.000 78.000 0.000 0.000 0.000 0.000 0.582 NoExpr Pending +chrX-135779451-135779452-C-T 1204.CT45A5.ENST00000617203.1.missense.120R/Q 1 CT45A5 R120Q 1 QEINADIKRKLVKEL ENST00000617203.1 1 DRB1*04:05 1 None 1 0 5009.080 4775.770 77.000 78.000 0.000 0.000 0.000 0.000 0.577 NoExpr Pending +chrX-135796713-135796714-C-T 1205.CT45A6.ENST00000612878.4.missense.120R/Q 1 CT45A6 R120Q 1 QEINADIKRKLVKEL ENST00000612878.4 1 DRB1*04:05 1 None 1 0 5009.080 4775.770 77.000 78.000 0.102 0.000 0.000 0.000 0.554 NoExpr Pending +chrX-7843975-7843976-C-T 1124.VCX.ENST00000381059.7.missense.194P/L 1 VCX P194L 1 EEPLSQESQVEEPLS ENST00000381059.7 1 DRB1*04:05 14 None 1 0 5398.050 6271.600 72.000 72.000 0.000 0.000 0.000 0.000 1.000 NoExpr Pending +chrX-8466116-8466117-G-C 1127.VCX3B.ENST00000381032.6.missense.159E/Q 1 VCX3B E159Q 1 EEPLSQESQVEEPLS ENST00000381032.6 5 DRB1*04:05 9 None 1 0 5398.050 7919.310 72.000 84.000 0.048 0.000 0.000 3.000 0.110 NoExpr Pending +chr1-111727105-111727106-G-T 50.INKA2.ENST00000357260.6.missense.252S/R 1 INKA2 S252R 1 VKKRRLSKGSGHFPF ENST00000357260.6 1 DRB1*04:05 5 None 1 0 6449.035 7542.075 80.000 85.000 2.143 0.000 0.000 29.000 0.063 NoExpr Pending +chr14-24068642-24068643-G-A 790.CARMIL3.ENST00000342740.6.missense.1248E/K 1 CARMIL3 E1248K 1 GKEEKEGTLFPERTL ENST00000342740.6 5 DRB1*04:05 2 None 1 0 7615.750 7815.315 86.000 87.000 1.601 0.000 0.000 25.000 0.185 NoExpr Pending +chr8-138737576-138737577-C-A 554.COL22A1.ENST00000303045.11.missense.696G/W 1 COL22A1 G696W 1 PPGLQGLRWKKGDMG ENST00000303045.11 1 DRB1*04:05 9 None 1 0 8119.750 9664.005 86.000 86.000 0.308 0.000 0.000 2.000 0.200 NoExpr Pending +chr21-44330789-44330813-AGGCAGCCGCGGCCCCTAGCGGCCC-A 1088.CFAP410.ENST00000397956.7.inframe_del.217-224GPLGAAAA/- 1 CFAP410 GPLGAAAA217-224- 1 SSHRGRVSGSAHCTH ENST00000397956.7 1 DRB1*04:05 9-10 None 1 0 9193.345 17908.385 87.000 96.000 6.570 0.000 0.000 18.000 0.376 NoExpr Pending +chr3-52517959-52517960-A-C 234.STAB1.ENST00000321725.10.missense.1573H/P 1 STAB1 H1573P 1 GQRTCTCDTAPTVGD ENST00000321725.10 1 DRB1*04:05 11 None 1 0 10740.270 13563.605 80.000 88.000 0.090 0.000 0.000 0.000 1.000 NoExpr Pending +chr7-39339738-39339739-G-C 420.POU6F2.ENST00000518318.7.missense.232Q/H 1 POU6F2 Q232H 1 PSTNHHPQPAPQAPS ENST00000518318.7 1 DRB1*04:05 5 None 1 0 13358.615 15114.250 93.000 94.000 0.273 0.000 0.000 0.000 0.299 NoExpr Pending +chr3-130409352-130409353-G-T 256.COL6A5.ENST00000312481.11.missense.1503G/W 1 COL6A5 G1503W 1 APWQYGEKGFPGDPG ENST00000312481.11 1 DRB1*04:05 3 None 1 0 14454.785 18429.165 86.000 90.000 0.001 0.000 0.000 0.000 0.306 NoExpr Pending +chr9-138120681-138120682-G-A 600.CACNA1B.ENST00000371372.6.missense.2097G/D 1 CACNA1B G2097D 1 GPTDCRRERERRQER ENST00000371372.6 5 DRB1*04:05 4 None 1 0 15249.780 15376.540 96.000 96.000 0.154 0.000 0.000 0.000 0.276 NoExpr Pending +chr3-44242057-44242058-G-A 231.TOPAZ1.ENST00000309765.4.missense.2R/Q 1 TOPAZ1 R2Q 1 QRPPPLGPTTASGPE ENST00000309765.4 5 DRB1*04:05 1 None 1 0 19740.006 19466.445 92.000 92.000 0.005 0.000 0.000 0.000 0.307 NoExpr Pending +chr22-37723212-37723213-GA-G 1100.TRIOBP.ENST00000644935.1.FS.219GA/G 1 TRIOBP FS219 1 GGGRSAGSTGQGSGE ENST00000644935.1 NA DRB1*04:05 8-15 None 1 0 21387.385 NA 95.000 NA 35.473 0.000 0.000 5.000 0.289 NoExpr Pending diff --git a/pvactools/tools/pvacseq/example_data/results/MHC_Class_II/server.R b/pvactools/tools/pvacseq/example_data/results/MHC_Class_II/server.R index 7a02784f..ae51ad03 100644 --- a/pvactools/tools/pvacseq/example_data/results/MHC_Class_II/server.R +++ b/pvactools/tools/pvacseq/example_data/results/MHC_Class_II/server.R @@ -24,7 +24,7 @@ options(shiny.port = 3333) server <- shinyServer(function(input, output, session) { ## pVACtools version - output$version <- renderText({"pVACtools version 4.4.0"}) + output$version <- renderText({"pVACtools version 5.0.1"}) ##############################DATA UPLOAD TAB################################### ## helper function defined for generating shinyInputs in mainTable (Evaluation dropdown menus) @@ -36,10 +36,10 @@ server <- shinyServer(function(input, output, session) { inputs } ## helper function defined for generating shinyInputs in mainTable (Investigate button) - shinyInputSelect <- function(FUN, len, id, ...) { - inputs <- character(len) - for (i in seq_len(len)) { - inputs[i] <- as.character(FUN(paste0(id, i), ...)) + shinyInputSelect <- function(FUN, row_ids, button_label, ...) { + inputs <- character(nrow(row_ids)) + for (i in 1:nrow(row_ids)) { + inputs[i] <- as.character(FUN(paste0(button_label, row_ids[i, "ID"]), ...)) } inputs } @@ -55,28 +55,29 @@ server <- shinyServer(function(input, output, session) { })) } #set button styling based on values in Evaluation column - setButtonStyling <- function(evaluations) { + setButtonStyling <- function(evaluations, ids) { for (i in 1:length(evaluations)){ evaluation <- evaluations[i] + id <- ids[i] if (evaluation == 'Accept') { - html <- paste0("#button-acpt_", i ," { color: red !important; }") + html <- paste0("#button-acpt_", id ," { color: green !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-rej_", i, ')')) - removeUI(selector = paste0("style:contains(#button-rev_", i, ')')) + removeUI(selector = paste0("style:contains(#button-rej_", id, ')')) + removeUI(selector = paste0("style:contains(#button-rev_", id, ')')) } else if (evaluation == 'Reject') { - html <- paste0("#button-rej_", i ," { color: red !important; }") + html <- paste0("#button-rej_", id ," { color: red !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-acpt_", i, ')')) - removeUI(selector = paste0("style:contains(#button-rev_", i, ')')) + removeUI(selector = paste0("style:contains(#button-acpt_", id, ')')) + removeUI(selector = paste0("style:contains(#button-rev_", id, ')')) } else if (evaluation == 'Review') { - html <- paste0("#button-rev_", i ," { color: red !important; }") + html <- paste0("#button-rev_", id ," { color: orange !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-acpt_", i, ')')) - removeUI(selector = paste0("style:contains(#button-rej_", i, ')')) + removeUI(selector = paste0("style:contains(#button-acpt_", id, ')')) + removeUI(selector = paste0("style:contains(#button-rej_", id, ')')) } else if (evaluation == 'Pending') { - removeUI(selector = paste0("style:contains(#button-acpt_", i, ')')) - removeUI(selector = paste0("style:contains(#button-rej_", i, ')')) - removeUI(selector = paste0("style:contains(#button-rev_", i, ')')) + removeUI(selector = paste0("style:contains(#button-acpt_", id, ')')) + removeUI(selector = paste0("style:contains(#button-rej_", id, ')')) + removeUI(selector = paste0("style:contains(#button-rev_", id, ')')) } } } @@ -106,15 +107,15 @@ server <- shinyServer(function(input, output, session) { colnames(mainData) <- mainData[1, ] mainData <- mainData[-1, ] row.names(mainData) <- NULL - setButtonStyling(mainData$Evaluation) - mainData$Acpt <- shinyInputSelect(actionButton, nrow(mainData), "button-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - mainData$Rej <- shinyInputSelect(actionButton, nrow(mainData), "button-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - mainData$Rev <- shinyInputSelect(actionButton, nrow(mainData), "button-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + setButtonStyling(mainData$Evaluation, mainData$ID) + mainData$Acpt <- shinyInputSelect(actionButton, mainData["ID"], "button-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + mainData$Rej <- shinyInputSelect(actionButton, mainData["ID"], "button-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + mainData$Rev <- shinyInputSelect(actionButton, mainData["ID"], "button-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") mainData$`IC50 MT` <- as.numeric(mainData$`IC50 MT`) mainData$`%ile MT` <- as.numeric(mainData$`%ile MT`) mainData$`RNA Depth` <- as.character(as.integer(mainData$`RNA Depth`)) mainData$`TSL`[is.na(mainData$`TSL`)] <- "NA" - df$evaluations <- mainData[c("ID", "Evaluation")] + df$evaluations <- data.frame(data = mainData$Evaluation, row.names = mainData$ID) df$mainTable <- mainData df$metricsData <- NULL df$lastSelectedRow <- 1 @@ -190,22 +191,22 @@ server <- shinyServer(function(input, output, session) { ## Class I demo aggregate report #session$sendCustomMessage("unbind-DT", "mainTable") withProgress(message = "Loading Demo Data", value = 0, { - load(url("https://github.com/griffithlab/pVACtools/raw/489a68cdd9e84e38b1bacc661aba15d78410282f/pvactools/tools/pvacview/data/HCC1395_demo_data.rda")) + load(url("https://github.com/griffithlab/pVACtools/raw/a3cc6d2b190a344d846438c1f0e5073e748dbd52/pvactools/tools/pvacview/data/HCC1395_demo_data.rda")) incProgress(0.3) #data <- getURL("https://raw.githubusercontent.com/griffithlab/pVACtools/c5a4f4c5b0bfa9c2832fc752e98dddea4c1c9eda/pvactools/tools/pvacview/data/H_NJ-HCC1395-HCC1395.Class_I.all_epitopes.aggregated.tsv") #mainData <- read.table(text = data, sep = "\t", header = FALSE, stringsAsFactors = FALSE, check.names = FALSE) colnames(mainData) <- mainData[1, ] mainData <- mainData[-1, ] row.names(mainData) <- NULL - setButtonStyling(mainData$Evaluation) - mainData$Acpt <- shinyInputSelect(actionButton, nrow(mainData), "button-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - mainData$Rej <- shinyInputSelect(actionButton, nrow(mainData), "button-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - mainData$Rev <- shinyInputSelect(actionButton, nrow(mainData), "button-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + setButtonStyling(mainData$Evaluation, mainData$ID) + mainData$Acpt <- shinyInputSelect(actionButton, mainData["ID"], "button-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + mainData$Rej <- shinyInputSelect(actionButton, mainData["ID"], "button-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + mainData$Rev <- shinyInputSelect(actionButton, mainData["ID"], "button-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") mainData$`IC50 MT` <- as.numeric(mainData$`IC50 MT`) mainData$`%ile MT` <- as.numeric(mainData$`%ile MT`) mainData$`RNA Depth` <- as.character(as.integer(mainData$`RNA Depth`)) mainData$`TSL`[is.na(mainData$`TSL`)] <- "NA" - df$evaluations <- mainData[c("ID", "Evaluation")] + df$evaluations <- data.frame(data = mainData$Evaluation, row.names = mainData$ID) df$mainTable <- mainData incProgress(0.1) ## Class I demo metrics file @@ -254,7 +255,7 @@ server <- shinyServer(function(input, output, session) { rownames(df$comments) <- df$mainTable$ID incProgress(0.2) ## Class II additional demo aggregate report - add_data <- getURL("https://raw.githubusercontent.com/griffithlab/pVACtools/489a68cdd9e84e38b1bacc661aba15d78410282f/pvactools/tools/pvacview/data/H_NJ-HCC1395-HCC1395.Class_II.all_epitopes.aggregated.tsv") + add_data <- getURL("https://raw.githubusercontent.com/griffithlab/pVACtools/a3cc6d2b190a344d846438c1f0e5073e748dbd52/pvactools/tools/pvacview/data/H_NJ-HCC1395-HCC1395.Class_II.all_epitopes.aggregated.tsv") addData <- read.table(text = add_data, sep = "\t", header = FALSE, stringsAsFactors = FALSE, check.names = FALSE) colnames(addData) <- addData[1, ] addData <- addData[-1, ] @@ -643,37 +644,34 @@ server <- shinyServer(function(input, output, session) { if (is.null(df$mainTable)) { return() } - selectedRow <- as.numeric(strsplit(input$accept_eval, "_")[[1]][2]) - selectedID <- df$mainTable$ID[selectedRow] - df$evaluations[df$evaluations$ID == selectedID, "Evaluation"] <- "Accept" - html <- paste0("#button-acpt_", selectedRow ," { color: red !important; }") + selectedID <- strsplit(input$accept_eval, "_")[[1]][2] + df$evaluations[selectedID, 1] <- "Accept" + html <- paste0("#button-acpt_", selectedID ," { color: green !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-rej_", selectedRow, ')'), multiple = TRUE) - removeUI(selector = paste0("style:contains(#button-rev_", selectedRow, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-rej_", selectedID, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-rev_", selectedID, ')'), multiple = TRUE) }) observeEvent(input$reject_eval, { if (is.null(df$mainTable)) { return() } - selectedRow <- as.numeric(strsplit(input$reject_eval, "_")[[1]][2]) - selectedID <- df$mainTable$ID[selectedRow] - df$evaluations[df$evaluations$ID == selectedID, "Evaluation"] <- "Reject" - html <- paste0("#button-rej_", selectedRow ," { color: red !important; }") + selectedID <- strsplit(input$reject_eval, "_")[[1]][2] + df$evaluations[selectedID, 1] <- "Reject" + html <- paste0("#button-rej_", selectedID ," { color: red !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-acpt_", selectedRow, ')'), multiple = TRUE) - removeUI(selector = paste0("style:contains(#button-rev_", selectedRow, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-acpt_", selectedID, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-rev_", selectedID, ')'), multiple = TRUE) }) observeEvent(input$review_eval, { if (is.null(df$mainTable)) { return() } - selectedRow <- as.numeric(strsplit(input$review_eval, "_")[[1]][2]) - selectedID <- df$mainTable$ID[selectedRow] - df$evaluations[df$evaluations$ID == selectedID, "Evaluation"] <- "Review" - html <- paste0("#button-rev_", selectedRow ," { color: red !important; }") + selectedID <- strsplit(input$review_eval, "_")[[1]][2] + df$evaluations[selectedID, 1] <- "Review" + html <- paste0("#button-rev_", selectedID ," { color: orange !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-acpt_", selectedRow, ')'), multiple = TRUE) - removeUI(selector = paste0("style:contains(#button-rej_", selectedRow, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-acpt_", selectedID, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-rej_", selectedID, ')'), multiple = TRUE) }) ##selected row text box output$selected <- renderText({ @@ -950,7 +948,10 @@ server <- shinyServer(function(input, output, session) { ##Anchor Heatmap overlayed on selected peptide sequences anchorPlotHeight <- reactive({ if (is.null(df$metricsData)) { - return(0) + return(100) + } + if (length(df$metricsData[[selectedID()]]$good_binders) == 0) { + return(100) } peptide_data <- df$metricsData[[selectedID()]]$good_binders[[selectedTranscriptSet()]]$`peptides` peptide_names <- names(peptide_data) @@ -1097,12 +1098,12 @@ server <- shinyServer(function(input, output, session) { hla_allele_count <- length(unique(bindingScoreDataIC50()$HLA_allele)) incProgress(0.5) p <- ggplot(data = bindingScoreDataIC50(), aes(x = Mutant, y = Score, color = Mutant), trim = FALSE) + geom_violin() + facet_grid(cols = vars(HLA_allele)) + scale_y_continuous(trans = "log10") + #coord_trans(y = "log10") + - stat_summary(fun.y = mean, fun.ymin = mean, fun.ymax = mean, geom = "crossbar", width = 0.25, position = position_dodge(width = .25)) + - geom_jitter(data = bindingScoreDataIC50(), aes(shape = algorithms), sizes = 5, stroke = 1, position = position_jitter(0.3)) + + stat_summary(fun = mean, fun.min = mean, fun.max = mean, geom = "crossbar", width = 0.25, position = position_dodge(width = .25)) + + geom_jitter(data = bindingScoreDataIC50(), aes(shape = algorithms), size = 5, stroke = 1, position = position_jitter(0.3)) + scale_shape_manual(values = 0:8) + geom_hline(aes(yintercept = yintercept, linetype = Cutoffs), line.data, color = rep(line.data$color, hla_allele_count)) + scale_color_manual(values = rep(c("MT" = "#D2B4DE", "WT" = "#F7DC6F"), hla_allele_count)) + - theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 15), axis.ticks = element_line(size = 3), legend.text = element_text(size = 15), legend.title = element_text(size = 15)) + theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 15), axis.ticks = element_line(linewidth = 3), legend.text = element_text(size = 15), legend.title = element_text(size = 15)) incProgress(0.5) print(p) }else { @@ -1155,12 +1156,12 @@ server <- shinyServer(function(input, output, session) { hla_allele_count <- length(unique(combinedBindingElutionDataPercentile()$HLA_allele)) incProgress(0.5) p <- ggplot(data = combinedBindingElutionDataPercentile(), aes(x = Mutant, y = Score, color = Mutant), trim = FALSE) + geom_violin() + facet_grid(cols = vars(HLA_allele)) + scale_y_continuous(trans = "log10") + #coord_trans(y = "log10") + - stat_summary(fun.y = mean, fun.ymin = mean, fun.ymax = mean, geom = "crossbar", width = 0.25, position = position_dodge(width = .25)) + + stat_summary(fun = mean, fun.min = mean, fun.max = mean, geom = "crossbar", width = 0.25, position = position_dodge(width = .25)) + geom_jitter(data = combinedBindingElutionDataPercentile(), aes(shape = algorithms), size = 5, stroke = 1, position = position_jitter(0.3)) + scale_shape_manual(values = 0:10) + geom_hline(aes(yintercept = yintercept, linetype = Cutoffs), line.data, color = rep(line.data$color, hla_allele_count)) + scale_color_manual(values = rep(c("MT" = "#D2B4DE", "WT" = "#F7DC6F"), hla_allele_count)) + - theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 15), axis.ticks = element_line(size = 3), legend.text = element_text(size = 15), legend.title = element_text(size = 15)) + theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 15), axis.ticks = element_line(linewidth = 3), legend.text = element_text(size = 15), legend.title = element_text(size = 15)) incProgress(0.5) print(p) }else { @@ -1432,16 +1433,16 @@ server <- shinyServer(function(input, output, session) { return(nchar(df$metricsData[[selectedID()]]$reference_matches$query_peptide) * 20) } } ) - ##############################EXPORT TAB############################################## #evalutation overview table output$checked <- renderTable({ if (is.null(df$evaluations)) { return() } - data <- as.data.frame(table(df$evaluations$Evaluation)) + data <- as.data.frame(table(df$evaluations)) colnames(data) <- c("Evaluation","Count") data }) + ##############################EXPORT TAB############################################## #export table display with options to download output$ExportTable <- renderDataTable({ if (is.null(df$mainTable)) { @@ -1452,8 +1453,8 @@ server <- shinyServer(function(input, output, session) { "Col RNA Depth", "Col DNA VAF", "Percentile Fail", "Has Prob Pos", "Acpt", "Rej", "Rev") data <- df$mainTable[, !(colsToDrop)] col_names <- colnames(data) - data <- plyr::join(data, df$evaluations, by='ID') - colnames(data) <- c(col_names, "Evaluation") + evaluations <- data.frame("ID" = row.names(df$evaluations), Evaluation = df$evaluations[, 1]) + data <- join(data, evaluations) comments <- data.frame("ID" = row.names(df$comments), Comments = df$comments[, 1]) data <- join(data, comments) data[is.na(data)] <- "NA" @@ -1551,16 +1552,16 @@ server <- shinyServer(function(input, output, session) { len <- nrow(df_neofox$mainTable_neofox) if ('Evaluation' %in% colnames(df_neofox$mainTable_neofox)) { - setButtonStyling(df_neofox$mainTable_neofox$Evaluation) + setButtonStyling(df_neofox$mainTable_neofox$Evaluation, df_neofox$mainTable_neofox$ID) } else { df_neofox$mainTable_neofox["Evaluation"] = "Pending" } df_neofox$mainTable_neofox <- cbind(ID = rownames(df_neofox$mainTable_neofox), df_neofox$mainTable_neofox) df_neofox$evaluations <- df_neofox$mainTable_neofox[c("ID", "Evaluation")] df_neofox$mainTable_neofox$Evaluation <- NULL - df_neofox$mainTable_neofox$Acpt <- shinyInputSelect(actionButton, nrow(mainData_neofox), "button-neofox-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - df_neofox$mainTable_neofox$Rej <- shinyInputSelect(actionButton, nrow(mainData_neofox), "button-neofox-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - df_neofox$mainTable_neofox$Rev <- shinyInputSelect(actionButton, nrow(mainData_neofox), "button-neofox-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + df_neofox$mainTable_neofox$Acpt <- shinyInputSelect(actionButton, df_neofox$mainTable_neofox["ID"], "button-neofox-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + df_neofox$mainTable_neofox$Rej <- shinyInputSelect(actionButton, df_neofox$mainTable_neofox["ID"], "button-neofox-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + df_neofox$mainTable_neofox$Rev <- shinyInputSelect(actionButton, df_neofox$mainTable_neofox["ID"], "button-neofox-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") if ("Comments" %in% colnames(df_neofox$mainTable_neofox)) { df_neofox$comments <- data.frame(data = df_neofox$mainTable_neofox$`Comments`, nrow = nrow(df_neofox$mainTable_neofox), ncol = 1) @@ -1633,16 +1634,16 @@ server <- shinyServer(function(input, output, session) { len <- nrow(df_neofox$mainTable_neofox) if ('Evaluation' %in% colnames(df_neofox$mainTable_neofox)) { - setButtonStyling(df_neofox$mainTable_neofox$Evaluation) + setButtonStyling(df_neofox$mainTable_neofox$Evaluation, df_neofox$mainTable_neofox$ID) } else { df_neofox$mainTable_neofox["Evaluation"] = "Pending" } df_neofox$mainTable_neofox <- cbind(ID = rownames(df_neofox$mainTable_neofox), df_neofox$mainTable_neofox) df_neofox$evaluations <- df_neofox$mainTable_neofox[c("ID", "Evaluation")] df_neofox$mainTable_neofox$Evaluation <- NULL - df_neofox$mainTable_neofox$Acpt <- shinyInputSelect(actionButton, nrow(mainData_neofox), "button-neofox-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - df_neofox$mainTable_neofox$Rej <- shinyInputSelect(actionButton, nrow(mainData_neofox), "button-neofox-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - df_neofox$mainTable_neofox$Rev <- shinyInputSelect(actionButton, nrow(mainData_neofox), "button-neofox-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + df_neofox$mainTable_neofox$Acpt <- shinyInputSelect(actionButton, df_neofox$mainTable_neofox["ID"], "button-neofox-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + df_neofox$mainTable_neofox$Rej <- shinyInputSelect(actionButton, df_neofox$mainTable_neofox["ID"], "button-neofox-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + df_neofox$mainTable_neofox$Rev <- shinyInputSelect(actionButton, df_neofox$mainTable_neofox["ID"], "button-neofox-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") if ("Comments" %in% colnames(df_neofox$mainTable_neofox)) { df_neofox$comments <- data.frame(data = df_neofox$mainTable_neofox$`Comments`, nrow = nrow(df_neofox$mainTable_neofox), ncol = 1) @@ -1747,34 +1748,34 @@ server <- shinyServer(function(input, output, session) { if (is.null(df_neofox$mainTable_neofox)) { return() } - selectedRow <- as.numeric(strsplit(input$accept_neofox_eval, "_")[[1]][2]) - df_neofox$evaluations[df_neofox$evaluations$ID == selectedRow, "Evaluation"] <- "Accept" - html <- paste0("#button-neofox-acpt_", selectedRow ," { color: red !important; }") + selectedID <- strsplit(input$accept_neofox_eval, "_")[[1]][2] + df_neofox$evaluations[df_neofox$evaluations$ID == selectedID, "Evaluation"] <- "Accept" + html <- paste0("#button-neofox-acpt_", selectedID ," { color: red !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-neofox-rej_", selectedRow, ')'), multiple = TRUE) - removeUI(selector = paste0("style:contains(#button-neofox-rev_", selectedRow, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-neofox-rej_", selectedID, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-neofox-rev_", selectedID, ')'), multiple = TRUE) }) observeEvent(input$reject_neofox_eval, { if (is.null(df_neofox$mainTable_neofox)) { return() } - selectedRow <- as.numeric(strsplit(input$reject_neofox_eval, "_")[[1]][2]) - df_neofox$evaluations[df_neofox$evaluations$ID == selectedRow, "Evaluation"] <- "Reject" - html <- paste0("#button-neofox-rej_", selectedRow ," { color: red !important; }") + selectedID <- as.numeric(strsplit(input$reject_neofox_eval, "_")[[1]][2]) + df_neofox$evaluations[df_neofox$evaluations$ID == selectedID, "Evaluation"] <- "Reject" + html <- paste0("#button-neofox-rej_", selectedID ," { color: red !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-neofox-acpt_", selectedRow, ')'), multiple = TRUE) - removeUI(selector = paste0("style:contains(#button-neofox-rev_", selectedRow, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-neofox-acpt_", selectedID, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-neofox-rev_", selectedID, ')'), multiple = TRUE) }) observeEvent(input$review_neofox_eval, { if (is.null(df_neofox$mainTable_neofox)) { return() } - selectedRow <- as.numeric(strsplit(input$review_neofox_eval, "_")[[1]][2]) - df_neofox$evaluations[df_neofox$evaluations$ID == selectedRow, "Evaluation"] <- "Review" - html <- paste0("#button-neofox-rev_", selectedRow ," { color: red !important; }") + selectedID <- as.numeric(strsplit(input$review_neofox_eval, "_")[[1]][2]) + df_neofox$evaluations[df_neofox$evaluations$ID == selectedID, "Evaluation"] <- "Review" + html <- paste0("#button-neofox-rev_", selectedID ," { color: red !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-neofox-acpt_", selectedRow, ')'), multiple = TRUE) - removeUI(selector = paste0("style:contains(#button-neofox-rej_", selectedRow, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-neofox-acpt_", selectedID, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-neofox-rej_", selectedID, ')'), multiple = TRUE) }) # NeoFox evalutation overview table @@ -1852,7 +1853,7 @@ server <- shinyServer(function(input, output, session) { scale_color_manual(values = c("No" = "#939094", "Yes" = "#f42409")) + labs(x = NULL) + facet_wrap(~Feature, scales="free", ncol=6) + - theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 10), axis.ticks = element_line(size = 3), legend.text = element_text(size = 10), legend.title = element_text(size = 10)) + theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 10), axis.ticks = element_line(linewidth = 3), legend.text = element_text(size = 10), legend.title = element_text(size = 10)) incProgress(0.5) print(p_neofox) @@ -2111,7 +2112,7 @@ server <- shinyServer(function(input, output, session) { "Gene:", .data[["gene"]]))) + geom_point(aes(color = .data[[input$color_scatter]], size = .data[[input$size_scatter]])) + # Correct placement of aes() here scale_color_gradient(low = input$min_col, high = input$max_col) + - theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 15), axis.ticks = element_line(size = 3), legend.text = element_text(size = 15), legend.title = element_text(size = 15)) + theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 15), axis.ticks = element_line(linewidth = 3), legend.text = element_text(size = 15), legend.title = element_text(size = 15)) scatter_plot <- ggplotly(scatter_plot) @@ -2309,7 +2310,8 @@ server <- shinyServer(function(input, output, session) { df_custom$group_inds <- row_ind_df row_ind_top <- apply(row_ind_df, 1, function(x) {unlist(x[1])[1]}) df_custom$mainTable_custom <- as.data.frame(reformat_data[row_ind_top, ]) - df_custom$mainTable_custom <- cbind(Select = shinyInputSelect(actionButton, nrow(df_custom$mainTable_custom), "button_", label = "Investigate", onclick = 'Shiny.onInputChange(\"custom_select_button\", this.id)'), df_custom$mainTable_custom) + df_custom$mainTable_custom["ID"] <- 1:nrow(df_custom$mainTable_custom) + df_custom$mainTable_custom <- cbind(Select = shinyInputSelect(actionButton, df_custom$mainTable_custom["ID"], "button_", label = "Investigate", onclick = 'Shiny.onInputChange(\"custom_select_button\", this.id)'), df_custom$mainTable_custom) df_custom$metricsData <- get_group_inds(df_custom$fullData, df_custom$group_inds) df_custom$peptide_features <- input$peptide_features updateTabItems(session, "custom_tabs", "custom_explore") @@ -2610,7 +2612,7 @@ server <- shinyServer(function(input, output, session) { strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 15), - axis.ticks = element_line(size = 3), + axis.ticks = element_line(linewidth = 3), legend.text = element_text(size = 15), legend.title = element_text(size = 15) ) diff --git a/pvactools/tools/pvacseq/example_data/results/MHC_Class_II/ui.R b/pvactools/tools/pvacseq/example_data/results/MHC_Class_II/ui.R index 45154935..e2730359 100644 --- a/pvactools/tools/pvacseq/example_data/results/MHC_Class_II/ui.R +++ b/pvactools/tools/pvacseq/example_data/results/MHC_Class_II/ui.R @@ -275,7 +275,7 @@ explore_tab <- tabItem( DTOutput(outputId = "bindingDatatable"), style = "overflow-x: scroll;" ), tabPanel("Elution and Immunogenicity Data", - h4("Prediction score table showing exact MHC scpres for elution, immunogenicity, and percentile calculations."), + h4("Prediction score table showing exact MHC scores for elution, immunogenicity, and percentile calculations."), DTOutput(outputId = "elutionDatatable"), br(), strong("BigMHC_EL / BigMHC_IM"), span(": A deep learning tool for predicting MHC-I (neo)epitope presentation and immunogenicity. ("), diff --git a/pvactools/tools/pvacseq/example_data/results/combined/HCC1395_TUMOR_DNA.all_epitopes.aggregated.metrics.json b/pvactools/tools/pvacseq/example_data/results/combined/HCC1395_TUMOR_DNA.all_epitopes.aggregated.metrics.json index cf942d18..00924f9e 100644 --- a/pvactools/tools/pvacseq/example_data/results/combined/HCC1395_TUMOR_DNA.all_epitopes.aggregated.metrics.json +++ b/pvactools/tools/pvacseq/example_data/results/combined/HCC1395_TUMOR_DNA.all_epitopes.aggregated.metrics.json @@ -59083,11 +59083,286 @@ "best_hla_allele": "DRB1*04:05" }, "chr1-111727105-111727106-G-T": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "RLSKGSGHF": { + "ic50s_MT": [ + "X", + 6086.81982421875, + "X" + ], + "percentiles_MT": [ + "X", + 4.800000190734863, + "X" + ], + "ic50s_WT": [ + "X", + 3915.305, + "X" + ], + "percentiles_WT": [ + "X", + 3.055, + "X" + ], + "hla_types": [ + "DRB1*04:05", + "HLA-A*29:02", + "HLA-B*45:01" + ], + "mutation_position": "1", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign" + ], + "MT": { + "HLA-A*29:02": [ + 821.2253847037994, + 5235.29, + "NA", + "NA", + 8147.13, + "NA", + 6095.65, + 6015.92, + 6128.72, + 6077.99, + 7429.68, + "NA" + ] + }, + "WT": { + "HLA-A*29:02": [ + 508.6269905117159, + 5061.76, + "NA", + "NA", + 4022.06, + "NA", + 2551.25, + 3665.32, + 7527.49, + 3808.55, + 4819.15, + "NA" + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign" + ], + "MT": { + "HLA-A*29:02": [ + 1.559749960899353, + 3.200000047683716, + "NA", + "NA", + 6.300000190734863, + "NA", + 7.300000190734863, + 3.299999952316284, + 16.0, + 13.0, + 15.0, + "NA" + ] + }, + "WT": { + "HLA-A*29:02": [ + 1.25875, + 2.41, + "NA", + "NA", + 3.7, + "NA", + 4.4, + 2.4, + 20.0, + 8.2, + 9.9, + "NA" + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "HLA-A*29:02": [ + 0.1072599105536937, + 0.140017892799247, + 0.0316, + "NA", + 0.0021173267, + 0.1212231 + ] + }, + "WT": { + "HLA-A*29:02": [ + 0.0495408065617084, + 0.1745092204070079, + 0.057, + "NA", + 0.010859818, + 0.17833187 + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "HLA-A*29:02": [ + "NA", + 2.334510869565136, + 1.9, + "NA", + "NA", + "NA" + ] + }, + "WT": { + "HLA-A*29:02": [ + "NA", + 2.012282608695557, + 1.4, + "NA", + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL" + ], + "MT": { + "HLA-A*29:02": [ + 1.559749960899353, + 3.200000047683716, + "NA", + "NA", + 6.300000190734863, + "NA", + 7.300000190734863, + 3.299999952316284, + 16.0, + 13.0, + 15.0, + "NA", + 2.334510869565136, + 1.9, + "NA" + ] + }, + "WT": { + "HLA-A*29:02": [ + 1.25875, + 2.41, + "NA", + "NA", + 3.7, + "NA", + 4.4, + 2.4, + 20.0, + 8.2, + 9.9, + "NA", + 2.012282608695557, + 1.4, + "NA" + ] + } + }, + "wt_peptide": "SLSKGSGHF" + } + }, + "transcripts": [ + "ENST00000357260.6-INKA2-S/R-252" + ], + "transcript_expr": [ + 1.081 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 297 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 1.081 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 1.081 + ], "DNA VAF": 0.063, "RNA VAF": 0.0, "gene_expr": 2.143, @@ -232849,40 +233124,27 @@ "best_hla_allele": "DRB1*04:05" }, "chr12-116009024-116009025-G-C": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 0.05, - "RNA VAF": 0.038, - "gene_expr": 77.827, - "best_peptide_mt": "FSAGPSSSSSLPPPG", - "best_peptide_wt": "FSAGPSSSSSLPPPA", - "best_hla_allele": "DRB1*04:05" - }, - "chr13-25541936-25541937-G-C": { "good_binders": { "Transcript Set 1": { "peptides": { - "LKIRQGLSHTAHMQT": { + "FSAGPSSSSSLPPPG": { "ic50s_MT": [ - 1216.1600341796875, + 6508.23486328125, "X", "X" ], "percentiles_MT": [ - 40.0, + 89.0, "X", "X" ], "ic50s_WT": [ - 794.9, + 6703.74, "X", "X" ], "percentiles_WT": [ - 32.0, + 88.0, "X", "X" ], @@ -232891,7 +233153,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "12", + "mutation_position": "15", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -232913,32 +233175,32 @@ "DRB1*04:05": [ "NA", "NA", - 151.58, - 1127.1, + 3859.27, + 10351.0, "NA", - 1305.22, + 9157.2, "NA", "NA", "NA", "NA", "NA", - 1335.0 + 1117.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 111.37, - 627.8, + 4934.64, + 9468.1, "NA", - 1374.77, + 8472.84, "NA", "NA", "NA", "NA", "NA", - 962.0 + 968.0 ] } }, @@ -232961,26 +233223,26 @@ "DRB1*04:05": [ "NA", "NA", - 5.980000019073486, - 38.0, + 42.41999816894531, + 90.0, "NA", - 47.0, + 92.0, "NA", "NA", "NA", "NA", "NA", - 40.0 + 35.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 4.49, - 27.0, + 47.09, + 88.0, "NA", - 48.0, + 91.0, "NA", "NA", "NA", @@ -233004,7 +233266,7 @@ "NA", "NA", "NA", - 0.0065, + 0.001, "NA", "NA" ] @@ -233014,7 +233276,7 @@ "NA", "NA", "NA", - 0.0109, + 0.0011, "NA", "NA" ] @@ -233034,7 +233296,7 @@ "NA", "NA", "NA", - 58.0, + 89.0, "NA", "NA" ] @@ -233044,7 +233306,7 @@ "NA", "NA", "NA", - 48.0, + 88.0, "NA", "NA" ] @@ -233072,29 +233334,29 @@ "DRB1*04:05": [ "NA", "NA", - 5.980000019073486, - 38.0, + 42.41999816894531, + 90.0, "NA", - 47.0, + 92.0, "NA", "NA", "NA", "NA", "NA", - 40.0, + 35.0, "NA", "NA", - 58.0 + 89.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 4.49, - 27.0, + 47.09, + 88.0, "NA", - 48.0, + 91.0, "NA", "NA", "NA", @@ -233103,30 +233365,74 @@ 32.0, "NA", "NA", - 48.0 + 88.0 ] } }, - "wt_peptide": "LKIRQGLSHTADMQT" - }, - "TNLKIRQGLSHTAHM": { + "wt_peptide": "FSAGPSSSSSLPPPA" + } + }, + "transcripts": [ + "ENST00000281928.9-MED13L-A/G-463" + ], + "transcript_expr": [ + 2.852 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 2210 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 2.852 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 2.852 + ], + "DNA VAF": 0.05, + "RNA VAF": 0.038, + "gene_expr": 77.827, + "best_peptide_mt": "FSAGPSSSSSLPPPG", + "best_peptide_wt": "FSAGPSSSSSLPPPA", + "best_hla_allele": "DRB1*04:05" + }, + "chr13-25541936-25541937-G-C": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "LKIRQGLSHTAHMQT": { "ic50s_MT": [ - 1400.7099609375, + 1216.1600341796875, "X", "X" ], "percentiles_MT": [ - 44.0, + 40.0, "X", "X" ], "ic50s_WT": [ - 1380.105, + 794.9, "X", "X" ], "percentiles_WT": [ - 39.0, + 32.0, "X", "X" ], @@ -233135,7 +233441,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "14", + "mutation_position": "12", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -233157,32 +233463,32 @@ "DRB1*04:05": [ "NA", "NA", - 829.87, - 1487.6, + 151.58, + 1127.1, "NA", - 1313.82, + 1305.22, "NA", "NA", "NA", "NA", "NA", - 1917.0 + 1335.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 327.01, - 1156.4, + 111.37, + 627.8, "NA", - 1603.81, + 1374.77, "NA", "NA", "NA", "NA", "NA", - 1723.0 + 962.0 ] } }, @@ -233205,8 +233511,8 @@ "DRB1*04:05": [ "NA", "NA", - 19.850000381469727, - 44.0, + 5.980000019073486, + 38.0, "NA", 47.0, "NA", @@ -233214,23 +233520,23 @@ "NA", "NA", "NA", - 50.0 + 40.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 10.99, - 39.0, + 4.49, + 27.0, "NA", - 52.0, + 48.0, "NA", "NA", "NA", "NA", "NA", - 47.0 + 32.0 ] } }, @@ -233248,7 +233554,7 @@ "NA", "NA", "NA", - 0.0134, + 0.0065, "NA", "NA" ] @@ -233258,7 +233564,7 @@ "NA", "NA", "NA", - 0.019, + 0.0109, "NA", "NA" ] @@ -233278,7 +233584,7 @@ "NA", "NA", "NA", - 44.0, + 58.0, "NA", "NA" ] @@ -233288,7 +233594,7 @@ "NA", "NA", "NA", - 39.0, + 48.0, "NA", "NA" ] @@ -233316,8 +233622,8 @@ "DRB1*04:05": [ "NA", "NA", - 19.850000381469727, - 44.0, + 5.980000019073486, + 38.0, "NA", 47.0, "NA", @@ -233325,52 +233631,52 @@ "NA", "NA", "NA", - 50.0, + 40.0, "NA", "NA", - 44.0 + 58.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 10.99, - 39.0, + 4.49, + 27.0, "NA", - 52.0, + 48.0, "NA", "NA", "NA", "NA", "NA", - 47.0, + 32.0, "NA", "NA", - 39.0 + 48.0 ] } }, - "wt_peptide": "TNLKIRQGLSHTADM" + "wt_peptide": "LKIRQGLSHTADMQT" }, - "KIRQGLSHTAHMQTR": { + "TNLKIRQGLSHTAHM": { "ic50s_MT": [ - 1405.72998046875, + 1400.7099609375, "X", "X" ], "percentiles_MT": [ - 50.0, + 44.0, "X", "X" ], "ic50s_WT": [ - 848.15, + 1380.105, "X", "X" ], "percentiles_WT": [ - 32.0, + 39.0, "X", "X" ], @@ -233379,7 +233685,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "11", + "mutation_position": "14", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -233401,32 +233707,32 @@ "DRB1*04:05": [ "NA", "NA", - 216.75, - 1109.4, + 829.87, + 1487.6, "NA", - 1702.06, + 1313.82, "NA", "NA", "NA", "NA", "NA", - 1894.0 + 1917.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 171.96, - 504.3, + 327.01, + 1156.4, "NA", - 1404.45, + 1603.81, "NA", "NA", "NA", "NA", "NA", - 1192.0 + 1723.0 ] } }, @@ -233449,10 +233755,10 @@ "DRB1*04:05": [ "NA", "NA", - 8.0600004196167, - 38.0, + 19.850000381469727, + 44.0, "NA", - 54.0, + 47.0, "NA", "NA", "NA", @@ -233465,16 +233771,16 @@ "DRB1*04:05": [ "NA", "NA", - 6.660000000000001, - 23.0, + 10.99, + 39.0, "NA", - 49.0, + 52.0, "NA", "NA", "NA", "NA", "NA", - 37.0 + 47.0 ] } }, @@ -233492,7 +233798,7 @@ "NA", "NA", "NA", - 0.0049, + 0.0134, "NA", "NA" ] @@ -233502,7 +233808,7 @@ "NA", "NA", "NA", - 0.029, + 0.019, "NA", "NA" ] @@ -233522,7 +233828,7 @@ "NA", "NA", "NA", - 64.0, + 44.0, "NA", "NA" ] @@ -233532,7 +233838,7 @@ "NA", "NA", "NA", - 32.0, + 39.0, "NA", "NA" ] @@ -233560,10 +233866,10 @@ "DRB1*04:05": [ "NA", "NA", - 8.0600004196167, - 38.0, + 19.850000381469727, + 44.0, "NA", - 54.0, + 47.0, "NA", "NA", "NA", @@ -233572,49 +233878,49 @@ 50.0, "NA", "NA", - 64.0 + 44.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 6.660000000000001, - 23.0, + 10.99, + 39.0, "NA", - 49.0, + 52.0, "NA", "NA", "NA", "NA", "NA", - 37.0, + 47.0, "NA", "NA", - 32.0 + 39.0 ] } }, - "wt_peptide": "KIRQGLSHTADMQTR" + "wt_peptide": "TNLKIRQGLSHTADM" }, - "NLKIRQGLSHTAHMQ": { + "KIRQGLSHTAHMQTR": { "ic50s_MT": [ - 1521.5250244140625, + 1405.72998046875, "X", "X" ], "percentiles_MT": [ - 42.0, + 50.0, "X", "X" ], "ic50s_WT": [ - 1352.7, + 848.15, "X", "X" ], "percentiles_WT": [ - 33.0, + 32.0, "X", "X" ], @@ -233623,7 +233929,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "13", + "mutation_position": "11", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -233645,32 +233951,276 @@ "DRB1*04:05": [ "NA", "NA", - 1696.55, - 1346.5, + 216.75, + 1109.4, "NA", - 1248.7, + 1702.06, "NA", "NA", "NA", "NA", "NA", - 2056.0 + 1894.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 1130.29, - 876.9, + 171.96, + 504.3, "NA", - 1575.11, + 1404.45, "NA", "NA", "NA", "NA", "NA", - 1829.0 + 1192.0 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + 8.0600004196167, + 38.0, + "NA", + 54.0, + "NA", + "NA", + "NA", + "NA", + "NA", + 50.0 + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + 6.660000000000001, + 23.0, + "NA", + 49.0, + "NA", + "NA", + "NA", + "NA", + "NA", + 37.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 0.0049, + "NA", + "NA" + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 0.029, + "NA", + "NA" + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 64.0, + "NA", + "NA" + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 32.0, + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + 8.0600004196167, + 38.0, + "NA", + 54.0, + "NA", + "NA", + "NA", + "NA", + "NA", + 50.0, + "NA", + "NA", + 64.0 + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + 6.660000000000001, + 23.0, + "NA", + 49.0, + "NA", + "NA", + "NA", + "NA", + "NA", + 37.0, + "NA", + "NA", + 32.0 + ] + } + }, + "wt_peptide": "KIRQGLSHTADMQTR" + }, + "NLKIRQGLSHTAHMQ": { + "ic50s_MT": [ + 1521.5250244140625, + "X", + "X" + ], + "percentiles_MT": [ + 42.0, + "X", + "X" + ], + "ic50s_WT": [ + 1352.7, + "X", + "X" + ], + "percentiles_WT": [ + 33.0, + "X", + "X" + ], + "hla_types": [ + "DRB1*04:05", + "HLA-A*29:02", + "HLA-B*45:01" + ], + "mutation_position": "13", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + 1696.55, + 1346.5, + "NA", + 1248.7, + "NA", + "NA", + "NA", + "NA", + "NA", + 2056.0 + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + 1130.29, + 876.9, + "NA", + 1575.11, + "NA", + "NA", + "NA", + "NA", + "NA", + 1829.0 ] } }, @@ -307021,40 +307571,27 @@ "best_hla_allele": "HLA-B*45:01" }, "chr15-40622778-40622779-C-T": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 0.444, - "RNA VAF": 0.492, - "gene_expr": 13.527, - "best_peptide_mt": "MDVLEDESVQKPKFS", - "best_peptide_wt": "MDVLEDESVQKPKFP", - "best_hla_allele": "DRB1*04:05" - }, - "chr15-40622778-40622780-CC-TT": { "good_binders": { "Transcript Set 1": { "peptides": { - "QKPKFLKEKQNVKIW": { + "MDVLEDESVQKPKFS": { "ic50s_MT": [ - 2983.0, + 5009.044921875, "X", "X" ], "percentiles_MT": [ - 63.0, + 70.0, "X", "X" ], "ic50s_WT": [ - 13258.14, + 6869.24, "X", "X" ], "percentiles_WT": [ - 96.0, + 73.48, "X", "X" ], @@ -307063,7 +307600,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "6", + "mutation_position": "15", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -307085,32 +307622,32 @@ "DRB1*04:05": [ "NA", "NA", - 2304.06, - 3318.2, + 3587.55, + 4214.5, "NA", - 2647.8, + 5803.59, "NA", "NA", "NA", "NA", "NA", - 3610.0 + 7556.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 4957.18, - 13887.0, + 16012.11, + 4237.0, "NA", - 12629.28, + 6124.48, "NA", "NA", "NA", "NA", "NA", - 27131.0 + 7614.0 ] } }, @@ -307133,32 +307670,32 @@ "DRB1*04:05": [ "NA", "NA", - 33.68000030517578, - 63.0, + 41.09000015258789, + 70.0, "NA", - 66.0, + 85.0, "NA", "NA", "NA", "NA", "NA", - 67.0 + 83.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 47.17, - 95.0, + 73.48, + 70.0, "NA", - 96.0, + 86.0, "NA", "NA", "NA", "NA", "NA", - 97.0 + 84.0 ] } }, @@ -307176,7 +307713,7 @@ "NA", "NA", "NA", - 0.0118, + 0.013, "NA", "NA" ] @@ -307186,7 +307723,7 @@ "NA", "NA", "NA", - 0.0004, + 0.0154, "NA", "NA" ] @@ -307206,7 +307743,7 @@ "NA", "NA", "NA", - 47.0, + 45.0, "NA", "NA" ] @@ -307216,7 +307753,7 @@ "NA", "NA", "NA", - 96.0, + 42.0, "NA", "NA" ] @@ -307244,46 +307781,90 @@ "DRB1*04:05": [ "NA", "NA", - 33.68000030517578, - 63.0, + 41.09000015258789, + 70.0, "NA", - 66.0, + 85.0, "NA", "NA", "NA", "NA", "NA", - 67.0, + 83.0, "NA", "NA", - 47.0 + 45.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 47.17, - 95.0, + 73.48, + 70.0, "NA", - 96.0, + 86.0, "NA", "NA", "NA", "NA", "NA", - 97.0, + 84.0, "NA", "NA", - 96.0 + 42.0 ] } }, - "wt_peptide": "QKPKFPKEKQNVKIW" - }, - "KPKFLKEKQNVKIWG": { + "wt_peptide": "MDVLEDESVQKPKFP" + } + }, + "transcripts": [ + "ENST00000346991.9-KNL1-P/S-865" + ], + "transcript_expr": [ + 0.345 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 2342 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0.345 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0.345 + ], + "DNA VAF": 0.444, + "RNA VAF": 0.492, + "gene_expr": 13.527, + "best_peptide_mt": "MDVLEDESVQKPKFS", + "best_peptide_wt": "MDVLEDESVQKPKFP", + "best_hla_allele": "DRB1*04:05" + }, + "chr15-40622778-40622780-CC-TT": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "QKPKFLKEKQNVKIW": { "ic50s_MT": [ - 3172.510009765625, + 2983.0, "X", "X" ], @@ -307293,12 +307874,12 @@ "X" ], "ic50s_WT": [ - 11504.445, + 13258.14, "X", "X" ], "percentiles_WT": [ - 94.0, + 96.0, "X", "X" ], @@ -307307,7 +307888,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "5", + "mutation_position": "6", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -307329,32 +307910,32 @@ "DRB1*04:05": [ "NA", "NA", - 2301.78, - 3279.0, + 2304.06, + 3318.2, "NA", - 3066.02, + 2647.8, "NA", "NA", "NA", "NA", "NA", - 3658.0 + 3610.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 10700.6, - 10863.4, + 4957.18, + 13887.0, "NA", - 12145.49, + 12629.28, "NA", "NA", "NA", "NA", "NA", - 24779.0 + 27131.0 ] } }, @@ -307377,10 +307958,10 @@ "DRB1*04:05": [ "NA", "NA", - 33.65999984741211, + 33.68000030517578, 63.0, "NA", - 70.0, + 66.0, "NA", "NA", "NA", @@ -307393,8 +307974,8 @@ "DRB1*04:05": [ "NA", "NA", - 63.63999999999999, - 91.0, + 47.17, + 95.0, "NA", 96.0, "NA", @@ -307420,7 +308001,7 @@ "NA", "NA", "NA", - 0.0178, + 0.0118, "NA", "NA" ] @@ -307430,7 +308011,7 @@ "NA", "NA", "NA", - 0.0006, + 0.0004, "NA", "NA" ] @@ -307450,7 +308031,7 @@ "NA", "NA", "NA", - 40.0, + 47.0, "NA", "NA" ] @@ -307460,7 +308041,7 @@ "NA", "NA", "NA", - 94.0, + 96.0, "NA", "NA" ] @@ -307488,10 +308069,10 @@ "DRB1*04:05": [ "NA", "NA", - 33.65999984741211, + 33.68000030517578, 63.0, "NA", - 70.0, + 66.0, "NA", "NA", "NA", @@ -307500,15 +308081,15 @@ 67.0, "NA", "NA", - 40.0 + 47.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 63.63999999999999, - 91.0, + 47.17, + 95.0, "NA", 96.0, "NA", @@ -307519,30 +308100,30 @@ 97.0, "NA", "NA", - 94.0 + 96.0 ] } }, - "wt_peptide": "KPKFPKEKQNVKIWG" + "wt_peptide": "QKPKFPKEKQNVKIW" }, - "VQKPKFLKEKQNVKI": { + "KPKFLKEKQNVKIWG": { "ic50s_MT": [ - 3241.2900390625, + 3172.510009765625, "X", "X" ], "percentiles_MT": [ - 65.0, + 63.0, "X", "X" ], "ic50s_WT": [ - 16898.24, + 11504.445, "X", "X" ], "percentiles_WT": [ - 97.0, + 94.0, "X", "X" ], @@ -307551,7 +308132,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "7", + "mutation_position": "5", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -307573,32 +308154,32 @@ "DRB1*04:05": [ "NA", "NA", - 2233.57, - 4146.1, + 2301.78, + 3279.0, "NA", - 3138.58, + 3066.02, "NA", "NA", "NA", "NA", "NA", - 3344.0 + 3658.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 5400.1, - 17918.7, + 10700.6, + 10863.4, "NA", - 15877.78, + 12145.49, "NA", "NA", "NA", "NA", "NA", - 25084.0 + 24779.0 ] } }, @@ -307621,8 +308202,8 @@ "DRB1*04:05": [ "NA", "NA", - 33.189998626708984, - 69.0, + 33.65999984741211, + 63.0, "NA", 70.0, "NA", @@ -307630,17 +308211,17 @@ "NA", "NA", "NA", - 65.0 + 67.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 48.89, - 97.0, + 63.63999999999999, + 91.0, "NA", - 98.0, + 96.0, "NA", "NA", "NA", @@ -307664,7 +308245,7 @@ "NA", "NA", "NA", - 0.0115, + 0.0178, "NA", "NA" ] @@ -307674,7 +308255,7 @@ "NA", "NA", "NA", - 0.0004, + 0.0006, "NA", "NA" ] @@ -307694,7 +308275,7 @@ "NA", "NA", "NA", - 47.0, + 40.0, "NA", "NA" ] @@ -307704,7 +308285,7 @@ "NA", "NA", "NA", - 96.0, + 94.0, "NA", "NA" ] @@ -307732,8 +308313,8 @@ "DRB1*04:05": [ "NA", "NA", - 33.189998626708984, - 69.0, + 33.65999984741211, + 63.0, "NA", 70.0, "NA", @@ -307741,20 +308322,20 @@ "NA", "NA", "NA", - 65.0, + 67.0, "NA", "NA", - 47.0 + 40.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 48.89, - 97.0, + 63.63999999999999, + 91.0, "NA", - 98.0, + 96.0, "NA", "NA", "NA", @@ -307763,30 +308344,30 @@ 97.0, "NA", "NA", - 96.0 + 94.0 ] } }, - "wt_peptide": "VQKPKFPKEKQNVKI" + "wt_peptide": "KPKFPKEKQNVKIWG" }, - "PKFLKEKQNVKIWGR": { + "VQKPKFLKEKQNVKI": { "ic50s_MT": [ - 3309.655029296875, + 3241.2900390625, "X", "X" ], "percentiles_MT": [ - 63.0, + 65.0, "X", "X" ], "ic50s_WT": [ - 9147.635, + 16898.24, "X", "X" ], "percentiles_WT": [ - 91.0, + 97.0, "X", "X" ], @@ -307795,7 +308376,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "4", + "mutation_position": "7", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -307817,32 +308398,32 @@ "DRB1*04:05": [ "NA", "NA", - 3353.51, - 3265.8, + 2233.57, + 4146.1, "NA", - 3200.52, + 3138.58, "NA", "NA", "NA", "NA", "NA", - 3413.0 + 3344.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 7306.54, - 8292.5, + 5400.1, + 17918.7, "NA", - 10002.77, + 15877.78, "NA", "NA", "NA", "NA", "NA", - 16091.0 + 25084.0 ] } }, @@ -307865,10 +308446,10 @@ "DRB1*04:05": [ "NA", "NA", - 39.900001525878906, - 63.0, + 33.189998626708984, + 69.0, "NA", - 71.0, + 70.0, "NA", "NA", "NA", @@ -307881,16 +308462,16 @@ "DRB1*04:05": [ "NA", "NA", - 55.14, - 86.0, + 48.89, + 97.0, "NA", - 94.0, + 98.0, "NA", "NA", "NA", "NA", "NA", - 93.0 + 97.0 ] } }, @@ -307908,7 +308489,7 @@ "NA", "NA", "NA", - 0.0066, + 0.0115, "NA", "NA" ] @@ -307918,7 +308499,7 @@ "NA", "NA", "NA", - 0.0008, + 0.0004, "NA", "NA" ] @@ -307938,7 +308519,7 @@ "NA", "NA", "NA", - 58.0, + 47.0, "NA", "NA" ] @@ -307948,7 +308529,251 @@ "NA", "NA", "NA", - 91.0, + 96.0, + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + 33.189998626708984, + 69.0, + "NA", + 70.0, + "NA", + "NA", + "NA", + "NA", + "NA", + 65.0, + "NA", + "NA", + 47.0 + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + 48.89, + 97.0, + "NA", + 98.0, + "NA", + "NA", + "NA", + "NA", + "NA", + 97.0, + "NA", + "NA", + 96.0 + ] + } + }, + "wt_peptide": "VQKPKFPKEKQNVKI" + }, + "PKFLKEKQNVKIWGR": { + "ic50s_MT": [ + 3309.655029296875, + "X", + "X" + ], + "percentiles_MT": [ + 63.0, + "X", + "X" + ], + "ic50s_WT": [ + 9147.635, + "X", + "X" + ], + "percentiles_WT": [ + 91.0, + "X", + "X" + ], + "hla_types": [ + "DRB1*04:05", + "HLA-A*29:02", + "HLA-B*45:01" + ], + "mutation_position": "4", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + 3353.51, + 3265.8, + "NA", + 3200.52, + "NA", + "NA", + "NA", + "NA", + "NA", + 3413.0 + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + 7306.54, + 8292.5, + "NA", + 10002.77, + "NA", + "NA", + "NA", + "NA", + "NA", + 16091.0 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + 39.900001525878906, + 63.0, + "NA", + 71.0, + "NA", + "NA", + "NA", + "NA", + "NA", + 65.0 + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + 55.14, + 86.0, + "NA", + 94.0, + "NA", + "NA", + "NA", + "NA", + "NA", + 93.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 0.0066, + "NA", + "NA" + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 0.0008, + "NA", + "NA" + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 58.0, + "NA", + "NA" + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 91.0, "NA", "NA" ] @@ -624164,40 +624989,27 @@ "best_hla_allele": "DRB1*04:05" }, "chr21-44330789-44330813-AGGCAGCCGCGGCCCCTAGCGGCCC-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 0.376, - "RNA VAF": 0.0, - "gene_expr": 6.57, - "best_peptide_mt": "SSHRGRVSGSAHCTH", - "best_peptide_wt": "SSHRGRVSGGPLGAA", - "best_hla_allele": "DRB1*04:05" - }, - "chr22-18606897-18606898-G-A": { "good_binders": { "Transcript Set 1": { "peptides": { - "YLSECNRQVGNIPGC": { + "SSHRGRVSGSAHCTH": { "ic50s_MT": [ - 3799.5, + 9193.3447265625, "X", "X" ], "percentiles_MT": [ - 63.43000030517578, + 87.0, "X", "X" ], "ic50s_WT": [ - 3556.9, + 17908.385, "X", "X" ], "percentiles_WT": [ - 68.14, + 96.0, "X", "X" ], @@ -624206,7 +625018,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "15", + "mutation_position": "9-10", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -624228,32 +625040,32 @@ "DRB1*04:05": [ "NA", "NA", - 10607.57, - 4722.0, + 5117.13, + 8116.1, "NA", - 2182.75, + 10270.59, "NA", "NA", "NA", "NA", "NA", - 2877.0 + 12886.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 12911.96, - 4280.8, + 20099.87, + 15716.9, "NA", - 2109.97, + 11626.91, "NA", "NA", "NA", "NA", "NA", - 2833.0 + 21607.0 ] } }, @@ -624276,32 +625088,32 @@ "DRB1*04:05": [ "NA", "NA", - 63.43000030517578, - 73.0, + 47.79999923706055, + 85.0, "NA", - 61.0, + 94.0, "NA", "NA", "NA", "NA", "NA", - 61.0 + 91.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 68.14, - 70.0, + 79.38, + 96.0, "NA", - 60.0, + 96.0, "NA", "NA", "NA", "NA", "NA", - 61.0 + 96.0 ] } }, @@ -624319,7 +625131,7 @@ "NA", "NA", "NA", - 0.0003, + 0.0012, "NA", "NA" ] @@ -624329,7 +625141,7 @@ "NA", "NA", "NA", - 0.0018, + 0.0009, "NA", "NA" ] @@ -624349,7 +625161,7 @@ "NA", "NA", "NA", - 98.0, + 87.0, "NA", "NA" ] @@ -624359,7 +625171,7 @@ "NA", "NA", "NA", - 82.0, + 91.0, "NA", "NA" ] @@ -624387,61 +625199,105 @@ "DRB1*04:05": [ "NA", "NA", - 63.43000030517578, - 73.0, + 47.79999923706055, + 85.0, "NA", - 61.0, + 94.0, "NA", "NA", "NA", "NA", "NA", - 61.0, + 91.0, "NA", "NA", - 98.0 + 87.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 68.14, - 70.0, + 79.38, + 96.0, "NA", - 60.0, + 96.0, "NA", "NA", "NA", "NA", "NA", - 61.0, + 96.0, "NA", "NA", - 82.0 + 91.0 ] } }, - "wt_peptide": "YLSECNRQVGNIPGR" - }, - "QVGNIPGCLVAEMEV": { + "wt_peptide": "SSHRGRVSGGPLGAA" + } + }, + "transcripts": [ + "ENST00000397956.7-CFAP410-GPLGAAAA/--217-224" + ], + "transcript_expr": [ + 0.0 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 375 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0.0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0.0 + ], + "DNA VAF": 0.376, + "RNA VAF": 0.0, + "gene_expr": 6.57, + "best_peptide_mt": "SSHRGRVSGSAHCTH", + "best_peptide_wt": "SSHRGRVSGGPLGAA", + "best_hla_allele": "DRB1*04:05" + }, + "chr22-18606897-18606898-G-A": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "YLSECNRQVGNIPGC": { "ic50s_MT": [ - 3908.074951171875, + 3799.5, "X", "X" ], "percentiles_MT": [ - 76.0, + 63.43000030517578, "X", "X" ], "ic50s_WT": [ - 3118.73, + 3556.9, "X", "X" ], "percentiles_WT": [ - 70.0, + 68.14, "X", "X" ], @@ -624450,7 +625306,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "8", + "mutation_position": "15", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -624472,32 +625328,32 @@ "DRB1*04:05": [ "NA", "NA", - 2408.02, - 6723.2, + 10607.57, + 4722.0, "NA", - 2664.15, + 2182.75, "NA", "NA", "NA", "NA", "NA", - 5152.0 + 2877.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 3173.76, - 8127.7, + 12911.96, + 4280.8, "NA", - 3063.7, + 2109.97, "NA", "NA", "NA", "NA", "NA", - 2220.0 + 2833.0 ] } }, @@ -624520,32 +625376,32 @@ "DRB1*04:05": [ "NA", "NA", - 34.380001068115234, - 81.0, + 63.43000030517578, + 73.0, "NA", - 66.0, + 61.0, "NA", "NA", "NA", "NA", "NA", - 76.0 + 61.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 38.940000000000005, - 85.0, - "NA", + 68.14, 70.0, "NA", + 60.0, + "NA", "NA", "NA", "NA", "NA", - 54.0 + 61.0 ] } }, @@ -624563,7 +625419,7 @@ "NA", "NA", "NA", - 0.0011, + 0.0003, "NA", "NA" ] @@ -624573,7 +625429,7 @@ "NA", "NA", "NA", - 0.0021, + 0.0018, "NA", "NA" ] @@ -624593,7 +625449,7 @@ "NA", "NA", "NA", - 89.0, + 98.0, "NA", "NA" ] @@ -624603,7 +625459,7 @@ "NA", "NA", "NA", - 79.0, + 82.0, "NA", "NA" ] @@ -624631,61 +625487,61 @@ "DRB1*04:05": [ "NA", "NA", - 34.380001068115234, - 81.0, + 63.43000030517578, + 73.0, "NA", - 66.0, + 61.0, "NA", "NA", "NA", "NA", "NA", - 76.0, + 61.0, "NA", "NA", - 89.0 + 98.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 38.940000000000005, - 85.0, - "NA", + 68.14, 70.0, "NA", + 60.0, "NA", "NA", "NA", "NA", - 54.0, + "NA", + 61.0, "NA", "NA", - 79.0 + 82.0 ] } }, - "wt_peptide": "QVGNIPGRLVAEMEV" + "wt_peptide": "YLSECNRQVGNIPGR" }, - "NIPGCLVAEMEVGTE": { + "QVGNIPGCLVAEMEV": { "ic50s_MT": [ - 3922.875, + 3908.074951171875, "X", "X" ], "percentiles_MT": [ - 75.0, + 76.0, "X", "X" ], "ic50s_WT": [ - 3179.745, + 3118.73, "X", "X" ], "percentiles_WT": [ - 52.0, + 70.0, "X", "X" ], @@ -624694,7 +625550,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "5", + "mutation_position": "8", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -624716,32 +625572,32 @@ "DRB1*04:05": [ "NA", "NA", - 1998.95, - 7929.6, + 2408.02, + 6723.2, "NA", - 3823.75, + 2664.15, "NA", "NA", "NA", "NA", "NA", - 4022.0 + 5152.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 3016.4, - 5475.6, + 3173.76, + 8127.7, "NA", - 3343.09, + 3063.7, "NA", "NA", "NA", "NA", "NA", - 2019.0 + 2220.0 ] } }, @@ -624764,32 +625620,32 @@ "DRB1*04:05": [ "NA", "NA", - 31.469999313354492, - 85.0, + 34.380001068115234, + 81.0, "NA", - 75.0, + 66.0, "NA", "NA", "NA", "NA", "NA", - 70.0 + 76.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 38.07, - 76.0, + 38.940000000000005, + 85.0, "NA", - 72.0, + 70.0, "NA", "NA", "NA", "NA", "NA", - 52.0 + 54.0 ] } }, @@ -624807,7 +625663,7 @@ "NA", "NA", "NA", - 0.0022, + 0.0011, "NA", "NA" ] @@ -624817,7 +625673,7 @@ "NA", "NA", "NA", - 0.0114, + 0.0021, "NA", "NA" ] @@ -624837,7 +625693,7 @@ "NA", "NA", "NA", - 78.0, + 89.0, "NA", "NA" ] @@ -624847,7 +625703,7 @@ "NA", "NA", "NA", - 47.0, + 79.0, "NA", "NA" ] @@ -624875,61 +625731,61 @@ "DRB1*04:05": [ "NA", "NA", - 31.469999313354492, - 85.0, + 34.380001068115234, + 81.0, "NA", - 75.0, + 66.0, "NA", "NA", "NA", "NA", "NA", - 70.0, + 76.0, "NA", "NA", - 78.0 + 89.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 38.07, - 76.0, + 38.940000000000005, + 85.0, "NA", - 72.0, + 70.0, "NA", "NA", "NA", "NA", "NA", - 52.0, + 54.0, "NA", "NA", - 47.0 + 79.0 ] } }, - "wt_peptide": "NIPGRLVAEMEVGTE" + "wt_peptide": "QVGNIPGRLVAEMEV" }, - "IPGCLVAEMEVGTEQ": { + "NIPGCLVAEMEVGTE": { "ic50s_MT": [ - 4297.52001953125, + 3922.875, "X", "X" ], "percentiles_MT": [ - 73.0, + 75.0, "X", "X" ], "ic50s_WT": [ - 3800.25, + 3179.745, "X", "X" ], "percentiles_WT": [ - 65.0, + 52.0, "X", "X" ], @@ -624938,7 +625794,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "4", + "mutation_position": "5", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -624960,32 +625816,32 @@ "DRB1*04:05": [ "NA", "NA", - 3759.04, - 6555.1, + 1998.95, + 7929.6, "NA", - 3457.49, + 3823.75, "NA", "NA", "NA", "NA", "NA", - 4836.0 + 4022.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 4988.4, - 4154.5, + 3016.4, + 5475.6, "NA", - 2555.4, + 3343.09, "NA", "NA", "NA", "NA", "NA", - 3446.0 + 2019.0 ] } }, @@ -625008,32 +625864,32 @@ "DRB1*04:05": [ "NA", "NA", - 41.93000030517578, - 80.0, + 31.469999313354492, + 85.0, "NA", - 73.0, + 75.0, "NA", "NA", "NA", "NA", "NA", - 74.0 + 70.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 47.3, - 69.0, + 38.07, + 76.0, "NA", - 65.0, + 72.0, "NA", "NA", "NA", "NA", "NA", - 66.0 + 52.0 ] } }, @@ -625051,7 +625907,7 @@ "NA", "NA", "NA", - 0.0089, + 0.0022, "NA", "NA" ] @@ -625061,7 +625917,7 @@ "NA", "NA", "NA", - 0.0752, + 0.0114, "NA", "NA" ] @@ -625081,7 +625937,7 @@ "NA", "NA", "NA", - 52.0, + 78.0, "NA", "NA" ] @@ -625091,7 +625947,7 @@ "NA", "NA", "NA", - 19.0, + 47.0, "NA", "NA" ] @@ -625119,61 +625975,61 @@ "DRB1*04:05": [ "NA", "NA", - 41.93000030517578, - 80.0, + 31.469999313354492, + 85.0, "NA", - 73.0, + 75.0, "NA", "NA", "NA", "NA", "NA", - 74.0, + 70.0, "NA", "NA", - 52.0 + 78.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 47.3, - 69.0, + 38.07, + 76.0, "NA", - 65.0, + 72.0, "NA", "NA", "NA", "NA", "NA", - 66.0, + 52.0, "NA", "NA", - 19.0 + 47.0 ] } }, - "wt_peptide": "IPGRLVAEMEVGTEQ" + "wt_peptide": "NIPGRLVAEMEVGTE" }, - "GNIPGCLVAEMEVGT": { + "IPGCLVAEMEVGTEQ": { "ic50s_MT": [ - 4340.10986328125, + 4297.52001953125, "X", "X" ], "percentiles_MT": [ - 77.0, + 73.0, "X", "X" ], "ic50s_WT": [ - 3103.385, + 3800.25, "X", "X" ], "percentiles_WT": [ - 60.0, + 65.0, "X", "X" ], @@ -625182,7 +626038,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "6", + "mutation_position": "4", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -625204,32 +626060,32 @@ "DRB1*04:05": [ "NA", "NA", - 1271.43, - 9846.0, + 3759.04, + 6555.1, "NA", - 4143.22, + 3457.49, "NA", "NA", "NA", "NA", "NA", - 4537.0 + 4836.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 1506.07, - 9323.9, + 4988.4, + 4154.5, "NA", - 4047.77, + 2555.4, "NA", "NA", "NA", "NA", "NA", - 2159.0 + 3446.0 ] } }, @@ -625252,32 +626108,32 @@ "DRB1*04:05": [ "NA", "NA", - 25.06999969482422, - 89.0, + 41.93000030517578, + 80.0, "NA", - 77.0, + 73.0, "NA", "NA", "NA", "NA", "NA", - 72.0 + 74.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 27.36, - 88.0, + 47.3, + 69.0, "NA", - 77.0, + 65.0, "NA", "NA", "NA", "NA", "NA", - 53.0 + 66.0 ] } }, @@ -625295,7 +626151,7 @@ "NA", "NA", "NA", - 0.0024, + 0.0089, "NA", "NA" ] @@ -625305,7 +626161,7 @@ "NA", "NA", "NA", - 0.0059, + 0.0752, "NA", "NA" ] @@ -625325,7 +626181,7 @@ "NA", "NA", "NA", - 77.0, + 52.0, "NA", "NA" ] @@ -625335,7 +626191,7 @@ "NA", "NA", "NA", - 60.0, + 19.0, "NA", "NA" ] @@ -625363,61 +626219,61 @@ "DRB1*04:05": [ "NA", "NA", - 25.06999969482422, - 89.0, + 41.93000030517578, + 80.0, "NA", - 77.0, + 73.0, "NA", "NA", "NA", "NA", "NA", - 72.0, + 74.0, "NA", "NA", - 77.0 + 52.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 27.36, - 88.0, + 47.3, + 69.0, "NA", - 77.0, + 65.0, "NA", "NA", "NA", "NA", "NA", - 53.0, + 66.0, "NA", "NA", - 60.0 + 19.0 ] } }, - "wt_peptide": "GNIPGRLVAEMEVGT" + "wt_peptide": "IPGRLVAEMEVGTEQ" }, - "PGCLVAEMEVGTEQT": { + "GNIPGCLVAEMEVGT": { "ic50s_MT": [ - 4416.77978515625, + 4340.10986328125, "X", "X" ], "percentiles_MT": [ - 74.0, + 77.0, "X", "X" ], "ic50s_WT": [ - 3056.4, + 3103.385, "X", "X" ], "percentiles_WT": [ - 63.0, + 60.0, "X", "X" ], @@ -625426,7 +626282,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "3", + "mutation_position": "6", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -625448,32 +626304,32 @@ "DRB1*04:05": [ "NA", "NA", - 717.74, - 6487.7, + 1271.43, + 9846.0, "NA", - 3689.56, + 4143.22, "NA", "NA", "NA", "NA", "NA", - 5144.0 + 4537.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 1119.25, - 4225.9, + 1506.07, + 9323.9, "NA", - 2347.8, + 4047.77, "NA", "NA", "NA", "NA", "NA", - 3765.0 + 2159.0 ] } }, @@ -625496,32 +626352,32 @@ "DRB1*04:05": [ "NA", "NA", - 18.260000228881836, - 80.0, + 25.06999969482422, + 89.0, "NA", - 74.0, + 77.0, "NA", "NA", "NA", "NA", "NA", - 75.0 + 72.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 23.42, - 70.0, + 27.36, + 88.0, "NA", - 63.0, + 77.0, "NA", "NA", "NA", "NA", "NA", - 68.0 + 53.0 ] } }, @@ -625539,7 +626395,7 @@ "NA", "NA", "NA", - 0.0182, + 0.0024, "NA", "NA" ] @@ -625549,7 +626405,7 @@ "NA", "NA", "NA", - 0.1471, + 0.0059, "NA", "NA" ] @@ -625569,7 +626425,7 @@ "NA", "NA", "NA", - 39.0, + 77.0, "NA", "NA" ] @@ -625579,7 +626435,7 @@ "NA", "NA", "NA", - 12.0, + 60.0, "NA", "NA" ] @@ -625607,56 +626463,56 @@ "DRB1*04:05": [ "NA", "NA", - 18.260000228881836, - 80.0, + 25.06999969482422, + 89.0, "NA", - 74.0, + 77.0, "NA", "NA", "NA", "NA", "NA", - 75.0, + 72.0, "NA", "NA", - 39.0 + 77.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 23.42, - 70.0, + 27.36, + 88.0, "NA", - 63.0, + 77.0, "NA", "NA", "NA", "NA", "NA", - 68.0, + 53.0, "NA", "NA", - 12.0 + 60.0 ] } }, - "wt_peptide": "PGRLVAEMEVGTEQT" + "wt_peptide": "GNIPGRLVAEMEVGT" }, - "GCLVAEMEVGTEQTD": { + "PGCLVAEMEVGTEQT": { "ic50s_MT": [ - 4423.0849609375, + 4416.77978515625, "X", "X" ], "percentiles_MT": [ - 73.0, + 74.0, "X", "X" ], "ic50s_WT": [ - 4250.055, + 3056.4, "X", "X" ], @@ -625670,7 +626526,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "2", + "mutation_position": "3", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -625692,32 +626548,32 @@ "DRB1*04:05": [ "NA", "NA", - 4140.17, - 6666.2, + 717.74, + 6487.7, "NA", - 4088.75, + 3689.56, "NA", "NA", "NA", "NA", "NA", - 4706.0 + 5144.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 4086.11, - 4646.0, + 1119.25, + 4225.9, "NA", - 2423.52, + 2347.8, "NA", "NA", "NA", "NA", "NA", - 4414.0 + 3765.0 ] } }, @@ -625740,24 +626596,24 @@ "DRB1*04:05": [ "NA", "NA", - 43.720001220703125, - 81.0, + 18.260000228881836, + 80.0, "NA", - 77.0, + 74.0, "NA", "NA", "NA", "NA", "NA", - 73.0 + 75.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 43.48, - 72.0, + 23.42, + 70.0, "NA", 63.0, "NA", @@ -625765,7 +626621,7 @@ "NA", "NA", "NA", - 72.0 + 68.0 ] } }, @@ -625783,7 +626639,7 @@ "NA", "NA", "NA", - 0.0395, + 0.0182, "NA", "NA" ] @@ -625793,7 +626649,7 @@ "NA", "NA", "NA", - 0.232, + 0.1471, "NA", "NA" ] @@ -625813,7 +626669,7 @@ "NA", "NA", "NA", - 27.0, + 39.0, "NA", "NA" ] @@ -625823,7 +626679,7 @@ "NA", "NA", "NA", - 7.6, + 12.0, "NA", "NA" ] @@ -625851,27 +626707,27 @@ "DRB1*04:05": [ "NA", "NA", - 43.720001220703125, - 81.0, + 18.260000228881836, + 80.0, "NA", - 77.0, + 74.0, "NA", "NA", "NA", "NA", "NA", - 73.0, + 75.0, "NA", "NA", - 27.0 + 39.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 43.48, - 72.0, + 23.42, + 70.0, "NA", 63.0, "NA", @@ -625879,33 +626735,33 @@ "NA", "NA", "NA", - 72.0, + 68.0, "NA", "NA", - 7.6 + 12.0 ] } }, - "wt_peptide": "GRLVAEMEVGTEQTD" + "wt_peptide": "PGRLVAEMEVGTEQT" }, - "VGNIPGCLVAEMEVG": { + "GCLVAEMEVGTEQTD": { "ic50s_MT": [ - 4885.46484375, + 4423.0849609375, "X", "X" ], "percentiles_MT": [ - 76.0, + 73.0, "X", "X" ], "ic50s_WT": [ - 4536.785, + 4250.055, "X", "X" ], "percentiles_WT": [ - 66.0, + 63.0, "X", "X" ], @@ -625914,7 +626770,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "7", + "mutation_position": "2", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -625936,32 +626792,32 @@ "DRB1*04:05": [ "NA", "NA", - 4597.93, - 8822.8, + 4140.17, + 6666.2, "NA", - 3812.97, + 4088.75, "NA", "NA", "NA", "NA", "NA", - 5173.0 + 4706.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 4918.64, - 11094.0, + 4086.11, + 4646.0, "NA", - 4154.93, + 2423.52, "NA", "NA", "NA", "NA", "NA", - 2236.0 + 4414.0 ] } }, @@ -625984,32 +626840,32 @@ "DRB1*04:05": [ "NA", "NA", - 45.72999954223633, - 87.0, + 43.720001220703125, + 81.0, "NA", - 75.0, + 77.0, "NA", "NA", "NA", "NA", "NA", - 76.0 + 73.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 47.03, - 91.0, + 43.48, + 72.0, "NA", - 77.0, + 63.0, "NA", "NA", "NA", "NA", "NA", - 54.0 + 72.0 ] } }, @@ -626027,7 +626883,7 @@ "NA", "NA", "NA", - 0.0023, + 0.0395, "NA", "NA" ] @@ -626037,7 +626893,7 @@ "NA", "NA", "NA", - 0.0044, + 0.232, "NA", "NA" ] @@ -626057,7 +626913,7 @@ "NA", "NA", "NA", - 78.0, + 27.0, "NA", "NA" ] @@ -626067,7 +626923,7 @@ "NA", "NA", "NA", - 66.0, + 7.6, "NA", "NA" ] @@ -626095,61 +626951,61 @@ "DRB1*04:05": [ "NA", "NA", - 45.72999954223633, - 87.0, + 43.720001220703125, + 81.0, "NA", - 75.0, + 77.0, "NA", "NA", "NA", "NA", "NA", - 76.0, + 73.0, "NA", "NA", - 78.0 + 27.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 47.03, - 91.0, + 43.48, + 72.0, "NA", - 77.0, + 63.0, "NA", "NA", "NA", "NA", "NA", - 54.0, + 72.0, "NA", "NA", - 66.0 + 7.6 ] } }, - "wt_peptide": "VGNIPGRLVAEMEVG" + "wt_peptide": "GRLVAEMEVGTEQTD" }, - "CLVAEMEVGTEQTDR": { + "VGNIPGCLVAEMEVG": { "ic50s_MT": [ - 4991.25, + 4885.46484375, "X", "X" ], "percentiles_MT": [ - 74.0, + 76.0, "X", "X" ], "ic50s_WT": [ - 4076.535, + 4536.785, "X", "X" ], "percentiles_WT": [ - 72.0, + 66.0, "X", "X" ], @@ -626158,7 +627014,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "1", + "mutation_position": "7", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -626180,32 +627036,32 @@ "DRB1*04:05": [ "NA", "NA", - 1732.59, - 6901.2, + 4597.93, + 8822.8, "NA", - 5053.5, + 3812.97, "NA", "NA", "NA", "NA", "NA", - 4929.0 + 5173.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 1453.19, - 5595.1, + 4918.64, + 11094.0, "NA", - 3375.07, + 4154.93, "NA", "NA", "NA", "NA", "NA", - 4778.0 + 2236.0 ] } }, @@ -626228,32 +627084,32 @@ "DRB1*04:05": [ "NA", "NA", - 29.350000381469727, - 81.0, + 45.72999954223633, + 87.0, "NA", - 82.0, + 75.0, "NA", "NA", "NA", "NA", "NA", - 74.0 + 76.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 26.87, - 77.0, + 47.03, + 91.0, "NA", - 72.0, + 77.0, "NA", "NA", "NA", "NA", "NA", - 74.0 + 54.0 ] } }, @@ -626271,7 +627127,7 @@ "NA", "NA", "NA", - 0.0196, + 0.0023, "NA", "NA" ] @@ -626281,7 +627137,7 @@ "NA", "NA", "NA", - 0.0516, + 0.0044, "NA", "NA" ] @@ -626301,7 +627157,7 @@ "NA", "NA", "NA", - 38.0, + 78.0, "NA", "NA" ] @@ -626311,7 +627167,7 @@ "NA", "NA", "NA", - 23.0, + 66.0, "NA", "NA" ] @@ -626339,105 +627195,61 @@ "DRB1*04:05": [ "NA", "NA", - 29.350000381469727, - 81.0, + 45.72999954223633, + 87.0, "NA", - 82.0, + 75.0, "NA", "NA", "NA", "NA", "NA", - 74.0, + 76.0, "NA", "NA", - 38.0 + 78.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 26.87, - 77.0, + 47.03, + 91.0, "NA", - 72.0, + 77.0, "NA", "NA", "NA", "NA", "NA", - 74.0, + 54.0, "NA", "NA", - 23.0 + 66.0 ] } }, - "wt_peptide": "RLVAEMEVGTEQTDR" - } - }, - "transcripts": [ - "ENST00000619918.1-RIMBP3-R/C-1513" - ], - "transcript_expr": [ - 207.888 - ], - "tsl": [ - "NA" - ], - "biotype": [ - "protein_coding" - ], - "transcript_length": [ - 1639 - ], - "transcript_count": 1, - "peptide_count": 9, - "total_expr": 207.888 - } - }, - "sets": [ - "Transcript Set 1" - ], - "transcript_counts": [ - 1 - ], - "peptide_counts": [ - 9 - ], - "set_expr": [ - 207.888 - ], - "DNA VAF": 0.504, - "RNA VAF": 1.0, - "gene_expr": 207.888, - "best_peptide_mt": "YLSECNRQVGNIPGC", - "best_peptide_wt": "YLSECNRQVGNIPGR", - "best_hla_allele": "DRB1*04:05" - }, - "chr22-26540809-26540810-G-T": { - "good_binders": { - "Transcript Set 1": { - "peptides": { - "HGGVSLSKIERSTDQ": { + "wt_peptide": "VGNIPGRLVAEMEVG" + }, + "CLVAEMEVGTEQTDR": { "ic50s_MT": [ - 999.5750122070312, + 4991.25, "X", "X" ], "percentiles_MT": [ - 19.989999771118164, + 74.0, "X", "X" ], "ic50s_WT": [ - 1155.44, + 4076.535, "X", "X" ], "percentiles_WT": [ - 24.92, + 72.0, "X", "X" ], @@ -626468,32 +627280,32 @@ "DRB1*04:05": [ "NA", "NA", - 840.05, - 1159.1, + 1732.59, + 6901.2, "NA", - 1780.09, + 5053.5, "NA", "NA", "NA", "NA", "NA", - 379.0 + 4929.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 1257.38, - 1053.5, + 1453.19, + 5595.1, "NA", - 1909.21, + 3375.07, "NA", "NA", "NA", "NA", "NA", - 377.0 + 4778.0 ] } }, @@ -626516,32 +627328,32 @@ "DRB1*04:05": [ "NA", "NA", - 19.989999771118164, - 39.0, + 29.350000381469727, + 81.0, "NA", - 55.0, + 82.0, "NA", "NA", "NA", "NA", "NA", - 14.0 + 74.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 24.92, - 36.0, + 26.87, + 77.0, "NA", - 57.0, + 72.0, "NA", "NA", "NA", "NA", "NA", - 14.0 + 74.0 ] } }, @@ -626559,7 +627371,7 @@ "NA", "NA", "NA", - 0.0781, + 0.0196, "NA", "NA" ] @@ -626569,7 +627381,7 @@ "NA", "NA", "NA", - 0.0893, + 0.0516, "NA", "NA" ] @@ -626589,7 +627401,7 @@ "NA", "NA", "NA", - 18.0, + 38.0, "NA", "NA" ] @@ -626599,7 +627411,7 @@ "NA", "NA", "NA", - 17.0, + 23.0, "NA", "NA" ] @@ -626627,61 +627439,105 @@ "DRB1*04:05": [ "NA", "NA", - 19.989999771118164, - 39.0, + 29.350000381469727, + 81.0, "NA", - 55.0, + 82.0, "NA", "NA", "NA", "NA", "NA", - 14.0, + 74.0, "NA", "NA", - 18.0 + 38.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 24.92, - 36.0, + 26.87, + 77.0, "NA", - 57.0, + 72.0, "NA", "NA", "NA", "NA", "NA", - 14.0, + 74.0, "NA", "NA", - 17.0 + 23.0 ] } }, - "wt_peptide": "PGGVSLSKIERSTDQ" - }, - "KHGGVSLSKIERSTD": { + "wt_peptide": "RLVAEMEVGTEQTDR" + } + }, + "transcripts": [ + "ENST00000619918.1-RIMBP3-R/C-1513" + ], + "transcript_expr": [ + 207.888 + ], + "tsl": [ + "NA" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 1639 + ], + "transcript_count": 1, + "peptide_count": 9, + "total_expr": 207.888 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 9 + ], + "set_expr": [ + 207.888 + ], + "DNA VAF": 0.504, + "RNA VAF": 1.0, + "gene_expr": 207.888, + "best_peptide_mt": "YLSECNRQVGNIPGC", + "best_peptide_wt": "YLSECNRQVGNIPGR", + "best_hla_allele": "DRB1*04:05" + }, + "chr22-26540809-26540810-G-T": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "HGGVSLSKIERSTDQ": { "ic50s_MT": [ - 1014.3900146484375, + 999.5750122070312, "X", "X" ], "percentiles_MT": [ - 23.0, + 19.989999771118164, "X", "X" ], "ic50s_WT": [ - 1091.785, + 1155.44, "X", "X" ], "percentiles_WT": [ - 21.0, + 24.92, "X", "X" ], @@ -626690,7 +627546,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "2", + "mutation_position": "1", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -626712,32 +627568,32 @@ "DRB1*04:05": [ "NA", "NA", - 630.78, - 1398.0, + 840.05, + 1159.1, "NA", - 1951.08, + 1780.09, "NA", "NA", "NA", "NA", "NA", - 383.0 + 379.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 863.07, - 1320.5, + 1257.38, + 1053.5, "NA", - 2168.01, + 1909.21, "NA", "NA", "NA", "NA", "NA", - 381.0 + 377.0 ] } }, @@ -626760,26 +627616,26 @@ "DRB1*04:05": [ "NA", "NA", - 16.90999984741211, - 43.0, + 19.989999771118164, + 39.0, "NA", - 58.0, + 55.0, "NA", "NA", "NA", "NA", "NA", - 15.0 + 14.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 20.29, - 42.0, + 24.92, + 36.0, "NA", - 61.0, + 57.0, "NA", "NA", "NA", @@ -626803,7 +627659,7 @@ "NA", "NA", "NA", - 0.0517, + 0.0781, "NA", "NA" ] @@ -626813,7 +627669,7 @@ "NA", "NA", "NA", - 0.0608, + 0.0893, "NA", "NA" ] @@ -626833,7 +627689,7 @@ "NA", "NA", "NA", - 23.0, + 18.0, "NA", "NA" ] @@ -626843,7 +627699,7 @@ "NA", "NA", "NA", - 21.0, + 17.0, "NA", "NA" ] @@ -626871,29 +627727,29 @@ "DRB1*04:05": [ "NA", "NA", - 16.90999984741211, - 43.0, + 19.989999771118164, + 39.0, "NA", - 58.0, + 55.0, "NA", "NA", "NA", "NA", "NA", - 15.0, + 14.0, "NA", "NA", - 23.0 + 18.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 20.29, - 42.0, + 24.92, + 36.0, "NA", - 61.0, + 57.0, "NA", "NA", "NA", @@ -626902,30 +627758,30 @@ 14.0, "NA", "NA", - 21.0 + 17.0 ] } }, - "wt_peptide": "KPGGVSLSKIERSTD" + "wt_peptide": "PGGVSLSKIERSTDQ" }, - "IGKHGGVSLSKIERS": { + "KHGGVSLSKIERSTD": { "ic50s_MT": [ - 1977.1949462890625, + 1014.3900146484375, "X", "X" ], "percentiles_MT": [ - 58.0, + 23.0, "X", "X" ], "ic50s_WT": [ - 2996.83, + 1091.785, "X", "X" ], "percentiles_WT": [ - 59.0, + 21.0, "X", "X" ], @@ -626934,7 +627790,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "4", + "mutation_position": "2", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -626956,32 +627812,32 @@ "DRB1*04:05": [ "NA", "NA", - 1363.64, - 2647.0, + 630.78, + 1398.0, "NA", - 2375.39, + 1951.08, "NA", "NA", "NA", "NA", "NA", - 1579.0 + 383.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 3462.89, - 2890.7, + 863.07, + 1320.5, "NA", - 3102.96, + 2168.01, "NA", "NA", "NA", "NA", "NA", - 1548.0 + 381.0 ] } }, @@ -627004,32 +627860,32 @@ "DRB1*04:05": [ "NA", "NA", - 26.0, - 58.0, + 16.90999984741211, + 43.0, "NA", - 63.0, + 58.0, "NA", "NA", "NA", "NA", "NA", - 45.0 + 15.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 40.46, - 60.0, + 20.29, + 42.0, "NA", - 70.0, + 61.0, "NA", "NA", "NA", "NA", "NA", - 44.0 + 14.0 ] } }, @@ -627047,7 +627903,7 @@ "NA", "NA", "NA", - 0.0053, + 0.0517, "NA", "NA" ] @@ -627057,7 +627913,7 @@ "NA", "NA", "NA", - 0.0062, + 0.0608, "NA", "NA" ] @@ -627077,7 +627933,7 @@ "NA", "NA", "NA", - 62.0, + 23.0, "NA", "NA" ] @@ -627087,7 +627943,7 @@ "NA", "NA", "NA", - 59.0, + 21.0, "NA", "NA" ] @@ -627115,61 +627971,61 @@ "DRB1*04:05": [ "NA", "NA", - 26.0, - 58.0, + 16.90999984741211, + 43.0, "NA", - 63.0, + 58.0, "NA", "NA", "NA", "NA", "NA", - 45.0, + 15.0, "NA", "NA", - 62.0 + 23.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 40.46, - 60.0, + 20.29, + 42.0, "NA", - 70.0, + 61.0, "NA", "NA", "NA", "NA", "NA", - 44.0, + 14.0, "NA", "NA", - 59.0 + 21.0 ] } }, - "wt_peptide": "IGKPGGVSLSKIERS" + "wt_peptide": "KPGGVSLSKIERSTD" }, - "GKHGGVSLSKIERST": { + "IGKHGGVSLSKIERS": { "ic50s_MT": [ - 2032.1500244140625, + 1977.1949462890625, "X", "X" ], "percentiles_MT": [ - 44.0, + 58.0, "X", "X" ], "ic50s_WT": [ - 2236.85, + 2996.83, "X", "X" ], "percentiles_WT": [ - 44.88, + 59.0, "X", "X" ], @@ -627178,7 +628034,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "3", + "mutation_position": "4", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -627200,32 +628056,32 @@ "DRB1*04:05": [ "NA", "NA", - 2412.38, - 2029.3, + 1363.64, + 2647.0, "NA", - 2035.0, + 2375.39, "NA", "NA", "NA", "NA", "NA", - 1567.0 + 1579.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 4401.06, - 2044.9, + 3462.89, + 2890.7, "NA", - 2428.8, + 3102.96, "NA", "NA", "NA", "NA", "NA", - 1529.0 + 1548.0 ] } }, @@ -627248,26 +628104,26 @@ "DRB1*04:05": [ "NA", "NA", - 34.400001525878906, - 51.0, + 26.0, + 58.0, "NA", - 59.0, + 63.0, "NA", "NA", "NA", "NA", "NA", - 44.0 + 45.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 44.88, - 51.0, + 40.46, + 60.0, "NA", - 64.0, + 70.0, "NA", "NA", "NA", @@ -627291,7 +628147,7 @@ "NA", "NA", "NA", - 0.0198, + 0.0053, "NA", "NA" ] @@ -627301,7 +628157,7 @@ "NA", "NA", "NA", - 0.0243, + 0.0062, "NA", "NA" ] @@ -627321,7 +628177,7 @@ "NA", "NA", "NA", - 38.0, + 62.0, "NA", "NA" ] @@ -627331,7 +628187,7 @@ "NA", "NA", "NA", - 34.0, + 59.0, "NA", "NA" ] @@ -627359,29 +628215,29 @@ "DRB1*04:05": [ "NA", "NA", - 34.400001525878906, - 51.0, + 26.0, + 58.0, "NA", - 59.0, + 63.0, "NA", "NA", "NA", "NA", "NA", - 44.0, + 45.0, "NA", "NA", - 38.0 + 62.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 44.88, - 51.0, + 40.46, + 60.0, "NA", - 64.0, + 70.0, "NA", "NA", "NA", @@ -627390,30 +628246,30 @@ 44.0, "NA", "NA", - 34.0 + 59.0 ] } }, - "wt_peptide": "GKPGGVSLSKIERST" + "wt_peptide": "IGKPGGVSLSKIERS" }, - "LIGKHGGVSLSKIER": { + "GKHGGVSLSKIERST": { "ic50s_MT": [ - 4915.21484375, + 2032.1500244140625, "X", "X" ], "percentiles_MT": [ - 79.0, + 44.0, "X", "X" ], "ic50s_WT": [ - 7788.45, + 2236.85, "X", "X" ], "percentiles_WT": [ - 85.0, + 44.88, "X", "X" ], @@ -627422,7 +628278,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "5", + "mutation_position": "3", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -627444,32 +628300,32 @@ "DRB1*04:05": [ "NA", "NA", - 1015.75, - 6172.5, + 2412.38, + 2029.3, "NA", - 4593.43, + 2035.0, "NA", "NA", "NA", "NA", "NA", - 5237.0 + 1567.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 2100.91, - 8202.9, + 4401.06, + 2044.9, "NA", - 8453.51, + 2428.8, "NA", "NA", "NA", "NA", "NA", - 7374.0 + 1529.0 ] } }, @@ -627492,32 +628348,32 @@ "DRB1*04:05": [ "NA", "NA", - 22.239999771118164, - 79.0, + 34.400001525878906, + 51.0, "NA", - 80.0, + 59.0, "NA", "NA", "NA", "NA", "NA", - 76.0 + 44.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 32.24, - 85.0, + 44.88, + 51.0, "NA", - 91.0, + 64.0, "NA", "NA", "NA", "NA", "NA", - 83.0 + 44.0 ] } }, @@ -627535,7 +628391,7 @@ "NA", "NA", "NA", - 0.0018, + 0.0198, "NA", "NA" ] @@ -627545,7 +628401,7 @@ "NA", "NA", "NA", - 0.0012, + 0.0243, "NA", "NA" ] @@ -627565,7 +628421,7 @@ "NA", "NA", "NA", - 82.0, + 38.0, "NA", "NA" ] @@ -627575,7 +628431,7 @@ "NA", "NA", "NA", - 87.0, + 34.0, "NA", "NA" ] @@ -627603,120 +628459,61 @@ "DRB1*04:05": [ "NA", "NA", - 22.239999771118164, - 79.0, + 34.400001525878906, + 51.0, "NA", - 80.0, + 59.0, "NA", "NA", "NA", "NA", "NA", - 76.0, + 44.0, "NA", "NA", - 82.0 + 38.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 32.24, - 85.0, + 44.88, + 51.0, "NA", - 91.0, + 64.0, "NA", "NA", "NA", "NA", "NA", - 83.0, + 44.0, "NA", "NA", - 87.0 + 34.0 ] } }, - "wt_peptide": "LIGKPGGVSLSKIER" - } - }, - "transcripts": [ - "ENST00000338754.9-TPST2-P/H-274", - "ENST00000398110.6-TPST2-P/H-274", - "ENST00000445720.1-TPST2-P/H-21", - "ENST00000403880.5-TPST2-P/H-274" - ], - "transcript_expr": [ - 3.495, - 22.641, - 0.748, - 0.425 - ], - "tsl": [ - 1, - 2, - 2, - 5 - ], - "biotype": [ - "protein_coding", - "protein_coding", - "protein_coding", - "protein_coding" - ], - "transcript_length": [ - 377, - 377, - 168, - 377 - ], - "transcript_count": 4, - "peptide_count": 5, - "total_expr": 27.309 - } - }, - "sets": [ - "Transcript Set 1" - ], - "transcript_counts": [ - 4 - ], - "peptide_counts": [ - 5 - ], - "set_expr": [ - 27.309 - ], - "DNA VAF": 0.203, - "RNA VAF": 0.21, - "gene_expr": 28.333, - "best_peptide_mt": "HGGVSLSKIERSTDQ", - "best_peptide_wt": "PGGVSLSKIERSTDQ", - "best_hla_allele": "DRB1*04:05" - }, - "chr22-37374977-37374978-G-A": { - "good_binders": { - "Transcript Set 1": { - "peptides": { - "SLMVCELAGNLFNCE": { + "wt_peptide": "GKPGGVSLSKIERST" + }, + "LIGKHGGVSLSKIER": { "ic50s_MT": [ - 1438.449951171875, + 4915.21484375, "X", "X" ], "percentiles_MT": [ - 46.0, + 79.0, "X", "X" ], "ic50s_WT": [ - 1998.055, + 7788.45, "X", "X" ], "percentiles_WT": [ - 55.0, + 85.0, "X", "X" ], @@ -627725,7 +628522,310 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "11", + "mutation_position": "5", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + 1015.75, + 6172.5, + "NA", + 4593.43, + "NA", + "NA", + "NA", + "NA", + "NA", + 5237.0 + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + 2100.91, + 8202.9, + "NA", + 8453.51, + "NA", + "NA", + "NA", + "NA", + "NA", + 7374.0 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + 22.239999771118164, + 79.0, + "NA", + 80.0, + "NA", + "NA", + "NA", + "NA", + "NA", + 76.0 + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + 32.24, + 85.0, + "NA", + 91.0, + "NA", + "NA", + "NA", + "NA", + "NA", + 83.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 0.0018, + "NA", + "NA" + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 0.0012, + "NA", + "NA" + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 82.0, + "NA", + "NA" + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 87.0, + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + 22.239999771118164, + 79.0, + "NA", + 80.0, + "NA", + "NA", + "NA", + "NA", + "NA", + 76.0, + "NA", + "NA", + 82.0 + ] + }, + "WT": { + 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"DRB1*04:05" + }, + "chr22-37374977-37374978-G-A": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "SLMVCELAGNLFNCE": { + "ic50s_MT": [ + 1438.449951171875, + "X", + "X" + ], + "percentiles_MT": [ + 46.0, + "X", + "X" + ], + "ic50s_WT": [ + 1998.055, + "X", + "X" + ], + "percentiles_WT": [ + 55.0, + "X", + "X" + ], + "hla_types": [ + "DRB1*04:05", + "HLA-A*29:02", + "HLA-B*45:01" + ], + "mutation_position": "11", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -659533,11 +660633,286 @@ "best_hla_allele": "DRB1*04:05" }, "chr3-44242057-44242058-G-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "MQRPPPLGPT": { + "ic50s_MT": [ + "X", + "X", + 18453.58984375 + ], + "percentiles_MT": [ + "X", + "X", + 18.5 + ], + "ic50s_WT": [ + "X", + "X", + 24155.798 + ], + "percentiles_WT": [ + "X", + "X", + 30.5 + ], + "hla_types": [ + "DRB1*04:05", + "HLA-A*29:02", + "HLA-B*45:01" + ], + "mutation_position": "2", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign" + ], + "MT": { + "HLA-B*45:01": [ + 18378.9089652236, + 36744.17, + "NA", + "NA", + 31132.66, + "NA", + 22695.78, + 18528.27, + 3167.62, + 13264.47, + 7779.11, + "NA" + ] + }, + "WT": { + "HLA-B*45:01": [ + 26222.09621678929, + 22089.5, + "NA", + "NA", + 39595.96, + "NA", + 34986.78, + 33597.82, + 20813.9, + 12962.54, + 16824.03, + "NA" + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign" + ], + "MT": { + "HLA-B*45:01": [ + 5.285624980926514, + 75.47000122070312, + "NA", + "NA", + 25.0, + "NA", + 12.0, + 7.400000095367432, + 4.5, + 36.0, + 25.0, + "NA" + ] + }, + "WT": { + "HLA-B*45:01": [ + 14.480874999999996, + 25.92, + "NA", + "NA", + 41.0, + "NA", + 33.0, + 28.0, + 27.0, + 35.0, + 42.0, + "NA" + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "HLA-B*45:01": [ + 0.0606379024684429, + 0.0066980467800002, + 0.00177, + "NA", + 0.0008481261, + 0.0030341588 + ] + }, + "WT": { + "HLA-B*45:01": [ + 0.0259483903646469, + 0.004205396760748, + 0.000164, + "NA", + 0.0002766934, + 0.00028116285 + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "HLA-B*45:01": [ + "NA", + 37.35904891304347, + 7.5, + "NA", + "NA", + "NA" + ] + }, + "WT": { + "HLA-B*45:01": [ + "NA", + 62.74467391304348, + 22.0, + "NA", + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL" + ], + "MT": { + "HLA-B*45:01": [ + 5.285624980926514, + 75.47000122070312, + "NA", + "NA", + 25.0, + "NA", + 12.0, + 7.400000095367432, + 4.5, + 36.0, + 25.0, + "NA", + 37.35904891304347, + 7.5, + "NA" + ] + }, + "WT": { + "HLA-B*45:01": [ + 14.480874999999996, + 25.92, + "NA", + "NA", + 41.0, + "NA", + 33.0, + 28.0, + 27.0, + 35.0, + 42.0, + "NA", + 62.74467391304348, + 22.0, + "NA" + ] + } + }, + "wt_peptide": "MRRPPPLGPT" + } + }, + "transcripts": [ + "ENST00000309765.4-TOPAZ1-R/Q-2" + ], + "transcript_expr": [ + 0.005 + ], + "tsl": [ + 5 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 1692 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0.005 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0.005 + ], "DNA VAF": 0.307, "RNA VAF": 0.0, "gene_expr": 0.005, @@ -663255,40 +664630,27 @@ "best_hla_allele": "DRB1*04:05" }, "chr3-52517959-52517960-A-C": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 1.0, - "RNA VAF": 0.0, - "gene_expr": 0.09, - "best_peptide_mt": "GQRTCTCDTAPTVGD", - "best_peptide_wt": "GQRTCTCDTAHTVGD", - "best_hla_allele": "DRB1*04:05" - }, - "chr3-56617278-56617279-G-C": { "good_binders": { "Transcript Set 1": { "peptides": { - "KQELTQDKGASLQKE": { + "GQRTCTCDTAPTVGD": { "ic50s_MT": [ - 4386.990234375, + 10740.26953125, "X", "X" ], "percentiles_MT": [ - 56.0, + 80.0, "X", "X" ], "ic50s_WT": [ - 5552.325, + 13563.605, "X", "X" ], "percentiles_WT": [ - 56.0, + 88.0, "X", "X" ], @@ -663297,7 +664659,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "13", + "mutation_position": "11", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -663319,32 +664681,32 @@ "DRB1*04:05": [ "NA", "NA", - 5127.52, - 6219.7, + 16994.83, + 6431.3, "NA", - 3646.46, + 8864.54, "NA", "NA", "NA", "NA", "NA", - 2352.0 + 12616.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 6994.87, - 7656.9, + 17974.51, + 9152.7, "NA", - 4109.78, + 8299.36, "NA", "NA", "NA", "NA", "NA", - 2378.0 + 18261.0 ] } }, @@ -663367,32 +664729,32 @@ "DRB1*04:05": [ "NA", "NA", - 47.84000015258789, - 79.0, + 74.98999786376953, + 80.0, "NA", - 74.0, + 92.0, "NA", "NA", "NA", "NA", "NA", - 56.0 + 91.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 54.2, - 84.0, + 76.44, + 88.0, "NA", - 77.0, + 91.0, "NA", "NA", "NA", "NA", "NA", - 56.0 + 95.0 ] } }, @@ -663410,7 +664772,7 @@ "NA", "NA", "NA", - 0.0748, + 0.0024, "NA", "NA" ] @@ -663420,7 +664782,7 @@ "NA", "NA", "NA", - 0.0776, + 0.0019, "NA", "NA" ] @@ -663440,7 +664802,7 @@ "NA", "NA", "NA", - 19.0, + 77.0, "NA", "NA" ] @@ -663450,7 +664812,7 @@ "NA", "NA", "NA", - 18.0, + 80.0, "NA", "NA" ] @@ -663478,46 +664840,90 @@ "DRB1*04:05": [ "NA", "NA", - 47.84000015258789, - 79.0, + 74.98999786376953, + 80.0, "NA", - 74.0, + 92.0, "NA", "NA", "NA", "NA", "NA", - 56.0, + 91.0, "NA", "NA", - 19.0 + 77.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 54.2, - 84.0, + 76.44, + 88.0, "NA", - 77.0, + 91.0, "NA", "NA", "NA", "NA", "NA", - 56.0, + 95.0, "NA", "NA", - 18.0 + 80.0 ] } }, - "wt_peptide": "KQELTQDKGASLEKE" - }, - "NKQELTQDKGASLQK": { + "wt_peptide": "GQRTCTCDTAHTVGD" + } + }, + "transcripts": [ + "ENST00000321725.10-STAB1-H/P-1573" + ], + "transcript_expr": [ + 0.012 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 2570 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0.012 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0.012 + ], + "DNA VAF": 1.0, + "RNA VAF": 0.0, + "gene_expr": 0.09, + "best_peptide_mt": "GQRTCTCDTAPTVGD", + "best_peptide_wt": "GQRTCTCDTAHTVGD", + "best_hla_allele": "DRB1*04:05" + }, + "chr3-56617278-56617279-G-C": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "KQELTQDKGASLQKE": { "ic50s_MT": [ - 4804.7548828125, + 4386.990234375, "X", "X" ], @@ -663527,12 +664933,12 @@ "X" ], "ic50s_WT": [ - 6254.34, + 5552.325, "X", "X" ], "percentiles_WT": [ - 58.34, + 56.0, "X", "X" ], @@ -663541,7 +664947,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "14", + "mutation_position": "13", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -663563,32 +664969,32 @@ "DRB1*04:05": [ "NA", "NA", - 5971.02, - 8856.2, + 5127.52, + 6219.7, "NA", - 3638.49, + 3646.46, "NA", "NA", "NA", "NA", "NA", - 2389.0 + 2352.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 8479.57, - 8918.0, + 6994.87, + 7656.9, "NA", - 4029.11, + 4109.78, "NA", "NA", "NA", "NA", "NA", - 2373.0 + 2378.0 ] } }, @@ -663611,8 +665017,8 @@ "DRB1*04:05": [ "NA", "NA", - 50.900001525878906, - 87.0, + 47.84000015258789, + 79.0, "NA", 74.0, "NA", @@ -663627,8 +665033,8 @@ "DRB1*04:05": [ "NA", "NA", - 58.34, - 87.0, + 54.2, + 84.0, "NA", 77.0, "NA", @@ -663654,7 +665060,7 @@ "NA", "NA", "NA", - 0.0551, + 0.0748, "NA", "NA" ] @@ -663664,7 +665070,7 @@ "NA", "NA", "NA", - 0.0576, + 0.0776, "NA", "NA" ] @@ -663684,7 +665090,7 @@ "NA", "NA", "NA", - 22.0, + 19.0, "NA", "NA" ] @@ -663694,7 +665100,7 @@ "NA", "NA", "NA", - 22.0, + 18.0, "NA", "NA" ] @@ -663722,8 +665128,8 @@ "DRB1*04:05": [ "NA", "NA", - 50.900001525878906, - 87.0, + 47.84000015258789, + 79.0, "NA", 74.0, "NA", @@ -663734,15 +665140,15 @@ 56.0, "NA", "NA", - 22.0 + 19.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 58.34, - 87.0, + 54.2, + 84.0, "NA", 77.0, "NA", @@ -663753,84 +665159,30 @@ 56.0, "NA", "NA", - 22.0 + 18.0 ] } }, - "wt_peptide": "NKQELTQDKGASLEK" - } - }, - "transcripts": [ - "ENST00000394672.8-CCDC66-E/Q-671", - "ENST00000326595.11-CCDC66-E/Q-637", - "ENST00000422222.5-CCDC66-E/Q-627" - ], - "transcript_expr": [ - 5.571, - 0.382, - 0.0 - ], - "tsl": [ - 1, - 1, - 5 - ], - "biotype": [ - "protein_coding", - "protein_coding", - "protein_coding" - ], - "transcript_length": [ - 948, - 914, - 633 - ], - "transcript_count": 3, - "peptide_count": 2, - "total_expr": 5.952999999999999 - } - }, - "sets": [ - "Transcript Set 1" - ], - "transcript_counts": [ - 3 - ], - "peptide_counts": [ - 2 - ], - "set_expr": [ - 5.952999999999999 - ], - "DNA VAF": 1.0, - "RNA VAF": 1.0, - "gene_expr": 24.974, - "best_peptide_mt": "KQELTQDKGASLQKE", - "best_peptide_wt": "KQELTQDKGASLEKE", - "best_hla_allele": "DRB1*04:05" - }, - "chr3-58210851-58210852-G-C": { - "good_binders": { - "Transcript Set 1": { - "peptides": { - "LLLLLSIHSAVAMRI": { + "wt_peptide": "KQELTQDKGASLEKE" + }, + "NKQELTQDKGASLQK": { "ic50s_MT": [ - 131.76499938964844, + 4804.7548828125, "X", "X" ], "percentiles_MT": [ - 5.5, + 56.0, "X", "X" ], "ic50s_WT": [ - 100.07, + 6254.34, "X", "X" ], "percentiles_WT": [ - 4.9, + 58.34, "X", "X" ], @@ -663839,7 +665191,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "11", + "mutation_position": "14", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -663861,32 +665213,32 @@ "DRB1*04:05": [ "NA", "NA", - 130.14, - 155.8, + 5971.02, + 8856.2, "NA", - 133.39, + 3638.49, "NA", "NA", "NA", "NA", "NA", - 109.0 + 2389.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 134.24, - 75.7, + 8479.57, + 8918.0, "NA", - 121.14, + 4029.11, "NA", "NA", "NA", "NA", "NA", - 79.0 + 2373.0 ] } }, @@ -663909,32 +665261,32 @@ "DRB1*04:05": [ "NA", "NA", - 5.210000038146973, - 8.300000190734863, + 50.900001525878906, + 87.0, "NA", - 5.5, + 74.0, "NA", "NA", "NA", "NA", "NA", - 2.9000000953674316 + 56.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 5.36, - 3.5, + 58.34, + 87.0, "NA", - 4.9, + 77.0, "NA", "NA", "NA", "NA", "NA", - 1.8 + 56.0 ] } }, @@ -663952,7 +665304,7 @@ "NA", "NA", "NA", - 0.0137, + 0.0551, "NA", "NA" ] @@ -663962,7 +665314,7 @@ "NA", "NA", "NA", - 0.0134, + 0.0576, "NA", "NA" ] @@ -663982,7 +665334,7 @@ "NA", "NA", "NA", - 44.0, + 22.0, "NA", "NA" ] @@ -663992,7 +665344,7 @@ "NA", "NA", "NA", - 45.0, + 22.0, "NA", "NA" ] @@ -664020,61 +665372,115 @@ "DRB1*04:05": [ "NA", "NA", - 5.210000038146973, - 8.300000190734863, + 50.900001525878906, + 87.0, "NA", - 5.5, + 74.0, "NA", "NA", "NA", "NA", "NA", - 2.9000000953674316, + 56.0, "NA", "NA", - 44.0 + 22.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 5.36, - 3.5, + 58.34, + 87.0, "NA", - 4.9, + 77.0, "NA", "NA", "NA", "NA", "NA", - 1.8, + 56.0, "NA", "NA", - 45.0 + 22.0 ] } }, - "wt_peptide": "LLLLLSIHSALAMRI" - }, - "PLLLLLLSIHSAVAM": { + "wt_peptide": "NKQELTQDKGASLEK" + } + }, + "transcripts": [ + "ENST00000394672.8-CCDC66-E/Q-671", + "ENST00000326595.11-CCDC66-E/Q-637", + "ENST00000422222.5-CCDC66-E/Q-627" + ], + "transcript_expr": [ + 5.571, + 0.382, + 0.0 + ], + "tsl": [ + 1, + 1, + 5 + ], + "biotype": [ + "protein_coding", + "protein_coding", + "protein_coding" + ], + "transcript_length": [ + 948, + 914, + 633 + ], + "transcript_count": 3, + "peptide_count": 2, + "total_expr": 5.952999999999999 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 3 + ], + "peptide_counts": [ + 2 + ], + "set_expr": [ + 5.952999999999999 + ], + "DNA VAF": 1.0, + "RNA VAF": 1.0, + "gene_expr": 24.974, + "best_peptide_mt": "KQELTQDKGASLQKE", + "best_peptide_wt": "KQELTQDKGASLEKE", + "best_hla_allele": "DRB1*04:05" + }, + "chr3-58210851-58210852-G-C": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "LLLLLSIHSAVAMRI": { "ic50s_MT": [ - 137.7050018310547, + 131.76499938964844, "X", "X" ], "percentiles_MT": [ - 8.199999809265137, + 5.5, "X", "X" ], "ic50s_WT": [ - 124.1, + 100.07, "X", "X" ], "percentiles_WT": [ - 6.24, + 4.9, "X", "X" ], @@ -664083,7 +665489,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "13", + "mutation_position": "11", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -664105,32 +665511,32 @@ "DRB1*04:05": [ "NA", "NA", - 121.21, - 154.2, + 130.14, + 155.8, "NA", - 234.52, + 133.39, "NA", "NA", "NA", "NA", "NA", - 47.0 + 109.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 159.5, - 88.7, + 134.24, + 75.7, "NA", - 228.61, + 121.14, "NA", "NA", "NA", "NA", "NA", - 44.0 + 79.0 ] } }, @@ -664153,32 +665559,32 @@ "DRB1*04:05": [ "NA", "NA", - 4.860000133514404, - 8.199999809265137, + 5.210000038146973, + 8.300000190734863, "NA", - 11.0, + 5.5, "NA", "NA", "NA", "NA", "NA", - 0.6399999856948853 + 2.9000000953674316 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 6.239999999999999, - 4.4, + 5.36, + 3.5, "NA", - 11.0, + 4.9, "NA", "NA", "NA", "NA", "NA", - 0.55 + 1.8 ] } }, @@ -664196,7 +665602,7 @@ "NA", "NA", "NA", - 0.0074, + 0.0137, "NA", "NA" ] @@ -664206,7 +665612,7 @@ "NA", "NA", "NA", - 0.0063, + 0.0134, "NA", "NA" ] @@ -664226,7 +665632,7 @@ "NA", "NA", "NA", - 56.0, + 44.0, "NA", "NA" ] @@ -664236,7 +665642,7 @@ "NA", "NA", "NA", - 59.0, + 45.0, "NA", "NA" ] @@ -664264,61 +665670,61 @@ "DRB1*04:05": [ "NA", "NA", - 4.860000133514404, - 8.199999809265137, + 5.210000038146973, + 8.300000190734863, "NA", - 11.0, + 5.5, "NA", "NA", "NA", "NA", "NA", - 0.6399999856948853, + 2.9000000953674316, "NA", "NA", - 56.0 + 44.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 6.239999999999999, - 4.4, + 5.36, + 3.5, "NA", - 11.0, + 4.9, "NA", "NA", "NA", "NA", "NA", - 0.55, + 1.8, "NA", "NA", - 59.0 + 45.0 ] } }, - "wt_peptide": "PLLLLLLSIHSALAM" + "wt_peptide": "LLLLLSIHSALAMRI" }, - "LLLLLLSIHSAVAMR": { + "PLLLLLLSIHSAVAM": { "ic50s_MT": [ - 156.4600067138672, + 137.7050018310547, "X", "X" ], "percentiles_MT": [ - 8.300000190734863, + 8.199999809265137, "X", "X" ], "ic50s_WT": [ - 114.16, + 124.1, "X", "X" ], "percentiles_WT": [ - 5.9, + 6.24, "X", "X" ], @@ -664327,7 +665733,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "12", + "mutation_position": "13", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -664349,32 +665755,32 @@ "DRB1*04:05": [ "NA", "NA", - 668.39, - 156.9, + 121.21, + 154.2, "NA", - 156.02, + 234.52, "NA", "NA", "NA", "NA", "NA", - 108.0 + 47.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 984.29, - 82.6, + 159.5, + 88.7, "NA", - 139.32, + 228.61, "NA", "NA", "NA", "NA", "NA", - 89.0 + 44.0 ] } }, @@ -664397,32 +665803,32 @@ "DRB1*04:05": [ "NA", "NA", - 17.489999771118164, - 8.300000190734863, + 4.860000133514404, + 8.199999809265137, "NA", - 6.800000190734863, + 11.0, "NA", "NA", "NA", "NA", "NA", - 2.799999952316284 + 0.6399999856948853 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 21.85, - 3.9, + 6.239999999999999, + 4.4, "NA", - 5.9, + 11.0, "NA", "NA", "NA", "NA", "NA", - 2.1 + 0.55 ] } }, @@ -664440,7 +665846,7 @@ "NA", "NA", "NA", - 0.0196, + 0.0074, "NA", "NA" ] @@ -664450,7 +665856,7 @@ "NA", "NA", "NA", - 0.0199, + 0.0063, "NA", "NA" ] @@ -664470,7 +665876,7 @@ "NA", "NA", "NA", - 38.0, + 56.0, "NA", "NA" ] @@ -664480,7 +665886,7 @@ "NA", "NA", "NA", - 38.0, + 59.0, "NA", "NA" ] @@ -664508,61 +665914,61 @@ "DRB1*04:05": [ "NA", "NA", - 17.489999771118164, - 8.300000190734863, + 4.860000133514404, + 8.199999809265137, "NA", - 6.800000190734863, + 11.0, "NA", "NA", "NA", "NA", "NA", - 2.799999952316284, + 0.6399999856948853, "NA", "NA", - 38.0 + 56.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 21.85, - 3.9, + 6.239999999999999, + 4.4, "NA", - 5.9, + 11.0, "NA", "NA", "NA", "NA", "NA", - 2.1, + 0.55, "NA", "NA", - 38.0 + 59.0 ] } }, - "wt_peptide": "LLLLLLSIHSALAMR" + "wt_peptide": "PLLLLLLSIHSALAM" }, - "LLLLSIHSAVAMRIC": { + "LLLLLLSIHSAVAMR": { "ic50s_MT": [ - 203.0, + 156.4600067138672, "X", "X" ], "percentiles_MT": [ - 8.430000305175781, + 8.300000190734863, "X", "X" ], "ic50s_WT": [ - 116.615, + 114.16, "X", "X" ], "percentiles_WT": [ - 5.1, + 5.9, "X", "X" ], @@ -664571,7 +665977,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "10", + "mutation_position": "12", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -664593,32 +665999,32 @@ "DRB1*04:05": [ "NA", "NA", - 229.76, - 186.0, + 668.39, + 156.9, "NA", - 146.88, + 156.02, "NA", "NA", "NA", "NA", "NA", - 220.0 + 108.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 294.64, - 87.6, + 984.29, + 82.6, "NA", - 127.23, + 139.32, "NA", "NA", "NA", "NA", "NA", - 106.0 + 89.0 ] } }, @@ -664641,32 +666047,32 @@ "DRB1*04:05": [ "NA", "NA", - 8.430000305175781, - 9.899999618530273, + 17.489999771118164, + 8.300000190734863, "NA", - 6.199999809265137, + 6.800000190734863, "NA", "NA", "NA", "NA", "NA", - 7.800000190734863 + 2.799999952316284 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 10.19, - 4.3, + 21.85, + 3.9, "NA", - 5.1, + 5.9, "NA", "NA", "NA", "NA", "NA", - 2.8 + 2.1 ] } }, @@ -664684,7 +666090,7 @@ "NA", "NA", "NA", - 0.0085, + 0.0196, "NA", "NA" ] @@ -664694,7 +666100,7 @@ "NA", "NA", "NA", - 0.0093, + 0.0199, "NA", "NA" ] @@ -664714,7 +666120,7 @@ "NA", "NA", "NA", - 53.0, + 38.0, "NA", "NA" ] @@ -664724,7 +666130,251 @@ "NA", "NA", "NA", - 51.0, + 38.0, + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + 17.489999771118164, + 8.300000190734863, + "NA", + 6.800000190734863, + "NA", + "NA", + "NA", + "NA", + "NA", + 2.799999952316284, + "NA", + "NA", + 38.0 + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + 21.85, + 3.9, + "NA", + 5.9, + "NA", + "NA", + "NA", + "NA", + "NA", + 2.1, + "NA", + "NA", + 38.0 + ] + } + }, + "wt_peptide": "LLLLLLSIHSALAMR" + }, + "LLLLSIHSAVAMRIC": { + "ic50s_MT": [ + 203.0, + "X", + "X" + ], + "percentiles_MT": [ + 8.430000305175781, + "X", + "X" + ], + "ic50s_WT": [ + 116.615, + "X", + "X" + ], + "percentiles_WT": [ + 5.1, + "X", + "X" + ], + "hla_types": [ + "DRB1*04:05", + "HLA-A*29:02", + "HLA-B*45:01" + ], + "mutation_position": "10", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + 229.76, + 186.0, + "NA", + 146.88, + "NA", + "NA", + "NA", + "NA", + "NA", + 220.0 + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + 294.64, + 87.6, + "NA", + 127.23, + "NA", + "NA", + "NA", + "NA", + "NA", + 106.0 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + 8.430000305175781, + 9.899999618530273, + "NA", + 6.199999809265137, + "NA", + "NA", + "NA", + "NA", + "NA", + 7.800000190734863 + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + 10.19, + 4.3, + "NA", + 5.1, + "NA", + "NA", + "NA", + "NA", + "NA", + 2.8 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 0.0085, + "NA", + "NA" + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 0.0093, + "NA", + "NA" + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 53.0, + "NA", + "NA" + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 51.0, "NA", "NA" ] @@ -709862,40 +711512,27 @@ "best_hla_allele": "DRB1*04:05" }, "chr4-48420360-48420361-A-G": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 0.29, - "RNA VAF": 0.312, - "gene_expr": 58.28, - "best_peptide_mt": "TTAMGSGLPRPSAPS", - "best_peptide_wt": "TTAMRSGLPRPSAPS", - "best_hla_allele": "DRB1*04:05" - }, - "chr4-103145955-103145956-C-G": { "good_binders": { "Transcript Set 1": { "peptides": { - "IEIEMLGLSKTLQES": { + "TTAMGSGLPRPSAPS": { "ic50s_MT": [ - 185.06500244140625, + 6773.23486328125, "X", "X" ], "percentiles_MT": [ - 8.800000190734863, + 86.0, "X", "X" ], "ic50s_WT": [ - 906.465, + 3940.11, "X", "X" ], "percentiles_WT": [ - 43.0, + 67.0, "X", "X" ], @@ -709904,7 +711541,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "11", + "mutation_position": "5", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -709926,32 +711563,32 @@ "DRB1*04:05": [ "NA", "NA", - 176.21, - 118.0, + 2962.21, + 16706.1, "NA", - 193.92, + 10514.47, "NA", "NA", "NA", "NA", "NA", - 462.0 + 3032.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 123.01, - 662.2, + 1977.27, + 8671.4, "NA", - 1150.73, + 5902.95, "NA", "NA", "NA", "NA", "NA", - 1545.0 + 1410.0 ] } }, @@ -709974,32 +711611,32 @@ "DRB1*04:05": [ "NA", "NA", - 6.800000190734863, - 6.199999809265137, + 37.7599983215332, + 97.0, "NA", - 8.800000190734863, + 94.0, "NA", "NA", "NA", "NA", "NA", - 17.0 + 62.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 4.94, - 28.0, + 31.31, + 86.0, "NA", - 43.0, + 85.0, "NA", "NA", "NA", "NA", "NA", - 44.0 + 41.0 ] } }, @@ -710017,7 +711654,7 @@ "NA", "NA", "NA", - 0.1387, + 0.0013, "NA", "NA" ] @@ -710027,7 +711664,7 @@ "NA", "NA", "NA", - 0.0061, + 0.0042, "NA", "NA" ] @@ -710047,7 +711684,7 @@ "NA", "NA", "NA", - 12.0, + 86.0, "NA", "NA" ] @@ -710057,7 +711694,7 @@ "NA", "NA", "NA", - 59.0, + 67.0, "NA", "NA" ] @@ -710085,61 +711722,105 @@ "DRB1*04:05": [ "NA", "NA", - 6.800000190734863, - 6.199999809265137, + 37.7599983215332, + 97.0, "NA", - 8.800000190734863, + 94.0, "NA", "NA", "NA", "NA", "NA", - 17.0, + 62.0, "NA", "NA", - 12.0 + 86.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 4.94, - 28.0, + 31.31, + 86.0, "NA", - 43.0, + 85.0, "NA", "NA", "NA", "NA", "NA", - 44.0, + 41.0, "NA", "NA", - 59.0 + 67.0 ] } }, - "wt_peptide": "IEIEMLGLSKRLQES" - }, - "EIEMLGLSKTLQESH": { + "wt_peptide": "TTAMRSGLPRPSAPS" + } + }, + "transcripts": [ + "ENST00000264313.11-SLAIN2-R/G-533" + ], + "transcript_expr": [ + 4.169 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 581 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 4.169 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 4.169 + ], + "DNA VAF": 0.29, + "RNA VAF": 0.312, + "gene_expr": 58.28, + "best_peptide_mt": "TTAMGSGLPRPSAPS", + "best_peptide_wt": "TTAMRSGLPRPSAPS", + "best_hla_allele": "DRB1*04:05" + }, + "chr4-103145955-103145956-C-G": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "IEIEMLGLSKTLQES": { "ic50s_MT": [ - 214.55999755859375, + 185.06500244140625, "X", "X" ], "percentiles_MT": [ - 7.599999904632568, + 8.800000190734863, "X", "X" ], "ic50s_WT": [ - 1102.75, + 906.465, "X", "X" ], "percentiles_WT": [ - 39.0, + 43.0, "X", "X" ], @@ -710148,7 +711829,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "10", + "mutation_position": "11", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -710170,32 +711851,32 @@ "DRB1*04:05": [ "NA", "NA", - 258.49, - 126.9, + 176.21, + 118.0, "NA", - 170.63, + 193.92, "NA", "NA", "NA", "NA", "NA", - 293.0 + 462.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 426.92, - 896.5, + 123.01, + 662.2, "NA", - 1392.57, + 1150.73, "NA", "NA", "NA", "NA", "NA", - 1309.0 + 1545.0 ] } }, @@ -710218,32 +711899,32 @@ "DRB1*04:05": [ "NA", "NA", - 9.239999771118164, - 6.699999809265137, + 6.800000190734863, + 6.199999809265137, "NA", - 7.599999904632568, + 8.800000190734863, "NA", "NA", "NA", "NA", "NA", - 11.0 + 17.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 13.2, - 33.0, + 4.94, + 28.0, "NA", - 48.0, + 43.0, "NA", "NA", "NA", "NA", "NA", - 39.0 + 44.0 ] } }, @@ -710261,7 +711942,7 @@ "NA", "NA", "NA", - 0.3014, + 0.1387, "NA", "NA" ] @@ -710271,7 +711952,7 @@ "NA", "NA", "NA", - 0.0089, + 0.0061, "NA", "NA" ] @@ -710291,7 +711972,7 @@ "NA", "NA", "NA", - 5.9, + 12.0, "NA", "NA" ] @@ -710301,7 +711982,7 @@ "NA", "NA", "NA", - 52.0, + 59.0, "NA", "NA" ] @@ -710329,61 +712010,61 @@ "DRB1*04:05": [ "NA", "NA", - 9.239999771118164, - 6.699999809265137, + 6.800000190734863, + 6.199999809265137, "NA", - 7.599999904632568, + 8.800000190734863, "NA", "NA", "NA", "NA", "NA", - 11.0, + 17.0, "NA", "NA", - 5.9 + 12.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 13.2, - 33.0, + 4.94, + 28.0, "NA", - 48.0, + 43.0, "NA", "NA", "NA", "NA", "NA", - 39.0, + 44.0, "NA", "NA", - 52.0 + 59.0 ] } }, - "wt_peptide": "EIEMLGLSKRLQESH" + "wt_peptide": "IEIEMLGLSKRLQES" }, - "EMLGLSKTLQESHDE": { + "EIEMLGLSKTLQESH": { "ic50s_MT": [ - 254.8000030517578, + 214.55999755859375, "X", "X" ], "percentiles_MT": [ - 11.0, + 7.599999904632568, "X", "X" ], "ic50s_WT": [ - 1265.45, + 1102.75, "X", "X" ], "percentiles_WT": [ - 45.0, + 39.0, "X", "X" ], @@ -710392,7 +712073,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "8", + "mutation_position": "10", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -710414,32 +712095,32 @@ "DRB1*04:05": [ "NA", "NA", - 136.86, - 203.6, + 258.49, + 126.9, "NA", - 480.54, + 170.63, "NA", "NA", "NA", "NA", "NA", - 306.0 + 293.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 397.16, - 1528.9, + 426.92, + 896.5, "NA", - 3059.22, + 1392.57, "NA", "NA", "NA", "NA", "NA", - 1002.0 + 1309.0 ] } }, @@ -710462,32 +712143,32 @@ "DRB1*04:05": [ "NA", "NA", - 5.460000038146973, - 11.0, + 9.239999771118164, + 6.699999809265137, "NA", - 23.0, + 7.599999904632568, "NA", "NA", "NA", "NA", "NA", - 12.0 + 11.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 12.58, - 45.0, + 13.2, + 33.0, "NA", - 70.0, + 48.0, "NA", "NA", "NA", "NA", "NA", - 33.0 + 39.0 ] } }, @@ -710505,7 +712186,7 @@ "NA", "NA", "NA", - 0.2014, + 0.3014, "NA", "NA" ] @@ -710515,7 +712196,7 @@ "NA", "NA", "NA", - 0.0042, + 0.0089, "NA", "NA" ] @@ -710535,7 +712216,7 @@ "NA", "NA", "NA", - 8.7, + 5.9, "NA", "NA" ] @@ -710545,7 +712226,7 @@ "NA", "NA", "NA", - 67.0, + 52.0, "NA", "NA" ] @@ -710573,46 +712254,46 @@ "DRB1*04:05": [ "NA", "NA", - 5.460000038146973, - 11.0, + 9.239999771118164, + 6.699999809265137, "NA", - 23.0, + 7.599999904632568, "NA", "NA", "NA", "NA", "NA", - 12.0, + 11.0, "NA", "NA", - 8.7 + 5.9 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 12.58, - 45.0, + 13.2, + 33.0, "NA", - 70.0, + 48.0, "NA", "NA", "NA", "NA", "NA", - 33.0, + 39.0, "NA", "NA", - 67.0 + 52.0 ] } }, - "wt_peptide": "EMLGLSKRLQESHDE" + "wt_peptide": "EIEMLGLSKRLQESH" }, - "IEMLGLSKTLQESHD": { + "EMLGLSKTLQESHDE": { "ic50s_MT": [ - 264.06500244140625, + 254.8000030517578, "X", "X" ], @@ -710622,12 +712303,12 @@ "X" ], "ic50s_WT": [ - 1572.635, + 1265.45, "X", "X" ], "percentiles_WT": [ - 40.0, + 45.0, "X", "X" ], @@ -710636,7 +712317,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "9", + "mutation_position": "8", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -710658,32 +712339,32 @@ "DRB1*04:05": [ "NA", "NA", - 555.62, - 140.4, + 136.86, + 203.6, "NA", - 239.13, + 480.54, "NA", "NA", "NA", "NA", "NA", - 289.0 + 306.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 2049.58, - 1229.0, + 397.16, + 1528.9, "NA", - 1916.27, + 3059.22, "NA", "NA", "NA", "NA", "NA", - 980.0 + 1002.0 ] } }, @@ -710706,32 +712387,32 @@ "DRB1*04:05": [ "NA", "NA", - 15.640000343322754, - 7.400000095367432, + 5.460000038146973, + 11.0, "NA", - 12.0, + 23.0, "NA", "NA", "NA", "NA", "NA", - 11.0 + 12.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 31.86, - 40.0, + 12.58, + 45.0, "NA", - 57.0, + 70.0, "NA", "NA", "NA", "NA", "NA", - 32.0 + 33.0 ] } }, @@ -710749,7 +712430,7 @@ "NA", "NA", "NA", - 0.4636, + 0.2014, "NA", "NA" ] @@ -710759,7 +712440,7 @@ "NA", "NA", "NA", - 0.011, + 0.0042, "NA", "NA" ] @@ -710779,7 +712460,7 @@ "NA", "NA", "NA", - 3.6, + 8.7, "NA", "NA" ] @@ -710789,7 +712470,7 @@ "NA", "NA", "NA", - 48.0, + 67.0, "NA", "NA" ] @@ -710817,61 +712498,61 @@ "DRB1*04:05": [ "NA", "NA", - 15.640000343322754, - 7.400000095367432, + 5.460000038146973, + 11.0, "NA", - 12.0, + 23.0, "NA", "NA", "NA", "NA", "NA", - 11.0, + 12.0, "NA", "NA", - 3.6 + 8.7 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 31.86, - 40.0, + 12.58, + 45.0, "NA", - 57.0, + 70.0, "NA", "NA", "NA", "NA", "NA", - 32.0, + 33.0, "NA", "NA", - 48.0 + 67.0 ] } }, - "wt_peptide": "IEMLGLSKRLQESHD" + "wt_peptide": "EMLGLSKRLQESHDE" }, - "RIEIEMLGLSKTLQE": { + "IEMLGLSKTLQESHD": { "ic50s_MT": [ - 310.29998779296875, + 264.06500244140625, "X", "X" ], "percentiles_MT": [ - 13.0, + 11.0, "X", "X" ], "ic50s_WT": [ - 705.615, + 1572.635, "X", "X" ], "percentiles_WT": [ - 36.0, + 40.0, "X", "X" ], @@ -710880,7 +712561,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "12", + "mutation_position": "9", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -710902,32 +712583,32 @@ "DRB1*04:05": [ "NA", "NA", - 344.46, - 143.6, + 555.62, + 140.4, "NA", - 276.14, + 239.13, "NA", "NA", "NA", "NA", "NA", - 421.0 + 289.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 264.06, - 560.0, + 2049.58, + 1229.0, "NA", - 851.23, + 1916.27, "NA", "NA", "NA", "NA", "NA", - 1204.0 + 980.0 ] } }, @@ -710950,32 +712631,32 @@ "DRB1*04:05": [ "NA", "NA", - 11.399999618530273, - 7.599999904632568, + 15.640000343322754, + 7.400000095367432, "NA", - 13.0, + 12.0, "NA", "NA", "NA", "NA", "NA", - 16.0 + 11.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 9.4, - 25.0, + 31.86, + 40.0, "NA", - 36.0, + 57.0, "NA", "NA", "NA", "NA", "NA", - 37.0 + 32.0 ] } }, @@ -710993,7 +712674,7 @@ "NA", "NA", "NA", - 0.0224, + 0.4636, "NA", "NA" ] @@ -711003,7 +712684,7 @@ "NA", "NA", "NA", - 0.0073, + 0.011, "NA", "NA" ] @@ -711023,7 +712704,7 @@ "NA", "NA", "NA", - 36.0, + 3.6, "NA", "NA" ] @@ -711033,7 +712714,7 @@ "NA", "NA", "NA", - 56.0, + 48.0, "NA", "NA" ] @@ -711061,61 +712742,61 @@ "DRB1*04:05": [ "NA", "NA", - 11.399999618530273, - 7.599999904632568, + 15.640000343322754, + 7.400000095367432, "NA", - 13.0, + 12.0, "NA", "NA", "NA", "NA", "NA", - 16.0, + 11.0, "NA", "NA", - 36.0 + 3.6 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 9.4, - 25.0, + 31.86, + 40.0, "NA", - 36.0, + 57.0, "NA", "NA", "NA", "NA", "NA", - 37.0, + 32.0, "NA", "NA", - 56.0 + 48.0 ] } }, - "wt_peptide": "RIEIEMLGLSKRLQE" + "wt_peptide": "IEMLGLSKRLQESHD" }, - "LRIEIEMLGLSKTLQ": { + "RIEIEMLGLSKTLQE": { "ic50s_MT": [ - 444.6600036621094, + 310.29998779296875, "X", "X" ], "percentiles_MT": [ - 23.0, + 13.0, "X", "X" ], "ic50s_WT": [ - 714.34, + 705.615, "X", "X" ], "percentiles_WT": [ - 30.0, + 36.0, "X", "X" ], @@ -711124,7 +712805,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "13", + "mutation_position": "12", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -711146,32 +712827,32 @@ "DRB1*04:05": [ "NA", "NA", - 306.45, - 495.5, + 344.46, + 143.6, "NA", - 393.82, + 276.14, "NA", "NA", "NA", "NA", "NA", - 1015.0 + 421.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 472.82, - 766.1, + 264.06, + 560.0, "NA", - 662.58, + 851.23, "NA", "NA", "NA", "NA", "NA", - 1700.0 + 1204.0 ] } }, @@ -711194,32 +712875,32 @@ "DRB1*04:05": [ "NA", "NA", - 10.5, - 23.0, + 11.399999618530273, + 7.599999904632568, "NA", - 19.0, + 13.0, "NA", "NA", "NA", "NA", "NA", - 33.0 + 16.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 14.09, - 30.0, + 9.4, + 25.0, "NA", - 30.0, + 36.0, "NA", "NA", "NA", "NA", "NA", - 47.0 + 37.0 ] } }, @@ -711237,7 +712918,7 @@ "NA", "NA", "NA", - 0.0085, + 0.0224, "NA", "NA" ] @@ -711247,7 +712928,7 @@ "NA", "NA", "NA", - 0.0046, + 0.0073, "NA", "NA" ] @@ -711267,7 +712948,7 @@ "NA", "NA", "NA", - 53.0, + 36.0, "NA", "NA" ] @@ -711277,7 +712958,7 @@ "NA", "NA", "NA", - 65.0, + 56.0, "NA", "NA" ] @@ -711305,61 +712986,61 @@ "DRB1*04:05": [ "NA", "NA", - 10.5, - 23.0, + 11.399999618530273, + 7.599999904632568, "NA", - 19.0, + 13.0, "NA", "NA", "NA", "NA", "NA", - 33.0, + 16.0, "NA", "NA", - 53.0 + 36.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 14.09, - 30.0, + 9.4, + 25.0, "NA", - 30.0, + 36.0, "NA", "NA", "NA", "NA", "NA", - 47.0, + 37.0, "NA", "NA", - 65.0 + 56.0 ] } }, - "wt_peptide": "LRIEIEMLGLSKRLQ" + "wt_peptide": "RIEIEMLGLSKRLQE" }, - "ALLRIEIEMLGLSKT": { + "LRIEIEMLGLSKTLQ": { "ic50s_MT": [ - 489.2699890136719, + 444.6600036621094, "X", "X" ], "percentiles_MT": [ - 22.0, + 23.0, "X", "X" ], "ic50s_WT": [ - 510.3, + 714.34, "X", "X" ], "percentiles_WT": [ - 23.0, + 30.0, "X", "X" ], @@ -711368,7 +713049,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "15", + "mutation_position": "13", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -711390,32 +713071,32 @@ "DRB1*04:05": [ "NA", "NA", - 470.54, - 516.4, + 306.45, + 495.5, "NA", - 453.83, + 393.82, "NA", "NA", "NA", "NA", "NA", - 508.0 + 1015.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 1136.11, - 511.6, + 472.82, + 766.1, "NA", - 482.0, + 662.58, "NA", "NA", "NA", "NA", "NA", - 509.0 + 1700.0 ] } }, @@ -711438,32 +713119,32 @@ "DRB1*04:05": [ "NA", "NA", - 14.050000190734863, + 10.5, 23.0, "NA", - 22.0, + 19.0, "NA", "NA", "NA", "NA", "NA", - 19.0 + 33.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 23.6, - 23.0, + 14.09, + 30.0, "NA", - 23.0, + 30.0, "NA", "NA", "NA", "NA", "NA", - 19.0 + 47.0 ] } }, @@ -711481,7 +713162,7 @@ "NA", "NA", "NA", - 0.0044, + 0.0085, "NA", "NA" ] @@ -711491,7 +713172,7 @@ "NA", "NA", "NA", - 0.0057, + 0.0046, "NA", "NA" ] @@ -711511,7 +713192,7 @@ "NA", "NA", "NA", - 66.0, + 53.0, "NA", "NA" ] @@ -711521,7 +713202,7 @@ "NA", "NA", "NA", - 61.0, + 65.0, "NA", "NA" ] @@ -711549,61 +713230,61 @@ "DRB1*04:05": [ "NA", "NA", - 14.050000190734863, + 10.5, 23.0, "NA", - 22.0, + 19.0, "NA", "NA", "NA", "NA", "NA", - 19.0, + 33.0, "NA", "NA", - 66.0 + 53.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 23.6, - 23.0, + 14.09, + 30.0, "NA", - 23.0, + 30.0, "NA", "NA", "NA", "NA", "NA", - 19.0, + 47.0, "NA", "NA", - 61.0 + 65.0 ] } }, - "wt_peptide": "ALLRIEIEMLGLSKR" + "wt_peptide": "LRIEIEMLGLSKRLQ" }, - "LLRIEIEMLGLSKTL": { + "ALLRIEIEMLGLSKT": { "ic50s_MT": [ - 501.82501220703125, + 489.2699890136719, "X", "X" ], "percentiles_MT": [ - 19.0, + 22.0, "X", "X" ], "ic50s_WT": [ - 635.585, + 510.3, "X", "X" ], "percentiles_WT": [ - 26.02, + 23.0, "X", "X" ], @@ -711612,7 +713293,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "14", + "mutation_position": "15", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -711634,32 +713315,32 @@ "DRB1*04:05": [ "NA", "NA", - 483.65, - 623.9, + 470.54, + 516.4, "NA", - 406.36, + 453.83, "NA", "NA", "NA", "NA", "NA", - 520.0 + 508.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 1365.39, - 713.8, + 1136.11, + 511.6, "NA", - 557.37, + 482.0, "NA", "NA", "NA", "NA", "NA", - 521.0 + 509.0 ] } }, @@ -711682,10 +713363,10 @@ "DRB1*04:05": [ "NA", "NA", - 14.3100004196167, - 27.0, + 14.050000190734863, + 23.0, "NA", - 19.0, + 22.0, "NA", "NA", "NA", @@ -711698,10 +713379,10 @@ "DRB1*04:05": [ "NA", "NA", - 26.02, - 29.0, + 23.6, + 23.0, "NA", - 26.0, + 23.0, "NA", "NA", "NA", @@ -711725,7 +713406,7 @@ "NA", "NA", "NA", - 0.0041, + 0.0044, "NA", "NA" ] @@ -711735,7 +713416,7 @@ "NA", "NA", "NA", - 0.0044, + 0.0057, "NA", "NA" ] @@ -711755,7 +713436,7 @@ "NA", "NA", "NA", - 67.0, + 66.0, "NA", "NA" ] @@ -711765,7 +713446,7 @@ "NA", "NA", "NA", - 66.0, + 61.0, "NA", "NA" ] @@ -711793,10 +713474,10 @@ "DRB1*04:05": [ "NA", "NA", - 14.3100004196167, - 27.0, + 14.050000190734863, + 23.0, "NA", - 19.0, + 22.0, "NA", "NA", "NA", @@ -711805,17 +713486,17 @@ 19.0, "NA", "NA", - 67.0 + 66.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 26.02, - 29.0, + 23.6, + 23.0, "NA", - 26.0, + 23.0, "NA", "NA", "NA", @@ -711824,30 +713505,30 @@ 19.0, "NA", "NA", - 66.0 + 61.0 ] } }, - "wt_peptide": "LLRIEIEMLGLSKRL" + "wt_peptide": "ALLRIEIEMLGLSKR" }, - "MLGLSKTLQESHDEM": { + "LLRIEIEMLGLSKTL": { "ic50s_MT": [ - 542.375, + 501.82501220703125, "X", "X" ], "percentiles_MT": [ - 21.0, + 19.0, "X", "X" ], "ic50s_WT": [ - 1688.75, + 635.585, "X", "X" ], "percentiles_WT": [ - 52.0, + 26.02, "X", "X" ], @@ -711856,7 +713537,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "7", + "mutation_position": "14", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -711878,32 +713559,32 @@ "DRB1*04:05": [ "NA", "NA", - 613.75, - 462.0, + 483.65, + 623.9, "NA", - 879.35, + 406.36, "NA", "NA", "NA", "NA", "NA", - 471.0 + 520.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 846.0, - 2060.5, + 1365.39, + 713.8, "NA", - 3663.74, + 557.37, "NA", "NA", "NA", "NA", "NA", - 1317.0 + 521.0 ] } }, @@ -711926,32 +713607,32 @@ "DRB1*04:05": [ "NA", "NA", - 16.6299991607666, - 21.0, + 14.3100004196167, + 27.0, "NA", - 37.0, + 19.0, "NA", "NA", "NA", "NA", "NA", - 18.0 + 19.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 20.07, - 52.0, + 26.02, + 29.0, "NA", - 74.0, + 26.0, "NA", "NA", "NA", "NA", "NA", - 40.0 + 19.0 ] } }, @@ -711969,7 +713650,7 @@ "NA", "NA", "NA", - 0.011, + 0.0041, "NA", "NA" ] @@ -711979,7 +713660,7 @@ "NA", "NA", "NA", - 0.0018, + 0.0044, "NA", "NA" ] @@ -711999,7 +713680,7 @@ "NA", "NA", "NA", - 48.0, + 67.0, "NA", "NA" ] @@ -712009,7 +713690,7 @@ "NA", "NA", "NA", - 82.0, + 66.0, "NA", "NA" ] @@ -712037,70 +713718,70 @@ "DRB1*04:05": [ "NA", "NA", - 16.6299991607666, - 21.0, + 14.3100004196167, + 27.0, "NA", - 37.0, + 19.0, "NA", "NA", "NA", "NA", "NA", - 18.0, + 19.0, "NA", "NA", - 48.0 + 67.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 20.07, - 52.0, + 26.02, + 29.0, "NA", - 74.0, + 26.0, "NA", "NA", "NA", "NA", "NA", - 40.0, + 19.0, "NA", "NA", - 82.0 + 66.0 ] } }, - "wt_peptide": "MLGLSKRLQESHDEM" + "wt_peptide": "LLRIEIEMLGLSKRL" }, - "IEMLGLSKT": { + "MLGLSKTLQESHDEM": { "ic50s_MT": [ + 542.375, "X", - "X", - 834.3800048828125 + "X" ], "percentiles_MT": [ + 21.0, "X", - "X", - 1.3919999599456787 + "X" ], "ic50s_WT": [ + 1688.75, "X", - "X", - 8114.15 + "X" ], "percentiles_WT": [ + 52.0, "X", - "X", - 7.85 + "X" ], "hla_types": [ "DRB1*04:05", "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "9", + "mutation_position": "7", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -712119,35 +713800,35 @@ "SMMalign" ], "MT": { - "HLA-B*45:01": [ - 223.4798891953436, - 9791.91, + "DRB1*04:05": [ "NA", "NA", - 790.51, + 613.75, + 462.0, "NA", - 1654.99, - 520.12, - 953.12, - 390.13, - 878.25, - "NA" + 879.35, + "NA", + "NA", + "NA", + "NA", + "NA", + 471.0 ] }, "WT": { - "HLA-B*45:01": [ - 4198.692961438009, - 13105.51, + "DRB1*04:05": [ "NA", "NA", - 11312.21, + 846.0, + 2060.5, "NA", - 11541.43, - 14297.39, - 2551.25, - 3021.41, - 4916.09, - "NA" + 3663.74, + "NA", + "NA", + "NA", + "NA", + "NA", + 1317.0 ] } }, @@ -712167,35 +713848,35 @@ "SMMalign" ], "MT": { - "HLA-B*45:01": [ - 0.5297499895095825, - 10.229999542236328, + "DRB1*04:05": [ "NA", "NA", - 1.2000000476837158, + 16.6299991607666, + 21.0, "NA", - 2.299999952316284, - 0.38999998569488525, - 3.0999999046325684, - 1.4, - 3.2, - "NA" + 37.0, + "NA", + "NA", + "NA", + "NA", + "NA", + 18.0 ] }, "WT": { - "HLA-B*45:01": [ - 2.052125, - 13.62, + "DRB1*04:05": [ "NA", "NA", - 7.8, + 20.07, + 52.0, "NA", - 6.4, - 5.3, - 7.9, - 12.0, - 15.0, - "NA" + 74.0, + "NA", + "NA", + "NA", + "NA", + "NA", + 40.0 ] } }, @@ -712209,23 +713890,23 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ - 0.0170274227857589, - 0.2952121690143259, - 0.264, + "DRB1*04:05": [ "NA", - 0.0018446883, - 0.00046415054 + "NA", + "NA", + 0.011, + "NA", + "NA" ] }, "WT": { - "HLA-B*45:01": [ - 0.0503677166998386, - 0.0265602431327407, - 0.0139, + "DRB1*04:05": [ "NA", - 0.00056617655, - 0.00037295002 + "NA", + "NA", + 0.0018, + "NA", + "NA" ] } }, @@ -712239,20 +713920,264 @@ "BigMHC_IM" ], "MT": { - "HLA-B*45:01": [ + "DRB1*04:05": [ "NA", - 1.384347826086881, - 0.44, "NA", "NA", + 48.0, + "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "DRB1*04:05": [ "NA", - 9.15535326086956, - 3.1, + "NA", + "NA", + 82.0, + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + 16.6299991607666, + 21.0, + "NA", + 37.0, + "NA", + "NA", + "NA", + "NA", + "NA", + 18.0, + "NA", + "NA", + 48.0 + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + 20.07, + 52.0, + "NA", + 74.0, + "NA", + "NA", + "NA", + "NA", + "NA", + 40.0, + "NA", + "NA", + 82.0 + ] + } + }, + "wt_peptide": "MLGLSKRLQESHDEM" + }, + "IEMLGLSKT": { + "ic50s_MT": [ + "X", + "X", + 834.3800048828125 + ], + "percentiles_MT": [ + "X", + "X", + 1.3919999599456787 + ], + "ic50s_WT": [ + "X", + "X", + 8114.15 + ], + "percentiles_WT": [ + "X", + "X", + 7.85 + ], + "hla_types": [ + "DRB1*04:05", + "HLA-A*29:02", + "HLA-B*45:01" + ], + "mutation_position": "9", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign" + ], + "MT": { + "HLA-B*45:01": [ + 223.4798891953436, + 9791.91, + "NA", + "NA", + 790.51, + "NA", + 1654.99, + 520.12, + 953.12, + 390.13, + 878.25, + "NA" + ] + }, + "WT": { + "HLA-B*45:01": [ + 4198.692961438009, + 13105.51, + "NA", + "NA", + 11312.21, + "NA", + 11541.43, + 14297.39, + 2551.25, + 3021.41, + 4916.09, + "NA" + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign" + ], + "MT": { + "HLA-B*45:01": [ + 0.5297499895095825, + 10.229999542236328, + "NA", + "NA", + 1.2000000476837158, + "NA", + 2.299999952316284, + 0.38999998569488525, + 3.0999999046325684, + 1.4, + 3.2, + "NA" + ] + }, + "WT": { + "HLA-B*45:01": [ + 2.052125, + 13.62, + "NA", + "NA", + 7.8, + "NA", + 6.4, + 5.3, + 7.9, + 12.0, + 15.0, + "NA" + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "HLA-B*45:01": [ + 0.0170274227857589, + 0.2952121690143259, + 0.264, + "NA", + 0.0018446883, + 0.00046415054 + ] + }, + "WT": { + "HLA-B*45:01": [ + 0.0503677166998386, + 0.0265602431327407, + 0.0139, + "NA", + 0.00056617655, + 0.00037295002 + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "HLA-B*45:01": [ + "NA", + 1.384347826086881, + 0.44, + "NA", + "NA", + "NA" + ] + }, + "WT": { + "HLA-B*45:01": [ + "NA", + 9.15535326086956, + 3.1, "NA", "NA", "NA" @@ -875237,54 +877162,28 @@ "best_hla_allele": "DRB1*04:05" }, "chr7-27130623-27130624-C-T": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 0.375, - "RNA VAF": 0.375, - "gene_expr": 1.689, - "best_peptide_mt": "GGPDGGPGY", - "best_peptide_wt": "GGPGGGPGY", - "best_hla_allele": "HLA-A*29:02" - }, - "chr7-39339738-39339739-G-C": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 0.299, - "RNA VAF": 0.0, - "gene_expr": 0.273, - "best_peptide_mt": "PSTNHHPQPAPQAPS", - "best_peptide_wt": "PSTNQHPQPAPQAPS", - "best_hla_allele": "DRB1*04:05" - }, - "chr7-47833094-47833095-G-A": { "good_binders": { "Transcript Set 1": { "peptides": { - "CPPHIQAPSSGLEGL": { + "GGPDGGPGY": { "ic50s_MT": [ - 4493.7900390625, "X", + 5038.81982421875, "X" ], "percentiles_MT": [ - 66.0, "X", + 3.799999952316284, "X" ], "ic50s_WT": [ - 13006.655, "X", + 5061.965, "X" ], "percentiles_WT": [ - 89.0, "X", + 3.8, "X" ], "hla_types": [ @@ -875292,7 +877191,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "5", + "mutation_position": "4", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -875311,35 +877210,35 @@ "SMMalign" ], "MT": { - "DRB1*04:05": [ - "NA", - "NA", - 4704.28, - 4283.3, - "NA", - 6834.06, - "NA", - "NA", + "HLA-A*29:02": [ + 662.1541320591791, + 5615.52, "NA", "NA", + 4517.58, "NA", - 3535.0 + 5560.06, + 12599.12, + 20368.33, + 983.47, + 1047.06, + "NA" ] }, "WT": { - "DRB1*04:05": [ - "NA", - "NA", - 16616.08, - 10403.3, - "NA", - 15610.01, - "NA", - "NA", + "HLA-A*29:02": [ + 674.7509303869019, + 5717.23, "NA", "NA", + 4442.25, "NA", - 10377.0 + 5681.68, + 11280.07, + 19088.05, + 1025.09, + 1051.89, + "NA" ] } }, @@ -875359,35 +877258,35 @@ "SMMalign" ], "MT": { - "DRB1*04:05": [ - "NA", - "NA", - 46.16999816894531, - 70.0, - "NA", - 88.0, - "NA", - "NA", + "HLA-A*29:02": [ + 1.4147499799728394, + 8.3100004196167, "NA", "NA", + 4.0, "NA", - 66.0 + 6.900000095367432, + 6.800000190734863, + 46.0, + 3.4, + 3.6, + "NA" ] }, "WT": { - "DRB1*04:05": [ - "NA", - "NA", - 74.42, - 90.0, - "NA", - 98.0, - "NA", - "NA", + "HLA-A*29:02": [ + 1.4302499999999998, + 12.48, "NA", "NA", + 4.0, "NA", - 89.0 + 7.0, + 6.1, + 44.0, + 3.6, + 3.6, + "NA" ] } }, @@ -875401,23 +877300,23 @@ "BigMHC_IM" ], "MT": { - "DRB1*04:05": [ - "NA", - "NA", - "NA", - 0.019, + "HLA-A*29:02": [ + 0.008780762553215, + 0.1240698407818478, + 0.0514, "NA", - "NA" + 0.039474797, + 0.2530218 ] }, "WT": { - "DRB1*04:05": [ - "NA", - "NA", - "NA", - 0.0017, + "HLA-A*29:02": [ + 0.011206429451704, + 0.1230170253007008, + 0.0451, "NA", - "NA" + 0.085912466, + 0.25358316 ] } }, @@ -875431,21 +877330,597 @@ "BigMHC_IM" ], "MT": { - "DRB1*04:05": [ - "NA", + "HLA-A*29:02": [ "NA", + 2.5301358695651146, + 1.5, "NA", - 39.0, "NA", "NA" ] }, "WT": { - "DRB1*04:05": [ - "NA", + "HLA-A*29:02": [ "NA", + 2.5436413043477444, + 1.6, "NA", - 82.0, + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL" + ], + "MT": { + "HLA-A*29:02": [ + 1.4147499799728394, + 8.3100004196167, + "NA", + "NA", + 4.0, + "NA", + 6.900000095367432, + 6.800000190734863, + 46.0, + 3.4, + 3.6, + "NA", + 2.5301358695651146, + 1.5, + "NA" + ] + }, + "WT": { + "HLA-A*29:02": [ + 1.4302499999999998, + 12.48, + "NA", + "NA", + 4.0, + "NA", + 7.0, + 6.1, + 44.0, + 3.6, + 3.6, + "NA", + 2.5436413043477444, + 1.6, + "NA" + ] + } + }, + "wt_peptide": "GGPGGGPGY" + } + }, + "transcripts": [ + "ENST00000360046.10-HOXA4-G/D-37" + ], + "transcript_expr": [ + 0.464 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 320 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0.464 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0.464 + ], + "DNA VAF": 0.375, + "RNA VAF": 0.375, + "gene_expr": 1.689, + 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"mutation_position": "5", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + 4704.28, + 4283.3, + "NA", + 6834.06, + "NA", + "NA", + "NA", + "NA", + "NA", + 3535.0 + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + 16616.08, + 10403.3, + "NA", + 15610.01, + "NA", + "NA", + "NA", + "NA", + "NA", + 10377.0 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + 46.16999816894531, + 70.0, + "NA", + 88.0, + "NA", + "NA", + "NA", + "NA", + "NA", + 66.0 + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + 74.42, + 90.0, + "NA", + 98.0, + "NA", + "NA", + "NA", + "NA", + "NA", + 89.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 0.019, + "NA", + "NA" + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 0.0017, + "NA", + "NA" + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 39.0, + "NA", + "NA" + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 82.0, "NA", "NA" ] @@ -973879,11 +976354,286 @@ "best_hla_allele": "DRB1*04:05" }, "chr8-138737576-138737577-C-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "PPGLQGLRWKKGDMG": { + "ic50s_MT": [ + 8119.75, + "X", + "X" + ], + "percentiles_MT": [ + 86.0, + "X", + "X" + ], + "ic50s_WT": [ + 9664.005, + "X", + "X" + ], + "percentiles_WT": [ + 86.0, + "X", + "X" + ], + "hla_types": [ + "DRB1*04:05", + "HLA-A*29:02", + "HLA-B*45:01" + ], + "mutation_position": "9", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + 7392.07, + 11812.3, + "NA", + 7716.5, + "NA", + "NA", + "NA", + "NA", + "NA", + 8523.0 + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + 16160.74, + 8618.0, + "NA", + 9859.01, + "NA", + "NA", + "NA", + "NA", + "NA", + 9469.0 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + 55.380001068115234, + 92.0, + "NA", + 90.0, + "NA", + "NA", + "NA", + "NA", + "NA", + 86.0 + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + 73.72, + 86.0, + "NA", + 93.0, + "NA", + "NA", + "NA", + "NA", + "NA", + 87.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 0.0014, + "NA", + "NA" + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 0.0172, + "NA", + "NA" + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 85.0, + "NA", + "NA" + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 40.0, + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + 55.380001068115234, + 92.0, + "NA", + 90.0, + "NA", + "NA", + "NA", + "NA", + "NA", + 86.0, + "NA", + "NA", + 85.0 + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + 73.72, + 86.0, + "NA", + 93.0, + "NA", + "NA", + "NA", + "NA", + "NA", + 87.0, + "NA", + "NA", + 40.0 + ] + } + }, + "wt_peptide": "PPGLQGLRGKKGDMG" + } + }, + "transcripts": [ + "ENST00000303045.11-COL22A1-G/W-696" + ], + "transcript_expr": [ + 0.049 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 1626 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0.049 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0.049 + ], "DNA VAF": 0.2, "RNA VAF": 0.0, "gene_expr": 0.308, @@ -1018109,49 +1020859,36 @@ "best_hla_allele": "DRB1*04:05" }, "chr9-138120681-138120682-G-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 0.276, - "RNA VAF": 0.0, - "gene_expr": 0.154, - "best_peptide_mt": "GEGPTDCRR", - "best_peptide_wt": "GEGPTGCRR", - "best_hla_allele": "HLA-B*45:01" - }, - "chrX-1419025-1419026-G-A": { "good_binders": { "Transcript Set 1": { "peptides": { - "VAMAFNLSRFSSACD": { + "GEGPTDCRR": { "ic50s_MT": [ - 215.9949951171875, "X", - "X" + "X", + 7694.03515625 ], "percentiles_MT": [ - 13.0, "X", - "X" + "X", + 11.8149995803833 ], "ic50s_WT": [ - 235.68, "X", - "X" + "X", + 7362.53 ], "percentiles_WT": [ - 10.29, "X", - "X" + "X", + 9.46 ], "hla_types": [ "DRB1*04:05", "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "3", + "mutation_position": "6", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -1018170,35 +1020907,35 @@ "SMMalign" ], "MT": { - "DRB1*04:05": [ - "NA", - "NA", - 471.98, - 67.6, - "NA", - 257.99, - "NA", - "NA", + "HLA-B*45:01": [ + 5582.474922586768, + 9040.32, "NA", "NA", + 23263.89, "NA", - 174.0 + 20040.43, + 30975.41, + 3725.78, + 6197.41, + 6347.75, + "NA" ] }, "WT": { - "DRB1*04:05": [ - "NA", - "NA", - 298.13, - 67.6, - "NA", - 297.36, - "NA", - "NA", + "HLA-B*45:01": [ + 4455.724537066623, + 9264.84, "NA", "NA", + 21173.23, "NA", - 174.0 + 12930.01, + 25207.23, + 3066.45, + 5460.22, + 4916.09, + "NA" ] } }, @@ -1018218,35 +1020955,35 @@ "SMMalign" ], "MT": { - "DRB1*04:05": [ - "NA", - "NA", - 14.079999923706055, - 2.9000000953674316, - "NA", - 13.0, - "NA", - "NA", + "HLA-B*45:01": [ + 2.304500102996826, + 9.510000228881836, "NA", "NA", + 17.0, "NA", - 5.800000190734863 + 9.100000381469727, + 22.0, + 12.0, + 17.0, + 18.0, + "NA" ] }, "WT": { - "DRB1*04:05": [ + "HLA-B*45:01": [ + 2.095625, + 9.72, "NA", "NA", - 10.29, - 2.9, + 16.0, "NA", + 6.8, 14.0, - "NA", - "NA", - "NA", - "NA", - "NA", - 5.8 + 9.2, + 16.0, + 15.0, + "NA" ] } }, @@ -1018260,23 +1020997,23 @@ "BigMHC_IM" ], "MT": { - "DRB1*04:05": [ - "NA", - "NA", - "NA", - 0.0034, + "HLA-B*45:01": [ + 0.0565916709601879, + 0.0207122957220581, + 0.00379, "NA", - "NA" + 4.8424463e-05, + 2.8045704e-05 ] }, "WT": { - "DRB1*04:05": [ - "NA", - "NA", - "NA", - 0.0039, + "HLA-B*45:01": [ + 0.1171552799642086, + 0.0315894860926236, + 0.00824, "NA", - "NA" + 9.265721e-05, + 4.0969946e-05 ] } }, @@ -1018290,21 +1021027,21 @@ "BigMHC_IM" ], "MT": { - "DRB1*04:05": [ - "NA", + "HLA-B*45:01": [ "NA", + 11.6303260869565, + 5.4, "NA", - 71.0, "NA", "NA" ] }, "WT": { - "DRB1*04:05": [ - "NA", + "HLA-B*45:01": [ "NA", + 7.778097826086963, + 3.9, "NA", - 68.0, "NA", "NA" ] @@ -1018329,64 +1021066,108 @@ "NetMHCIIpanEL" ], "MT": { - "DRB1*04:05": [ - "NA", - "NA", - 14.079999923706055, - 2.9000000953674316, - "NA", - 13.0, - "NA", - "NA", - "NA", + "HLA-B*45:01": [ + 2.304500102996826, + 9.510000228881836, "NA", "NA", - 5.800000190734863, + 17.0, "NA", + 9.100000381469727, + 22.0, + 12.0, + 17.0, + 18.0, "NA", - 71.0 + 11.6303260869565, + 5.4, + "NA" ] }, "WT": { - "DRB1*04:05": [ + "HLA-B*45:01": [ + 2.095625, + 9.72, "NA", "NA", - 10.29, - 2.9, + 16.0, "NA", + 6.8, 14.0, + 9.2, + 16.0, + 15.0, "NA", - "NA", - "NA", - "NA", - "NA", - 5.8, - "NA", - "NA", - 68.0 + 7.778097826086963, + 3.9, + "NA" ] } }, - "wt_peptide": "VATAFNLSRFSSACD" - }, - "CQVAMAFNLSRFSSA": { + "wt_peptide": "GEGPTGCRR" + } + }, + "transcripts": [ + "ENST00000371372.6-CACNA1B-G/D-2097" + ], + "transcript_expr": [ + 0.036 + ], + "tsl": [ + 5 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 2339 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0.036 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0.036 + ], + "DNA VAF": 0.276, + "RNA VAF": 0.0, + "gene_expr": 0.154, + "best_peptide_mt": "GEGPTDCRR", + "best_peptide_wt": "GEGPTGCRR", + "best_hla_allele": "HLA-B*45:01" + }, + "chrX-1419025-1419026-G-A": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "VAMAFNLSRFSSACD": { "ic50s_MT": [ - 363.82501220703125, + 215.9949951171875, "X", "X" ], "percentiles_MT": [ - 16.0, + 13.0, "X", "X" ], "ic50s_WT": [ - 485.235, + 235.68, "X", "X" ], "percentiles_WT": [ - 25.0, + 10.29, "X", "X" ], @@ -1018395,7 +1021176,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "5", + "mutation_position": "3", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -1018417,32 +1021198,32 @@ "DRB1*04:05": [ "NA", "NA", - 190.33, - 509.8, + 471.98, + 67.6, 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"DRB1*04:05": [ + "NA", + "NA", + "NA", + 0.5634, + "NA", + "NA" + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 0.0227, + "NA", + "NA" + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL", + "BigMHC_EL", + "BigMHC_IM" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 2.5, + "NA", + "NA" + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + "NA", + 36.0, + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "NetMHCIIpanEL" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + 26.110000610351562, + 14.0, + "NA", + 7.599999904632568, + "NA", + "NA", + "NA", + "NA", + "NA", + 23.0, + "NA", + "NA", + 2.5 + ] + }, + "WT": { + "DRB1*04:05": [ + "NA", + "NA", + 45.79, + 64.0, + "NA", + 58.0, + "NA", + "NA", + "NA", + "NA", + "NA", + 59.0, + "NA", + "NA", + 36.0 + ] + } + }, + "wt_peptide": "PKRSKLEETSLVPRA" + }, + "STPKRIKLEETSLVP": { + "ic50s_MT": [ + 462.70001220703125, + "X", + "X" + ], + "percentiles_MT": [ + 15.0, + "X", + "X" + ], + "ic50s_WT": [ + 3886.305, + "X", + "X" + ], + "percentiles_WT": [ + 60.0, + "X", + "X" + ], + "hla_types": [ + "DRB1*04:05", + "HLA-A*29:02", + "HLA-B*45:01" + ], + "mutation_position": "6", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "MHCnuggetsII", + "NNalign", + "NetMHC", + "NetMHCIIpan", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "SMMalign" + ], + "MT": { + "DRB1*04:05": [ + "NA", + "NA", + 1617.62, + 285.4, "NA", - 1654.63, + 270.79, "NA", "NA", "NA", "NA", "NA", - 2120.0 + 640.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 5977.81, - 2393.2, + 7878.35, + 4455.5, "NA", - 1271.07, + 3317.11, "NA", "NA", "NA", "NA", "NA", - 1997.0 + 2816.0 ] } }, @@ -1063615,32 +1067421,32 @@ "DRB1*04:05": [ "NA", "NA", - 56.65999984741211, - 59.0, + 28.350000381469727, + 15.0, "NA", - 53.0, + 13.0, "NA", "NA", "NA", "NA", "NA", - 53.0 + 23.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 50.92, - 55.0, + 56.75, + 71.0, "NA", - 46.0, + 72.0, "NA", "NA", "NA", "NA", "NA", - 51.0 + 60.0 ] } }, @@ -1063658,7 +1067464,7 @@ "NA", "NA", "NA", - 0.0016, + 0.3093, "NA", "NA" ] @@ -1063668,7 +1067474,7 @@ "NA", "NA", "NA", - 0.0025, + 0.0068, "NA", "NA" ] @@ -1063688,7 +1067494,7 @@ "NA", "NA", "NA", - 83.0, + 5.7, "NA", "NA" ] @@ -1063698,7 +1067504,7 @@ "NA", "NA", "NA", - 76.0, + 57.0, "NA", "NA" ] @@ -1063726,110 +1067532,61 @@ "DRB1*04:05": [ "NA", "NA", - 56.65999984741211, - 59.0, + 28.350000381469727, + 15.0, "NA", - 53.0, + 13.0, "NA", "NA", "NA", "NA", "NA", - 53.0, + 23.0, "NA", "NA", - 83.0 + 5.7 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 50.92, - 55.0, + 56.75, + 71.0, "NA", - 46.0, + 72.0, "NA", "NA", "NA", "NA", "NA", - 51.0, + 60.0, "NA", "NA", - 76.0 + 57.0 ] } }, - "wt_peptide": "NVEFPETLLMDRIRL" - } - }, - "transcripts": [ - "ENST00000642911.1-TCP11X2-R/W-318", - "ENST00000618302.2-ENSG00000284800-R/W-22" - ], - "transcript_expr": [ - 0.0, - 0.0 - ], - "tsl": [ - "NA", - 2 - ], - "biotype": [ - "protein_coding", - "nonsense_mediated_decay" - ], - "transcript_length": [ - 502, - 142 - ], - "transcript_count": 2, - "peptide_count": 15, - "total_expr": 0.0 - } - }, - "sets": [ - "Transcript Set 1" - ], - "transcript_counts": [ - 2 - ], - "peptide_counts": [ - 15 - ], - "set_expr": [ - 0.0 - ], - "DNA VAF": 0.481, - "RNA VAF": 0.0, - "gene_expr": 0.0, - "best_peptide_mt": "PETLLMDRIWLQELA", - "best_peptide_wt": "PETLLMDRIRLQELA", - "best_hla_allele": "DRB1*04:05" - }, - "chrX-107601385-107601386-G-T": { - "good_binders": { - "Transcript Set 1": { - "peptides": { - "TPKRIKLEETSLVPR": { + "wt_peptide": "STPKRSKLEETSLVP" + }, + "ESTPKRIKLEETSLV": { "ic50s_MT": [ - 443.6000061035156, + 551.7000122070312, "X", "X" ], "percentiles_MT": [ - 13.0, + 22.0, "X", "X" ], "ic50s_WT": [ - 3077.75, + 5325.62, "X", "X" ], "percentiles_WT": [ - 59.0, + 76.0, "X", "X" ], @@ -1063838,7 +1067595,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "5", + "mutation_position": "7", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -1063860,32 +1067617,32 @@ "DRB1*04:05": [ "NA", "NA", - 1330.32, - 236.2, + 1177.27, + 486.4, "NA", - 198.67, + 361.99, "NA", "NA", "NA", "NA", "NA", - 651.0 + 617.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 5396.44, - 3528.5, + 7807.65, + 6709.7, "NA", - 2407.37, + 3941.54, "NA", "NA", "NA", "NA", "NA", - 2627.0 + 2715.0 ] } }, @@ -1063908,32 +1067665,32 @@ "DRB1*04:05": [ "NA", "NA", - 25.670000076293945, - 13.0, + 24.06999969482422, + 22.0, "NA", - 9.100000381469727, + 17.0, "NA", "NA", "NA", "NA", "NA", - 23.0 + 22.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 48.870000000000005, - 65.0, + 56.56, + 81.0, "NA", - 63.0, + 76.0, "NA", "NA", "NA", "NA", "NA", - 59.0 + 60.0 ] } }, @@ -1063951,7 +1067708,7 @@ "NA", "NA", "NA", - 0.5, + 0.0496, "NA", "NA" ] @@ -1063961,7 +1067718,7 @@ "NA", "NA", "NA", - 0.0161, + 0.0016, "NA", "NA" ] @@ -1063981,7 +1067738,7 @@ "NA", "NA", "NA", - 3.1, + 24.0, "NA", "NA" ] @@ -1063991,7 +1067748,7 @@ "NA", "NA", "NA", - 41.0, + 83.0, "NA", "NA" ] @@ -1064019,61 +1067776,61 @@ "DRB1*04:05": [ "NA", "NA", - 25.670000076293945, - 13.0, + 24.06999969482422, + 22.0, "NA", - 9.100000381469727, + 17.0, "NA", "NA", "NA", "NA", "NA", - 23.0, + 22.0, "NA", "NA", - 3.1 + 24.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 48.870000000000005, - 65.0, + 56.56, + 81.0, "NA", - 63.0, + 76.0, "NA", "NA", "NA", "NA", "NA", - 59.0, + 60.0, "NA", "NA", - 41.0 + 83.0 ] } }, - "wt_peptide": "TPKRSKLEETSLVPR" + "wt_peptide": "ESTPKRSKLEETSLV" }, - "PKRIKLEETSLVPRA": { + "KRIKLEETSLVPRAT": { "ic50s_MT": [ - 453.20001220703125, + 603.4500122070312, "X", "X" ], "percentiles_MT": [ - 14.0, + 20.0, "X", "X" ], "ic50s_WT": [ - 3018.4, + 3905.5, "X", "X" ], "percentiles_WT": [ - 58.0, + 57.0, "X", "X" ], @@ -1064082,7 +1067839,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "4", + "mutation_position": "3", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -1064104,32 +1067861,32 @@ "DRB1*04:05": [ "NA", "NA", - 1374.7, - 256.4, + 3077.62, + 425.9, "NA", - 171.73, + 169.77, "NA", "NA", "NA", "NA", "NA", - 650.0 + 781.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 4613.97, - 3392.8, + 5130.26, + 4400.0, "NA", - 1956.68, + 1887.25, "NA", "NA", "NA", "NA", "NA", - 2644.0 + 3411.0 ] } }, @@ -1064152,8 +1067909,8 @@ "DRB1*04:05": [ "NA", "NA", - 26.110000610351562, - 14.0, + 38.40999984741211, + 20.0, "NA", 7.599999904632568, "NA", @@ -1064161,23 +1067918,23 @@ "NA", "NA", "NA", - 23.0 + 27.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 45.79, - 64.0, + 47.85, + 71.0, "NA", - 58.0, + 57.0, "NA", "NA", "NA", "NA", "NA", - 59.0 + 65.0 ] } }, @@ -1064195,7 +1067952,7 @@ "NA", "NA", "NA", - 0.5634, + 0.2245, "NA", "NA" ] @@ -1064205,7 +1067962,7 @@ "NA", "NA", "NA", - 0.0227, + 0.0069, "NA", "NA" ] @@ -1064225,7 +1067982,7 @@ "NA", "NA", "NA", - 2.5, + 7.8, "NA", "NA" ] @@ -1064235,7 +1067992,7 @@ "NA", "NA", "NA", - 36.0, + 57.0, "NA", "NA" ] @@ -1064263,8 +1068020,8 @@ "DRB1*04:05": [ "NA", "NA", - 26.110000610351562, - 14.0, + 38.40999984741211, + 20.0, "NA", 7.599999904632568, "NA", @@ -1064272,52 +1068029,52 @@ "NA", "NA", "NA", - 23.0, + 27.0, "NA", "NA", - 2.5 + 7.8 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 45.79, - 64.0, + 47.85, + 71.0, "NA", - 58.0, + 57.0, "NA", "NA", "NA", "NA", "NA", - 59.0, + 65.0, "NA", "NA", - 36.0 + 57.0 ] } }, - "wt_peptide": "PKRSKLEETSLVPRA" + "wt_peptide": "KRSKLEETSLVPRAT" }, - "STPKRIKLEETSLVP": { + "RIKLEETSLVPRATY": { "ic50s_MT": [ - 462.70001220703125, + 1554.800048828125, "X", "X" ], "percentiles_MT": [ - 15.0, + 38.0, "X", "X" ], "ic50s_WT": [ - 3886.305, + 3343.89, "X", "X" ], "percentiles_WT": [ - 60.0, + 62.0, "X", "X" ], @@ -1064326,7 +1068083,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "6", + "mutation_position": "2", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -1064348,32 +1068105,32 @@ "DRB1*04:05": [ "NA", "NA", - 1617.62, - 285.4, + 1892.63, + 1242.6, "NA", - 270.79, + 341.82, "NA", "NA", "NA", "NA", "NA", - 640.0 + 1867.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 7878.35, - 4455.5, + 2681.78, + 6640.0, "NA", - 3317.11, + 2260.75, "NA", "NA", "NA", "NA", "NA", - 2816.0 + 4006.0 ] } }, @@ -1064396,32 +1068153,32 @@ "DRB1*04:05": [ "NA", "NA", - 28.350000381469727, - 15.0, + 30.65999984741211, + 40.0, "NA", - 13.0, + 17.0, "NA", "NA", "NA", "NA", "NA", - 23.0 + 50.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 56.75, - 71.0, + 36.13, + 81.0, "NA", - 72.0, + 62.0, "NA", "NA", "NA", "NA", "NA", - 60.0 + 69.0 ] } }, @@ -1064439,7 +1068196,7 @@ "NA", "NA", "NA", - 0.3093, + 0.0193, "NA", "NA" ] @@ -1064449,7 +1068206,7 @@ "NA", "NA", "NA", - 0.0068, + 0.0057, "NA", "NA" ] @@ -1064469,7 +1068226,7 @@ "NA", "NA", "NA", - 5.7, + 38.0, "NA", "NA" ] @@ -1064479,7 +1068236,7 @@ "NA", "NA", "NA", - 57.0, + 61.0, "NA", "NA" ] @@ -1064507,61 +1068264,61 @@ "DRB1*04:05": [ "NA", "NA", - 28.350000381469727, - 15.0, + 30.65999984741211, + 40.0, "NA", - 13.0, + 17.0, "NA", "NA", "NA", "NA", "NA", - 23.0, + 50.0, "NA", "NA", - 5.7 + 38.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 56.75, - 71.0, + 36.13, + 81.0, "NA", - 72.0, + 62.0, "NA", "NA", "NA", "NA", "NA", - 60.0, + 69.0, "NA", "NA", - 57.0 + 61.0 ] } }, - "wt_peptide": "STPKRSKLEETSLVP" + "wt_peptide": "RSKLEETSLVPRATY" }, - "ESTPKRIKLEETSLV": { + "IKLEETSLVPRATYP": { "ic50s_MT": [ - 551.7000122070312, + 3017.840087890625, "X", "X" ], "percentiles_MT": [ - 22.0, + 54.0, "X", "X" ], "ic50s_WT": [ - 5325.62, + 4379.44, "X", "X" ], "percentiles_WT": [ - 76.0, + 73.0, "X", "X" ], @@ -1064570,7 +1068327,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "7", + "mutation_position": "1", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -1064592,32 +1068349,32 @@ "DRB1*04:05": [ "NA", "NA", - 1177.27, - 486.4, + 3845.68, + 5290.2, "NA", - 361.99, + 1549.57, "NA", "NA", "NA", "NA", "NA", - 617.0 + 2190.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 7807.65, - 6709.7, + 4073.88, + 9468.3, "NA", - 3941.54, + 3946.53, "NA", "NA", "NA", "NA", "NA", - 2715.0 + 4685.0 ] } }, @@ -1064640,24 +1068397,24 @@ "DRB1*04:05": [ "NA", "NA", - 24.06999969482422, - 22.0, + 42.36000061035156, + 75.0, "NA", - 17.0, + 51.0, "NA", "NA", "NA", "NA", "NA", - 22.0 + 54.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 56.56, - 81.0, + 43.42, + 88.0, "NA", 76.0, "NA", @@ -1064665,7 +1068422,7 @@ "NA", "NA", "NA", - 60.0 + 73.0 ] } }, @@ -1064683,7 +1068440,7 @@ "NA", "NA", "NA", - 0.0496, + 0.0051, "NA", "NA" ] @@ -1064693,7 +1068450,7 @@ "NA", "NA", "NA", - 0.0016, + 0.006, "NA", "NA" ] @@ -1064713,7 +1068470,7 @@ "NA", "NA", "NA", - 24.0, + 63.0, "NA", "NA" ] @@ -1064723,7 +1068480,7 @@ "NA", "NA", "NA", - 83.0, + 60.0, "NA", "NA" ] @@ -1064751,27 +1068508,27 @@ "DRB1*04:05": [ "NA", "NA", - 24.06999969482422, - 22.0, + 42.36000061035156, + 75.0, "NA", - 17.0, + 51.0, "NA", "NA", "NA", "NA", "NA", - 22.0, + 54.0, "NA", "NA", - 24.0 + 63.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 56.56, - 81.0, + 43.42, + 88.0, "NA", 76.0, "NA", @@ -1064779,33 +1068536,33 @@ "NA", "NA", "NA", - 60.0, + 73.0, "NA", "NA", - 83.0 + 60.0 ] } }, - "wt_peptide": "ESTPKRSKLEETSLV" + "wt_peptide": "SKLEETSLVPRATYP" }, - "KRIKLEETSLVPRAT": { + "GEKAQLESTPKRIKL": { "ic50s_MT": [ - 603.4500122070312, + 3960.52490234375, "X", "X" ], "percentiles_MT": [ - 20.0, + 68.0, "X", "X" ], "ic50s_WT": [ - 3905.5, + 3498.995, "X", "X" ], "percentiles_WT": [ - 57.0, + 67.0, "X", "X" ], @@ -1064814,7 +1068571,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "3", + "mutation_position": "13", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -1064836,32 +1068593,32 @@ "DRB1*04:05": [ "NA", "NA", - 3077.62, - 425.9, + 3778.65, + 4142.4, "NA", - 169.77, + 5637.59, "NA", "NA", "NA", "NA", "NA", - 781.0 + 2687.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 5130.26, - 4400.0, + 3226.79, + 3771.2, "NA", - 1887.25, + 7444.23, "NA", "NA", "NA", "NA", "NA", - 3411.0 + 2751.0 ] } }, @@ -1064884,32 +1068641,32 @@ "DRB1*04:05": [ "NA", "NA", - 38.40999984741211, - 20.0, + 42.029998779296875, + 69.0, "NA", - 7.599999904632568, + 84.0, "NA", "NA", "NA", "NA", "NA", - 27.0 + 59.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 47.85, - 71.0, + 39.23, + 67.0, "NA", - 57.0, + 89.0, "NA", "NA", "NA", "NA", "NA", - 65.0 + 60.0 ] } }, @@ -1064927,7 +1068684,7 @@ "NA", "NA", "NA", - 0.2245, + 0.0039, "NA", "NA" ] @@ -1064937,7 +1068694,7 @@ "NA", "NA", "NA", - 0.0069, + 0.0038, "NA", "NA" ] @@ -1064957,7 +1068714,7 @@ "NA", "NA", "NA", - 7.8, + 68.0, "NA", "NA" ] @@ -1064967,7 +1068724,7 @@ "NA", "NA", "NA", - 57.0, + 68.0, "NA", "NA" ] @@ -1064995,61 +1068752,61 @@ "DRB1*04:05": [ "NA", "NA", - 38.40999984741211, - 20.0, + 42.029998779296875, + 69.0, "NA", - 7.599999904632568, + 84.0, "NA", "NA", "NA", "NA", "NA", - 27.0, + 59.0, "NA", "NA", - 7.8 + 68.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 47.85, - 71.0, + 39.23, + 67.0, "NA", - 57.0, + 89.0, "NA", "NA", "NA", "NA", "NA", - 65.0, + 60.0, "NA", "NA", - 57.0 + 68.0 ] } }, - "wt_peptide": "KRSKLEETSLVPRAT" + "wt_peptide": "GEKAQLESTPKRSKL" }, - "RIKLEETSLVPRATY": { + "QGEKAQLESTPKRIK": { "ic50s_MT": [ - 1554.800048828125, + 4357.75, "X", "X" ], "percentiles_MT": [ - 38.0, + 65.0, "X", "X" ], "ic50s_WT": [ - 3343.89, + 4408.6, "X", "X" ], "percentiles_WT": [ - 62.0, + 63.0, "X", "X" ], @@ -1065058,7 +1068815,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "2", + "mutation_position": "14", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -1065080,32 +1068837,32 @@ "DRB1*04:05": [ "NA", "NA", - 1892.63, - 1242.6, + 5138.1, + 3577.4, "NA", - 341.82, + 6907.89, "NA", "NA", "NA", "NA", "NA", - 1867.0 + 2425.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 2681.78, - 6640.0, + 5504.5, + 3312.7, "NA", - 2260.75, + 8711.46, "NA", "NA", "NA", "NA", "NA", - 4006.0 + 2500.0 ] } }, @@ -1065128,32 +1068885,32 @@ "DRB1*04:05": [ "NA", "NA", - 30.65999984741211, - 40.0, + 47.880001068115234, + 65.0, "NA", - 17.0, + 88.0, "NA", "NA", "NA", "NA", "NA", - 50.0 + 56.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 36.13, - 81.0, + 49.27, + 63.0, "NA", - 62.0, + 92.0, "NA", "NA", "NA", "NA", "NA", - 69.0 + 57.0 ] } }, @@ -1065171,7 +1068928,7 @@ "NA", "NA", "NA", - 0.0193, + 0.0039, "NA", "NA" ] @@ -1065181,7 +1068938,7 @@ "NA", "NA", "NA", - 0.0057, + 0.0044, "NA", "NA" ] @@ -1065201,7 +1068958,7 @@ "NA", "NA", "NA", - 38.0, + 68.0, "NA", "NA" ] @@ -1065211,7 +1068968,7 @@ "NA", "NA", "NA", - 61.0, + 66.0, "NA", "NA" ] @@ -1065239,61 +1068996,61 @@ "DRB1*04:05": [ "NA", "NA", - 30.65999984741211, - 40.0, + 47.880001068115234, + 65.0, "NA", - 17.0, + 88.0, "NA", "NA", "NA", "NA", "NA", - 50.0, + 56.0, "NA", "NA", - 38.0 + 68.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 36.13, - 81.0, + 49.27, + 63.0, "NA", - 62.0, + 92.0, "NA", "NA", "NA", "NA", "NA", - 69.0, + 57.0, "NA", "NA", - 61.0 + 66.0 ] } }, - "wt_peptide": "RSKLEETSLVPRATY" + "wt_peptide": "QGEKAQLESTPKRSK" }, - "IKLEETSLVPRATYP": { + "SQGEKAQLESTPKRI": { "ic50s_MT": [ - 3017.840087890625, + 4752.615234375, "X", "X" ], "percentiles_MT": [ - 54.0, + 68.0, "X", "X" ], "ic50s_WT": [ - 4379.44, + 6073.64, "X", "X" ], "percentiles_WT": [ - 73.0, + 67.0, "X", "X" ], @@ -1065302,7 +1069059,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "1", + "mutation_position": "15", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -1065324,32 +1069081,32 @@ "DRB1*04:05": [ "NA", "NA", - 3845.68, - 5290.2, + 5542.63, + 3962.6, "NA", - 1549.57, + 8634.14, "NA", "NA", "NA", "NA", "NA", - 2190.0 + 2440.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 4073.88, - 9468.3, + 8410.08, + 3737.2, "NA", - 3946.53, + 10606.68, "NA", "NA", "NA", "NA", "NA", - 4685.0 + 2537.0 ] } }, @@ -1065372,32 +1069129,32 @@ "DRB1*04:05": [ "NA", "NA", - 42.36000061035156, - 75.0, + 49.400001525878906, + 68.0, "NA", - 51.0, + 92.0, "NA", "NA", "NA", "NA", "NA", - 54.0 + 57.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 43.42, - 88.0, + 58.17, + 67.0, "NA", - 76.0, + 94.0, "NA", "NA", "NA", "NA", "NA", - 73.0 + 58.0 ] } }, @@ -1065415,7 +1069172,7 @@ "NA", "NA", "NA", - 0.0051, + 0.002, "NA", "NA" ] @@ -1065425,7 +1069182,7 @@ "NA", "NA", "NA", - 0.006, + 0.0023, "NA", "NA" ] @@ -1065445,7 +1069202,7 @@ "NA", "NA", "NA", - 63.0, + 80.0, "NA", "NA" ] @@ -1065455,7 +1069212,7 @@ "NA", "NA", "NA", - 60.0, + 78.0, "NA", "NA" ] @@ -1065483,61 +1069240,61 @@ "DRB1*04:05": [ "NA", "NA", - 42.36000061035156, - 75.0, + 49.400001525878906, + 68.0, "NA", - 51.0, + 92.0, "NA", "NA", "NA", "NA", "NA", - 54.0, + 57.0, "NA", "NA", - 63.0 + 80.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 43.42, - 88.0, + 58.17, + 67.0, "NA", - 76.0, + 94.0, "NA", "NA", "NA", "NA", "NA", - 73.0, + 58.0, "NA", "NA", - 60.0 + 78.0 ] } }, - "wt_peptide": "SKLEETSLVPRATYP" + "wt_peptide": "SQGEKAQLESTPKRS" }, - "GEKAQLESTPKRIKL": { + "LESTPKRIKLEETSL": { "ic50s_MT": [ - 3960.52490234375, + 4880.830078125, "X", "X" ], "percentiles_MT": [ - 68.0, + 70.0, "X", "X" ], "ic50s_WT": [ - 3498.995, + 11652.085, "X", "X" ], "percentiles_WT": [ - 67.0, + 91.0, "X", "X" ], @@ -1065546,7 +1069303,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "13", + "mutation_position": "8", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -1065568,32 +1069325,32 @@ "DRB1*04:05": [ "NA", "NA", - 3778.65, - 4142.4, + 5494.96, + 4266.7, "NA", - 5637.59, + 7403.98, "NA", "NA", "NA", "NA", "NA", - 2687.0 + 1855.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 3226.79, - 3771.2, + 11117.21, + 15187.2, "NA", - 7444.23, + 12186.96, "NA", "NA", "NA", "NA", "NA", - 2751.0 + 3500.0 ] } }, @@ -1065616,32 +1069373,32 @@ "DRB1*04:05": [ "NA", "NA", - 42.029998779296875, - 69.0, + 49.2400016784668, + 70.0, "NA", - 84.0, + 89.0, "NA", "NA", "NA", "NA", "NA", - 59.0 + 49.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 39.23, - 67.0, + 64.55, + 96.0, "NA", - 89.0, + 96.0, "NA", "NA", "NA", "NA", "NA", - 60.0 + 66.0 ] } }, @@ -1065659,7 +1069416,7 @@ "NA", "NA", "NA", - 0.0039, + 0.0014, "NA", "NA" ] @@ -1065669,7 +1069426,7 @@ "NA", "NA", "NA", - 0.0038, + 0.0009, "NA", "NA" ] @@ -1065689,7 +1069446,7 @@ "NA", "NA", "NA", - 68.0, + 85.0, "NA", "NA" ] @@ -1065699,7 +1069456,7 @@ "NA", "NA", "NA", - 68.0, + 91.0, "NA", "NA" ] @@ -1065727,61 +1069484,120 @@ "DRB1*04:05": [ "NA", "NA", - 42.029998779296875, - 69.0, + 49.2400016784668, + 70.0, "NA", - 84.0, + 89.0, "NA", "NA", "NA", "NA", "NA", - 59.0, + 49.0, "NA", "NA", - 68.0 + 85.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 39.23, - 67.0, + 64.55, + 96.0, "NA", - 89.0, + 96.0, "NA", "NA", "NA", "NA", "NA", - 60.0, + 66.0, "NA", "NA", - 68.0 + 91.0 ] } }, - "wt_peptide": "GEKAQLESTPKRSKL" - }, - "QGEKAQLESTPKRIK": { + "wt_peptide": "LESTPKRSKLEETSL" + } + }, + "transcripts": [ + "ENST00000276185.9-FRMPD3-S/I-1116", + "ENST00000439554.1-FRMPD3-S/I-1097", + "ENST00000683843.1-FRMPD3-S/I-1116", + "ENST00000684358.1-FRMPD3-S/I-981" + ], + "transcript_expr": [ + 0.0, + 0.045, + 0.0, + 0.0 + ], + "tsl": [ + 5, + 5, + "NA", + "NA" + ], + "biotype": [ + "protein_coding", + "protein_coding", + "protein_coding", + "protein_coding" + ], + "transcript_length": [ + 1777, + 1758, + 1777, + 1642 + ], + "transcript_count": 4, + "peptide_count": 11, + "total_expr": 0.045 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 4 + ], + "peptide_counts": [ + 11 + ], + "set_expr": [ + 0.045 + ], + "DNA VAF": 0.391, + "RNA VAF": 0.5, + "gene_expr": 0.1, + "best_peptide_mt": "TPKRIKLEETSLVPR", + "best_peptide_wt": "TPKRSKLEETSLVPR", + "best_hla_allele": "DRB1*04:05" + }, + "chrX-135721216-135721217-G-A": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "QEINADIKRKLVKEL": { "ic50s_MT": [ - 4357.75, + 5009.080078125, "X", "X" ], "percentiles_MT": [ - 65.0, + 77.0, "X", "X" ], "ic50s_WT": [ - 4408.6, + 4775.77, "X", "X" ], "percentiles_WT": [ - 63.0, + 78.0, "X", "X" ], @@ -1065790,7 +1069606,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "14", + "mutation_position": "1", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -1065812,32 +1069628,32 @@ "DRB1*04:05": [ "NA", "NA", - 5138.1, - 3577.4, + 4813.9, + 11918.2, "NA", - 6907.89, + 5204.26, "NA", "NA", "NA", "NA", "NA", - 2425.0 + 3496.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 5504.5, - 3312.7, + 4642.85, + 11397.5, "NA", - 8711.46, + 4908.69, "NA", "NA", "NA", "NA", "NA", - 2500.0 + 3459.0 ] } }, @@ -1065860,32 +1069676,32 @@ "DRB1*04:05": [ "NA", "NA", - 47.880001068115234, - 65.0, + 46.61000061035156, + 92.0, "NA", - 88.0, + 82.0, "NA", "NA", "NA", "NA", "NA", - 56.0 + 66.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 49.27, - 63.0, + 45.91, + 91.0, "NA", - 92.0, + 81.0, "NA", "NA", "NA", "NA", "NA", - 57.0 + 66.0 ] } }, @@ -1065903,7 +1069719,7 @@ "NA", "NA", "NA", - 0.0039, + 0.0024, "NA", "NA" ] @@ -1065913,7 +1069729,7 @@ "NA", "NA", "NA", - 0.0044, + 0.0023, "NA", "NA" ] @@ -1065933,7 +1069749,7 @@ "NA", "NA", "NA", - 68.0, + 77.0, "NA", "NA" ] @@ -1065943,7 +1069759,7 @@ "NA", "NA", "NA", - 66.0, + 78.0, "NA", "NA" ] @@ -1065971,61 +1069787,105 @@ "DRB1*04:05": [ "NA", "NA", - 47.880001068115234, - 65.0, + 46.61000061035156, + 92.0, "NA", - 88.0, + 82.0, "NA", "NA", "NA", "NA", "NA", - 56.0, + 66.0, "NA", "NA", - 68.0 + 77.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 49.27, - 63.0, + 45.91, + 91.0, "NA", - 92.0, + 81.0, "NA", "NA", "NA", "NA", "NA", - 57.0, + 66.0, "NA", "NA", - 66.0 + 78.0 ] } }, - "wt_peptide": "QGEKAQLESTPKRSK" - }, - "SQGEKAQLESTPKRI": { + "wt_peptide": "REINADIKRKLVKEL" + } + }, + "transcripts": [ + "ENST00000594117.4-CT45A1-R/Q-120" + ], + "transcript_expr": [ + 0.0 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 189 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0.0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0.0 + ], + "DNA VAF": 0.582, + "RNA VAF": 0.0, + "gene_expr": 0.0, + "best_peptide_mt": "QEINADIKRKLVKEL", + "best_peptide_wt": "REINADIKRKLVKEL", + "best_hla_allele": "DRB1*04:05" + }, + "chrX-135779451-135779452-C-T": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "QEINADIKRKLVKEL": { "ic50s_MT": [ - 4752.615234375, + 5009.080078125, "X", "X" ], "percentiles_MT": [ - 68.0, + 77.0, "X", "X" ], "ic50s_WT": [ - 6073.64, + 4775.77, "X", "X" ], "percentiles_WT": [ - 67.0, + 78.0, "X", "X" ], @@ -1066034,7 +1069894,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "15", + "mutation_position": "1", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -1066056,32 +1069916,32 @@ "DRB1*04:05": [ "NA", "NA", - 5542.63, - 3962.6, + 4813.9, + 11918.2, "NA", - 8634.14, + 5204.26, "NA", "NA", "NA", "NA", "NA", - 2440.0 + 3496.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 8410.08, - 3737.2, + 4642.85, + 11397.5, "NA", - 10606.68, + 4908.69, "NA", "NA", "NA", "NA", "NA", - 2537.0 + 3459.0 ] } }, @@ -1066104,32 +1069964,32 @@ "DRB1*04:05": [ "NA", "NA", - 49.400001525878906, - 68.0, - "NA", + 46.61000061035156, 92.0, "NA", + 82.0, "NA", "NA", "NA", "NA", - 57.0 + "NA", + 66.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 58.17, - 67.0, + 45.91, + 91.0, "NA", - 94.0, + 81.0, "NA", "NA", "NA", "NA", "NA", - 58.0 + 66.0 ] } }, @@ -1066147,7 +1070007,7 @@ "NA", "NA", "NA", - 0.002, + 0.0024, "NA", "NA" ] @@ -1066177,7 +1070037,7 @@ "NA", "NA", "NA", - 80.0, + 77.0, "NA", "NA" ] @@ -1066215,61 +1070075,105 @@ "DRB1*04:05": [ "NA", "NA", - 49.400001525878906, - 68.0, - "NA", + 46.61000061035156, 92.0, "NA", + 82.0, "NA", "NA", "NA", "NA", - 57.0, "NA", + 66.0, "NA", - 80.0 + "NA", + 77.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 58.17, - 67.0, + 45.91, + 91.0, "NA", - 94.0, + 81.0, "NA", "NA", "NA", "NA", "NA", - 58.0, + 66.0, "NA", "NA", 78.0 ] } }, - "wt_peptide": "SQGEKAQLESTPKRS" - }, - "LESTPKRIKLEETSL": { + "wt_peptide": "REINADIKRKLVKEL" + } + }, + "transcripts": [ + "ENST00000617203.1-CT45A5-R/Q-120" + ], + "transcript_expr": [ + 0.0 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 189 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0.0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0.0 + ], + "DNA VAF": 0.577, + "RNA VAF": 0.0, + "gene_expr": 0.0, + "best_peptide_mt": "QEINADIKRKLVKEL", + "best_peptide_wt": "REINADIKRKLVKEL", + "best_hla_allele": "DRB1*04:05" + }, + "chrX-135796713-135796714-C-T": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "QEINADIKRKLVKEL": { "ic50s_MT": [ - 4880.830078125, + 5009.080078125, "X", "X" ], "percentiles_MT": [ - 70.0, + 77.0, "X", "X" ], "ic50s_WT": [ - 11652.085, + 4775.77, "X", "X" ], "percentiles_WT": [ - 91.0, + 78.0, "X", "X" ], @@ -1066278,7 +1070182,7 @@ "HLA-A*29:02", "HLA-B*45:01" ], - "mutation_position": "8", + "mutation_position": "1", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -1066300,32 +1070204,32 @@ "DRB1*04:05": [ "NA", "NA", - 5494.96, - 4266.7, + 4813.9, + 11918.2, "NA", - 7403.98, + 5204.26, "NA", "NA", "NA", "NA", "NA", - 1855.0 + 3496.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 11117.21, - 15187.2, + 4642.85, + 11397.5, "NA", - 12186.96, + 4908.69, "NA", "NA", "NA", "NA", "NA", - 3500.0 + 3459.0 ] } }, @@ -1066348,26 +1070252,26 @@ "DRB1*04:05": [ "NA", "NA", - 49.2400016784668, - 70.0, + 46.61000061035156, + 92.0, "NA", - 89.0, + 82.0, "NA", "NA", "NA", "NA", "NA", - 49.0 + 66.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 64.55, - 96.0, + 45.91, + 91.0, "NA", - 96.0, + 81.0, "NA", "NA", "NA", @@ -1066391,7 +1070295,7 @@ "NA", "NA", "NA", - 0.0014, + 0.0024, "NA", "NA" ] @@ -1066401,7 +1070305,7 @@ "NA", "NA", "NA", - 0.0009, + 0.0023, "NA", "NA" ] @@ -1066421,7 +1070325,7 @@ "NA", "NA", "NA", - 85.0, + 77.0, "NA", "NA" ] @@ -1066431,7 +1070335,7 @@ "NA", "NA", "NA", - 91.0, + 78.0, "NA", "NA" ] @@ -1066459,29 +1070363,29 @@ "DRB1*04:05": [ "NA", "NA", - 49.2400016784668, - 70.0, + 46.61000061035156, + 92.0, "NA", - 89.0, + 82.0, "NA", "NA", "NA", "NA", "NA", - 49.0, + 66.0, "NA", "NA", - 85.0 + 77.0 ] }, "WT": { "DRB1*04:05": [ "NA", "NA", - 64.55, - 96.0, + 45.91, + 91.0, "NA", - 96.0, + 81.0, "NA", "NA", "NA", @@ -1066490,99 +1070394,45 @@ 66.0, "NA", "NA", - 91.0 + 78.0 ] } }, - "wt_peptide": "LESTPKRSKLEETSL" + "wt_peptide": "REINADIKRKLVKEL" } }, "transcripts": [ - "ENST00000276185.9-FRMPD3-S/I-1116", - "ENST00000439554.1-FRMPD3-S/I-1097", - "ENST00000683843.1-FRMPD3-S/I-1116", - "ENST00000684358.1-FRMPD3-S/I-981" + "ENST00000612878.4-CT45A6-R/Q-120" ], "transcript_expr": [ - 0.0, - 0.045, - 0.0, 0.0 ], "tsl": [ - 5, - 5, - "NA", - "NA" + 1 ], "biotype": [ - "protein_coding", - "protein_coding", - "protein_coding", "protein_coding" ], "transcript_length": [ - 1777, - 1758, - 1777, - 1642 + 189 ], - "transcript_count": 4, - "peptide_count": 11, - "total_expr": 0.045 + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0.0 } }, "sets": [ "Transcript Set 1" ], "transcript_counts": [ - 4 + 1 ], "peptide_counts": [ - 11 + 1 ], "set_expr": [ - 0.045 + 0.0 ], - "DNA VAF": 0.391, - "RNA VAF": 0.5, - "gene_expr": 0.1, - "best_peptide_mt": "TPKRIKLEETSLVPR", - "best_peptide_wt": "TPKRSKLEETSLVPR", - "best_hla_allele": "DRB1*04:05" - }, - "chrX-135721216-135721217-G-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 0.582, - "RNA VAF": 0.0, - "gene_expr": 0.0, - "best_peptide_mt": "QEINADIKRKLVKEL", - "best_peptide_wt": "REINADIKRKLVKEL", - "best_hla_allele": "DRB1*04:05" - }, - "chrX-135779451-135779452-C-T": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 0.577, - "RNA VAF": 0.0, - "gene_expr": 0.0, - "best_peptide_mt": "QEINADIKRKLVKEL", - "best_peptide_wt": "REINADIKRKLVKEL", - "best_hla_allele": "DRB1*04:05" - }, - "chrX-135796713-135796714-C-T": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], "DNA VAF": 0.554, "RNA VAF": 0.0, "gene_expr": 0.102, diff --git a/pvactools/tools/pvacseq/example_data/results/combined/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv b/pvactools/tools/pvacseq/example_data/results/combined/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv index d584e202..ae0d8f1e 100644 --- a/pvactools/tools/pvacseq/example_data/results/combined/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv +++ b/pvactools/tools/pvacseq/example_data/results/combined/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv @@ -182,7 +182,7 @@ chr6-3723707-3723708-C-G 359.PXDC1.ENST00000380283.5.missense.203E/Q 6 3 PXDC1 chr17-82961144-82961145-G-C 982.B3GNTL1.ENST00000320865.4.missense.198L/V 9 2 1 B3GNTL1 L198V 3 VRKGGGVIRVDQSLL ENST00000320865.4 1 DRB1*04:05 1 None 12 0 925.400 925.700 35.000 35.000 10.001 0.235 2.350 81.000 0.221 Poor Pending chr6-43340177-43340178-C-G 382.ZNF318.ENST00000361428.3.missense.1274G/R 10 ZNF318 G1274R 1 SSFRKFSWKKPEKEE ENST00000361428.3 1 DRB1*04:05 4 None 10 0 1245.530 2434.105 34.000 57.000 12.831 0.377 4.837 106.000 0.347 Poor Pending chr1-16972417-16972418-C-G 5.CROCC.ENST00000375541.10.missense.2009S/C 5 CROCC S2009C 1 QLQQELRRSSAPFCP ENST00000375541.10 5 DRB1*04:05 14 None 5 0 2445.435 678.045 59.000 24.000 11.754 1.000 11.754 56.000 0.988 Poor Pending -chr4-48420360-48420361-A-G 295.SLAIN2.ENST00000264313.11.missense.533R/G SLAIN2 R533G 0 TTAMGSGLPRPSAPS ENST00000264313.11 1 DRB1*04:05 5 None 0 0 6773.235 3940.110 86.000 67.000 58.280 0.312 18.183 365.000 0.290 Poor Pending +chr4-48420360-48420361-A-G 295.SLAIN2.ENST00000264313.11.missense.533R/G 1 SLAIN2 R533G 1 TTAMGSGLPRPSAPS ENST00000264313.11 1 DRB1*04:05 5 None 1 0 6773.235 3940.110 86.000 67.000 58.280 0.312 18.183 365.000 0.290 Poor Pending chr19-12580947-12580948-G-A 1009.ZNF490.ENST00000311437.11.missense.376S/F 11 2 ZNF490 S376F 2 CGEAFKSSSFCEVHE ENST00000311437.11 1 DRB1*04:05 10 None 13 0 1407.650 698.550 48.000 26.000 15.981 0.257 4.107 167.000 0.351 Poor Pending chr19-422192-422193-G-C 993.SHC2.ENST00000264554.11.missense.525H/D 11 SHC2 H525D 1 PGQYVLTGMDAGQPK ENST00000264554.11 1 DRB1*04:05 10 None 11 0 808.575 988.595 27.000 35.000 8.139 0.070 0.570 115.000 0.110 Poor Pending chr8-143805313-143805314-A-C 561.SCRIB.ENST00000320476.7.missense.823V/G 10 1 SCRIB V823G 6 ENAGTITPLRPEDDY ENST00000320476.7 1 DRB1*04:05 4 None 11 0 1418.095 966.460 42.000 26.000 61.627 0.055 3.389 402.000 0.164 Poor Pending @@ -199,11 +199,11 @@ chr11-6410863-6410864-C-T 688.APBB1.ENST00000311051.7.missense.162E/K 1 APBB1 chr9-4286160-4286161-G-T 568.GLIS3.ENST00000477901.5.missense.89Q/K 12 1 GLIS3 Q89K 4 AESRIHLPALSPRRK ENST00000477901.5 1 DRB1*04:05 15 None 13 0 833.650 1088.480 35.000 35.000 2.761 0.043 0.119 23.000 0.153 Poor Pending chr14-32773880-32773881-G-T 800.AKAP6.ENST00000280979.9.missense.1192M/I 15 AKAP6 M1192I 3 VMQAVQWQTRLQKKI ENST00000280979.9 1 DRB1*04:05 15 None 15 0 2055.985 2087.975 58.000 59.000 2.905 1.000 2.905 6.000 0.607 Poor Pending chr13-25541936-25541938-GA-CT 751.ATP8A2.ENST00000381655.7.missense.224D/L 15 ATP8A2 D224L 6 LSHTALMQTREVLMK ENST00000381655.7 1 DRB1*04:05 6 None 15 0 785.420 3555.080 33.000 75.000 0.145 NA NA NA 0.319 Poor Pending -chr15-40622778-40622779-C-T 846.KNL1.ENST00000346991.9.missense.865P/S KNL1 P865S 0 MDVLEDESVQKPKFS ENST00000346991.9 1 DRB1*04:05 15 None 0 0 5009.045 6869.240 70.000 73.480 13.527 0.492 6.655 128.000 0.444 Poor Pending +chr15-40622778-40622779-C-T 846.KNL1.ENST00000346991.9.missense.865P/S 1 KNL1 P865S 1 MDVLEDESVQKPKFS ENST00000346991.9 1 DRB1*04:05 15 None 1 0 5009.045 6869.240 70.000 73.480 13.527 0.492 6.655 128.000 0.444 Poor Pending chr10-104021651-104021652-G-T 618.SLK.ENST00000369755.4.missense.1160E/D 10 SLK E1160D 2 QLQNEKCHLLVEHDT ENST00000369755.4 1 DRB1*04:05 14 None 10 0 1775.345 1915.105 62.000 66.000 21.369 0.057 1.218 418.000 0.068 Poor Pending chrX-149930830-149930831-G-A 1209.HSFX4.ENST00000457775.3.missense.243R/H 9 HSFX4 R243H 1 TQSFRHSGMWSKKSA ENST00000457775.3 3 DRB1*04:05 6 None 9 0 993.555 870.825 46.000 45.000 0.012 0.286 0.003 7.000 0.422 Poor Pending chr7-128815875-128815876-C-G 474.CCDC136.ENST00000297788.9.missense.1103S/C 2 5 CCDC136 S1103C 2 SEEEEDDADC ENST00000297788.9 1 HLA-B*45:01 10 None 7 0 2356.280 2591.060 4.350 5.425 4.998 0.250 1.250 32.000 0.200 Poor Pending -chr12-116009024-116009025-G-C 740.MED13L.ENST00000281928.9.missense.463A/G MED13L A463G 0 FSAGPSSSSSLPPPG ENST00000281928.9 1 DRB1*04:05 15 None 0 0 6508.235 6703.740 89.000 88.000 77.827 0.038 2.957 586.000 0.050 Poor Pending +chr12-116009024-116009025-G-C 740.MED13L.ENST00000281928.9.missense.463A/G 1 MED13L A463G 1 FSAGPSSSSSLPPPG ENST00000281928.9 1 DRB1*04:05 15 None 1 0 6508.235 6703.740 89.000 88.000 77.827 0.038 2.957 586.000 0.050 Poor Pending chr22-37374977-37374978-G-A 1094.ELFN2.ENST00000402918.7.missense.186P/L 11 3 1 ELFN2 P186L 1 SLMVCELAGNLFNCE ENST00000402918.7 4 DRB1*04:05 11 None 15 0 1438.450 1998.055 46.000 55.000 0.890 0.368 0.328 19.000 0.168 Poor Pending chr15-30089755-30089756-C-G 845.GOLGA8J.ENST00000567927.2.missense.311L/V 10 3 GOLGA8J L311V 1 SEVELQHV ENST00000567927.2 5 HLA-B*45:01 8 None 13 0 1580.310 4878.700 0.955 2.200 0.354 1.000 0.354 10.000 0.119 Poor Pending chrX-43656385-43656386-C-A 1164.MAOA.ENST00000338702.4.missense.15D/E 8 1 2 MAOA D15E 2 SIAGHMFEVVVIGGG ENST00000338702.4 1 DRB1*04:05 8 None 11 0 2394.765 2643.590 45.000 48.000 0.784 1.000 0.784 2.000 1.000 Poor Pending @@ -213,7 +213,7 @@ chr2-106425181-106425182-C-T 158.RGPD3.ENST00000409886.4.missense.929E/K 7 RGP chr22-37570267-37570268-C-G 1095.LGALS2.ENST00000215886.6.missense.132E/Q 1 LGALS2 E132Q 1 SVRGGFNMSSFKLKQ ENST00000215886.6 1 DRB1*04:05 15 None 1 0 1299.075 737.795 38.000 33.000 0.067 0.222 0.015 9.000 0.484 Poor Pending chr7-157005551-157005552-G-A 485.MNX1.ENST00000252971.11.missense.392P/S 1 MNX1 P392S 2 SEDDSPPSRP ENST00000252971.11 1 HLA-B*45:01 8 None 1 0 2653.235 2299.625 4.670 3.855 18.982 0.040 0.759 101.000 0.054 Poor Pending chr17-7588499-7588500-G-C 943.SOX15.ENST00000250055.3.missense.194Q/E 2 SOX15 Q194E 2 ESDPRLQGELLPTYT ENST00000250055.3 1 DRB1*04:05 1 None 2 0 3658.650 3642.200 74.000 75.000 0.580 0.692 0.401 13.000 0.722 Poor Pending -chr7-27130623-27130624-C-T 416.HOXA4.ENST00000360046.10.missense.37G/D HOXA4 G37D 0 GGPDGGPGY ENST00000360046.10 1 HLA-A*29:02 4 None 0 0 5038.820 5061.965 3.800 3.800 1.689 0.375 0.633 16.000 0.375 Poor Pending +chr7-27130623-27130624-C-T 416.HOXA4.ENST00000360046.10.missense.37G/D 1 HOXA4 G37D 1 GGPDGGPGY ENST00000360046.10 1 HLA-A*29:02 4 None 1 0 5038.820 5061.965 3.800 3.800 1.689 0.375 0.633 16.000 0.375 Poor Pending chr1-36179726-36179728-GG-AA 17.MAP7D1.ENST00000373151.6.missense.764-765EE/EK 3 3 MAP7D1 EE764-765EK 4 KEKPIPQEP ENST00000373151.6 1 HLA-B*45:01 3 None 6 0 1880.870 1720.405 3.850 3.210 93.193 NA NA NA 0.361 Poor Pending chr3-184239802-184239803-C-T 286.VWA5B2.ENST00000426955.6.missense.836A/V 4 VWA5B2 A836V 3 PQVPRCHVVIRGLCG ENST00000426955.6 1 DRB1*04:05 3 None 4 0 3031.620 3623.450 66.000 66.000 0.083 1.000 0.083 2.000 0.429 Poor Pending chr15-40622778-40622780-CC-TT 848.KNL1.ENST00000346991.9.missense.865P/L 7 KNL1 P865L 2 QKPKFLKEKQNVKIW ENST00000346991.9 1 DRB1*04:05 6 None 7 0 2983.000 13258.140 63.000 96.000 13.527 NA NA NA 0.450 Poor Pending @@ -353,13 +353,13 @@ chr1-196995755-196995756-A-G 80.CFHR5.ENST00000256785.5.missense.216N/S 1 CFHR chr14-24068642-24068643-G-A 790.CARMIL3.ENST00000342740.6.missense.1248E/K 1 CARMIL3 E1248K 1 KEEKEGTLFP ENST00000342740.6 5 HLA-B*45:01 1 None 1 0 3676.090 2462.670 4.450 2.353 1.601 0.000 0.000 25.000 0.185 NoExpr Pending chr6-32223881-32223881-T-TAGCAGC 377.NOTCH4.ENST00000375023.3.inframe_ins.16L/LLL 1 1 NOTCH4 L16LLL 1 LLLLLLLLL ENST00000375023.3 1 HLA-A*29:02 9 None 2 0 3852.573 7483.750 5.400 13.975 1.260 0.000 0.000 0.000 0.187 NoExpr Pending chr7-47833094-47833095-G-A 421.PKD1L1.ENST00000289672.7.missense.2111T/I 1 PKD1L1 T2111I 3 CPPHIQAPSSGLEGL ENST00000289672.7 1 DRB1*04:05 5 None 1 0 4493.790 13006.655 66.000 89.000 0.696 0.000 0.000 0.000 0.322 NoExpr Pending -chrX-135721216-135721217-G-A 1201.CT45A1.ENST00000594117.4.missense.120R/Q CT45A1 R120Q 0 QEINADIKRKLVKEL ENST00000594117.4 1 DRB1*04:05 1 None 0 0 5009.080 4775.770 77.000 78.000 0.000 0.000 0.000 0.000 0.582 NoExpr Pending -chrX-135779451-135779452-C-T 1204.CT45A5.ENST00000617203.1.missense.120R/Q CT45A5 R120Q 0 QEINADIKRKLVKEL ENST00000617203.1 1 DRB1*04:05 1 None 0 0 5009.080 4775.770 77.000 78.000 0.000 0.000 0.000 0.000 0.577 NoExpr Pending -chrX-135796713-135796714-C-T 1205.CT45A6.ENST00000612878.4.missense.120R/Q CT45A6 R120Q 0 QEINADIKRKLVKEL ENST00000612878.4 1 DRB1*04:05 1 None 0 0 5009.080 4775.770 77.000 78.000 0.102 0.000 0.000 0.000 0.554 NoExpr Pending -chr1-111727105-111727106-G-T 50.INKA2.ENST00000357260.6.missense.252S/R INKA2 S252R 0 RLSKGSGHF ENST00000357260.6 1 HLA-A*29:02 1 None 0 0 6086.820 3915.305 4.800 3.055 2.143 0.000 0.000 29.000 0.063 NoExpr Pending -chr9-138120681-138120682-G-A 600.CACNA1B.ENST00000371372.6.missense.2097G/D CACNA1B G2097D 0 GEGPTDCRR ENST00000371372.6 5 HLA-B*45:01 6 None 0 0 7694.035 7362.530 11.815 9.460 0.154 0.000 0.000 0.000 0.276 NoExpr Pending -chr8-138737576-138737577-C-A 554.COL22A1.ENST00000303045.11.missense.696G/W COL22A1 G696W 0 PPGLQGLRWKKGDMG ENST00000303045.11 1 DRB1*04:05 9 None 0 0 8119.750 9664.005 86.000 86.000 0.308 0.000 0.000 2.000 0.200 NoExpr Pending -chr21-44330789-44330813-AGGCAGCCGCGGCCCCTAGCGGCCC-A 1088.CFAP410.ENST00000397956.7.inframe_del.217-224GPLGAAAA/- CFAP410 GPLGAAAA217-224- 0 SSHRGRVSGSAHCTH ENST00000397956.7 1 DRB1*04:05 9-10 None 0 0 9193.345 17908.385 87.000 96.000 6.570 0.000 0.000 18.000 0.376 NoExpr Pending -chr3-52517959-52517960-A-C 234.STAB1.ENST00000321725.10.missense.1573H/P STAB1 H1573P 0 GQRTCTCDTAPTVGD ENST00000321725.10 1 DRB1*04:05 11 None 0 0 10740.270 13563.605 80.000 88.000 0.090 0.000 0.000 0.000 1.000 NoExpr Pending -chr7-39339738-39339739-G-C 420.POU6F2.ENST00000518318.7.missense.232Q/H POU6F2 Q232H 0 PSTNHHPQPAPQAPS ENST00000518318.7 1 DRB1*04:05 5 None 0 0 13358.615 15114.250 93.000 94.000 0.273 0.000 0.000 0.000 0.299 NoExpr Pending -chr3-44242057-44242058-G-A 231.TOPAZ1.ENST00000309765.4.missense.2R/Q TOPAZ1 R2Q 0 MQRPPPLGPT ENST00000309765.4 5 HLA-B*45:01 2 None 0 0 18453.590 24155.798 18.500 30.500 0.005 0.000 0.000 0.000 0.307 NoExpr Pending +chrX-135721216-135721217-G-A 1201.CT45A1.ENST00000594117.4.missense.120R/Q 1 CT45A1 R120Q 1 QEINADIKRKLVKEL ENST00000594117.4 1 DRB1*04:05 1 None 1 0 5009.080 4775.770 77.000 78.000 0.000 0.000 0.000 0.000 0.582 NoExpr Pending +chrX-135779451-135779452-C-T 1204.CT45A5.ENST00000617203.1.missense.120R/Q 1 CT45A5 R120Q 1 QEINADIKRKLVKEL ENST00000617203.1 1 DRB1*04:05 1 None 1 0 5009.080 4775.770 77.000 78.000 0.000 0.000 0.000 0.000 0.577 NoExpr Pending +chrX-135796713-135796714-C-T 1205.CT45A6.ENST00000612878.4.missense.120R/Q 1 CT45A6 R120Q 1 QEINADIKRKLVKEL ENST00000612878.4 1 DRB1*04:05 1 None 1 0 5009.080 4775.770 77.000 78.000 0.102 0.000 0.000 0.000 0.554 NoExpr Pending +chr1-111727105-111727106-G-T 50.INKA2.ENST00000357260.6.missense.252S/R 1 INKA2 S252R 1 RLSKGSGHF ENST00000357260.6 1 HLA-A*29:02 1 None 1 0 6086.820 3915.305 4.800 3.055 2.143 0.000 0.000 29.000 0.063 NoExpr Pending +chr9-138120681-138120682-G-A 600.CACNA1B.ENST00000371372.6.missense.2097G/D 1 CACNA1B G2097D 1 GEGPTDCRR ENST00000371372.6 5 HLA-B*45:01 6 None 1 0 7694.035 7362.530 11.815 9.460 0.154 0.000 0.000 0.000 0.276 NoExpr Pending +chr8-138737576-138737577-C-A 554.COL22A1.ENST00000303045.11.missense.696G/W 1 COL22A1 G696W 1 PPGLQGLRWKKGDMG ENST00000303045.11 1 DRB1*04:05 9 None 1 0 8119.750 9664.005 86.000 86.000 0.308 0.000 0.000 2.000 0.200 NoExpr Pending +chr21-44330789-44330813-AGGCAGCCGCGGCCCCTAGCGGCCC-A 1088.CFAP410.ENST00000397956.7.inframe_del.217-224GPLGAAAA/- 1 CFAP410 GPLGAAAA217-224- 1 SSHRGRVSGSAHCTH ENST00000397956.7 1 DRB1*04:05 9-10 None 1 0 9193.345 17908.385 87.000 96.000 6.570 0.000 0.000 18.000 0.376 NoExpr Pending +chr3-52517959-52517960-A-C 234.STAB1.ENST00000321725.10.missense.1573H/P 1 STAB1 H1573P 1 GQRTCTCDTAPTVGD ENST00000321725.10 1 DRB1*04:05 11 None 1 0 10740.270 13563.605 80.000 88.000 0.090 0.000 0.000 0.000 1.000 NoExpr Pending +chr7-39339738-39339739-G-C 420.POU6F2.ENST00000518318.7.missense.232Q/H 1 POU6F2 Q232H 1 PSTNHHPQPAPQAPS ENST00000518318.7 1 DRB1*04:05 5 None 1 0 13358.615 15114.250 93.000 94.000 0.273 0.000 0.000 0.000 0.299 NoExpr Pending +chr3-44242057-44242058-G-A 231.TOPAZ1.ENST00000309765.4.missense.2R/Q 1 TOPAZ1 R2Q 1 MQRPPPLGPT ENST00000309765.4 5 HLA-B*45:01 2 None 1 0 18453.590 24155.798 18.500 30.500 0.005 0.000 0.000 0.000 0.307 NoExpr Pending diff --git a/pvactools/tools/pvacseq/example_data/results/combined/server.R b/pvactools/tools/pvacseq/example_data/results/combined/server.R index 7a02784f..ae51ad03 100644 --- a/pvactools/tools/pvacseq/example_data/results/combined/server.R +++ b/pvactools/tools/pvacseq/example_data/results/combined/server.R @@ -24,7 +24,7 @@ options(shiny.port = 3333) server <- shinyServer(function(input, output, session) { ## pVACtools version - output$version <- renderText({"pVACtools version 4.4.0"}) + output$version <- renderText({"pVACtools version 5.0.1"}) ##############################DATA UPLOAD TAB################################### ## helper function defined for generating shinyInputs in mainTable (Evaluation dropdown menus) @@ -36,10 +36,10 @@ server <- shinyServer(function(input, output, session) { inputs } ## helper function defined for generating shinyInputs in mainTable (Investigate button) - shinyInputSelect <- function(FUN, len, id, ...) { - inputs <- character(len) - for (i in seq_len(len)) { - inputs[i] <- as.character(FUN(paste0(id, i), ...)) + shinyInputSelect <- function(FUN, row_ids, button_label, ...) { + inputs <- character(nrow(row_ids)) + for (i in 1:nrow(row_ids)) { + inputs[i] <- as.character(FUN(paste0(button_label, row_ids[i, "ID"]), ...)) } inputs } @@ -55,28 +55,29 @@ server <- shinyServer(function(input, output, session) { })) } #set button styling based on values in Evaluation column - setButtonStyling <- function(evaluations) { + setButtonStyling <- function(evaluations, ids) { for (i in 1:length(evaluations)){ evaluation <- evaluations[i] + id <- ids[i] if (evaluation == 'Accept') { - html <- paste0("#button-acpt_", i ," { color: red !important; }") + html <- paste0("#button-acpt_", id ," { color: green !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-rej_", i, ')')) - removeUI(selector = paste0("style:contains(#button-rev_", i, ')')) + removeUI(selector = paste0("style:contains(#button-rej_", id, ')')) + removeUI(selector = paste0("style:contains(#button-rev_", id, ')')) } else if (evaluation == 'Reject') { - html <- paste0("#button-rej_", i ," { color: red !important; }") + html <- paste0("#button-rej_", id ," { color: red !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-acpt_", i, ')')) - removeUI(selector = paste0("style:contains(#button-rev_", i, ')')) + removeUI(selector = paste0("style:contains(#button-acpt_", id, ')')) + removeUI(selector = paste0("style:contains(#button-rev_", id, ')')) } else if (evaluation == 'Review') { - html <- paste0("#button-rev_", i ," { color: red !important; }") + html <- paste0("#button-rev_", id ," { color: orange !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-acpt_", i, ')')) - removeUI(selector = paste0("style:contains(#button-rej_", i, ')')) + removeUI(selector = paste0("style:contains(#button-acpt_", id, ')')) + removeUI(selector = paste0("style:contains(#button-rej_", id, ')')) } else if (evaluation == 'Pending') { - removeUI(selector = paste0("style:contains(#button-acpt_", i, ')')) - removeUI(selector = paste0("style:contains(#button-rej_", i, ')')) - removeUI(selector = paste0("style:contains(#button-rev_", i, ')')) + removeUI(selector = paste0("style:contains(#button-acpt_", id, ')')) + removeUI(selector = paste0("style:contains(#button-rej_", id, ')')) + removeUI(selector = paste0("style:contains(#button-rev_", id, ')')) } } } @@ -106,15 +107,15 @@ server <- shinyServer(function(input, output, session) { colnames(mainData) <- mainData[1, ] mainData <- mainData[-1, ] row.names(mainData) <- NULL - setButtonStyling(mainData$Evaluation) - mainData$Acpt <- shinyInputSelect(actionButton, nrow(mainData), "button-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - mainData$Rej <- shinyInputSelect(actionButton, nrow(mainData), "button-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - mainData$Rev <- shinyInputSelect(actionButton, nrow(mainData), "button-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + setButtonStyling(mainData$Evaluation, mainData$ID) + mainData$Acpt <- shinyInputSelect(actionButton, mainData["ID"], "button-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + mainData$Rej <- shinyInputSelect(actionButton, mainData["ID"], "button-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + mainData$Rev <- shinyInputSelect(actionButton, mainData["ID"], "button-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") mainData$`IC50 MT` <- as.numeric(mainData$`IC50 MT`) mainData$`%ile MT` <- as.numeric(mainData$`%ile MT`) mainData$`RNA Depth` <- as.character(as.integer(mainData$`RNA Depth`)) mainData$`TSL`[is.na(mainData$`TSL`)] <- "NA" - df$evaluations <- mainData[c("ID", "Evaluation")] + df$evaluations <- data.frame(data = mainData$Evaluation, row.names = mainData$ID) df$mainTable <- mainData df$metricsData <- NULL df$lastSelectedRow <- 1 @@ -190,22 +191,22 @@ server <- shinyServer(function(input, output, session) { ## Class I demo aggregate report #session$sendCustomMessage("unbind-DT", "mainTable") withProgress(message = "Loading Demo Data", value = 0, { - load(url("https://github.com/griffithlab/pVACtools/raw/489a68cdd9e84e38b1bacc661aba15d78410282f/pvactools/tools/pvacview/data/HCC1395_demo_data.rda")) + load(url("https://github.com/griffithlab/pVACtools/raw/a3cc6d2b190a344d846438c1f0e5073e748dbd52/pvactools/tools/pvacview/data/HCC1395_demo_data.rda")) incProgress(0.3) #data <- getURL("https://raw.githubusercontent.com/griffithlab/pVACtools/c5a4f4c5b0bfa9c2832fc752e98dddea4c1c9eda/pvactools/tools/pvacview/data/H_NJ-HCC1395-HCC1395.Class_I.all_epitopes.aggregated.tsv") #mainData <- read.table(text = data, sep = "\t", header = FALSE, stringsAsFactors = FALSE, check.names = FALSE) colnames(mainData) <- mainData[1, ] mainData <- mainData[-1, ] row.names(mainData) <- NULL - setButtonStyling(mainData$Evaluation) - mainData$Acpt <- shinyInputSelect(actionButton, nrow(mainData), "button-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - mainData$Rej <- shinyInputSelect(actionButton, nrow(mainData), "button-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - mainData$Rev <- shinyInputSelect(actionButton, nrow(mainData), "button-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + setButtonStyling(mainData$Evaluation, mainData$ID) + mainData$Acpt <- shinyInputSelect(actionButton, mainData["ID"], "button-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + mainData$Rej <- shinyInputSelect(actionButton, mainData["ID"], "button-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + mainData$Rev <- shinyInputSelect(actionButton, mainData["ID"], "button-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") mainData$`IC50 MT` <- as.numeric(mainData$`IC50 MT`) mainData$`%ile MT` <- as.numeric(mainData$`%ile MT`) mainData$`RNA Depth` <- as.character(as.integer(mainData$`RNA Depth`)) mainData$`TSL`[is.na(mainData$`TSL`)] <- "NA" - df$evaluations <- mainData[c("ID", "Evaluation")] + df$evaluations <- data.frame(data = mainData$Evaluation, row.names = mainData$ID) df$mainTable <- mainData incProgress(0.1) ## Class I demo metrics file @@ -254,7 +255,7 @@ server <- shinyServer(function(input, output, session) { rownames(df$comments) <- df$mainTable$ID incProgress(0.2) ## Class II additional demo aggregate report - add_data <- getURL("https://raw.githubusercontent.com/griffithlab/pVACtools/489a68cdd9e84e38b1bacc661aba15d78410282f/pvactools/tools/pvacview/data/H_NJ-HCC1395-HCC1395.Class_II.all_epitopes.aggregated.tsv") + add_data <- getURL("https://raw.githubusercontent.com/griffithlab/pVACtools/a3cc6d2b190a344d846438c1f0e5073e748dbd52/pvactools/tools/pvacview/data/H_NJ-HCC1395-HCC1395.Class_II.all_epitopes.aggregated.tsv") addData <- read.table(text = add_data, sep = "\t", header = FALSE, stringsAsFactors = FALSE, check.names = FALSE) colnames(addData) <- addData[1, ] addData <- addData[-1, ] @@ -643,37 +644,34 @@ server <- shinyServer(function(input, output, session) { if (is.null(df$mainTable)) { return() } - selectedRow <- as.numeric(strsplit(input$accept_eval, "_")[[1]][2]) - selectedID <- df$mainTable$ID[selectedRow] - df$evaluations[df$evaluations$ID == selectedID, "Evaluation"] <- "Accept" - html <- paste0("#button-acpt_", selectedRow ," { color: red !important; }") + selectedID <- strsplit(input$accept_eval, "_")[[1]][2] + df$evaluations[selectedID, 1] <- "Accept" + html <- paste0("#button-acpt_", selectedID ," { color: green !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-rej_", selectedRow, ')'), multiple = TRUE) - removeUI(selector = paste0("style:contains(#button-rev_", selectedRow, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-rej_", selectedID, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-rev_", selectedID, ')'), multiple = TRUE) }) observeEvent(input$reject_eval, { if (is.null(df$mainTable)) { return() } - selectedRow <- as.numeric(strsplit(input$reject_eval, "_")[[1]][2]) - selectedID <- df$mainTable$ID[selectedRow] - df$evaluations[df$evaluations$ID == selectedID, "Evaluation"] <- "Reject" - html <- paste0("#button-rej_", selectedRow ," { color: red !important; }") + selectedID <- strsplit(input$reject_eval, "_")[[1]][2] + df$evaluations[selectedID, 1] <- "Reject" + html <- paste0("#button-rej_", selectedID ," { color: red !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-acpt_", selectedRow, ')'), multiple = TRUE) - removeUI(selector = paste0("style:contains(#button-rev_", selectedRow, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-acpt_", selectedID, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-rev_", selectedID, ')'), multiple = TRUE) }) observeEvent(input$review_eval, { if (is.null(df$mainTable)) { return() } - selectedRow <- as.numeric(strsplit(input$review_eval, "_")[[1]][2]) - selectedID <- df$mainTable$ID[selectedRow] - df$evaluations[df$evaluations$ID == selectedID, "Evaluation"] <- "Review" - html <- paste0("#button-rev_", selectedRow ," { color: red !important; }") + selectedID <- strsplit(input$review_eval, "_")[[1]][2] + df$evaluations[selectedID, 1] <- "Review" + html <- paste0("#button-rev_", selectedID ," { color: orange !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-acpt_", selectedRow, ')'), multiple = TRUE) - removeUI(selector = paste0("style:contains(#button-rej_", selectedRow, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-acpt_", selectedID, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-rej_", selectedID, ')'), multiple = TRUE) }) ##selected row text box output$selected <- renderText({ @@ -950,7 +948,10 @@ server <- shinyServer(function(input, output, session) { ##Anchor Heatmap overlayed on selected peptide sequences anchorPlotHeight <- reactive({ if (is.null(df$metricsData)) { - return(0) + return(100) + } + if (length(df$metricsData[[selectedID()]]$good_binders) == 0) { + return(100) } peptide_data <- df$metricsData[[selectedID()]]$good_binders[[selectedTranscriptSet()]]$`peptides` peptide_names <- names(peptide_data) @@ -1097,12 +1098,12 @@ server <- shinyServer(function(input, output, session) { hla_allele_count <- length(unique(bindingScoreDataIC50()$HLA_allele)) incProgress(0.5) p <- ggplot(data = bindingScoreDataIC50(), aes(x = Mutant, y = Score, color = Mutant), trim = FALSE) + geom_violin() + facet_grid(cols = vars(HLA_allele)) + scale_y_continuous(trans = "log10") + #coord_trans(y = "log10") + - stat_summary(fun.y = mean, fun.ymin = mean, fun.ymax = mean, geom = "crossbar", width = 0.25, position = position_dodge(width = .25)) + - geom_jitter(data = bindingScoreDataIC50(), aes(shape = algorithms), sizes = 5, stroke = 1, position = position_jitter(0.3)) + + stat_summary(fun = mean, fun.min = mean, fun.max = mean, geom = "crossbar", width = 0.25, position = position_dodge(width = .25)) + + geom_jitter(data = bindingScoreDataIC50(), aes(shape = algorithms), size = 5, stroke = 1, position = position_jitter(0.3)) + scale_shape_manual(values = 0:8) + geom_hline(aes(yintercept = yintercept, linetype = Cutoffs), line.data, color = rep(line.data$color, hla_allele_count)) + scale_color_manual(values = rep(c("MT" = "#D2B4DE", "WT" = "#F7DC6F"), hla_allele_count)) + - theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 15), axis.ticks = element_line(size = 3), legend.text = element_text(size = 15), legend.title = element_text(size = 15)) + theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 15), axis.ticks = element_line(linewidth = 3), legend.text = element_text(size = 15), legend.title = element_text(size = 15)) incProgress(0.5) print(p) }else { @@ -1155,12 +1156,12 @@ server <- shinyServer(function(input, output, session) { hla_allele_count <- length(unique(combinedBindingElutionDataPercentile()$HLA_allele)) incProgress(0.5) p <- ggplot(data = combinedBindingElutionDataPercentile(), aes(x = Mutant, y = Score, color = Mutant), trim = FALSE) + geom_violin() + facet_grid(cols = vars(HLA_allele)) + scale_y_continuous(trans = "log10") + #coord_trans(y = "log10") + - stat_summary(fun.y = mean, fun.ymin = mean, fun.ymax = mean, geom = "crossbar", width = 0.25, position = position_dodge(width = .25)) + + stat_summary(fun = mean, fun.min = mean, fun.max = mean, geom = "crossbar", width = 0.25, position = position_dodge(width = .25)) + geom_jitter(data = combinedBindingElutionDataPercentile(), aes(shape = algorithms), size = 5, stroke = 1, position = position_jitter(0.3)) + scale_shape_manual(values = 0:10) + geom_hline(aes(yintercept = yintercept, linetype = Cutoffs), line.data, color = rep(line.data$color, hla_allele_count)) + scale_color_manual(values = rep(c("MT" = "#D2B4DE", "WT" = "#F7DC6F"), hla_allele_count)) + - theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 15), axis.ticks = element_line(size = 3), legend.text = element_text(size = 15), legend.title = element_text(size = 15)) + theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 15), axis.ticks = element_line(linewidth = 3), legend.text = element_text(size = 15), legend.title = element_text(size = 15)) incProgress(0.5) print(p) }else { @@ -1432,16 +1433,16 @@ server <- shinyServer(function(input, output, session) { return(nchar(df$metricsData[[selectedID()]]$reference_matches$query_peptide) * 20) } } ) - ##############################EXPORT TAB############################################## #evalutation overview table output$checked <- renderTable({ if (is.null(df$evaluations)) { return() } - data <- as.data.frame(table(df$evaluations$Evaluation)) + data <- as.data.frame(table(df$evaluations)) colnames(data) <- c("Evaluation","Count") data }) + ##############################EXPORT TAB############################################## #export table display with options to download output$ExportTable <- renderDataTable({ if (is.null(df$mainTable)) { @@ -1452,8 +1453,8 @@ server <- shinyServer(function(input, output, session) { "Col RNA Depth", "Col DNA VAF", "Percentile Fail", "Has Prob Pos", "Acpt", "Rej", "Rev") data <- df$mainTable[, !(colsToDrop)] col_names <- colnames(data) - data <- plyr::join(data, df$evaluations, by='ID') - colnames(data) <- c(col_names, "Evaluation") + evaluations <- data.frame("ID" = row.names(df$evaluations), Evaluation = df$evaluations[, 1]) + data <- join(data, evaluations) comments <- data.frame("ID" = row.names(df$comments), Comments = df$comments[, 1]) data <- join(data, comments) data[is.na(data)] <- "NA" @@ -1551,16 +1552,16 @@ server <- shinyServer(function(input, output, session) { len <- nrow(df_neofox$mainTable_neofox) if ('Evaluation' %in% colnames(df_neofox$mainTable_neofox)) { - setButtonStyling(df_neofox$mainTable_neofox$Evaluation) + setButtonStyling(df_neofox$mainTable_neofox$Evaluation, df_neofox$mainTable_neofox$ID) } else { df_neofox$mainTable_neofox["Evaluation"] = "Pending" } df_neofox$mainTable_neofox <- cbind(ID = rownames(df_neofox$mainTable_neofox), df_neofox$mainTable_neofox) df_neofox$evaluations <- df_neofox$mainTable_neofox[c("ID", "Evaluation")] df_neofox$mainTable_neofox$Evaluation <- NULL - df_neofox$mainTable_neofox$Acpt <- shinyInputSelect(actionButton, nrow(mainData_neofox), "button-neofox-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - df_neofox$mainTable_neofox$Rej <- shinyInputSelect(actionButton, nrow(mainData_neofox), "button-neofox-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - df_neofox$mainTable_neofox$Rev <- shinyInputSelect(actionButton, nrow(mainData_neofox), "button-neofox-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + df_neofox$mainTable_neofox$Acpt <- shinyInputSelect(actionButton, df_neofox$mainTable_neofox["ID"], "button-neofox-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + df_neofox$mainTable_neofox$Rej <- shinyInputSelect(actionButton, df_neofox$mainTable_neofox["ID"], "button-neofox-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + df_neofox$mainTable_neofox$Rev <- shinyInputSelect(actionButton, df_neofox$mainTable_neofox["ID"], "button-neofox-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") if ("Comments" %in% colnames(df_neofox$mainTable_neofox)) { df_neofox$comments <- data.frame(data = df_neofox$mainTable_neofox$`Comments`, nrow = nrow(df_neofox$mainTable_neofox), ncol = 1) @@ -1633,16 +1634,16 @@ server <- shinyServer(function(input, output, session) { len <- nrow(df_neofox$mainTable_neofox) if ('Evaluation' %in% colnames(df_neofox$mainTable_neofox)) { - setButtonStyling(df_neofox$mainTable_neofox$Evaluation) + setButtonStyling(df_neofox$mainTable_neofox$Evaluation, df_neofox$mainTable_neofox$ID) } else { df_neofox$mainTable_neofox["Evaluation"] = "Pending" } df_neofox$mainTable_neofox <- cbind(ID = rownames(df_neofox$mainTable_neofox), df_neofox$mainTable_neofox) df_neofox$evaluations <- df_neofox$mainTable_neofox[c("ID", "Evaluation")] df_neofox$mainTable_neofox$Evaluation <- NULL - df_neofox$mainTable_neofox$Acpt <- shinyInputSelect(actionButton, nrow(mainData_neofox), "button-neofox-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - df_neofox$mainTable_neofox$Rej <- shinyInputSelect(actionButton, nrow(mainData_neofox), "button-neofox-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") - df_neofox$mainTable_neofox$Rev <- shinyInputSelect(actionButton, nrow(mainData_neofox), "button-neofox-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + df_neofox$mainTable_neofox$Acpt <- shinyInputSelect(actionButton, df_neofox$mainTable_neofox["ID"], "button-neofox-acpt_", icon = icon("thumbs-up"), label = "", onclick = 'Shiny.onInputChange(\"accept_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + df_neofox$mainTable_neofox$Rej <- shinyInputSelect(actionButton, df_neofox$mainTable_neofox["ID"], "button-neofox-rej_", icon = icon("thumbs-down"), label = "", onclick = 'Shiny.onInputChange(\"reject_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") + df_neofox$mainTable_neofox$Rev <- shinyInputSelect(actionButton, df_neofox$mainTable_neofox["ID"], "button-neofox-rev_", icon = icon("flag"), label = "", onclick = 'Shiny.onInputChange(\"review_neofox_eval\", this.id, {priority: "event"})', onmousedown = "event.preventDefault(); event.stopPropagation();") if ("Comments" %in% colnames(df_neofox$mainTable_neofox)) { df_neofox$comments <- data.frame(data = df_neofox$mainTable_neofox$`Comments`, nrow = nrow(df_neofox$mainTable_neofox), ncol = 1) @@ -1747,34 +1748,34 @@ server <- shinyServer(function(input, output, session) { if (is.null(df_neofox$mainTable_neofox)) { return() } - selectedRow <- as.numeric(strsplit(input$accept_neofox_eval, "_")[[1]][2]) - df_neofox$evaluations[df_neofox$evaluations$ID == selectedRow, "Evaluation"] <- "Accept" - html <- paste0("#button-neofox-acpt_", selectedRow ," { color: red !important; }") + selectedID <- strsplit(input$accept_neofox_eval, "_")[[1]][2] + df_neofox$evaluations[df_neofox$evaluations$ID == selectedID, "Evaluation"] <- "Accept" + html <- paste0("#button-neofox-acpt_", selectedID ," { color: red !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-neofox-rej_", selectedRow, ')'), multiple = TRUE) - removeUI(selector = paste0("style:contains(#button-neofox-rev_", selectedRow, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-neofox-rej_", selectedID, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-neofox-rev_", selectedID, ')'), multiple = TRUE) }) observeEvent(input$reject_neofox_eval, { if (is.null(df_neofox$mainTable_neofox)) { return() } - selectedRow <- as.numeric(strsplit(input$reject_neofox_eval, "_")[[1]][2]) - df_neofox$evaluations[df_neofox$evaluations$ID == selectedRow, "Evaluation"] <- "Reject" - html <- paste0("#button-neofox-rej_", selectedRow ," { color: red !important; }") + selectedID <- as.numeric(strsplit(input$reject_neofox_eval, "_")[[1]][2]) + df_neofox$evaluations[df_neofox$evaluations$ID == selectedID, "Evaluation"] <- "Reject" + html <- paste0("#button-neofox-rej_", selectedID ," { color: red !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-neofox-acpt_", selectedRow, ')'), multiple = TRUE) - removeUI(selector = paste0("style:contains(#button-neofox-rev_", selectedRow, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-neofox-acpt_", selectedID, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-neofox-rev_", selectedID, ')'), multiple = TRUE) }) observeEvent(input$review_neofox_eval, { if (is.null(df_neofox$mainTable_neofox)) { return() } - selectedRow <- as.numeric(strsplit(input$review_neofox_eval, "_")[[1]][2]) - df_neofox$evaluations[df_neofox$evaluations$ID == selectedRow, "Evaluation"] <- "Review" - html <- paste0("#button-neofox-rev_", selectedRow ," { color: red !important; }") + selectedID <- as.numeric(strsplit(input$review_neofox_eval, "_")[[1]][2]) + df_neofox$evaluations[df_neofox$evaluations$ID == selectedID, "Evaluation"] <- "Review" + html <- paste0("#button-neofox-rev_", selectedID ," { color: red !important; }") insertUI("head", ui = tags$style(HTML(html))) - removeUI(selector = paste0("style:contains(#button-neofox-acpt_", selectedRow, ')'), multiple = TRUE) - removeUI(selector = paste0("style:contains(#button-neofox-rej_", selectedRow, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-neofox-acpt_", selectedID, ')'), multiple = TRUE) + removeUI(selector = paste0("style:contains(#button-neofox-rej_", selectedID, ')'), multiple = TRUE) }) # NeoFox evalutation overview table @@ -1852,7 +1853,7 @@ server <- shinyServer(function(input, output, session) { scale_color_manual(values = c("No" = "#939094", "Yes" = "#f42409")) + labs(x = NULL) + facet_wrap(~Feature, scales="free", ncol=6) + - theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 10), axis.ticks = element_line(size = 3), legend.text = element_text(size = 10), legend.title = element_text(size = 10)) + theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 10), axis.ticks = element_line(linewidth = 3), legend.text = element_text(size = 10), legend.title = element_text(size = 10)) incProgress(0.5) print(p_neofox) @@ -2111,7 +2112,7 @@ server <- shinyServer(function(input, output, session) { "Gene:", .data[["gene"]]))) + geom_point(aes(color = .data[[input$color_scatter]], size = .data[[input$size_scatter]])) + # Correct placement of aes() here scale_color_gradient(low = input$min_col, high = input$max_col) + - theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 15), axis.ticks = element_line(size = 3), legend.text = element_text(size = 15), legend.title = element_text(size = 15)) + theme(strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 15), axis.ticks = element_line(linewidth = 3), legend.text = element_text(size = 15), legend.title = element_text(size = 15)) scatter_plot <- ggplotly(scatter_plot) @@ -2309,7 +2310,8 @@ server <- shinyServer(function(input, output, session) { df_custom$group_inds <- row_ind_df row_ind_top <- apply(row_ind_df, 1, function(x) {unlist(x[1])[1]}) df_custom$mainTable_custom <- as.data.frame(reformat_data[row_ind_top, ]) - df_custom$mainTable_custom <- cbind(Select = shinyInputSelect(actionButton, nrow(df_custom$mainTable_custom), "button_", label = "Investigate", onclick = 'Shiny.onInputChange(\"custom_select_button\", this.id)'), df_custom$mainTable_custom) + df_custom$mainTable_custom["ID"] <- 1:nrow(df_custom$mainTable_custom) + df_custom$mainTable_custom <- cbind(Select = shinyInputSelect(actionButton, df_custom$mainTable_custom["ID"], "button_", label = "Investigate", onclick = 'Shiny.onInputChange(\"custom_select_button\", this.id)'), df_custom$mainTable_custom) df_custom$metricsData <- get_group_inds(df_custom$fullData, df_custom$group_inds) df_custom$peptide_features <- input$peptide_features updateTabItems(session, "custom_tabs", "custom_explore") @@ -2610,7 +2612,7 @@ server <- shinyServer(function(input, output, session) { strip.text = element_text(size = 15), axis.text = element_text(size = 10), axis.title = element_text(size = 15), - axis.ticks = element_line(size = 3), + axis.ticks = element_line(linewidth = 3), legend.text = element_text(size = 15), legend.title = element_text(size = 15) ) diff --git a/pvactools/tools/pvacseq/example_data/results/combined/ui.R b/pvactools/tools/pvacseq/example_data/results/combined/ui.R index 45154935..e2730359 100644 --- a/pvactools/tools/pvacseq/example_data/results/combined/ui.R +++ b/pvactools/tools/pvacseq/example_data/results/combined/ui.R @@ -275,7 +275,7 @@ explore_tab <- tabItem( DTOutput(outputId = "bindingDatatable"), style = "overflow-x: scroll;" ), tabPanel("Elution and Immunogenicity Data", - h4("Prediction score table showing exact MHC scpres for elution, immunogenicity, and percentile calculations."), + h4("Prediction score table showing exact MHC scores for elution, immunogenicity, and percentile calculations."), DTOutput(outputId = "elutionDatatable"), br(), strong("BigMHC_EL / BigMHC_IM"), span(": A deep learning tool for predicting MHC-I (neo)epitope presentation and immunogenicity. ("), diff --git a/pvactools/tools/pvacsplice/example_data/results/MHC_Class_I/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv b/pvactools/tools/pvacsplice/example_data/results/MHC_Class_I/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv index dcee30cd..0711bea2 100644 --- a/pvactools/tools/pvacsplice/example_data/results/MHC_Class_I/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv +++ b/pvactools/tools/pvacsplice/example_data/results/MHC_Class_I/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv @@ -1,116 +1,116 @@ -ID A*29:02 B*45:01 Gene Transcript Junction Name AA Change Best Peptide TSL Allele Pos Prob Pos Num Passing Peptides IC50 MT %ile MT RNA Expr RNA VAF Allele Expr RNA Depth DNA VAF Tier Evaluation -LDHB.ENST00000350669.JUNC00000053.chr12:21654541-21654542.D 6 LDHB ENST00000350669.5 JUNC00000053 NA HMMFNLSHY 1 HLA-A*29:02 48 None 6 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Pass Pending -LDHB.ENST00000350669.JUNC00000046.chr12:21654541-21654542.A 8 LDHB ENST00000350669.5 JUNC00000046 NA EEESLADELA 1 HLA-B*45:01 14 None 8 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Pass Pending -DBN1.ENST00000292385.JUNC00000178.chr5:177460555-177460556.D 11 DBN1 ENST00000292385.9 JUNC00000178 NA SESEVEAAA 1 HLA-B*45:01 274 None 11 29.935 0.040 109.087 0.070 7.636 129.000 0.290 Pass Pending -DBN1.ENST00000309007.JUNC00000178.chr5:177460555-177460556.D 11 DBN1 ENST00000309007.9 JUNC00000178 NA SESEVEAAA 1 HLA-B*45:01 272 None 11 29.935 0.040 109.087 0.070 7.636 129.000 0.290 Pass Pending -SEC24D.ENST00000280551.JUNC00000155.chr4:118740662-118740663.A 3 3 SEC24D ENST00000280551.11 JUNC00000155 Q VIESCAVLY 1 HLA-A*29:02 747 None 6 92.091 0.310 67.286 0.120 8.074 575.000 0.205 Pass Pending -SEC24D.ENST00000511481.JUNC00000155.chr4:118740662-118740663.A 3 3 SEC24D ENST00000511481.5 JUNC00000155 Q VIESCAVLY 1 HLA-A*29:02 378 None 6 92.091 0.310 67.286 0.120 8.074 575.000 0.205 Pass Pending -DBN1.ENST00000292385.JUNC00000177.chr5:177460555-177460556.D 2 12 DBN1 ENST00000292385.9 JUNC00000177 NA KESHRPLRAA 1 HLA-B*45:01 298 None 14 311.785 0.570 109.087 0.070 7.636 129.000 0.290 Pass Pending -DBN1.ENST00000309007.JUNC00000177.chr5:177460555-177460556.D 2 12 DBN1 ENST00000309007.9 JUNC00000177 NA KESHRPLRAA 1 HLA-B*45:01 296 None 14 311.785 0.570 109.087 0.070 7.636 129.000 0.290 Pass Pending -DBN1.ENST00000292385.JUNC00000178.chr5:177460554-177460555.D 11 DBN1 ENST00000292385.9 JUNC00000178 E/K SESEVEAAA 1 HLA-B*45:01 274 None 11 29.935 0.040 109.087 0.009 0.982 1076.000 0.285 LowExpr Pending -DBN1.ENST00000309007.JUNC00000178.chr5:177460554-177460555.D 11 DBN1 ENST00000309007.9 JUNC00000178 E/K SESEVEAAA 1 HLA-B*45:01 272 None 11 29.935 0.040 109.087 0.009 0.982 1076.000 0.285 LowExpr Pending -DBN1.ENST00000292385.JUNC00000177.chr5:177460554-177460555.D 2 12 DBN1 ENST00000292385.9 JUNC00000177 E/K KESHRPLRAA 1 HLA-B*45:01 298 None 14 311.785 0.570 109.087 0.009 0.982 1076.000 0.285 LowExpr Pending -DBN1.ENST00000309007.JUNC00000177.chr5:177460554-177460555.D 2 12 DBN1 ENST00000309007.9 JUNC00000177 E/K KESHRPLRAA 1 HLA-B*45:01 296 None 14 311.785 0.570 109.087 0.009 0.982 1076.000 0.285 LowExpr Pending -LDHB.ENST00000396075.JUNC00000053.chr12:21654541-21654542.D 6 LDHB ENST00000396075.5 JUNC00000053 NA HMMFNLSHY 3 HLA-A*29:02 48 None 6 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396076.JUNC00000053.chr12:21654541-21654542.D 6 LDHB ENST00000396076.5 JUNC00000053 NA HMMFNLSHY 5 HLA-A*29:02 48 None 6 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000450584.JUNC00000053.chr12:21654541-21654542.D 6 LDHB ENST00000450584.5 JUNC00000053 NA HMMFNLSHY 3 HLA-A*29:02 48 None 6 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000539782.JUNC00000053.chr12:21654541-21654542.D 6 LDHB ENST00000539782.1 JUNC00000053 NA HMMFNLSHY 3 HLA-A*29:02 48 None 6 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000673047.JUNC00000053.chr12:21654541-21654542.D 6 LDHB ENST00000673047.2 JUNC00000053 NA HMMFNLSHY NA HLA-A*29:02 48 None 6 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396075.JUNC00000046.chr12:21654541-21654542.A 8 LDHB ENST00000396075.5 JUNC00000046 NA EEESLADELA 3 HLA-B*45:01 14 None 8 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396076.JUNC00000046.chr12:21654541-21654542.A 8 LDHB ENST00000396076.5 JUNC00000046 NA EEESLADELA 5 HLA-B*45:01 14 None 8 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000450584.JUNC00000046.chr12:21654541-21654542.A 8 LDHB ENST00000450584.5 JUNC00000046 NA EEESLADELA 3 HLA-B*45:01 14 None 8 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000539782.JUNC00000046.chr12:21654541-21654542.A 8 LDHB ENST00000539782.1 JUNC00000046 NA EEESLADELA 3 HLA-B*45:01 14 None 8 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000673047.JUNC00000046.chr12:21654541-21654542.A 8 LDHB ENST00000673047.2 JUNC00000046 NA EEESLADELA NA HLA-B*45:01 14 None 8 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Poor Pending -DBN1.ENST00000393565.JUNC00000178.chr5:177460555-177460556.D 11 DBN1 ENST00000393565.6 JUNC00000178 NA SESEVEAAA 5 HLA-B*45:01 272 None 11 29.935 0.040 109.087 0.070 7.636 129.000 0.290 Poor Pending -DBN1.ENST00000477391.JUNC00000178.chr5:177460555-177460556.D 11 DBN1 ENST00000477391.6 JUNC00000178 NA SESEVEAAA 3 HLA-B*45:01 271 None 11 29.935 0.040 109.087 0.070 7.636 129.000 0.290 Poor Pending -DBN1.ENST00000512501.JUNC00000178.chr5:177460555-177460556.D 11 DBN1 ENST00000512501.1 JUNC00000178 NA SESEVEAAA 3 HLA-B*45:01 4 None 11 29.935 0.040 109.087 0.070 7.636 129.000 0.290 Poor Pending -SEC24D.ENST00000419654.JUNC00000155.chr4:118740662-118740663.A 3 3 SEC24D ENST00000419654.6 JUNC00000155 Q VIESCAVLY 5 HLA-A*29:02 303 None 6 92.091 0.310 67.286 0.120 8.074 575.000 0.205 Poor Pending -DBN1.ENST00000393565.JUNC00000178.chr5:177460554-177460555.D 11 DBN1 ENST00000393565.6 JUNC00000178 E/K SESEVEAAA 5 HLA-B*45:01 272 None 11 29.935 0.040 109.087 0.009 0.982 1076.000 0.285 Poor Pending -DBN1.ENST00000477391.JUNC00000178.chr5:177460554-177460555.D 11 DBN1 ENST00000477391.6 JUNC00000178 E/K SESEVEAAA 3 HLA-B*45:01 271 None 11 29.935 0.040 109.087 0.009 0.982 1076.000 0.285 Poor Pending -DBN1.ENST00000512501.JUNC00000178.chr5:177460554-177460555.D 11 DBN1 ENST00000512501.1 JUNC00000178 E/K SESEVEAAA 3 HLA-B*45:01 4 None 11 29.935 0.040 109.087 0.009 0.982 1076.000 0.285 Poor Pending -PRDM4.ENST00000228437.JUNC00000069.chr12:107746273-107746274.A 3 5 PRDM4 ENST00000228437.10 JUNC00000069 NA LEKPFLCGLA 2 HLA-B*45:01 435 None 8 477.255 0.900 13.577 1.000 13.577 71.000 0.980 Poor Pending -DBN1.ENST00000393565.JUNC00000177.chr5:177460555-177460556.D 2 11 DBN1 ENST00000393565.6 JUNC00000177 NA KESHRPLRAA 5 HLA-B*45:01 296 None 13 311.785 0.570 109.087 0.070 7.636 129.000 0.290 Poor Pending -DBN1.ENST00000477391.JUNC00000177.chr5:177460555-177460556.D 2 11 DBN1 ENST00000477391.6 JUNC00000177 NA KESHRPLRAA 3 HLA-B*45:01 295 None 13 311.785 0.570 109.087 0.070 7.636 129.000 0.290 Poor Pending -DBN1.ENST00000512501.JUNC00000177.chr5:177460555-177460556.D 2 12 DBN1 ENST00000512501.1 JUNC00000177 NA KESHRPLRAA 3 HLA-B*45:01 28 None 14 311.785 0.570 109.087 0.070 7.636 129.000 0.290 Poor Pending -UBE2I.ENST00000325437.JUNC00000100.chr16:1320436-1320437.D 2 UBE2I ENST00000325437.9 JUNC00000100 NA PAITIKQEY 3 HLA-A*29:02 105 None 2 2590.400 2.500 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000355803.JUNC00000100.chr16:1320436-1320437.D 2 UBE2I ENST00000355803.8 JUNC00000100 NA PAITIKQEY 2 HLA-A*29:02 105 None 2 2590.400 2.500 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000397514.JUNC00000100.chr16:1320436-1320437.D 2 UBE2I ENST00000397514.8 JUNC00000100 NA PAITIKQEY 1 HLA-A*29:02 105 None 2 2590.400 2.500 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000397515.JUNC00000100.chr16:1320436-1320437.D 2 UBE2I ENST00000397515.6 JUNC00000100 NA PAITIKQEY 3 HLA-A*29:02 105 None 2 2590.400 2.500 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000402301.JUNC00000100.chr16:1320436-1320437.D 2 UBE2I ENST00000402301.5 JUNC00000100 NA PAITIKQEY 1 HLA-A*29:02 105 None 2 2590.400 2.500 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000403747.JUNC00000100.chr16:1320436-1320437.D 2 UBE2I ENST00000403747.6 JUNC00000100 NA PAITIKQEY 5 HLA-A*29:02 105 None 2 2590.400 2.500 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000406620.JUNC00000100.chr16:1320436-1320437.D 2 UBE2I ENST00000406620.6 JUNC00000100 NA PAITIKQEY 2 HLA-A*29:02 105 None 2 2590.400 2.500 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000562470.JUNC00000100.chr16:1320436-1320437.D 2 UBE2I ENST00000562470.3 JUNC00000100 NA PAITIKQEY 2 HLA-A*29:02 105 None 2 2590.400 2.500 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000566587.JUNC00000100.chr16:1320436-1320437.D 2 UBE2I ENST00000566587.5 JUNC00000100 NA PAITIKQEY 2 HLA-A*29:02 105 None 2 2590.400 2.500 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000567074.JUNC00000100.chr16:1320436-1320437.D 2 UBE2I ENST00000567074.6 JUNC00000100 NA PAITIKQEY 1 HLA-A*29:02 105 None 2 2590.400 2.500 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000567383.JUNC00000100.chr16:1320436-1320437.D 2 UBE2I ENST00000567383.6 JUNC00000100 NA PAITIKQEY 4 HLA-A*29:02 105 None 2 2590.400 2.500 58.799 0.385 22.638 26.000 0.602 Poor Pending -SEC24D.ENST00000280551.JUNC00000153.chr4:118740662-118740663.NDA 2 SEC24D ENST00000280551.11 JUNC00000153 Q STAFKAVLH 1 HLA-A*29:02 696 None 2 2297.120 2.600 67.286 0.120 8.074 575.000 0.205 Poor Pending -SEC24D.ENST00000419654.JUNC00000153.chr4:118740662-118740663.NDA 2 SEC24D ENST00000419654.6 JUNC00000153 Q STAFKAVLH 5 HLA-A*29:02 252 None 2 2297.120 2.600 67.286 0.120 8.074 575.000 0.205 Poor Pending -SEC24D.ENST00000511481.JUNC00000153.chr4:118740662-118740663.NDA 2 SEC24D ENST00000511481.5 JUNC00000153 Q STAFKAVLH 1 HLA-A*29:02 327 None 2 2297.120 2.600 67.286 0.120 8.074 575.000 0.205 Poor Pending -DBN1.ENST00000393565.JUNC00000177.chr5:177460554-177460555.D 2 11 DBN1 ENST00000393565.6 JUNC00000177 E/K KESHRPLRAA 5 HLA-B*45:01 296 None 13 311.785 0.570 109.087 0.009 0.982 1076.000 0.285 Poor Pending -DBN1.ENST00000477391.JUNC00000177.chr5:177460554-177460555.D 2 11 DBN1 ENST00000477391.6 JUNC00000177 E/K KESHRPLRAA 3 HLA-B*45:01 295 None 13 311.785 0.570 109.087 0.009 0.982 1076.000 0.285 Poor Pending -DBN1.ENST00000512501.JUNC00000177.chr5:177460554-177460555.D 2 12 DBN1 ENST00000512501.1 JUNC00000177 E/K KESHRPLRAA 3 HLA-B*45:01 28 None 14 311.785 0.570 109.087 0.009 0.982 1076.000 0.285 Poor Pending -PODXL.ENST00000322985.JUNC00000200.chr7:131504507-131504508.D 1 15 PODXL ENST00000322985.9 JUNC00000200 Q/* SEMQEKKVV 1 HLA-B*45:01 487 None 16 256.275 0.410 0.630 0.455 0.287 11.000 0.124 Poor Pending -PODXL.ENST00000378555.JUNC00000200.chr7:131504507-131504508.D 1 15 PODXL ENST00000378555.8 JUNC00000200 Q/* SEMQEKKVV 1 HLA-B*45:01 519 None 16 256.275 0.410 0.630 0.455 0.287 11.000 0.124 Poor Pending -CCDC18.ENST00000343253.JUNC00000006.chr1:93226448-93226449.NDA 1 3 CCDC18 ENST00000343253.11 JUNC00000006 E EETIKVYCL 5 HLA-B*45:01 720 None 4 520.055 1.400 18.750 0.300 5.625 20.000 0.628 Poor Pending -CCDC18.ENST00000370276.JUNC00000006.chr1:93226448-93226449.NDA 1 3 CCDC18 ENST00000370276.6 JUNC00000006 E EETIKVYCL 5 HLA-B*45:01 720 None 4 520.055 1.400 18.750 0.300 5.625 20.000 0.628 Poor Pending -CCDC18.ENST00000401026.JUNC00000006.chr1:93226448-93226449.NDA 1 3 CCDC18 ENST00000401026.7 JUNC00000006 E EETIKVYCL 1 HLA-B*45:01 721 None 4 520.055 1.400 18.750 0.300 5.625 20.000 0.628 Poor Pending -CCDC18.ENST00000690025.JUNC00000006.chr1:93226448-93226449.NDA 1 3 CCDC18 ENST00000690025.1 JUNC00000006 E EETIKVYCL NA HLA-B*45:01 721 None 4 520.055 1.400 18.750 0.300 5.625 20.000 0.628 Poor Pending -UBE2I.ENST00000325437.JUNC00000102.chr16:1320436-1320437.NDA 1 UBE2I ENST00000325437.9 JUNC00000102 NA REKGPSTSQ 3 HLA-B*45:01 118 None 1 4951.980 5.400 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000355803.JUNC00000102.chr16:1320436-1320437.NDA 1 UBE2I ENST00000355803.8 JUNC00000102 NA REKGPSTSQ 2 HLA-B*45:01 118 None 1 4951.980 5.400 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000397514.JUNC00000102.chr16:1320436-1320437.NDA 1 UBE2I ENST00000397514.8 JUNC00000102 NA REKGPSTSQ 1 HLA-B*45:01 118 None 1 4951.980 5.400 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000397515.JUNC00000102.chr16:1320436-1320437.NDA 1 UBE2I ENST00000397515.6 JUNC00000102 NA REKGPSTSQ 3 HLA-B*45:01 118 None 1 4951.980 5.400 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000403747.JUNC00000102.chr16:1320436-1320437.NDA 1 UBE2I ENST00000403747.6 JUNC00000102 NA REKGPSTSQ 5 HLA-B*45:01 118 None 1 4951.980 5.400 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000406620.JUNC00000102.chr16:1320436-1320437.NDA 1 UBE2I ENST00000406620.6 JUNC00000102 NA REKGPSTSQ 2 HLA-B*45:01 118 None 1 4951.980 5.400 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000562470.JUNC00000102.chr16:1320436-1320437.NDA 1 UBE2I ENST00000562470.3 JUNC00000102 NA REKGPSTSQ 2 HLA-B*45:01 118 None 1 4951.980 5.400 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000566587.JUNC00000102.chr16:1320436-1320437.NDA 1 UBE2I ENST00000566587.5 JUNC00000102 NA REKGPSTSQ 2 HLA-B*45:01 118 None 1 4951.980 5.400 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000567074.JUNC00000102.chr16:1320436-1320437.NDA 1 UBE2I ENST00000567074.6 JUNC00000102 NA REKGPSTSQ 1 HLA-B*45:01 118 None 1 4951.980 5.400 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000567383.JUNC00000102.chr16:1320436-1320437.NDA 1 UBE2I ENST00000567383.6 JUNC00000102 NA REKGPSTSQ 4 HLA-B*45:01 118 None 1 4951.980 5.400 58.799 0.385 22.638 26.000 0.602 Poor Pending -EPS15L1.ENST00000455140.JUNC00000110.chr19:16361781-16361782.NDA 1 EPS15L1 ENST00000455140.7 JUNC00000110 T FADFSQMSKF 2 HLA-A*29:02 741 None 1 4361.370 5.500 21.206 0.311 6.595 90.000 0.199 Poor Pending -LDHB.ENST00000350669.JUNC00000044.chr12:21654541-21654542.A LDHB ENST00000350669.5 JUNC00000044 NA GQSLADELA 1 HLA-B*45:01 30 None 0 7496.556 6.100 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396075.JUNC00000044.chr12:21654541-21654542.A LDHB ENST00000396075.5 JUNC00000044 NA GQSLADELA 3 HLA-B*45:01 30 None 0 7496.556 6.100 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396076.JUNC00000044.chr12:21654541-21654542.A LDHB ENST00000396076.5 JUNC00000044 NA GQSLADELA 5 HLA-B*45:01 30 None 0 7496.556 6.100 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000450584.JUNC00000044.chr12:21654541-21654542.A LDHB ENST00000450584.5 JUNC00000044 NA GQSLADELA 3 HLA-B*45:01 30 None 0 7496.556 6.100 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000539782.JUNC00000044.chr12:21654541-21654542.A LDHB ENST00000539782.1 JUNC00000044 NA GQSLADELA 3 HLA-B*45:01 30 None 0 7496.556 6.100 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000673047.JUNC00000044.chr12:21654541-21654542.A LDHB ENST00000673047.2 JUNC00000044 NA GQSLADELA NA HLA-B*45:01 30 None 0 7496.556 6.100 203.702 0.881 179.461 118.000 0.780 Poor Pending -TIPRL.ENST00000367830.JUNC00000028.chr1:168179177-168179178.D TIPRL ENST00000367830.3 JUNC00000028 E/V KSADVVKQRF 1 HLA-A*29:02 29 None 0 7201.105 9.300 55.746 0.332 18.508 927.000 0.273 Poor Pending -TIPRL.ENST00000367833.JUNC00000028.chr1:168179177-168179178.D TIPRL ENST00000367833.7 JUNC00000028 E/V KSADVVKQRF 1 HLA-A*29:02 29 None 0 7201.105 9.300 55.746 0.332 18.508 927.000 0.273 Poor Pending -CCDC18.ENST00000343253.JUNC00000011.chr1:93226448-93226449.D 1 CCDC18 ENST00000343253.11 JUNC00000011 E EEKELKIKN 5 HLA-B*45:01 762 None 1 4893.975 6.000 18.750 0.300 5.625 20.000 0.628 Poor Pending -CCDC18.ENST00000370276.JUNC00000011.chr1:93226448-93226449.D 1 CCDC18 ENST00000370276.6 JUNC00000011 E EEKELKIKN 5 HLA-B*45:01 762 None 1 4893.975 6.000 18.750 0.300 5.625 20.000 0.628 Poor Pending -CCDC18.ENST00000401026.JUNC00000011.chr1:93226448-93226449.D 1 CCDC18 ENST00000401026.7 JUNC00000011 E EEKELKIKN 1 HLA-B*45:01 763 None 1 4893.975 6.000 18.750 0.300 5.625 20.000 0.628 Poor Pending -CCDC18.ENST00000690025.JUNC00000011.chr1:93226448-93226449.D 1 CCDC18 ENST00000690025.1 JUNC00000011 E EEKELKIKN NA HLA-B*45:01 763 None 1 4893.975 6.000 18.750 0.300 5.625 20.000 0.628 Poor Pending -LDHB.ENST00000350669.JUNC00000045.chr12:21654541-21654542.A LDHB ENST00000350669.5 JUNC00000045 NA NNKITVSLA 1 HLA-B*45:01 21 None 0 10849.410 9.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396075.JUNC00000045.chr12:21654541-21654542.A LDHB ENST00000396075.5 JUNC00000045 NA NNKITVSLA 3 HLA-B*45:01 21 None 0 10849.410 9.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396076.JUNC00000045.chr12:21654541-21654542.A LDHB ENST00000396076.5 JUNC00000045 NA NNKITVSLA 5 HLA-B*45:01 21 None 0 10849.410 9.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000450584.JUNC00000045.chr12:21654541-21654542.A LDHB ENST00000450584.5 JUNC00000045 NA NNKITVSLA 3 HLA-B*45:01 21 None 0 10849.410 9.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000539782.JUNC00000045.chr12:21654541-21654542.A LDHB ENST00000539782.1 JUNC00000045 NA NNKITVSLA 3 HLA-B*45:01 21 None 0 10849.410 9.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000673047.JUNC00000045.chr12:21654541-21654542.A LDHB ENST00000673047.2 JUNC00000045 NA NNKITVSLA NA HLA-B*45:01 21 None 0 10849.410 9.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -TIPRL.ENST00000367830.JUNC00000027.chr1:168179177-168179178.D TIPRL ENST00000367830.3 JUNC00000027 E/V IMKSADVVNR 1 HLA-A*29:02 27 None 0 9431.964 13.000 55.746 0.332 18.508 927.000 0.273 Poor Pending -TIPRL.ENST00000367833.JUNC00000027.chr1:168179177-168179178.D TIPRL ENST00000367833.7 JUNC00000027 E/V IMKSADVVNR 1 HLA-A*29:02 27 None 0 9431.964 13.000 55.746 0.332 18.508 927.000 0.273 Poor Pending -LDHB.ENST00000350669.JUNC00000043.chr12:21654541-21654542.A LDHB ENST00000350669.5 JUNC00000043 NA TVVGVGQVV 1 HLA-A*29:02 25 None 0 19305.740 22.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396075.JUNC00000043.chr12:21654541-21654542.A LDHB ENST00000396075.5 JUNC00000043 NA TVVGVGQVV 3 HLA-A*29:02 25 None 0 19305.740 22.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396076.JUNC00000043.chr12:21654541-21654542.A LDHB ENST00000396076.5 JUNC00000043 NA TVVGVGQVV 5 HLA-A*29:02 25 None 0 19305.740 22.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000450584.JUNC00000043.chr12:21654541-21654542.A LDHB ENST00000450584.5 JUNC00000043 NA TVVGVGQVV 3 HLA-A*29:02 25 None 0 19305.740 22.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000539782.JUNC00000043.chr12:21654541-21654542.A LDHB ENST00000539782.1 JUNC00000043 NA TVVGVGQVV 3 HLA-A*29:02 25 None 0 19305.740 22.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000673047.JUNC00000043.chr12:21654541-21654542.A LDHB ENST00000673047.2 JUNC00000043 NA TVVGVGQVV NA HLA-A*29:02 25 None 0 19305.740 22.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -PRDM4.ENST00000228437.JUNC00000071.chr12:107746273-107746274.NDA PRDM4 ENST00000228437.10 JUNC00000071 NA MATLFTICV 2 HLA-B*45:01 369 None 0 10084.895 9.900 13.577 1.000 13.577 71.000 0.980 Poor Pending -TIPRL.ENST00000367830.JUNC00000025.chr1:168179177-168179178.D TIPRL ENST00000367830.3 JUNC00000025 E/V KVKCKLTQSF 1 HLA-A*29:02 35 None 0 13897.785 15.000 55.746 0.332 18.508 927.000 0.273 Poor Pending -TIPRL.ENST00000367833.JUNC00000025.chr1:168179177-168179178.D TIPRL ENST00000367833.7 JUNC00000025 E/V KVKCKLTQSF 1 HLA-A*29:02 35 None 0 13897.785 15.000 55.746 0.332 18.508 927.000 0.273 Poor Pending -EPS15L1.ENST00000455140.JUNC00000108.chr19:16361781-16361782.A EPS15L1 ENST00000455140.7 JUNC00000108 T PPSGKSTPF 2 HLA-A*29:02 791 None 0 21948.110 31.000 21.206 0.311 6.595 90.000 0.199 Poor Pending -EPS15L1.ENST00000455140.JUNC00000109.chr19:16361781-16361782.NDA EPS15L1 ENST00000455140.7 JUNC00000109 T APPRPKPPSV 2 HLA-B*45:01 785 None 0 29042.080 23.000 21.206 0.311 6.595 90.000 0.199 Poor Pending -WASHC5.ENST00000318410.JUNC00000210.chr8:125067719-125067720.D 10 1 WASHC5 ENST00000318410.12 JUNC00000210 NA HTADSDIFY 1 HLA-A*29:02 379 None 11 75.509 0.160 65.088 0.000 0.000 25.000 0.062 NoExpr Pending -WASHC5.ENST00000517845.JUNC00000210.chr8:125067719-125067720.D 10 1 WASHC5 ENST00000517845.5 JUNC00000210 NA HTADSDIFY 2 HLA-A*29:02 231 None 11 75.509 0.160 65.088 0.000 0.000 25.000 0.062 NoExpr Pending -WASHC5.ENST00000318410.JUNC00000207.chr8:125067719-125067720.A 6 2 WASHC5 ENST00000318410.12 JUNC00000207 NA REALDENQVA 1 HLA-B*45:01 415 None 8 213.655 0.350 65.088 0.000 0.000 25.000 0.062 NoExpr Pending -WASHC5.ENST00000517845.JUNC00000207.chr8:125067719-125067720.A 6 2 WASHC5 ENST00000517845.5 JUNC00000207 NA REALDENQVA 2 HLA-B*45:01 267 None 8 213.655 0.350 65.088 0.000 0.000 25.000 0.062 NoExpr Pending -WASHC5.ENST00000318410.JUNC00000205.chr8:125067719-125067720.NDA 2 WASHC5 ENST00000318410.12 JUNC00000205 NA ADSDVQANA 1 HLA-B*45:01 381 None 2 2549.435 2.000 65.088 0.000 0.000 25.000 0.062 NoExpr Pending -WASHC5.ENST00000517845.JUNC00000205.chr8:125067719-125067720.NDA 2 WASHC5 ENST00000517845.5 JUNC00000205 NA ADSDVQANA 2 HLA-B*45:01 233 None 2 2549.435 2.000 65.088 0.000 0.000 25.000 0.062 NoExpr Pending -CUL9.ENST00000252050.JUNC00000183.chr6:43187095-43187096.NDA 1 CUL9 ENST00000252050.9 JUNC00000183 NA HFPPGTGILW 5 HLA-A*29:02 418 None 1 4667.000 6.400 16.683 0.000 0.000 6.000 0.252 NoExpr Pending -CUL9.ENST00000372647.JUNC00000183.chr6:43187095-43187096.NDA 1 CUL9 ENST00000372647.6 JUNC00000183 NA HFPPGTGILW 1 HLA-A*29:02 418 None 1 4667.000 6.400 16.683 0.000 0.000 6.000 0.252 NoExpr Pending -AGPS.ENST00000264167.JUNC00000129.chr2:177513816-177513817.D AGPS ENST00000264167.11 JUNC00000129 NA FETSAPWDRS 1 HLA-B*45:01 528 None 0 7486.430 6.800 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000637633.JUNC00000129.chr2:177513816-177513817.D AGPS ENST00000637633.2 JUNC00000129 NA FETSAPWDRS 5 HLA-B*45:01 528 None 0 7486.430 6.800 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000642466.JUNC00000129.chr2:177513816-177513817.D AGPS ENST00000642466.2 JUNC00000129 NA FETSAPWDRS NA HLA-B*45:01 528 None 0 7486.430 6.800 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000679459.JUNC00000129.chr2:177513816-177513817.D AGPS ENST00000679459.1 JUNC00000129 NA FETSAPWDRS NA HLA-B*45:01 528 None 0 7486.430 6.800 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000679478.JUNC00000129.chr2:177513816-177513817.D AGPS ENST00000679478.1 JUNC00000129 NA FETSAPWDRS NA HLA-B*45:01 438 None 0 7486.430 6.800 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000679994.JUNC00000129.chr2:177513816-177513817.D AGPS ENST00000679994.1 JUNC00000129 NA FETSAPWDRS NA HLA-B*45:01 438 None 0 7486.430 6.800 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000680155.JUNC00000129.chr2:177513816-177513817.D AGPS ENST00000680155.1 JUNC00000129 NA FETSAPWDRS NA HLA-B*45:01 438 None 0 7486.430 6.800 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000680770.JUNC00000129.chr2:177513816-177513817.D AGPS ENST00000680770.1 JUNC00000129 NA FETSAPWDRS NA HLA-B*45:01 528 None 0 7486.430 6.800 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000681449.JUNC00000129.chr2:177513816-177513817.D AGPS ENST00000681449.1 JUNC00000129 NA FETSAPWDRS NA HLA-B*45:01 438 None 0 7486.430 6.800 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +ID A*29:02 B*45:01 Gene Transcript Junction Name AA Change Best Peptide TSL Allele Pos Prob Pos Num Included Peptides Num Passing Peptides IC50 MT %ile MT RNA Expr RNA VAF Allele Expr RNA Depth DNA VAF Tier Evaluation +LDHB.ENST00000350669.JUNC00000053.chr12:21654541-21654542.D 6 LDHB ENST00000350669.5 JUNC00000053 NA HMMFNLSHY 1 HLA-A*29:02 48 None 6 3 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Pass Pending +LDHB.ENST00000350669.JUNC00000046.chr12:21654541-21654542.A 8 LDHB ENST00000350669.5 JUNC00000046 NA EEESLADELA 1 HLA-B*45:01 14 None 8 2 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Pass Pending +DBN1.ENST00000292385.JUNC00000178.chr5:177460555-177460556.D 11 DBN1 ENST00000292385.9 JUNC00000178 NA SESEVEAAA 1 HLA-B*45:01 274 None 11 5 29.935 0.040 109.087 0.070 7.636 129.000 0.290 Pass Pending +DBN1.ENST00000309007.JUNC00000178.chr5:177460555-177460556.D 11 DBN1 ENST00000309007.9 JUNC00000178 NA SESEVEAAA 1 HLA-B*45:01 272 None 11 5 29.935 0.040 109.087 0.070 7.636 129.000 0.290 Pass Pending +SEC24D.ENST00000280551.JUNC00000155.chr4:118740662-118740663.A 3 3 SEC24D ENST00000280551.11 JUNC00000155 Q VIESCAVLY 1 HLA-A*29:02 747 None 6 2 92.091 0.310 67.286 0.120 8.074 575.000 0.205 Pass Pending +SEC24D.ENST00000511481.JUNC00000155.chr4:118740662-118740663.A 3 3 SEC24D ENST00000511481.5 JUNC00000155 Q VIESCAVLY 1 HLA-A*29:02 378 None 6 2 92.091 0.310 67.286 0.120 8.074 575.000 0.205 Pass Pending +DBN1.ENST00000292385.JUNC00000177.chr5:177460555-177460556.D 2 12 DBN1 ENST00000292385.9 JUNC00000177 NA KESHRPLRAA 1 HLA-B*45:01 298 None 14 1 311.785 0.570 109.087 0.070 7.636 129.000 0.290 Pass Pending +DBN1.ENST00000309007.JUNC00000177.chr5:177460555-177460556.D 2 12 DBN1 ENST00000309007.9 JUNC00000177 NA KESHRPLRAA 1 HLA-B*45:01 296 None 14 1 311.785 0.570 109.087 0.070 7.636 129.000 0.290 Pass Pending +DBN1.ENST00000292385.JUNC00000178.chr5:177460554-177460555.D 11 DBN1 ENST00000292385.9 JUNC00000178 E/K SESEVEAAA 1 HLA-B*45:01 274 None 11 5 29.935 0.040 109.087 0.009 0.982 1076.000 0.285 LowExpr Pending +DBN1.ENST00000309007.JUNC00000178.chr5:177460554-177460555.D 11 DBN1 ENST00000309007.9 JUNC00000178 E/K SESEVEAAA 1 HLA-B*45:01 272 None 11 5 29.935 0.040 109.087 0.009 0.982 1076.000 0.285 LowExpr Pending +DBN1.ENST00000292385.JUNC00000177.chr5:177460554-177460555.D 2 12 DBN1 ENST00000292385.9 JUNC00000177 E/K KESHRPLRAA 1 HLA-B*45:01 298 None 14 1 311.785 0.570 109.087 0.009 0.982 1076.000 0.285 LowExpr Pending +DBN1.ENST00000309007.JUNC00000177.chr5:177460554-177460555.D 2 12 DBN1 ENST00000309007.9 JUNC00000177 E/K KESHRPLRAA 1 HLA-B*45:01 296 None 14 1 311.785 0.570 109.087 0.009 0.982 1076.000 0.285 LowExpr Pending +LDHB.ENST00000396075.JUNC00000053.chr12:21654541-21654542.D 6 LDHB ENST00000396075.5 JUNC00000053 NA HMMFNLSHY 3 HLA-A*29:02 48 None 6 3 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396076.JUNC00000053.chr12:21654541-21654542.D 6 LDHB ENST00000396076.5 JUNC00000053 NA HMMFNLSHY 5 HLA-A*29:02 48 None 6 3 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000450584.JUNC00000053.chr12:21654541-21654542.D 6 LDHB ENST00000450584.5 JUNC00000053 NA HMMFNLSHY 3 HLA-A*29:02 48 None 6 3 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000539782.JUNC00000053.chr12:21654541-21654542.D 6 LDHB ENST00000539782.1 JUNC00000053 NA HMMFNLSHY 3 HLA-A*29:02 48 None 6 3 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000673047.JUNC00000053.chr12:21654541-21654542.D 6 LDHB ENST00000673047.2 JUNC00000053 NA HMMFNLSHY NA HLA-A*29:02 48 None 6 3 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396075.JUNC00000046.chr12:21654541-21654542.A 8 LDHB ENST00000396075.5 JUNC00000046 NA EEESLADELA 3 HLA-B*45:01 14 None 8 2 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396076.JUNC00000046.chr12:21654541-21654542.A 8 LDHB ENST00000396076.5 JUNC00000046 NA EEESLADELA 5 HLA-B*45:01 14 None 8 2 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000450584.JUNC00000046.chr12:21654541-21654542.A 8 LDHB ENST00000450584.5 JUNC00000046 NA EEESLADELA 3 HLA-B*45:01 14 None 8 2 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000539782.JUNC00000046.chr12:21654541-21654542.A 8 LDHB ENST00000539782.1 JUNC00000046 NA EEESLADELA 3 HLA-B*45:01 14 None 8 2 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000673047.JUNC00000046.chr12:21654541-21654542.A 8 LDHB ENST00000673047.2 JUNC00000046 NA EEESLADELA NA HLA-B*45:01 14 None 8 2 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Poor Pending +DBN1.ENST00000393565.JUNC00000178.chr5:177460555-177460556.D 11 DBN1 ENST00000393565.6 JUNC00000178 NA SESEVEAAA 5 HLA-B*45:01 272 None 11 5 29.935 0.040 109.087 0.070 7.636 129.000 0.290 Poor Pending +DBN1.ENST00000477391.JUNC00000178.chr5:177460555-177460556.D 11 DBN1 ENST00000477391.6 JUNC00000178 NA SESEVEAAA 3 HLA-B*45:01 271 None 11 5 29.935 0.040 109.087 0.070 7.636 129.000 0.290 Poor Pending +DBN1.ENST00000512501.JUNC00000178.chr5:177460555-177460556.D 11 DBN1 ENST00000512501.1 JUNC00000178 NA SESEVEAAA 3 HLA-B*45:01 4 None 11 5 29.935 0.040 109.087 0.070 7.636 129.000 0.290 Poor Pending +SEC24D.ENST00000419654.JUNC00000155.chr4:118740662-118740663.A 3 3 SEC24D ENST00000419654.6 JUNC00000155 Q VIESCAVLY 5 HLA-A*29:02 303 None 6 2 92.091 0.310 67.286 0.120 8.074 575.000 0.205 Poor Pending +DBN1.ENST00000393565.JUNC00000178.chr5:177460554-177460555.D 11 DBN1 ENST00000393565.6 JUNC00000178 E/K SESEVEAAA 5 HLA-B*45:01 272 None 11 5 29.935 0.040 109.087 0.009 0.982 1076.000 0.285 Poor Pending +DBN1.ENST00000477391.JUNC00000178.chr5:177460554-177460555.D 11 DBN1 ENST00000477391.6 JUNC00000178 E/K SESEVEAAA 3 HLA-B*45:01 271 None 11 5 29.935 0.040 109.087 0.009 0.982 1076.000 0.285 Poor Pending +DBN1.ENST00000512501.JUNC00000178.chr5:177460554-177460555.D 11 DBN1 ENST00000512501.1 JUNC00000178 E/K SESEVEAAA 3 HLA-B*45:01 4 None 11 5 29.935 0.040 109.087 0.009 0.982 1076.000 0.285 Poor Pending +PRDM4.ENST00000228437.JUNC00000069.chr12:107746273-107746274.A 3 5 PRDM4 ENST00000228437.10 JUNC00000069 NA LEKPFLCGLA 2 HLA-B*45:01 435 None 8 2 477.255 0.900 13.577 1.000 13.577 71.000 0.980 Poor Pending +DBN1.ENST00000393565.JUNC00000177.chr5:177460555-177460556.D 2 11 DBN1 ENST00000393565.6 JUNC00000177 NA KESHRPLRAA 5 HLA-B*45:01 296 None 13 1 311.785 0.570 109.087 0.070 7.636 129.000 0.290 Poor Pending +DBN1.ENST00000477391.JUNC00000177.chr5:177460555-177460556.D 2 11 DBN1 ENST00000477391.6 JUNC00000177 NA KESHRPLRAA 3 HLA-B*45:01 295 None 13 1 311.785 0.570 109.087 0.070 7.636 129.000 0.290 Poor Pending +DBN1.ENST00000512501.JUNC00000177.chr5:177460555-177460556.D 2 12 DBN1 ENST00000512501.1 JUNC00000177 NA KESHRPLRAA 3 HLA-B*45:01 28 None 14 1 311.785 0.570 109.087 0.070 7.636 129.000 0.290 Poor Pending +UBE2I.ENST00000325437.JUNC00000100.chr16:1320436-1320437.D 2 UBE2I ENST00000325437.9 JUNC00000100 NA PAITIKQEY 3 HLA-A*29:02 105 None 2 0 2590.400 2.500 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000355803.JUNC00000100.chr16:1320436-1320437.D 2 UBE2I ENST00000355803.8 JUNC00000100 NA PAITIKQEY 2 HLA-A*29:02 105 None 2 0 2590.400 2.500 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000397514.JUNC00000100.chr16:1320436-1320437.D 2 UBE2I ENST00000397514.8 JUNC00000100 NA PAITIKQEY 1 HLA-A*29:02 105 None 2 0 2590.400 2.500 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000397515.JUNC00000100.chr16:1320436-1320437.D 2 UBE2I ENST00000397515.6 JUNC00000100 NA PAITIKQEY 3 HLA-A*29:02 105 None 2 0 2590.400 2.500 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000402301.JUNC00000100.chr16:1320436-1320437.D 2 UBE2I ENST00000402301.5 JUNC00000100 NA PAITIKQEY 1 HLA-A*29:02 105 None 2 0 2590.400 2.500 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000403747.JUNC00000100.chr16:1320436-1320437.D 2 UBE2I ENST00000403747.6 JUNC00000100 NA PAITIKQEY 5 HLA-A*29:02 105 None 2 0 2590.400 2.500 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000406620.JUNC00000100.chr16:1320436-1320437.D 2 UBE2I ENST00000406620.6 JUNC00000100 NA PAITIKQEY 2 HLA-A*29:02 105 None 2 0 2590.400 2.500 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000562470.JUNC00000100.chr16:1320436-1320437.D 2 UBE2I ENST00000562470.3 JUNC00000100 NA PAITIKQEY 2 HLA-A*29:02 105 None 2 0 2590.400 2.500 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000566587.JUNC00000100.chr16:1320436-1320437.D 2 UBE2I ENST00000566587.5 JUNC00000100 NA PAITIKQEY 2 HLA-A*29:02 105 None 2 0 2590.400 2.500 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000567074.JUNC00000100.chr16:1320436-1320437.D 2 UBE2I ENST00000567074.6 JUNC00000100 NA PAITIKQEY 1 HLA-A*29:02 105 None 2 0 2590.400 2.500 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000567383.JUNC00000100.chr16:1320436-1320437.D 2 UBE2I ENST00000567383.6 JUNC00000100 NA PAITIKQEY 4 HLA-A*29:02 105 None 2 0 2590.400 2.500 58.799 0.385 22.638 26.000 0.602 Poor Pending +SEC24D.ENST00000280551.JUNC00000153.chr4:118740662-118740663.NDA 2 SEC24D ENST00000280551.11 JUNC00000153 Q STAFKAVLH 1 HLA-A*29:02 696 None 2 0 2297.120 2.600 67.286 0.120 8.074 575.000 0.205 Poor Pending +SEC24D.ENST00000419654.JUNC00000153.chr4:118740662-118740663.NDA 2 SEC24D ENST00000419654.6 JUNC00000153 Q STAFKAVLH 5 HLA-A*29:02 252 None 2 0 2297.120 2.600 67.286 0.120 8.074 575.000 0.205 Poor Pending +SEC24D.ENST00000511481.JUNC00000153.chr4:118740662-118740663.NDA 2 SEC24D ENST00000511481.5 JUNC00000153 Q STAFKAVLH 1 HLA-A*29:02 327 None 2 0 2297.120 2.600 67.286 0.120 8.074 575.000 0.205 Poor Pending +DBN1.ENST00000393565.JUNC00000177.chr5:177460554-177460555.D 2 11 DBN1 ENST00000393565.6 JUNC00000177 E/K KESHRPLRAA 5 HLA-B*45:01 296 None 13 1 311.785 0.570 109.087 0.009 0.982 1076.000 0.285 Poor Pending +DBN1.ENST00000477391.JUNC00000177.chr5:177460554-177460555.D 2 11 DBN1 ENST00000477391.6 JUNC00000177 E/K KESHRPLRAA 3 HLA-B*45:01 295 None 13 1 311.785 0.570 109.087 0.009 0.982 1076.000 0.285 Poor Pending +DBN1.ENST00000512501.JUNC00000177.chr5:177460554-177460555.D 2 12 DBN1 ENST00000512501.1 JUNC00000177 E/K KESHRPLRAA 3 HLA-B*45:01 28 None 14 1 311.785 0.570 109.087 0.009 0.982 1076.000 0.285 Poor Pending +PODXL.ENST00000322985.JUNC00000200.chr7:131504507-131504508.D 1 14 PODXL ENST00000322985.9 JUNC00000200 Q/* SEMQEKKVV 1 HLA-B*45:01 487 None 15 2 256.275 0.410 0.630 0.455 0.287 11.000 0.124 Poor Pending +PODXL.ENST00000378555.JUNC00000200.chr7:131504507-131504508.D 1 14 PODXL ENST00000378555.8 JUNC00000200 Q/* SEMQEKKVV 1 HLA-B*45:01 519 None 15 2 256.275 0.410 0.630 0.455 0.287 11.000 0.124 Poor Pending +CCDC18.ENST00000343253.JUNC00000006.chr1:93226448-93226449.NDA 1 3 CCDC18 ENST00000343253.11 JUNC00000006 E EETIKVYCL 5 HLA-B*45:01 720 None 4 0 520.055 1.400 18.750 0.300 5.625 20.000 0.628 Poor Pending +CCDC18.ENST00000370276.JUNC00000006.chr1:93226448-93226449.NDA 1 3 CCDC18 ENST00000370276.6 JUNC00000006 E EETIKVYCL 5 HLA-B*45:01 720 None 4 0 520.055 1.400 18.750 0.300 5.625 20.000 0.628 Poor Pending +CCDC18.ENST00000401026.JUNC00000006.chr1:93226448-93226449.NDA 1 3 CCDC18 ENST00000401026.7 JUNC00000006 E EETIKVYCL 1 HLA-B*45:01 721 None 4 0 520.055 1.400 18.750 0.300 5.625 20.000 0.628 Poor Pending +CCDC18.ENST00000690025.JUNC00000006.chr1:93226448-93226449.NDA 1 3 CCDC18 ENST00000690025.1 JUNC00000006 E EETIKVYCL NA HLA-B*45:01 721 None 4 0 520.055 1.400 18.750 0.300 5.625 20.000 0.628 Poor Pending +UBE2I.ENST00000325437.JUNC00000102.chr16:1320436-1320437.NDA 1 UBE2I ENST00000325437.9 JUNC00000102 NA REKGPSTSQ 3 HLA-B*45:01 118 None 1 0 4951.980 5.400 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000355803.JUNC00000102.chr16:1320436-1320437.NDA 1 UBE2I ENST00000355803.8 JUNC00000102 NA REKGPSTSQ 2 HLA-B*45:01 118 None 1 0 4951.980 5.400 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000397514.JUNC00000102.chr16:1320436-1320437.NDA 1 UBE2I ENST00000397514.8 JUNC00000102 NA REKGPSTSQ 1 HLA-B*45:01 118 None 1 0 4951.980 5.400 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000397515.JUNC00000102.chr16:1320436-1320437.NDA 1 UBE2I ENST00000397515.6 JUNC00000102 NA REKGPSTSQ 3 HLA-B*45:01 118 None 1 0 4951.980 5.400 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000403747.JUNC00000102.chr16:1320436-1320437.NDA 1 UBE2I ENST00000403747.6 JUNC00000102 NA REKGPSTSQ 5 HLA-B*45:01 118 None 1 0 4951.980 5.400 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000406620.JUNC00000102.chr16:1320436-1320437.NDA 1 UBE2I ENST00000406620.6 JUNC00000102 NA REKGPSTSQ 2 HLA-B*45:01 118 None 1 0 4951.980 5.400 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000562470.JUNC00000102.chr16:1320436-1320437.NDA 1 UBE2I ENST00000562470.3 JUNC00000102 NA REKGPSTSQ 2 HLA-B*45:01 118 None 1 0 4951.980 5.400 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000566587.JUNC00000102.chr16:1320436-1320437.NDA 1 UBE2I ENST00000566587.5 JUNC00000102 NA REKGPSTSQ 2 HLA-B*45:01 118 None 1 0 4951.980 5.400 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000567074.JUNC00000102.chr16:1320436-1320437.NDA 1 UBE2I ENST00000567074.6 JUNC00000102 NA REKGPSTSQ 1 HLA-B*45:01 118 None 1 0 4951.980 5.400 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000567383.JUNC00000102.chr16:1320436-1320437.NDA 1 UBE2I ENST00000567383.6 JUNC00000102 NA REKGPSTSQ 4 HLA-B*45:01 118 None 1 0 4951.980 5.400 58.799 0.385 22.638 26.000 0.602 Poor Pending +EPS15L1.ENST00000455140.JUNC00000110.chr19:16361781-16361782.NDA 1 EPS15L1 ENST00000455140.7 JUNC00000110 T FADFSQMSKF 2 HLA-A*29:02 741 None 1 0 4361.370 5.500 21.206 0.311 6.595 90.000 0.199 Poor Pending +LDHB.ENST00000350669.JUNC00000044.chr12:21654541-21654542.A 1 LDHB ENST00000350669.5 JUNC00000044 NA GQSLADELA 1 HLA-B*45:01 30 None 1 0 7496.556 6.100 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396075.JUNC00000044.chr12:21654541-21654542.A 1 LDHB ENST00000396075.5 JUNC00000044 NA GQSLADELA 3 HLA-B*45:01 30 None 1 0 7496.556 6.100 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396076.JUNC00000044.chr12:21654541-21654542.A 1 LDHB ENST00000396076.5 JUNC00000044 NA GQSLADELA 5 HLA-B*45:01 30 None 1 0 7496.556 6.100 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000450584.JUNC00000044.chr12:21654541-21654542.A 1 LDHB ENST00000450584.5 JUNC00000044 NA GQSLADELA 3 HLA-B*45:01 30 None 1 0 7496.556 6.100 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000539782.JUNC00000044.chr12:21654541-21654542.A 1 LDHB ENST00000539782.1 JUNC00000044 NA GQSLADELA 3 HLA-B*45:01 30 None 1 0 7496.556 6.100 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000673047.JUNC00000044.chr12:21654541-21654542.A 1 LDHB ENST00000673047.2 JUNC00000044 NA GQSLADELA NA HLA-B*45:01 30 None 1 0 7496.556 6.100 203.702 0.881 179.461 118.000 0.780 Poor Pending +TIPRL.ENST00000367830.JUNC00000028.chr1:168179177-168179178.D 1 TIPRL ENST00000367830.3 JUNC00000028 E/V KSADVVKQRF 1 HLA-A*29:02 29 None 1 0 7201.105 9.300 55.746 0.332 18.508 927.000 0.273 Poor Pending +TIPRL.ENST00000367833.JUNC00000028.chr1:168179177-168179178.D 1 TIPRL ENST00000367833.7 JUNC00000028 E/V KSADVVKQRF 1 HLA-A*29:02 29 None 1 0 7201.105 9.300 55.746 0.332 18.508 927.000 0.273 Poor Pending +CCDC18.ENST00000343253.JUNC00000011.chr1:93226448-93226449.D 1 CCDC18 ENST00000343253.11 JUNC00000011 E EEKELKIKN 5 HLA-B*45:01 762 None 1 0 4893.975 6.000 18.750 0.300 5.625 20.000 0.628 Poor Pending +CCDC18.ENST00000370276.JUNC00000011.chr1:93226448-93226449.D 1 CCDC18 ENST00000370276.6 JUNC00000011 E EEKELKIKN 5 HLA-B*45:01 762 None 1 0 4893.975 6.000 18.750 0.300 5.625 20.000 0.628 Poor Pending +CCDC18.ENST00000401026.JUNC00000011.chr1:93226448-93226449.D 1 CCDC18 ENST00000401026.7 JUNC00000011 E EEKELKIKN 1 HLA-B*45:01 763 None 1 0 4893.975 6.000 18.750 0.300 5.625 20.000 0.628 Poor Pending +CCDC18.ENST00000690025.JUNC00000011.chr1:93226448-93226449.D 1 CCDC18 ENST00000690025.1 JUNC00000011 E EEKELKIKN NA HLA-B*45:01 763 None 1 0 4893.975 6.000 18.750 0.300 5.625 20.000 0.628 Poor Pending +LDHB.ENST00000350669.JUNC00000045.chr12:21654541-21654542.A 1 LDHB ENST00000350669.5 JUNC00000045 NA NNKITVSLA 1 HLA-B*45:01 21 None 1 0 10849.410 9.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396075.JUNC00000045.chr12:21654541-21654542.A 1 LDHB ENST00000396075.5 JUNC00000045 NA NNKITVSLA 3 HLA-B*45:01 21 None 1 0 10849.410 9.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396076.JUNC00000045.chr12:21654541-21654542.A 1 LDHB ENST00000396076.5 JUNC00000045 NA NNKITVSLA 5 HLA-B*45:01 21 None 1 0 10849.410 9.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000450584.JUNC00000045.chr12:21654541-21654542.A 1 LDHB ENST00000450584.5 JUNC00000045 NA NNKITVSLA 3 HLA-B*45:01 21 None 1 0 10849.410 9.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000539782.JUNC00000045.chr12:21654541-21654542.A 1 LDHB ENST00000539782.1 JUNC00000045 NA NNKITVSLA 3 HLA-B*45:01 21 None 1 0 10849.410 9.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000673047.JUNC00000045.chr12:21654541-21654542.A 1 LDHB ENST00000673047.2 JUNC00000045 NA NNKITVSLA NA HLA-B*45:01 21 None 1 0 10849.410 9.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +TIPRL.ENST00000367830.JUNC00000027.chr1:168179177-168179178.D 1 TIPRL ENST00000367830.3 JUNC00000027 E/V IMKSADVVNR 1 HLA-A*29:02 27 None 1 0 9431.964 13.000 55.746 0.332 18.508 927.000 0.273 Poor Pending +TIPRL.ENST00000367833.JUNC00000027.chr1:168179177-168179178.D 1 TIPRL ENST00000367833.7 JUNC00000027 E/V IMKSADVVNR 1 HLA-A*29:02 27 None 1 0 9431.964 13.000 55.746 0.332 18.508 927.000 0.273 Poor Pending +LDHB.ENST00000350669.JUNC00000043.chr12:21654541-21654542.A 1 LDHB ENST00000350669.5 JUNC00000043 NA TVVGVGQVV 1 HLA-A*29:02 25 None 1 0 19305.740 22.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396075.JUNC00000043.chr12:21654541-21654542.A 1 LDHB ENST00000396075.5 JUNC00000043 NA TVVGVGQVV 3 HLA-A*29:02 25 None 1 0 19305.740 22.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396076.JUNC00000043.chr12:21654541-21654542.A 1 LDHB ENST00000396076.5 JUNC00000043 NA TVVGVGQVV 5 HLA-A*29:02 25 None 1 0 19305.740 22.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000450584.JUNC00000043.chr12:21654541-21654542.A 1 LDHB ENST00000450584.5 JUNC00000043 NA TVVGVGQVV 3 HLA-A*29:02 25 None 1 0 19305.740 22.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000539782.JUNC00000043.chr12:21654541-21654542.A 1 LDHB ENST00000539782.1 JUNC00000043 NA TVVGVGQVV 3 HLA-A*29:02 25 None 1 0 19305.740 22.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000673047.JUNC00000043.chr12:21654541-21654542.A 1 LDHB ENST00000673047.2 JUNC00000043 NA TVVGVGQVV NA HLA-A*29:02 25 None 1 0 19305.740 22.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +PRDM4.ENST00000228437.JUNC00000071.chr12:107746273-107746274.NDA 1 PRDM4 ENST00000228437.10 JUNC00000071 NA MATLFTICV 2 HLA-B*45:01 369 None 1 0 10084.895 9.900 13.577 1.000 13.577 71.000 0.980 Poor Pending +TIPRL.ENST00000367830.JUNC00000025.chr1:168179177-168179178.D 1 TIPRL ENST00000367830.3 JUNC00000025 E/V KVKCKLTQSF 1 HLA-A*29:02 35 None 1 0 13897.785 15.000 55.746 0.332 18.508 927.000 0.273 Poor Pending +TIPRL.ENST00000367833.JUNC00000025.chr1:168179177-168179178.D 1 TIPRL ENST00000367833.7 JUNC00000025 E/V KVKCKLTQSF 1 HLA-A*29:02 35 None 1 0 13897.785 15.000 55.746 0.332 18.508 927.000 0.273 Poor Pending +EPS15L1.ENST00000455140.JUNC00000108.chr19:16361781-16361782.A 1 EPS15L1 ENST00000455140.7 JUNC00000108 T PPSGKSTPF 2 HLA-A*29:02 791 None 1 0 21948.110 31.000 21.206 0.311 6.595 90.000 0.199 Poor Pending +EPS15L1.ENST00000455140.JUNC00000109.chr19:16361781-16361782.NDA 1 EPS15L1 ENST00000455140.7 JUNC00000109 T APPRPKPPSV 2 HLA-B*45:01 785 None 1 0 29042.080 23.000 21.206 0.311 6.595 90.000 0.199 Poor Pending +WASHC5.ENST00000318410.JUNC00000210.chr8:125067719-125067720.D 10 1 WASHC5 ENST00000318410.12 JUNC00000210 NA HTADSDIFY 1 HLA-A*29:02 379 None 11 2 75.509 0.160 65.088 0.000 0.000 25.000 0.062 NoExpr Pending +WASHC5.ENST00000517845.JUNC00000210.chr8:125067719-125067720.D 10 1 WASHC5 ENST00000517845.5 JUNC00000210 NA HTADSDIFY 2 HLA-A*29:02 231 None 11 2 75.509 0.160 65.088 0.000 0.000 25.000 0.062 NoExpr Pending +WASHC5.ENST00000318410.JUNC00000207.chr8:125067719-125067720.A 6 2 WASHC5 ENST00000318410.12 JUNC00000207 NA REALDENQVA 1 HLA-B*45:01 415 None 8 1 213.655 0.350 65.088 0.000 0.000 25.000 0.062 NoExpr Pending +WASHC5.ENST00000517845.JUNC00000207.chr8:125067719-125067720.A 6 2 WASHC5 ENST00000517845.5 JUNC00000207 NA REALDENQVA 2 HLA-B*45:01 267 None 8 1 213.655 0.350 65.088 0.000 0.000 25.000 0.062 NoExpr Pending +WASHC5.ENST00000318410.JUNC00000205.chr8:125067719-125067720.NDA 2 WASHC5 ENST00000318410.12 JUNC00000205 NA ADSDVQANA 1 HLA-B*45:01 381 None 2 0 2549.435 2.000 65.088 0.000 0.000 25.000 0.062 NoExpr Pending +WASHC5.ENST00000517845.JUNC00000205.chr8:125067719-125067720.NDA 2 WASHC5 ENST00000517845.5 JUNC00000205 NA ADSDVQANA 2 HLA-B*45:01 233 None 2 0 2549.435 2.000 65.088 0.000 0.000 25.000 0.062 NoExpr Pending +CUL9.ENST00000252050.JUNC00000183.chr6:43187095-43187096.NDA 1 CUL9 ENST00000252050.9 JUNC00000183 NA HFPPGTGILW 5 HLA-A*29:02 418 None 1 0 4667.000 6.400 16.683 0.000 0.000 6.000 0.252 NoExpr Pending +CUL9.ENST00000372647.JUNC00000183.chr6:43187095-43187096.NDA 1 CUL9 ENST00000372647.6 JUNC00000183 NA HFPPGTGILW 1 HLA-A*29:02 418 None 1 0 4667.000 6.400 16.683 0.000 0.000 6.000 0.252 NoExpr Pending +AGPS.ENST00000264167.JUNC00000129.chr2:177513816-177513817.D 1 AGPS ENST00000264167.11 JUNC00000129 NA FETSAPWDRS 1 HLA-B*45:01 528 None 1 0 7486.430 6.800 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000637633.JUNC00000129.chr2:177513816-177513817.D 1 AGPS ENST00000637633.2 JUNC00000129 NA FETSAPWDRS 5 HLA-B*45:01 528 None 1 0 7486.430 6.800 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000642466.JUNC00000129.chr2:177513816-177513817.D 1 AGPS ENST00000642466.2 JUNC00000129 NA FETSAPWDRS NA HLA-B*45:01 528 None 1 0 7486.430 6.800 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000679459.JUNC00000129.chr2:177513816-177513817.D 1 AGPS ENST00000679459.1 JUNC00000129 NA FETSAPWDRS NA HLA-B*45:01 528 None 1 0 7486.430 6.800 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000679478.JUNC00000129.chr2:177513816-177513817.D 1 AGPS ENST00000679478.1 JUNC00000129 NA FETSAPWDRS NA HLA-B*45:01 438 None 1 0 7486.430 6.800 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000679994.JUNC00000129.chr2:177513816-177513817.D 1 AGPS ENST00000679994.1 JUNC00000129 NA FETSAPWDRS NA HLA-B*45:01 438 None 1 0 7486.430 6.800 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000680155.JUNC00000129.chr2:177513816-177513817.D 1 AGPS ENST00000680155.1 JUNC00000129 NA FETSAPWDRS NA HLA-B*45:01 438 None 1 0 7486.430 6.800 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000680770.JUNC00000129.chr2:177513816-177513817.D 1 AGPS ENST00000680770.1 JUNC00000129 NA FETSAPWDRS NA HLA-B*45:01 528 None 1 0 7486.430 6.800 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000681449.JUNC00000129.chr2:177513816-177513817.D 1 AGPS ENST00000681449.1 JUNC00000129 NA FETSAPWDRS NA HLA-B*45:01 438 None 1 0 7486.430 6.800 38.437 0.000 0.000 9.000 0.237 NoExpr Pending diff --git a/pvactools/tools/pvacsplice/example_data/results/MHC_Class_II/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv b/pvactools/tools/pvacsplice/example_data/results/MHC_Class_II/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv index 4558c240..61fa46d4 100644 --- a/pvactools/tools/pvacsplice/example_data/results/MHC_Class_II/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv +++ b/pvactools/tools/pvacsplice/example_data/results/MHC_Class_II/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv @@ -1,116 +1,116 @@ -ID DRB1*04:05 Gene Transcript Junction Name AA Change Best Peptide TSL Allele Pos Prob Pos Num Passing Peptides IC50 MT %ile MT RNA Expr RNA VAF Allele Expr RNA Depth DNA VAF Tier Evaluation -LDHB.ENST00000350669.JUNC00000053.chr12:21654541-21654542.D 14 LDHB ENST00000350669.5 JUNC00000053 NA GKTIRRHMMFNLSHY 1 DRB1*04:05 42 None 14 198.980 13.000 203.702 0.881 179.461 118.000 0.780 Pass Pending -SEC24D.ENST00000280551.JUNC00000153.chr4:118740662-118740663.NDA 14 SEC24D ENST00000280551.11 JUNC00000153 Q TSTAFKAVLHQPLKV 1 DRB1*04:05 695 None 14 71.040 3.720 67.286 0.120 8.074 575.000 0.205 Pass Pending -SEC24D.ENST00000511481.JUNC00000153.chr4:118740662-118740663.NDA 14 SEC24D ENST00000511481.5 JUNC00000153 Q TSTAFKAVLHQPLKV 1 DRB1*04:05 326 None 14 71.040 3.720 67.286 0.120 8.074 575.000 0.205 Pass Pending -UBE2I.ENST00000397514.JUNC00000100.chr16:1320436-1320437.D 5 UBE2I ENST00000397514.8 JUNC00000100 NA DKDWRPAITIKQEYR 1 DRB1*04:05 100 None 5 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Pass Pending -UBE2I.ENST00000402301.JUNC00000100.chr16:1320436-1320437.D 5 UBE2I ENST00000402301.5 JUNC00000100 NA DKDWRPAITIKQEYR 1 DRB1*04:05 100 None 5 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Pass Pending -UBE2I.ENST00000567074.JUNC00000100.chr16:1320436-1320437.D 5 UBE2I ENST00000567074.6 JUNC00000100 NA DKDWRPAITIKQEYR 1 DRB1*04:05 100 None 5 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Pass Pending -SEC24D.ENST00000280551.JUNC00000155.chr4:118740662-118740663.A 18 SEC24D ENST00000280551.11 JUNC00000155 Q SCAVLYTTISGQRRL 1 DRB1*04:05 750 None 18 322.830 14.000 67.286 0.120 8.074 575.000 0.205 Pass Pending -SEC24D.ENST00000511481.JUNC00000155.chr4:118740662-118740663.A 18 SEC24D ENST00000511481.5 JUNC00000155 Q SCAVLYTTISGQRRL 1 DRB1*04:05 381 None 18 322.830 14.000 67.286 0.120 8.074 575.000 0.205 Pass Pending -TIPRL.ENST00000367830.JUNC00000028.chr1:168179177-168179178.D 12 TIPRL ENST00000367830.3 JUNC00000028 E/V SKTHIMKSADVVKQR 1 DRB1*04:05 23 None 12 442.135 20.000 55.746 0.332 18.508 927.000 0.273 Pass Pending -TIPRL.ENST00000367833.JUNC00000028.chr1:168179177-168179178.D 12 TIPRL ENST00000367833.7 JUNC00000028 E/V SKTHIMKSADVVKQR 1 DRB1*04:05 23 None 12 442.135 20.000 55.746 0.332 18.508 927.000 0.273 Pass Pending -TIPRL.ENST00000367830.JUNC00000027.chr1:168179177-168179178.D 2 TIPRL ENST00000367830.3 JUNC00000027 E/V ASKTHIMKSADVVNR 1 DRB1*04:05 22 None 2 485.250 21.000 55.746 0.332 18.508 927.000 0.273 Pass Pending -TIPRL.ENST00000367833.JUNC00000027.chr1:168179177-168179178.D 2 TIPRL ENST00000367833.7 JUNC00000027 E/V ASKTHIMKSADVVNR 1 DRB1*04:05 22 None 2 485.250 21.000 55.746 0.332 18.508 927.000 0.273 Pass Pending -LDHB.ENST00000396075.JUNC00000053.chr12:21654541-21654542.D 14 LDHB ENST00000396075.5 JUNC00000053 NA GKTIRRHMMFNLSHY 3 DRB1*04:05 42 None 14 198.980 13.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396076.JUNC00000053.chr12:21654541-21654542.D 14 LDHB ENST00000396076.5 JUNC00000053 NA GKTIRRHMMFNLSHY 5 DRB1*04:05 42 None 14 198.980 13.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000450584.JUNC00000053.chr12:21654541-21654542.D 14 LDHB ENST00000450584.5 JUNC00000053 NA GKTIRRHMMFNLSHY 3 DRB1*04:05 42 None 14 198.980 13.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000539782.JUNC00000053.chr12:21654541-21654542.D 14 LDHB ENST00000539782.1 JUNC00000053 NA GKTIRRHMMFNLSHY 3 DRB1*04:05 42 None 14 198.980 13.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000673047.JUNC00000053.chr12:21654541-21654542.D 14 LDHB ENST00000673047.2 JUNC00000053 NA GKTIRRHMMFNLSHY NA DRB1*04:05 42 None 14 198.980 13.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -SEC24D.ENST00000419654.JUNC00000153.chr4:118740662-118740663.NDA 14 SEC24D ENST00000419654.6 JUNC00000153 Q TSTAFKAVLHQPLKV 5 DRB1*04:05 251 None 14 71.040 3.720 67.286 0.120 8.074 575.000 0.205 Poor Pending -PRDM4.ENST00000228437.JUNC00000069.chr12:107746273-107746274.A 19 PRDM4 ENST00000228437.10 JUNC00000069 NA KQLVLRQSIVGAEVD 2 DRB1*04:05 412 None 19 298.575 15.000 13.577 1.000 13.577 71.000 0.980 Poor Pending -UBE2I.ENST00000325437.JUNC00000100.chr16:1320436-1320437.D 5 UBE2I ENST00000325437.9 JUNC00000100 NA DKDWRPAITIKQEYR 3 DRB1*04:05 100 None 5 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000355803.JUNC00000100.chr16:1320436-1320437.D 5 UBE2I ENST00000355803.8 JUNC00000100 NA DKDWRPAITIKQEYR 2 DRB1*04:05 100 None 5 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000397515.JUNC00000100.chr16:1320436-1320437.D 5 UBE2I ENST00000397515.6 JUNC00000100 NA DKDWRPAITIKQEYR 3 DRB1*04:05 100 None 5 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000403747.JUNC00000100.chr16:1320436-1320437.D 5 UBE2I ENST00000403747.6 JUNC00000100 NA DKDWRPAITIKQEYR 5 DRB1*04:05 100 None 5 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000406620.JUNC00000100.chr16:1320436-1320437.D 5 UBE2I ENST00000406620.6 JUNC00000100 NA DKDWRPAITIKQEYR 2 DRB1*04:05 100 None 5 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000562470.JUNC00000100.chr16:1320436-1320437.D 5 UBE2I ENST00000562470.3 JUNC00000100 NA DKDWRPAITIKQEYR 2 DRB1*04:05 100 None 5 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000566587.JUNC00000100.chr16:1320436-1320437.D 5 UBE2I ENST00000566587.5 JUNC00000100 NA DKDWRPAITIKQEYR 2 DRB1*04:05 100 None 5 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000567383.JUNC00000100.chr16:1320436-1320437.D 5 UBE2I ENST00000567383.6 JUNC00000100 NA DKDWRPAITIKQEYR 4 DRB1*04:05 100 None 5 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending -SEC24D.ENST00000419654.JUNC00000155.chr4:118740662-118740663.A 18 SEC24D ENST00000419654.6 JUNC00000155 Q SCAVLYTTISGQRRL 5 DRB1*04:05 306 None 18 322.830 14.000 67.286 0.120 8.074 575.000 0.205 Poor Pending -LDHB.ENST00000350669.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000350669.5 JUNC00000045 NA VSLADELALVDVLED 1 DRB1*04:05 26 None 12 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396075.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000396075.5 JUNC00000045 NA VSLADELALVDVLED 3 DRB1*04:05 26 None 12 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396076.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000396076.5 JUNC00000045 NA VSLADELALVDVLED 5 DRB1*04:05 26 None 12 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000450584.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000450584.5 JUNC00000045 NA VSLADELALVDVLED 3 DRB1*04:05 26 None 12 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000539782.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000539782.1 JUNC00000045 NA VSLADELALVDVLED 3 DRB1*04:05 26 None 12 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000673047.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000673047.2 JUNC00000045 NA VSLADELALVDVLED NA DRB1*04:05 26 None 12 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -TIPRL.ENST00000367830.JUNC00000025.chr1:168179177-168179178.D 7 TIPRL ENST00000367830.3 JUNC00000025 E/V SKTHIMKSADVVKVK 1 DRB1*04:05 23 None 7 512.505 23.000 55.746 0.332 18.508 927.000 0.273 Poor Pending -TIPRL.ENST00000367833.JUNC00000025.chr1:168179177-168179178.D 7 TIPRL ENST00000367833.7 JUNC00000025 E/V SKTHIMKSADVVKVK 1 DRB1*04:05 23 None 7 512.505 23.000 55.746 0.332 18.508 927.000 0.273 Poor Pending -UBE2I.ENST00000325437.JUNC00000102.chr16:1320436-1320437.NDA 6 UBE2I ENST00000325437.9 JUNC00000102 NA KDWRPAITIKQPKQS 3 DRB1*04:05 101 None 6 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000355803.JUNC00000102.chr16:1320436-1320437.NDA 6 UBE2I ENST00000355803.8 JUNC00000102 NA KDWRPAITIKQPKQS 2 DRB1*04:05 101 None 6 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000397514.JUNC00000102.chr16:1320436-1320437.NDA 6 UBE2I ENST00000397514.8 JUNC00000102 NA KDWRPAITIKQPKQS 1 DRB1*04:05 101 None 6 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000397515.JUNC00000102.chr16:1320436-1320437.NDA 6 UBE2I ENST00000397515.6 JUNC00000102 NA KDWRPAITIKQPKQS 3 DRB1*04:05 101 None 6 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000403747.JUNC00000102.chr16:1320436-1320437.NDA 6 UBE2I ENST00000403747.6 JUNC00000102 NA KDWRPAITIKQPKQS 5 DRB1*04:05 101 None 6 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000406620.JUNC00000102.chr16:1320436-1320437.NDA 6 UBE2I ENST00000406620.6 JUNC00000102 NA KDWRPAITIKQPKQS 2 DRB1*04:05 101 None 6 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000562470.JUNC00000102.chr16:1320436-1320437.NDA 6 UBE2I ENST00000562470.3 JUNC00000102 NA KDWRPAITIKQPKQS 2 DRB1*04:05 101 None 6 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000566587.JUNC00000102.chr16:1320436-1320437.NDA 6 UBE2I ENST00000566587.5 JUNC00000102 NA KDWRPAITIKQPKQS 2 DRB1*04:05 101 None 6 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000567074.JUNC00000102.chr16:1320436-1320437.NDA 6 UBE2I ENST00000567074.6 JUNC00000102 NA KDWRPAITIKQPKQS 1 DRB1*04:05 101 None 6 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000567383.JUNC00000102.chr16:1320436-1320437.NDA 6 UBE2I ENST00000567383.6 JUNC00000102 NA KDWRPAITIKQPKQS 4 DRB1*04:05 101 None 6 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending -LDHB.ENST00000350669.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000350669.5 JUNC00000044 NA QSLADELALVDVLED 1 DRB1*04:05 31 None 14 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396075.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000396075.5 JUNC00000044 NA QSLADELALVDVLED 3 DRB1*04:05 31 None 14 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396076.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000396076.5 JUNC00000044 NA QSLADELALVDVLED 5 DRB1*04:05 31 None 14 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000450584.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000450584.5 JUNC00000044 NA QSLADELALVDVLED 3 DRB1*04:05 31 None 14 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000539782.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000539782.1 JUNC00000044 NA QSLADELALVDVLED 3 DRB1*04:05 31 None 14 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000673047.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000673047.2 JUNC00000044 NA QSLADELALVDVLED NA DRB1*04:05 31 None 14 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending -PODXL.ENST00000322985.JUNC00000200.chr7:131504507-131504508.D 40 PODXL ENST00000322985.9 JUNC00000200 Q/* DNPTLEVMETSSEMQ 1 DRB1*04:05 476 None 40 294.275 12.000 0.630 0.455 0.287 11.000 0.124 Poor Pending -PODXL.ENST00000378555.JUNC00000200.chr7:131504507-131504508.D 40 PODXL ENST00000378555.8 JUNC00000200 Q/* DNPTLEVMETSSEMQ 1 DRB1*04:05 508 None 40 294.275 12.000 0.630 0.455 0.287 11.000 0.124 Poor Pending -LDHB.ENST00000350669.JUNC00000046.chr12:21654541-21654542.A 12 LDHB ENST00000350669.5 JUNC00000046 NA ESLADELALVDVLED 1 DRB1*04:05 16 None 12 692.480 26.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396075.JUNC00000046.chr12:21654541-21654542.A 12 LDHB ENST00000396075.5 JUNC00000046 NA ESLADELALVDVLED 3 DRB1*04:05 16 None 12 692.480 26.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396076.JUNC00000046.chr12:21654541-21654542.A 12 LDHB ENST00000396076.5 JUNC00000046 NA ESLADELALVDVLED 5 DRB1*04:05 16 None 12 692.480 26.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000450584.JUNC00000046.chr12:21654541-21654542.A 12 LDHB ENST00000450584.5 JUNC00000046 NA ESLADELALVDVLED 3 DRB1*04:05 16 None 12 692.480 26.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000539782.JUNC00000046.chr12:21654541-21654542.A 12 LDHB ENST00000539782.1 JUNC00000046 NA ESLADELALVDVLED 3 DRB1*04:05 16 None 12 692.480 26.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000673047.JUNC00000046.chr12:21654541-21654542.A 12 LDHB ENST00000673047.2 JUNC00000046 NA ESLADELALVDVLED NA DRB1*04:05 16 None 12 692.480 26.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -PRDM4.ENST00000228437.JUNC00000071.chr12:107746273-107746274.NDA 15 PRDM4 ENST00000228437.10 JUNC00000071 NA LFTICVWTGETIPVR 2 DRB1*04:05 372 None 15 715.145 32.000 13.577 1.000 13.577 71.000 0.980 Poor Pending -DBN1.ENST00000292385.JUNC00000177.chr5:177460555-177460556.D 52 DBN1 ENST00000292385.9 JUNC00000177 NA TGGWRPLPSPRGARL 1 DRB1*04:05 325 None 52 791.680 9.900 109.087 0.070 7.636 129.000 0.290 Poor Pending -DBN1.ENST00000309007.JUNC00000177.chr5:177460555-177460556.D 52 DBN1 ENST00000309007.9 JUNC00000177 NA TGGWRPLPSPRGARL 1 DRB1*04:05 323 None 52 791.680 9.900 109.087 0.070 7.636 129.000 0.290 Poor Pending -DBN1.ENST00000512501.JUNC00000177.chr5:177460555-177460556.D 47 DBN1 ENST00000512501.1 JUNC00000177 NA TGGWRPLPSPRGARL 3 DRB1*04:05 55 None 47 791.680 9.900 109.087 0.070 7.636 129.000 0.290 Poor Pending -CCDC18.ENST00000343253.JUNC00000006.chr1:93226448-93226449.NDA 12 CCDC18 ENST00000343253.11 JUNC00000006 E EETIKVYCLQKELKI 5 DRB1*04:05 720 None 12 806.315 31.000 18.750 0.300 5.625 20.000 0.628 Poor Pending -CCDC18.ENST00000370276.JUNC00000006.chr1:93226448-93226449.NDA 12 CCDC18 ENST00000370276.6 JUNC00000006 E EETIKVYCLQKELKI 5 DRB1*04:05 720 None 12 806.315 31.000 18.750 0.300 5.625 20.000 0.628 Poor Pending -CCDC18.ENST00000401026.JUNC00000006.chr1:93226448-93226449.NDA 12 CCDC18 ENST00000401026.7 JUNC00000006 E EETIKVYCLQKELKI 1 DRB1*04:05 721 None 12 806.315 31.000 18.750 0.300 5.625 20.000 0.628 Poor Pending -CCDC18.ENST00000690025.JUNC00000006.chr1:93226448-93226449.NDA 12 CCDC18 ENST00000690025.1 JUNC00000006 E EETIKVYCLQKELKI NA DRB1*04:05 721 None 12 806.315 31.000 18.750 0.300 5.625 20.000 0.628 Poor Pending -DBN1.ENST00000292385.JUNC00000177.chr5:177460554-177460555.D 52 DBN1 ENST00000292385.9 JUNC00000177 E/K TGGWRPLPSPRGARL 1 DRB1*04:05 325 None 52 791.680 9.900 109.087 0.009 0.982 1076.000 0.285 Poor Pending -DBN1.ENST00000309007.JUNC00000177.chr5:177460554-177460555.D 52 DBN1 ENST00000309007.9 JUNC00000177 E/K TGGWRPLPSPRGARL 1 DRB1*04:05 323 None 52 791.680 9.900 109.087 0.009 0.982 1076.000 0.285 Poor Pending -DBN1.ENST00000393565.JUNC00000177.chr5:177460555-177460556.D 38 DBN1 ENST00000393565.6 JUNC00000177 NA SEVEQLLLPSGLTTQ 5 DRB1*04:05 274 None 38 989.330 43.000 109.087 0.070 7.636 129.000 0.290 Poor Pending -DBN1.ENST00000477391.JUNC00000177.chr5:177460555-177460556.D 31 DBN1 ENST00000477391.6 JUNC00000177 NA SEVEQLLLPSGLTTQ 3 DRB1*04:05 273 None 31 989.330 43.000 109.087 0.070 7.636 129.000 0.290 Poor Pending -DBN1.ENST00000512501.JUNC00000177.chr5:177460554-177460555.D 47 DBN1 ENST00000512501.1 JUNC00000177 E/K TGGWRPLPSPRGARL 3 DRB1*04:05 55 None 47 791.680 9.900 109.087 0.009 0.982 1076.000 0.285 Poor Pending -LDHB.ENST00000350669.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000350669.5 JUNC00000043 NA NNKITVVGVGQVVSG 1 DRB1*04:05 21 None 3 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396075.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000396075.5 JUNC00000043 NA NNKITVVGVGQVVSG 3 DRB1*04:05 21 None 3 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396076.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000396076.5 JUNC00000043 NA NNKITVVGVGQVVSG 5 DRB1*04:05 21 None 3 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000450584.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000450584.5 JUNC00000043 NA NNKITVVGVGQVVSG 3 DRB1*04:05 21 None 3 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000539782.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000539782.1 JUNC00000043 NA NNKITVVGVGQVVSG 3 DRB1*04:05 21 None 3 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000673047.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000673047.2 JUNC00000043 NA NNKITVVGVGQVVSG NA DRB1*04:05 21 None 3 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -EPS15L1.ENST00000455140.JUNC00000110.chr19:16361781-16361782.NDA 12 EPS15L1 ENST00000455140.7 JUNC00000110 T DFSQMSKFGNEEQQL 2 DRB1*04:05 743 None 12 1108.365 37.000 21.206 0.311 6.595 90.000 0.199 Poor Pending -DBN1.ENST00000292385.JUNC00000178.chr5:177460555-177460556.D 11 DBN1 ENST00000292385.9 JUNC00000178 NA ESEVEAAAIIAQRPD 1 DRB1*04:05 275 None 11 1881.890 46.000 109.087 0.070 7.636 129.000 0.290 Poor Pending -DBN1.ENST00000309007.JUNC00000178.chr5:177460555-177460556.D 11 DBN1 ENST00000309007.9 JUNC00000178 NA ESEVEAAAIIAQRPD 1 DRB1*04:05 273 None 11 1881.890 46.000 109.087 0.070 7.636 129.000 0.290 Poor Pending -DBN1.ENST00000393565.JUNC00000177.chr5:177460554-177460555.D 38 DBN1 ENST00000393565.6 JUNC00000177 E/K SEVEQLLLPSGLTTQ 5 DRB1*04:05 274 None 38 989.330 43.000 109.087 0.009 0.982 1076.000 0.285 Poor Pending -DBN1.ENST00000393565.JUNC00000178.chr5:177460555-177460556.D 11 DBN1 ENST00000393565.6 JUNC00000178 NA ESEVEAAAIIAQRPD 5 DRB1*04:05 273 None 11 1881.890 46.000 109.087 0.070 7.636 129.000 0.290 Poor Pending -DBN1.ENST00000477391.JUNC00000177.chr5:177460554-177460555.D 31 DBN1 ENST00000477391.6 JUNC00000177 E/K SEVEQLLLPSGLTTQ 3 DRB1*04:05 273 None 31 989.330 43.000 109.087 0.009 0.982 1076.000 0.285 Poor Pending -DBN1.ENST00000477391.JUNC00000178.chr5:177460555-177460556.D 11 DBN1 ENST00000477391.6 JUNC00000178 NA ESEVEAAAIIAQRPD 3 DRB1*04:05 272 None 11 1881.890 46.000 109.087 0.070 7.636 129.000 0.290 Poor Pending -DBN1.ENST00000512501.JUNC00000178.chr5:177460555-177460556.D 7 DBN1 ENST00000512501.1 JUNC00000178 NA ESEVEAAAIIAQRPD 3 DRB1*04:05 5 None 7 1881.890 46.000 109.087 0.070 7.636 129.000 0.290 Poor Pending -CCDC18.ENST00000343253.JUNC00000011.chr1:93226448-93226449.D 4 CCDC18 ENST00000343253.11 JUNC00000011 E EKELKIKNHSLQETS 5 DRB1*04:05 763 None 4 1786.600 36.000 18.750 0.300 5.625 20.000 0.628 Poor Pending -CCDC18.ENST00000370276.JUNC00000011.chr1:93226448-93226449.D 4 CCDC18 ENST00000370276.6 JUNC00000011 E EKELKIKNHSLQETS 5 DRB1*04:05 763 None 4 1786.600 36.000 18.750 0.300 5.625 20.000 0.628 Poor Pending -CCDC18.ENST00000401026.JUNC00000011.chr1:93226448-93226449.D 4 CCDC18 ENST00000401026.7 JUNC00000011 E EKELKIKNHSLQETS 1 DRB1*04:05 764 None 4 1786.600 36.000 18.750 0.300 5.625 20.000 0.628 Poor Pending -CCDC18.ENST00000690025.JUNC00000011.chr1:93226448-93226449.D 4 CCDC18 ENST00000690025.1 JUNC00000011 E EKELKIKNHSLQETS NA DRB1*04:05 764 None 4 1786.600 36.000 18.750 0.300 5.625 20.000 0.628 Poor Pending -DBN1.ENST00000292385.JUNC00000178.chr5:177460554-177460555.D 11 DBN1 ENST00000292385.9 JUNC00000178 E/K ESEVEAAAIIAQRPD 1 DRB1*04:05 275 None 11 1881.890 46.000 109.087 0.009 0.982 1076.000 0.285 Poor Pending -DBN1.ENST00000309007.JUNC00000178.chr5:177460554-177460555.D 11 DBN1 ENST00000309007.9 JUNC00000178 E/K ESEVEAAAIIAQRPD 1 DRB1*04:05 273 None 11 1881.890 46.000 109.087 0.009 0.982 1076.000 0.285 Poor Pending -DBN1.ENST00000393565.JUNC00000178.chr5:177460554-177460555.D 11 DBN1 ENST00000393565.6 JUNC00000178 E/K ESEVEAAAIIAQRPD 5 DRB1*04:05 273 None 11 1881.890 46.000 109.087 0.009 0.982 1076.000 0.285 Poor Pending -DBN1.ENST00000477391.JUNC00000178.chr5:177460554-177460555.D 11 DBN1 ENST00000477391.6 JUNC00000178 E/K ESEVEAAAIIAQRPD 3 DRB1*04:05 272 None 11 1881.890 46.000 109.087 0.009 0.982 1076.000 0.285 Poor Pending -DBN1.ENST00000512501.JUNC00000178.chr5:177460554-177460555.D 7 DBN1 ENST00000512501.1 JUNC00000178 E/K ESEVEAAAIIAQRPD 3 DRB1*04:05 5 None 7 1881.890 46.000 109.087 0.009 0.982 1076.000 0.285 Poor Pending -EPS15L1.ENST00000455140.JUNC00000108.chr19:16361781-16361782.A EPS15L1 ENST00000455140.7 JUNC00000108 T KSTPFGNEEQQLAWA 2 DRB1*04:05 795 None 0 5252.645 75.000 21.206 0.311 6.595 90.000 0.199 Poor Pending -EPS15L1.ENST00000455140.JUNC00000109.chr19:16361781-16361782.NDA EPS15L1 ENST00000455140.7 JUNC00000109 T PKKPAPPRPKPPSVW 2 DRB1*04:05 781 None 0 27220.365 100.000 21.206 0.311 6.595 90.000 0.199 Poor Pending -WASHC5.ENST00000318410.JUNC00000207.chr8:125067719-125067720.A 32 WASHC5 ENST00000318410.12 JUNC00000207 NA TLRIRTYFTMQSGLA 1 DRB1*04:05 399 None 32 42.905 2.100 65.088 0.000 0.000 25.000 0.062 NoExpr Pending -WASHC5.ENST00000517845.JUNC00000207.chr8:125067719-125067720.A 32 WASHC5 ENST00000517845.5 JUNC00000207 NA TLRIRTYFTMQSGLA 2 DRB1*04:05 251 None 32 42.905 2.100 65.088 0.000 0.000 25.000 0.062 NoExpr Pending -WASHC5.ENST00000318410.JUNC00000205.chr8:125067719-125067720.NDA 19 WASHC5 ENST00000318410.12 JUNC00000205 NA AIRWLMLHTADSDVQ 1 DRB1*04:05 372 None 19 47.320 1.800 65.088 0.000 0.000 25.000 0.062 NoExpr Pending -WASHC5.ENST00000517845.JUNC00000205.chr8:125067719-125067720.NDA 19 WASHC5 ENST00000517845.5 JUNC00000205 NA AIRWLMLHTADSDVQ 2 DRB1*04:05 224 None 19 47.320 1.800 65.088 0.000 0.000 25.000 0.062 NoExpr Pending -WASHC5.ENST00000318410.JUNC00000210.chr8:125067719-125067720.D 28 WASHC5 ENST00000318410.12 JUNC00000210 NA AIRWLMLHTADSDIF 1 DRB1*04:05 372 None 28 47.575 1.900 65.088 0.000 0.000 25.000 0.062 NoExpr Pending -WASHC5.ENST00000517845.JUNC00000210.chr8:125067719-125067720.D 28 WASHC5 ENST00000517845.5 JUNC00000210 NA AIRWLMLHTADSDIF 2 DRB1*04:05 224 None 28 47.575 1.900 65.088 0.000 0.000 25.000 0.062 NoExpr Pending -CUL9.ENST00000252050.JUNC00000183.chr6:43187095-43187096.NDA 16 CUL9 ENST00000252050.9 JUNC00000183 NA GCTLCRTSSPNLRRM 5 DRB1*04:05 429 None 16 928.575 37.000 16.683 0.000 0.000 6.000 0.252 NoExpr Pending -CUL9.ENST00000372647.JUNC00000183.chr6:43187095-43187096.NDA 16 CUL9 ENST00000372647.6 JUNC00000183 NA GCTLCRTSSPNLRRM 1 DRB1*04:05 429 None 16 928.575 37.000 16.683 0.000 0.000 6.000 0.252 NoExpr Pending -AGPS.ENST00000264167.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000264167.11 JUNC00000129 NA LGESFETSAPWDRSL 1 DRB1*04:05 524 None 2 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000637633.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000637633.2 JUNC00000129 NA LGESFETSAPWDRSL 5 DRB1*04:05 524 None 2 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000642466.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000642466.2 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 524 None 2 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000679459.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000679459.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 524 None 2 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000679478.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000679478.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 434 None 2 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000679994.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000679994.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 434 None 2 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000680155.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000680155.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 434 None 2 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000680770.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000680770.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 524 None 2 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000681449.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000681449.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 434 None 2 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +ID DRB1*04:05 Gene Transcript Junction Name AA Change Best Peptide TSL Allele Pos Prob Pos Num Included Peptides Num Passing Peptides IC50 MT %ile MT RNA Expr RNA VAF Allele Expr RNA Depth DNA VAF Tier Evaluation +LDHB.ENST00000350669.JUNC00000053.chr12:21654541-21654542.D 14 LDHB ENST00000350669.5 JUNC00000053 NA GKTIRRHMMFNLSHY 1 DRB1*04:05 42 None 14 3 198.980 13.000 203.702 0.881 179.461 118.000 0.780 Pass Pending +SEC24D.ENST00000280551.JUNC00000153.chr4:118740662-118740663.NDA 14 SEC24D ENST00000280551.11 JUNC00000153 Q TSTAFKAVLHQPLKV 1 DRB1*04:05 695 None 14 12 71.040 3.720 67.286 0.120 8.074 575.000 0.205 Pass Pending +SEC24D.ENST00000511481.JUNC00000153.chr4:118740662-118740663.NDA 14 SEC24D ENST00000511481.5 JUNC00000153 Q TSTAFKAVLHQPLKV 1 DRB1*04:05 326 None 14 12 71.040 3.720 67.286 0.120 8.074 575.000 0.205 Pass Pending +UBE2I.ENST00000397514.JUNC00000100.chr16:1320436-1320437.D 5 UBE2I ENST00000397514.8 JUNC00000100 NA DKDWRPAITIKQEYR 1 DRB1*04:05 100 None 5 4 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Pass Pending +UBE2I.ENST00000402301.JUNC00000100.chr16:1320436-1320437.D 5 UBE2I ENST00000402301.5 JUNC00000100 NA DKDWRPAITIKQEYR 1 DRB1*04:05 100 None 5 4 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Pass Pending +UBE2I.ENST00000567074.JUNC00000100.chr16:1320436-1320437.D 5 UBE2I ENST00000567074.6 JUNC00000100 NA DKDWRPAITIKQEYR 1 DRB1*04:05 100 None 5 4 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Pass Pending +SEC24D.ENST00000280551.JUNC00000155.chr4:118740662-118740663.A 15 SEC24D ENST00000280551.11 JUNC00000155 Q SCAVLYTTISGQRRL 1 DRB1*04:05 750 None 15 3 322.830 14.000 67.286 0.120 8.074 575.000 0.205 Pass Pending +SEC24D.ENST00000511481.JUNC00000155.chr4:118740662-118740663.A 15 SEC24D ENST00000511481.5 JUNC00000155 Q SCAVLYTTISGQRRL 1 DRB1*04:05 381 None 15 3 322.830 14.000 67.286 0.120 8.074 575.000 0.205 Pass Pending +TIPRL.ENST00000367830.JUNC00000028.chr1:168179177-168179178.D 12 TIPRL ENST00000367830.3 JUNC00000028 E/V SKTHIMKSADVVKQR 1 DRB1*04:05 23 None 12 1 442.135 20.000 55.746 0.332 18.508 927.000 0.273 Pass Pending +TIPRL.ENST00000367833.JUNC00000028.chr1:168179177-168179178.D 12 TIPRL ENST00000367833.7 JUNC00000028 E/V SKTHIMKSADVVKQR 1 DRB1*04:05 23 None 12 1 442.135 20.000 55.746 0.332 18.508 927.000 0.273 Pass Pending +TIPRL.ENST00000367830.JUNC00000027.chr1:168179177-168179178.D 2 TIPRL ENST00000367830.3 JUNC00000027 E/V ASKTHIMKSADVVNR 1 DRB1*04:05 22 None 2 1 485.250 21.000 55.746 0.332 18.508 927.000 0.273 Pass Pending +TIPRL.ENST00000367833.JUNC00000027.chr1:168179177-168179178.D 2 TIPRL ENST00000367833.7 JUNC00000027 E/V ASKTHIMKSADVVNR 1 DRB1*04:05 22 None 2 1 485.250 21.000 55.746 0.332 18.508 927.000 0.273 Pass Pending +LDHB.ENST00000396075.JUNC00000053.chr12:21654541-21654542.D 14 LDHB ENST00000396075.5 JUNC00000053 NA GKTIRRHMMFNLSHY 3 DRB1*04:05 42 None 14 3 198.980 13.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396076.JUNC00000053.chr12:21654541-21654542.D 14 LDHB ENST00000396076.5 JUNC00000053 NA GKTIRRHMMFNLSHY 5 DRB1*04:05 42 None 14 3 198.980 13.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000450584.JUNC00000053.chr12:21654541-21654542.D 14 LDHB ENST00000450584.5 JUNC00000053 NA GKTIRRHMMFNLSHY 3 DRB1*04:05 42 None 14 3 198.980 13.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000539782.JUNC00000053.chr12:21654541-21654542.D 14 LDHB ENST00000539782.1 JUNC00000053 NA GKTIRRHMMFNLSHY 3 DRB1*04:05 42 None 14 3 198.980 13.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000673047.JUNC00000053.chr12:21654541-21654542.D 14 LDHB ENST00000673047.2 JUNC00000053 NA GKTIRRHMMFNLSHY NA DRB1*04:05 42 None 14 3 198.980 13.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +SEC24D.ENST00000419654.JUNC00000153.chr4:118740662-118740663.NDA 14 SEC24D ENST00000419654.6 JUNC00000153 Q TSTAFKAVLHQPLKV 5 DRB1*04:05 251 None 14 12 71.040 3.720 67.286 0.120 8.074 575.000 0.205 Poor Pending +PRDM4.ENST00000228437.JUNC00000069.chr12:107746273-107746274.A 15 PRDM4 ENST00000228437.10 JUNC00000069 NA KQLVLRQSIVGAEVD 2 DRB1*04:05 412 None 15 2 298.575 15.000 13.577 1.000 13.577 71.000 0.980 Poor Pending +UBE2I.ENST00000325437.JUNC00000100.chr16:1320436-1320437.D 5 UBE2I ENST00000325437.9 JUNC00000100 NA DKDWRPAITIKQEYR 3 DRB1*04:05 100 None 5 4 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000355803.JUNC00000100.chr16:1320436-1320437.D 5 UBE2I ENST00000355803.8 JUNC00000100 NA DKDWRPAITIKQEYR 2 DRB1*04:05 100 None 5 4 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000397515.JUNC00000100.chr16:1320436-1320437.D 5 UBE2I ENST00000397515.6 JUNC00000100 NA DKDWRPAITIKQEYR 3 DRB1*04:05 100 None 5 4 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000403747.JUNC00000100.chr16:1320436-1320437.D 5 UBE2I ENST00000403747.6 JUNC00000100 NA DKDWRPAITIKQEYR 5 DRB1*04:05 100 None 5 4 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000406620.JUNC00000100.chr16:1320436-1320437.D 5 UBE2I ENST00000406620.6 JUNC00000100 NA DKDWRPAITIKQEYR 2 DRB1*04:05 100 None 5 4 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000562470.JUNC00000100.chr16:1320436-1320437.D 5 UBE2I ENST00000562470.3 JUNC00000100 NA DKDWRPAITIKQEYR 2 DRB1*04:05 100 None 5 4 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000566587.JUNC00000100.chr16:1320436-1320437.D 5 UBE2I ENST00000566587.5 JUNC00000100 NA DKDWRPAITIKQEYR 2 DRB1*04:05 100 None 5 4 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000567383.JUNC00000100.chr16:1320436-1320437.D 5 UBE2I ENST00000567383.6 JUNC00000100 NA DKDWRPAITIKQEYR 4 DRB1*04:05 100 None 5 4 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending +SEC24D.ENST00000419654.JUNC00000155.chr4:118740662-118740663.A 15 SEC24D ENST00000419654.6 JUNC00000155 Q SCAVLYTTISGQRRL 5 DRB1*04:05 306 None 15 3 322.830 14.000 67.286 0.120 8.074 575.000 0.205 Poor Pending +LDHB.ENST00000350669.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000350669.5 JUNC00000045 NA VSLADELALVDVLED 1 DRB1*04:05 26 None 12 0 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396075.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000396075.5 JUNC00000045 NA VSLADELALVDVLED 3 DRB1*04:05 26 None 12 0 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396076.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000396076.5 JUNC00000045 NA VSLADELALVDVLED 5 DRB1*04:05 26 None 12 0 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000450584.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000450584.5 JUNC00000045 NA VSLADELALVDVLED 3 DRB1*04:05 26 None 12 0 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000539782.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000539782.1 JUNC00000045 NA VSLADELALVDVLED 3 DRB1*04:05 26 None 12 0 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000673047.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000673047.2 JUNC00000045 NA VSLADELALVDVLED NA DRB1*04:05 26 None 12 0 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +TIPRL.ENST00000367830.JUNC00000025.chr1:168179177-168179178.D 7 TIPRL ENST00000367830.3 JUNC00000025 E/V SKTHIMKSADVVKVK 1 DRB1*04:05 23 None 7 0 512.505 23.000 55.746 0.332 18.508 927.000 0.273 Poor Pending +TIPRL.ENST00000367833.JUNC00000025.chr1:168179177-168179178.D 7 TIPRL ENST00000367833.7 JUNC00000025 E/V SKTHIMKSADVVKVK 1 DRB1*04:05 23 None 7 0 512.505 23.000 55.746 0.332 18.508 927.000 0.273 Poor Pending +UBE2I.ENST00000325437.JUNC00000102.chr16:1320436-1320437.NDA 6 UBE2I ENST00000325437.9 JUNC00000102 NA KDWRPAITIKQPKQS 3 DRB1*04:05 101 None 6 0 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000355803.JUNC00000102.chr16:1320436-1320437.NDA 6 UBE2I ENST00000355803.8 JUNC00000102 NA KDWRPAITIKQPKQS 2 DRB1*04:05 101 None 6 0 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000397514.JUNC00000102.chr16:1320436-1320437.NDA 6 UBE2I ENST00000397514.8 JUNC00000102 NA KDWRPAITIKQPKQS 1 DRB1*04:05 101 None 6 0 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000397515.JUNC00000102.chr16:1320436-1320437.NDA 6 UBE2I ENST00000397515.6 JUNC00000102 NA KDWRPAITIKQPKQS 3 DRB1*04:05 101 None 6 0 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000403747.JUNC00000102.chr16:1320436-1320437.NDA 6 UBE2I ENST00000403747.6 JUNC00000102 NA KDWRPAITIKQPKQS 5 DRB1*04:05 101 None 6 0 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000406620.JUNC00000102.chr16:1320436-1320437.NDA 6 UBE2I ENST00000406620.6 JUNC00000102 NA KDWRPAITIKQPKQS 2 DRB1*04:05 101 None 6 0 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000562470.JUNC00000102.chr16:1320436-1320437.NDA 6 UBE2I ENST00000562470.3 JUNC00000102 NA KDWRPAITIKQPKQS 2 DRB1*04:05 101 None 6 0 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000566587.JUNC00000102.chr16:1320436-1320437.NDA 6 UBE2I ENST00000566587.5 JUNC00000102 NA KDWRPAITIKQPKQS 2 DRB1*04:05 101 None 6 0 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000567074.JUNC00000102.chr16:1320436-1320437.NDA 6 UBE2I ENST00000567074.6 JUNC00000102 NA KDWRPAITIKQPKQS 1 DRB1*04:05 101 None 6 0 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000567383.JUNC00000102.chr16:1320436-1320437.NDA 6 UBE2I ENST00000567383.6 JUNC00000102 NA KDWRPAITIKQPKQS 4 DRB1*04:05 101 None 6 0 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending +LDHB.ENST00000350669.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000350669.5 JUNC00000044 NA QSLADELALVDVLED 1 DRB1*04:05 31 None 14 0 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396075.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000396075.5 JUNC00000044 NA QSLADELALVDVLED 3 DRB1*04:05 31 None 14 0 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396076.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000396076.5 JUNC00000044 NA QSLADELALVDVLED 5 DRB1*04:05 31 None 14 0 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000450584.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000450584.5 JUNC00000044 NA QSLADELALVDVLED 3 DRB1*04:05 31 None 14 0 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000539782.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000539782.1 JUNC00000044 NA QSLADELALVDVLED 3 DRB1*04:05 31 None 14 0 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000673047.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000673047.2 JUNC00000044 NA QSLADELALVDVLED NA DRB1*04:05 31 None 14 0 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending +PODXL.ENST00000322985.JUNC00000200.chr7:131504507-131504508.D 15 PODXL ENST00000322985.9 JUNC00000200 Q/* DNPTLEVMETSSEMQ 1 DRB1*04:05 476 None 15 9 294.275 12.000 0.630 0.455 0.287 11.000 0.124 Poor Pending +PODXL.ENST00000378555.JUNC00000200.chr7:131504507-131504508.D 15 PODXL ENST00000378555.8 JUNC00000200 Q/* DNPTLEVMETSSEMQ 1 DRB1*04:05 508 None 15 9 294.275 12.000 0.630 0.455 0.287 11.000 0.124 Poor Pending +LDHB.ENST00000350669.JUNC00000046.chr12:21654541-21654542.A 12 LDHB ENST00000350669.5 JUNC00000046 NA ESLADELALVDVLED 1 DRB1*04:05 16 None 12 0 692.480 26.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396075.JUNC00000046.chr12:21654541-21654542.A 12 LDHB ENST00000396075.5 JUNC00000046 NA ESLADELALVDVLED 3 DRB1*04:05 16 None 12 0 692.480 26.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396076.JUNC00000046.chr12:21654541-21654542.A 12 LDHB ENST00000396076.5 JUNC00000046 NA ESLADELALVDVLED 5 DRB1*04:05 16 None 12 0 692.480 26.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000450584.JUNC00000046.chr12:21654541-21654542.A 12 LDHB ENST00000450584.5 JUNC00000046 NA ESLADELALVDVLED 3 DRB1*04:05 16 None 12 0 692.480 26.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000539782.JUNC00000046.chr12:21654541-21654542.A 12 LDHB ENST00000539782.1 JUNC00000046 NA ESLADELALVDVLED 3 DRB1*04:05 16 None 12 0 692.480 26.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000673047.JUNC00000046.chr12:21654541-21654542.A 12 LDHB ENST00000673047.2 JUNC00000046 NA ESLADELALVDVLED NA DRB1*04:05 16 None 12 0 692.480 26.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +PRDM4.ENST00000228437.JUNC00000071.chr12:107746273-107746274.NDA 15 PRDM4 ENST00000228437.10 JUNC00000071 NA LFTICVWTGETIPVR 2 DRB1*04:05 372 None 15 0 715.145 32.000 13.577 1.000 13.577 71.000 0.980 Poor Pending +DBN1.ENST00000292385.JUNC00000177.chr5:177460555-177460556.D 15 DBN1 ENST00000292385.9 JUNC00000177 NA TGGWRPLPSPRGARL 1 DRB1*04:05 325 None 15 0 791.680 9.900 109.087 0.070 7.636 129.000 0.290 Poor Pending +DBN1.ENST00000309007.JUNC00000177.chr5:177460555-177460556.D 15 DBN1 ENST00000309007.9 JUNC00000177 NA TGGWRPLPSPRGARL 1 DRB1*04:05 323 None 15 0 791.680 9.900 109.087 0.070 7.636 129.000 0.290 Poor Pending +DBN1.ENST00000512501.JUNC00000177.chr5:177460555-177460556.D 15 DBN1 ENST00000512501.1 JUNC00000177 NA TGGWRPLPSPRGARL 3 DRB1*04:05 55 None 15 0 791.680 9.900 109.087 0.070 7.636 129.000 0.290 Poor Pending +CCDC18.ENST00000343253.JUNC00000006.chr1:93226448-93226449.NDA 12 CCDC18 ENST00000343253.11 JUNC00000006 E EETIKVYCLQKELKI 5 DRB1*04:05 720 None 12 0 806.315 31.000 18.750 0.300 5.625 20.000 0.628 Poor Pending +CCDC18.ENST00000370276.JUNC00000006.chr1:93226448-93226449.NDA 12 CCDC18 ENST00000370276.6 JUNC00000006 E EETIKVYCLQKELKI 5 DRB1*04:05 720 None 12 0 806.315 31.000 18.750 0.300 5.625 20.000 0.628 Poor Pending +CCDC18.ENST00000401026.JUNC00000006.chr1:93226448-93226449.NDA 12 CCDC18 ENST00000401026.7 JUNC00000006 E EETIKVYCLQKELKI 1 DRB1*04:05 721 None 12 0 806.315 31.000 18.750 0.300 5.625 20.000 0.628 Poor Pending +CCDC18.ENST00000690025.JUNC00000006.chr1:93226448-93226449.NDA 12 CCDC18 ENST00000690025.1 JUNC00000006 E EETIKVYCLQKELKI NA DRB1*04:05 721 None 12 0 806.315 31.000 18.750 0.300 5.625 20.000 0.628 Poor Pending +DBN1.ENST00000292385.JUNC00000177.chr5:177460554-177460555.D 15 DBN1 ENST00000292385.9 JUNC00000177 E/K TGGWRPLPSPRGARL 1 DRB1*04:05 325 None 15 0 791.680 9.900 109.087 0.009 0.982 1076.000 0.285 Poor Pending +DBN1.ENST00000309007.JUNC00000177.chr5:177460554-177460555.D 15 DBN1 ENST00000309007.9 JUNC00000177 E/K TGGWRPLPSPRGARL 1 DRB1*04:05 323 None 15 0 791.680 9.900 109.087 0.009 0.982 1076.000 0.285 Poor Pending +DBN1.ENST00000393565.JUNC00000177.chr5:177460555-177460556.D 15 DBN1 ENST00000393565.6 JUNC00000177 NA SEVEQLLLPSGLTTQ 5 DRB1*04:05 274 None 15 0 989.330 43.000 109.087 0.070 7.636 129.000 0.290 Poor Pending +DBN1.ENST00000477391.JUNC00000177.chr5:177460555-177460556.D 15 DBN1 ENST00000477391.6 JUNC00000177 NA SEVEQLLLPSGLTTQ 3 DRB1*04:05 273 None 15 0 989.330 43.000 109.087 0.070 7.636 129.000 0.290 Poor Pending +DBN1.ENST00000512501.JUNC00000177.chr5:177460554-177460555.D 15 DBN1 ENST00000512501.1 JUNC00000177 E/K TGGWRPLPSPRGARL 3 DRB1*04:05 55 None 15 0 791.680 9.900 109.087 0.009 0.982 1076.000 0.285 Poor Pending +LDHB.ENST00000350669.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000350669.5 JUNC00000043 NA NNKITVVGVGQVVSG 1 DRB1*04:05 21 None 3 0 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396075.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000396075.5 JUNC00000043 NA NNKITVVGVGQVVSG 3 DRB1*04:05 21 None 3 0 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396076.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000396076.5 JUNC00000043 NA NNKITVVGVGQVVSG 5 DRB1*04:05 21 None 3 0 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000450584.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000450584.5 JUNC00000043 NA NNKITVVGVGQVVSG 3 DRB1*04:05 21 None 3 0 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000539782.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000539782.1 JUNC00000043 NA NNKITVVGVGQVVSG 3 DRB1*04:05 21 None 3 0 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000673047.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000673047.2 JUNC00000043 NA NNKITVVGVGQVVSG NA DRB1*04:05 21 None 3 0 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +EPS15L1.ENST00000455140.JUNC00000110.chr19:16361781-16361782.NDA 12 EPS15L1 ENST00000455140.7 JUNC00000110 T DFSQMSKFGNEEQQL 2 DRB1*04:05 743 None 12 0 1108.365 37.000 21.206 0.311 6.595 90.000 0.199 Poor Pending +DBN1.ENST00000292385.JUNC00000178.chr5:177460555-177460556.D 11 DBN1 ENST00000292385.9 JUNC00000178 NA ESEVEAAAIIAQRPD 1 DRB1*04:05 275 None 11 0 1881.890 46.000 109.087 0.070 7.636 129.000 0.290 Poor Pending +DBN1.ENST00000309007.JUNC00000178.chr5:177460555-177460556.D 11 DBN1 ENST00000309007.9 JUNC00000178 NA ESEVEAAAIIAQRPD 1 DRB1*04:05 273 None 11 0 1881.890 46.000 109.087 0.070 7.636 129.000 0.290 Poor Pending +DBN1.ENST00000393565.JUNC00000177.chr5:177460554-177460555.D 15 DBN1 ENST00000393565.6 JUNC00000177 E/K SEVEQLLLPSGLTTQ 5 DRB1*04:05 274 None 15 0 989.330 43.000 109.087 0.009 0.982 1076.000 0.285 Poor Pending +DBN1.ENST00000393565.JUNC00000178.chr5:177460555-177460556.D 11 DBN1 ENST00000393565.6 JUNC00000178 NA ESEVEAAAIIAQRPD 5 DRB1*04:05 273 None 11 0 1881.890 46.000 109.087 0.070 7.636 129.000 0.290 Poor Pending +DBN1.ENST00000477391.JUNC00000177.chr5:177460554-177460555.D 15 DBN1 ENST00000477391.6 JUNC00000177 E/K SEVEQLLLPSGLTTQ 3 DRB1*04:05 273 None 15 0 989.330 43.000 109.087 0.009 0.982 1076.000 0.285 Poor Pending +DBN1.ENST00000477391.JUNC00000178.chr5:177460555-177460556.D 11 DBN1 ENST00000477391.6 JUNC00000178 NA ESEVEAAAIIAQRPD 3 DRB1*04:05 272 None 11 0 1881.890 46.000 109.087 0.070 7.636 129.000 0.290 Poor Pending +DBN1.ENST00000512501.JUNC00000178.chr5:177460555-177460556.D 7 DBN1 ENST00000512501.1 JUNC00000178 NA ESEVEAAAIIAQRPD 3 DRB1*04:05 5 None 7 0 1881.890 46.000 109.087 0.070 7.636 129.000 0.290 Poor Pending +CCDC18.ENST00000343253.JUNC00000011.chr1:93226448-93226449.D 4 CCDC18 ENST00000343253.11 JUNC00000011 E EKELKIKNHSLQETS 5 DRB1*04:05 763 None 4 0 1786.600 36.000 18.750 0.300 5.625 20.000 0.628 Poor Pending +CCDC18.ENST00000370276.JUNC00000011.chr1:93226448-93226449.D 4 CCDC18 ENST00000370276.6 JUNC00000011 E EKELKIKNHSLQETS 5 DRB1*04:05 763 None 4 0 1786.600 36.000 18.750 0.300 5.625 20.000 0.628 Poor Pending +CCDC18.ENST00000401026.JUNC00000011.chr1:93226448-93226449.D 4 CCDC18 ENST00000401026.7 JUNC00000011 E EKELKIKNHSLQETS 1 DRB1*04:05 764 None 4 0 1786.600 36.000 18.750 0.300 5.625 20.000 0.628 Poor Pending +CCDC18.ENST00000690025.JUNC00000011.chr1:93226448-93226449.D 4 CCDC18 ENST00000690025.1 JUNC00000011 E EKELKIKNHSLQETS NA DRB1*04:05 764 None 4 0 1786.600 36.000 18.750 0.300 5.625 20.000 0.628 Poor Pending +DBN1.ENST00000292385.JUNC00000178.chr5:177460554-177460555.D 11 DBN1 ENST00000292385.9 JUNC00000178 E/K ESEVEAAAIIAQRPD 1 DRB1*04:05 275 None 11 0 1881.890 46.000 109.087 0.009 0.982 1076.000 0.285 Poor Pending +DBN1.ENST00000309007.JUNC00000178.chr5:177460554-177460555.D 11 DBN1 ENST00000309007.9 JUNC00000178 E/K ESEVEAAAIIAQRPD 1 DRB1*04:05 273 None 11 0 1881.890 46.000 109.087 0.009 0.982 1076.000 0.285 Poor Pending +DBN1.ENST00000393565.JUNC00000178.chr5:177460554-177460555.D 11 DBN1 ENST00000393565.6 JUNC00000178 E/K ESEVEAAAIIAQRPD 5 DRB1*04:05 273 None 11 0 1881.890 46.000 109.087 0.009 0.982 1076.000 0.285 Poor Pending +DBN1.ENST00000477391.JUNC00000178.chr5:177460554-177460555.D 11 DBN1 ENST00000477391.6 JUNC00000178 E/K ESEVEAAAIIAQRPD 3 DRB1*04:05 272 None 11 0 1881.890 46.000 109.087 0.009 0.982 1076.000 0.285 Poor Pending +DBN1.ENST00000512501.JUNC00000178.chr5:177460554-177460555.D 7 DBN1 ENST00000512501.1 JUNC00000178 E/K ESEVEAAAIIAQRPD 3 DRB1*04:05 5 None 7 0 1881.890 46.000 109.087 0.009 0.982 1076.000 0.285 Poor Pending +EPS15L1.ENST00000455140.JUNC00000108.chr19:16361781-16361782.A 1 EPS15L1 ENST00000455140.7 JUNC00000108 T KSTPFGNEEQQLAWA 2 DRB1*04:05 795 None 1 0 5252.645 75.000 21.206 0.311 6.595 90.000 0.199 Poor Pending +EPS15L1.ENST00000455140.JUNC00000109.chr19:16361781-16361782.NDA 1 EPS15L1 ENST00000455140.7 JUNC00000109 T PKKPAPPRPKPPSVW 2 DRB1*04:05 781 None 1 0 27220.365 100.000 21.206 0.311 6.595 90.000 0.199 Poor Pending +WASHC5.ENST00000318410.JUNC00000207.chr8:125067719-125067720.A 15 WASHC5 ENST00000318410.12 JUNC00000207 NA TLRIRTYFTMQSGLA 1 DRB1*04:05 399 None 15 15 42.905 2.100 65.088 0.000 0.000 25.000 0.062 NoExpr Pending +WASHC5.ENST00000517845.JUNC00000207.chr8:125067719-125067720.A 15 WASHC5 ENST00000517845.5 JUNC00000207 NA TLRIRTYFTMQSGLA 2 DRB1*04:05 251 None 15 15 42.905 2.100 65.088 0.000 0.000 25.000 0.062 NoExpr Pending +WASHC5.ENST00000318410.JUNC00000205.chr8:125067719-125067720.NDA 15 WASHC5 ENST00000318410.12 JUNC00000205 NA AIRWLMLHTADSDVQ 1 DRB1*04:05 372 None 15 5 47.320 1.800 65.088 0.000 0.000 25.000 0.062 NoExpr Pending +WASHC5.ENST00000517845.JUNC00000205.chr8:125067719-125067720.NDA 15 WASHC5 ENST00000517845.5 JUNC00000205 NA AIRWLMLHTADSDVQ 2 DRB1*04:05 224 None 15 5 47.320 1.800 65.088 0.000 0.000 25.000 0.062 NoExpr Pending +WASHC5.ENST00000318410.JUNC00000210.chr8:125067719-125067720.D 15 WASHC5 ENST00000318410.12 JUNC00000210 NA AIRWLMLHTADSDIF 1 DRB1*04:05 372 None 15 15 47.575 1.900 65.088 0.000 0.000 25.000 0.062 NoExpr Pending +WASHC5.ENST00000517845.JUNC00000210.chr8:125067719-125067720.D 15 WASHC5 ENST00000517845.5 JUNC00000210 NA AIRWLMLHTADSDIF 2 DRB1*04:05 224 None 15 15 47.575 1.900 65.088 0.000 0.000 25.000 0.062 NoExpr Pending +CUL9.ENST00000252050.JUNC00000183.chr6:43187095-43187096.NDA 15 CUL9 ENST00000252050.9 JUNC00000183 NA GCTLCRTSSPNLRRM 5 DRB1*04:05 429 None 15 0 928.575 37.000 16.683 0.000 0.000 6.000 0.252 NoExpr Pending +CUL9.ENST00000372647.JUNC00000183.chr6:43187095-43187096.NDA 15 CUL9 ENST00000372647.6 JUNC00000183 NA GCTLCRTSSPNLRRM 1 DRB1*04:05 429 None 15 0 928.575 37.000 16.683 0.000 0.000 6.000 0.252 NoExpr Pending +AGPS.ENST00000264167.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000264167.11 JUNC00000129 NA LGESFETSAPWDRSL 1 DRB1*04:05 524 None 2 0 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000637633.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000637633.2 JUNC00000129 NA LGESFETSAPWDRSL 5 DRB1*04:05 524 None 2 0 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000642466.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000642466.2 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 524 None 2 0 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000679459.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000679459.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 524 None 2 0 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000679478.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000679478.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 434 None 2 0 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000679994.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000679994.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 434 None 2 0 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000680155.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000680155.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 434 None 2 0 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000680770.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000680770.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 524 None 2 0 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000681449.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000681449.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 434 None 2 0 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending diff --git a/pvactools/tools/pvacsplice/example_data/results/combined/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv b/pvactools/tools/pvacsplice/example_data/results/combined/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv index 0ce6ca93..bf25db74 100644 --- a/pvactools/tools/pvacsplice/example_data/results/combined/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv +++ b/pvactools/tools/pvacsplice/example_data/results/combined/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv @@ -1,116 +1,116 @@ -ID DRB1*04:05 A*29:02 B*45:01 Gene Transcript Junction Name AA Change Best Peptide TSL Allele Pos Prob Pos Num Passing Peptides IC50 MT %ile MT RNA Expr RNA VAF Allele Expr RNA Depth DNA VAF Tier Evaluation -LDHB.ENST00000350669.JUNC00000053.chr12:21654541-21654542.D 14 6 LDHB ENST00000350669.5 JUNC00000053 NA HMMFNLSHY 1 HLA-A*29:02 48 None 20 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Pass Pending -DBN1.ENST00000292385.JUNC00000178.chr5:177460555-177460556.D 11 11 DBN1 ENST00000292385.9 JUNC00000178 NA SESEVEAAA 1 HLA-B*45:01 274 None 22 29.935 0.040 109.087 0.070 7.636 129.000 0.290 Pass Pending -DBN1.ENST00000309007.JUNC00000178.chr5:177460555-177460556.D 11 11 DBN1 ENST00000309007.9 JUNC00000178 NA SESEVEAAA 1 HLA-B*45:01 272 None 22 29.935 0.040 109.087 0.070 7.636 129.000 0.290 Pass Pending -LDHB.ENST00000350669.JUNC00000046.chr12:21654541-21654542.A 12 8 LDHB ENST00000350669.5 JUNC00000046 NA EEESLADELA 1 HLA-B*45:01 14 None 20 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Pass Pending -SEC24D.ENST00000280551.JUNC00000153.chr4:118740662-118740663.NDA 14 2 SEC24D ENST00000280551.11 JUNC00000153 Q TSTAFKAVLHQPLKV 1 DRB1*04:05 695 None 16 71.040 3.720 67.286 0.120 8.074 575.000 0.205 Pass Pending -SEC24D.ENST00000511481.JUNC00000153.chr4:118740662-118740663.NDA 14 2 SEC24D ENST00000511481.5 JUNC00000153 Q TSTAFKAVLHQPLKV 1 DRB1*04:05 326 None 16 71.040 3.720 67.286 0.120 8.074 575.000 0.205 Pass Pending -SEC24D.ENST00000280551.JUNC00000155.chr4:118740662-118740663.A 18 3 3 SEC24D ENST00000280551.11 JUNC00000155 Q VIESCAVLY 1 HLA-A*29:02 747 None 24 92.091 0.310 67.286 0.120 8.074 575.000 0.205 Pass Pending -SEC24D.ENST00000511481.JUNC00000155.chr4:118740662-118740663.A 18 3 3 SEC24D ENST00000511481.5 JUNC00000155 Q VIESCAVLY 1 HLA-A*29:02 378 None 24 92.091 0.310 67.286 0.120 8.074 575.000 0.205 Pass Pending -UBE2I.ENST00000397514.JUNC00000100.chr16:1320436-1320437.D 5 2 UBE2I ENST00000397514.8 JUNC00000100 NA DKDWRPAITIKQEYR 1 DRB1*04:05 100 None 7 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Pass Pending -UBE2I.ENST00000402301.JUNC00000100.chr16:1320436-1320437.D 5 2 UBE2I ENST00000402301.5 JUNC00000100 NA DKDWRPAITIKQEYR 1 DRB1*04:05 100 None 7 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Pass Pending -UBE2I.ENST00000567074.JUNC00000100.chr16:1320436-1320437.D 5 2 UBE2I ENST00000567074.6 JUNC00000100 NA DKDWRPAITIKQEYR 1 DRB1*04:05 100 None 7 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Pass Pending -TIPRL.ENST00000367830.JUNC00000028.chr1:168179177-168179178.D 12 TIPRL ENST00000367830.3 JUNC00000028 E/V SKTHIMKSADVVKQR 1 DRB1*04:05 23 None 12 442.135 20.000 55.746 0.332 18.508 927.000 0.273 Pass Pending -TIPRL.ENST00000367833.JUNC00000028.chr1:168179177-168179178.D 12 TIPRL ENST00000367833.7 JUNC00000028 E/V SKTHIMKSADVVKQR 1 DRB1*04:05 23 None 12 442.135 20.000 55.746 0.332 18.508 927.000 0.273 Pass Pending -DBN1.ENST00000292385.JUNC00000177.chr5:177460555-177460556.D 52 2 12 DBN1 ENST00000292385.9 JUNC00000177 NA KESHRPLRAA 1 HLA-B*45:01 298 None 66 311.785 0.570 109.087 0.070 7.636 129.000 0.290 Pass Pending -DBN1.ENST00000309007.JUNC00000177.chr5:177460555-177460556.D 52 2 12 DBN1 ENST00000309007.9 JUNC00000177 NA KESHRPLRAA 1 HLA-B*45:01 296 None 66 311.785 0.570 109.087 0.070 7.636 129.000 0.290 Pass Pending -TIPRL.ENST00000367830.JUNC00000027.chr1:168179177-168179178.D 2 TIPRL ENST00000367830.3 JUNC00000027 E/V ASKTHIMKSADVVNR 1 DRB1*04:05 22 None 2 485.250 21.000 55.746 0.332 18.508 927.000 0.273 Pass Pending -TIPRL.ENST00000367833.JUNC00000027.chr1:168179177-168179178.D 2 TIPRL ENST00000367833.7 JUNC00000027 E/V ASKTHIMKSADVVNR 1 DRB1*04:05 22 None 2 485.250 21.000 55.746 0.332 18.508 927.000 0.273 Pass Pending -DBN1.ENST00000292385.JUNC00000178.chr5:177460554-177460555.D 11 11 DBN1 ENST00000292385.9 JUNC00000178 E/K SESEVEAAA 1 HLA-B*45:01 274 None 22 29.935 0.040 109.087 0.009 0.982 1076.000 0.285 LowExpr Pending -DBN1.ENST00000309007.JUNC00000178.chr5:177460554-177460555.D 11 11 DBN1 ENST00000309007.9 JUNC00000178 E/K SESEVEAAA 1 HLA-B*45:01 272 None 22 29.935 0.040 109.087 0.009 0.982 1076.000 0.285 LowExpr Pending -DBN1.ENST00000292385.JUNC00000177.chr5:177460554-177460555.D 52 2 12 DBN1 ENST00000292385.9 JUNC00000177 E/K KESHRPLRAA 1 HLA-B*45:01 298 None 66 311.785 0.570 109.087 0.009 0.982 1076.000 0.285 LowExpr Pending -DBN1.ENST00000309007.JUNC00000177.chr5:177460554-177460555.D 52 2 12 DBN1 ENST00000309007.9 JUNC00000177 E/K KESHRPLRAA 1 HLA-B*45:01 296 None 66 311.785 0.570 109.087 0.009 0.982 1076.000 0.285 LowExpr Pending -LDHB.ENST00000396075.JUNC00000053.chr12:21654541-21654542.D 14 6 LDHB ENST00000396075.5 JUNC00000053 NA HMMFNLSHY 3 HLA-A*29:02 48 None 20 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396076.JUNC00000053.chr12:21654541-21654542.D 14 6 LDHB ENST00000396076.5 JUNC00000053 NA HMMFNLSHY 5 HLA-A*29:02 48 None 20 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000450584.JUNC00000053.chr12:21654541-21654542.D 14 6 LDHB ENST00000450584.5 JUNC00000053 NA HMMFNLSHY 3 HLA-A*29:02 48 None 20 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000539782.JUNC00000053.chr12:21654541-21654542.D 14 6 LDHB ENST00000539782.1 JUNC00000053 NA HMMFNLSHY 3 HLA-A*29:02 48 None 20 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000673047.JUNC00000053.chr12:21654541-21654542.D 14 6 LDHB ENST00000673047.2 JUNC00000053 NA HMMFNLSHY NA HLA-A*29:02 48 None 20 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Poor Pending -DBN1.ENST00000393565.JUNC00000178.chr5:177460555-177460556.D 11 11 DBN1 ENST00000393565.6 JUNC00000178 NA SESEVEAAA 5 HLA-B*45:01 272 None 22 29.935 0.040 109.087 0.070 7.636 129.000 0.290 Poor Pending -DBN1.ENST00000477391.JUNC00000178.chr5:177460555-177460556.D 11 11 DBN1 ENST00000477391.6 JUNC00000178 NA SESEVEAAA 3 HLA-B*45:01 271 None 22 29.935 0.040 109.087 0.070 7.636 129.000 0.290 Poor Pending -DBN1.ENST00000512501.JUNC00000178.chr5:177460555-177460556.D 7 11 DBN1 ENST00000512501.1 JUNC00000178 NA SESEVEAAA 3 HLA-B*45:01 4 None 18 29.935 0.040 109.087 0.070 7.636 129.000 0.290 Poor Pending -LDHB.ENST00000396075.JUNC00000046.chr12:21654541-21654542.A 12 8 LDHB ENST00000396075.5 JUNC00000046 NA EEESLADELA 3 HLA-B*45:01 14 None 20 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396076.JUNC00000046.chr12:21654541-21654542.A 12 8 LDHB ENST00000396076.5 JUNC00000046 NA EEESLADELA 5 HLA-B*45:01 14 None 20 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000450584.JUNC00000046.chr12:21654541-21654542.A 12 8 LDHB ENST00000450584.5 JUNC00000046 NA EEESLADELA 3 HLA-B*45:01 14 None 20 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000539782.JUNC00000046.chr12:21654541-21654542.A 12 8 LDHB ENST00000539782.1 JUNC00000046 NA EEESLADELA 3 HLA-B*45:01 14 None 20 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000673047.JUNC00000046.chr12:21654541-21654542.A 12 8 LDHB ENST00000673047.2 JUNC00000046 NA EEESLADELA NA HLA-B*45:01 14 None 20 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Poor Pending -DBN1.ENST00000393565.JUNC00000178.chr5:177460554-177460555.D 11 11 DBN1 ENST00000393565.6 JUNC00000178 E/K SESEVEAAA 5 HLA-B*45:01 272 None 22 29.935 0.040 109.087 0.009 0.982 1076.000 0.285 Poor Pending -DBN1.ENST00000477391.JUNC00000178.chr5:177460554-177460555.D 11 11 DBN1 ENST00000477391.6 JUNC00000178 E/K SESEVEAAA 3 HLA-B*45:01 271 None 22 29.935 0.040 109.087 0.009 0.982 1076.000 0.285 Poor Pending -DBN1.ENST00000512501.JUNC00000178.chr5:177460554-177460555.D 7 11 DBN1 ENST00000512501.1 JUNC00000178 E/K SESEVEAAA 3 HLA-B*45:01 4 None 18 29.935 0.040 109.087 0.009 0.982 1076.000 0.285 Poor Pending -SEC24D.ENST00000419654.JUNC00000153.chr4:118740662-118740663.NDA 14 2 SEC24D ENST00000419654.6 JUNC00000153 Q TSTAFKAVLHQPLKV 5 DRB1*04:05 251 None 16 71.040 3.720 67.286 0.120 8.074 575.000 0.205 Poor Pending -SEC24D.ENST00000419654.JUNC00000155.chr4:118740662-118740663.A 18 3 3 SEC24D ENST00000419654.6 JUNC00000155 Q VIESCAVLY 5 HLA-A*29:02 303 None 24 92.091 0.310 67.286 0.120 8.074 575.000 0.205 Poor Pending -PRDM4.ENST00000228437.JUNC00000069.chr12:107746273-107746274.A 19 3 5 PRDM4 ENST00000228437.10 JUNC00000069 NA KQLVLRQSIVGAEVD 2 DRB1*04:05 412 None 27 298.575 15.000 13.577 1.000 13.577 71.000 0.980 Poor Pending -UBE2I.ENST00000325437.JUNC00000100.chr16:1320436-1320437.D 5 2 UBE2I ENST00000325437.9 JUNC00000100 NA DKDWRPAITIKQEYR 3 DRB1*04:05 100 None 7 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000355803.JUNC00000100.chr16:1320436-1320437.D 5 2 UBE2I ENST00000355803.8 JUNC00000100 NA DKDWRPAITIKQEYR 2 DRB1*04:05 100 None 7 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000397515.JUNC00000100.chr16:1320436-1320437.D 5 2 UBE2I ENST00000397515.6 JUNC00000100 NA DKDWRPAITIKQEYR 3 DRB1*04:05 100 None 7 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000403747.JUNC00000100.chr16:1320436-1320437.D 5 2 UBE2I ENST00000403747.6 JUNC00000100 NA DKDWRPAITIKQEYR 5 DRB1*04:05 100 None 7 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000406620.JUNC00000100.chr16:1320436-1320437.D 5 2 UBE2I ENST00000406620.6 JUNC00000100 NA DKDWRPAITIKQEYR 2 DRB1*04:05 100 None 7 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000562470.JUNC00000100.chr16:1320436-1320437.D 5 2 UBE2I ENST00000562470.3 JUNC00000100 NA DKDWRPAITIKQEYR 2 DRB1*04:05 100 None 7 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000566587.JUNC00000100.chr16:1320436-1320437.D 5 2 UBE2I ENST00000566587.5 JUNC00000100 NA DKDWRPAITIKQEYR 2 DRB1*04:05 100 None 7 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000567383.JUNC00000100.chr16:1320436-1320437.D 5 2 UBE2I ENST00000567383.6 JUNC00000100 NA DKDWRPAITIKQEYR 4 DRB1*04:05 100 None 7 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending -DBN1.ENST00000393565.JUNC00000177.chr5:177460555-177460556.D 38 2 11 DBN1 ENST00000393565.6 JUNC00000177 NA KESHRPLRAA 5 HLA-B*45:01 296 None 51 311.785 0.570 109.087 0.070 7.636 129.000 0.290 Poor Pending -DBN1.ENST00000477391.JUNC00000177.chr5:177460555-177460556.D 31 2 11 DBN1 ENST00000477391.6 JUNC00000177 NA KESHRPLRAA 3 HLA-B*45:01 295 None 44 311.785 0.570 109.087 0.070 7.636 129.000 0.290 Poor Pending -DBN1.ENST00000512501.JUNC00000177.chr5:177460555-177460556.D 47 2 12 DBN1 ENST00000512501.1 JUNC00000177 NA KESHRPLRAA 3 HLA-B*45:01 28 None 61 311.785 0.570 109.087 0.070 7.636 129.000 0.290 Poor Pending -TIPRL.ENST00000367830.JUNC00000025.chr1:168179177-168179178.D 7 TIPRL ENST00000367830.3 JUNC00000025 E/V SKTHIMKSADVVKVK 1 DRB1*04:05 23 None 7 512.505 23.000 55.746 0.332 18.508 927.000 0.273 Poor Pending -TIPRL.ENST00000367833.JUNC00000025.chr1:168179177-168179178.D 7 TIPRL ENST00000367833.7 JUNC00000025 E/V SKTHIMKSADVVKVK 1 DRB1*04:05 23 None 7 512.505 23.000 55.746 0.332 18.508 927.000 0.273 Poor Pending -LDHB.ENST00000350669.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000350669.5 JUNC00000045 NA VSLADELALVDVLED 1 DRB1*04:05 26 None 12 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396075.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000396075.5 JUNC00000045 NA VSLADELALVDVLED 3 DRB1*04:05 26 None 12 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396076.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000396076.5 JUNC00000045 NA VSLADELALVDVLED 5 DRB1*04:05 26 None 12 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000450584.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000450584.5 JUNC00000045 NA VSLADELALVDVLED 3 DRB1*04:05 26 None 12 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000539782.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000539782.1 JUNC00000045 NA VSLADELALVDVLED 3 DRB1*04:05 26 None 12 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000673047.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000673047.2 JUNC00000045 NA VSLADELALVDVLED NA DRB1*04:05 26 None 12 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -PODXL.ENST00000322985.JUNC00000200.chr7:131504507-131504508.D 40 1 15 PODXL ENST00000322985.9 JUNC00000200 Q/* SEMQEKKVV 1 HLA-B*45:01 487 None 56 256.275 0.410 0.630 0.455 0.287 11.000 0.124 Poor Pending -PODXL.ENST00000378555.JUNC00000200.chr7:131504507-131504508.D 40 1 15 PODXL ENST00000378555.8 JUNC00000200 Q/* SEMQEKKVV 1 HLA-B*45:01 519 None 56 256.275 0.410 0.630 0.455 0.287 11.000 0.124 Poor Pending -UBE2I.ENST00000325437.JUNC00000102.chr16:1320436-1320437.NDA 6 1 UBE2I ENST00000325437.9 JUNC00000102 NA KDWRPAITIKQPKQS 3 DRB1*04:05 101 None 7 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000355803.JUNC00000102.chr16:1320436-1320437.NDA 6 1 UBE2I ENST00000355803.8 JUNC00000102 NA KDWRPAITIKQPKQS 2 DRB1*04:05 101 None 7 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000397514.JUNC00000102.chr16:1320436-1320437.NDA 6 1 UBE2I ENST00000397514.8 JUNC00000102 NA KDWRPAITIKQPKQS 1 DRB1*04:05 101 None 7 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000397515.JUNC00000102.chr16:1320436-1320437.NDA 6 1 UBE2I ENST00000397515.6 JUNC00000102 NA KDWRPAITIKQPKQS 3 DRB1*04:05 101 None 7 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000403747.JUNC00000102.chr16:1320436-1320437.NDA 6 1 UBE2I ENST00000403747.6 JUNC00000102 NA KDWRPAITIKQPKQS 5 DRB1*04:05 101 None 7 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000406620.JUNC00000102.chr16:1320436-1320437.NDA 6 1 UBE2I ENST00000406620.6 JUNC00000102 NA KDWRPAITIKQPKQS 2 DRB1*04:05 101 None 7 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000562470.JUNC00000102.chr16:1320436-1320437.NDA 6 1 UBE2I ENST00000562470.3 JUNC00000102 NA KDWRPAITIKQPKQS 2 DRB1*04:05 101 None 7 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000566587.JUNC00000102.chr16:1320436-1320437.NDA 6 1 UBE2I ENST00000566587.5 JUNC00000102 NA KDWRPAITIKQPKQS 2 DRB1*04:05 101 None 7 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000567074.JUNC00000102.chr16:1320436-1320437.NDA 6 1 UBE2I ENST00000567074.6 JUNC00000102 NA KDWRPAITIKQPKQS 1 DRB1*04:05 101 None 7 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending -UBE2I.ENST00000567383.JUNC00000102.chr16:1320436-1320437.NDA 6 1 UBE2I ENST00000567383.6 JUNC00000102 NA KDWRPAITIKQPKQS 4 DRB1*04:05 101 None 7 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending -DBN1.ENST00000393565.JUNC00000177.chr5:177460554-177460555.D 38 2 11 DBN1 ENST00000393565.6 JUNC00000177 E/K KESHRPLRAA 5 HLA-B*45:01 296 None 51 311.785 0.570 109.087 0.009 0.982 1076.000 0.285 Poor Pending -DBN1.ENST00000477391.JUNC00000177.chr5:177460554-177460555.D 31 2 11 DBN1 ENST00000477391.6 JUNC00000177 E/K KESHRPLRAA 3 HLA-B*45:01 295 None 44 311.785 0.570 109.087 0.009 0.982 1076.000 0.285 Poor Pending -DBN1.ENST00000512501.JUNC00000177.chr5:177460554-177460555.D 47 2 12 DBN1 ENST00000512501.1 JUNC00000177 E/K KESHRPLRAA 3 HLA-B*45:01 28 None 61 311.785 0.570 109.087 0.009 0.982 1076.000 0.285 Poor Pending -LDHB.ENST00000350669.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000350669.5 JUNC00000044 NA QSLADELALVDVLED 1 DRB1*04:05 31 None 14 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396075.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000396075.5 JUNC00000044 NA QSLADELALVDVLED 3 DRB1*04:05 31 None 14 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396076.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000396076.5 JUNC00000044 NA QSLADELALVDVLED 5 DRB1*04:05 31 None 14 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000450584.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000450584.5 JUNC00000044 NA QSLADELALVDVLED 3 DRB1*04:05 31 None 14 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000539782.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000539782.1 JUNC00000044 NA QSLADELALVDVLED 3 DRB1*04:05 31 None 14 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000673047.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000673047.2 JUNC00000044 NA QSLADELALVDVLED NA DRB1*04:05 31 None 14 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending -CCDC18.ENST00000343253.JUNC00000006.chr1:93226448-93226449.NDA 12 1 3 CCDC18 ENST00000343253.11 JUNC00000006 E EETIKVYCL 5 HLA-B*45:01 720 None 16 520.055 1.400 18.750 0.300 5.625 20.000 0.628 Poor Pending -CCDC18.ENST00000370276.JUNC00000006.chr1:93226448-93226449.NDA 12 1 3 CCDC18 ENST00000370276.6 JUNC00000006 E EETIKVYCL 5 HLA-B*45:01 720 None 16 520.055 1.400 18.750 0.300 5.625 20.000 0.628 Poor Pending -CCDC18.ENST00000401026.JUNC00000006.chr1:93226448-93226449.NDA 12 1 3 CCDC18 ENST00000401026.7 JUNC00000006 E EETIKVYCL 1 HLA-B*45:01 721 None 16 520.055 1.400 18.750 0.300 5.625 20.000 0.628 Poor Pending -CCDC18.ENST00000690025.JUNC00000006.chr1:93226448-93226449.NDA 12 1 3 CCDC18 ENST00000690025.1 JUNC00000006 E EETIKVYCL NA HLA-B*45:01 721 None 16 520.055 1.400 18.750 0.300 5.625 20.000 0.628 Poor Pending -PRDM4.ENST00000228437.JUNC00000071.chr12:107746273-107746274.NDA 15 PRDM4 ENST00000228437.10 JUNC00000071 NA LFTICVWTGETIPVR 2 DRB1*04:05 372 None 15 715.145 32.000 13.577 1.000 13.577 71.000 0.980 Poor Pending -LDHB.ENST00000350669.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000350669.5 JUNC00000043 NA NNKITVVGVGQVVSG 1 DRB1*04:05 21 None 3 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396075.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000396075.5 JUNC00000043 NA NNKITVVGVGQVVSG 3 DRB1*04:05 21 None 3 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000396076.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000396076.5 JUNC00000043 NA NNKITVVGVGQVVSG 5 DRB1*04:05 21 None 3 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000450584.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000450584.5 JUNC00000043 NA NNKITVVGVGQVVSG 3 DRB1*04:05 21 None 3 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000539782.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000539782.1 JUNC00000043 NA NNKITVVGVGQVVSG 3 DRB1*04:05 21 None 3 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -LDHB.ENST00000673047.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000673047.2 JUNC00000043 NA NNKITVVGVGQVVSG NA DRB1*04:05 21 None 3 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending -EPS15L1.ENST00000455140.JUNC00000110.chr19:16361781-16361782.NDA 12 1 EPS15L1 ENST00000455140.7 JUNC00000110 T DFSQMSKFGNEEQQL 2 DRB1*04:05 743 None 13 1108.365 37.000 21.206 0.311 6.595 90.000 0.199 Poor Pending -CCDC18.ENST00000343253.JUNC00000011.chr1:93226448-93226449.D 4 1 CCDC18 ENST00000343253.11 JUNC00000011 E EKELKIKNHSLQETS 5 DRB1*04:05 763 None 5 1786.600 36.000 18.750 0.300 5.625 20.000 0.628 Poor Pending -CCDC18.ENST00000370276.JUNC00000011.chr1:93226448-93226449.D 4 1 CCDC18 ENST00000370276.6 JUNC00000011 E EKELKIKNHSLQETS 5 DRB1*04:05 763 None 5 1786.600 36.000 18.750 0.300 5.625 20.000 0.628 Poor Pending -CCDC18.ENST00000401026.JUNC00000011.chr1:93226448-93226449.D 4 1 CCDC18 ENST00000401026.7 JUNC00000011 E EKELKIKNHSLQETS 1 DRB1*04:05 764 None 5 1786.600 36.000 18.750 0.300 5.625 20.000 0.628 Poor Pending -CCDC18.ENST00000690025.JUNC00000011.chr1:93226448-93226449.D 4 1 CCDC18 ENST00000690025.1 JUNC00000011 E EKELKIKNHSLQETS NA DRB1*04:05 764 None 5 1786.600 36.000 18.750 0.300 5.625 20.000 0.628 Poor Pending -EPS15L1.ENST00000455140.JUNC00000108.chr19:16361781-16361782.A EPS15L1 ENST00000455140.7 JUNC00000108 T KSTPFGNEEQQLAWA 2 DRB1*04:05 795 None 0 5252.645 75.000 21.206 0.311 6.595 90.000 0.199 Poor Pending -EPS15L1.ENST00000455140.JUNC00000109.chr19:16361781-16361782.NDA EPS15L1 ENST00000455140.7 JUNC00000109 T PKKPAPPRPKPPSVW 2 DRB1*04:05 781 None 0 27220.365 100.000 21.206 0.311 6.595 90.000 0.199 Poor Pending -WASHC5.ENST00000318410.JUNC00000207.chr8:125067719-125067720.A 32 6 2 WASHC5 ENST00000318410.12 JUNC00000207 NA TLRIRTYFTMQSGLA 1 DRB1*04:05 399 None 40 42.905 2.100 65.088 0.000 0.000 25.000 0.062 NoExpr Pending -WASHC5.ENST00000517845.JUNC00000207.chr8:125067719-125067720.A 32 6 2 WASHC5 ENST00000517845.5 JUNC00000207 NA TLRIRTYFTMQSGLA 2 DRB1*04:05 251 None 40 42.905 2.100 65.088 0.000 0.000 25.000 0.062 NoExpr Pending -WASHC5.ENST00000318410.JUNC00000205.chr8:125067719-125067720.NDA 19 2 WASHC5 ENST00000318410.12 JUNC00000205 NA AIRWLMLHTADSDVQ 1 DRB1*04:05 372 None 21 47.320 1.800 65.088 0.000 0.000 25.000 0.062 NoExpr Pending -WASHC5.ENST00000517845.JUNC00000205.chr8:125067719-125067720.NDA 19 2 WASHC5 ENST00000517845.5 JUNC00000205 NA AIRWLMLHTADSDVQ 2 DRB1*04:05 224 None 21 47.320 1.800 65.088 0.000 0.000 25.000 0.062 NoExpr Pending -WASHC5.ENST00000318410.JUNC00000210.chr8:125067719-125067720.D 28 10 1 WASHC5 ENST00000318410.12 JUNC00000210 NA AIRWLMLHTADSDIF 1 DRB1*04:05 372 None 39 47.575 1.900 65.088 0.000 0.000 25.000 0.062 NoExpr Pending -WASHC5.ENST00000517845.JUNC00000210.chr8:125067719-125067720.D 28 10 1 WASHC5 ENST00000517845.5 JUNC00000210 NA AIRWLMLHTADSDIF 2 DRB1*04:05 224 None 39 47.575 1.900 65.088 0.000 0.000 25.000 0.062 NoExpr Pending -CUL9.ENST00000252050.JUNC00000183.chr6:43187095-43187096.NDA 16 1 CUL9 ENST00000252050.9 JUNC00000183 NA GCTLCRTSSPNLRRM 5 DRB1*04:05 429 None 17 928.575 37.000 16.683 0.000 0.000 6.000 0.252 NoExpr Pending -CUL9.ENST00000372647.JUNC00000183.chr6:43187095-43187096.NDA 16 1 CUL9 ENST00000372647.6 JUNC00000183 NA GCTLCRTSSPNLRRM 1 DRB1*04:05 429 None 17 928.575 37.000 16.683 0.000 0.000 6.000 0.252 NoExpr Pending -AGPS.ENST00000264167.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000264167.11 JUNC00000129 NA LGESFETSAPWDRSL 1 DRB1*04:05 524 None 2 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000637633.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000637633.2 JUNC00000129 NA LGESFETSAPWDRSL 5 DRB1*04:05 524 None 2 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000642466.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000642466.2 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 524 None 2 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000679459.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000679459.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 524 None 2 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000679478.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000679478.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 434 None 2 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000679994.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000679994.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 434 None 2 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000680155.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000680155.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 434 None 2 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000680770.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000680770.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 524 None 2 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending -AGPS.ENST00000681449.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000681449.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 434 None 2 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +ID DRB1*04:05 A*29:02 B*45:01 Gene Transcript Junction Name AA Change Best Peptide TSL Allele Pos Prob Pos Num Included Peptides Num Passing Peptides IC50 MT %ile MT RNA Expr RNA VAF Allele Expr RNA Depth DNA VAF Tier Evaluation +LDHB.ENST00000350669.JUNC00000053.chr12:21654541-21654542.D 11 4 LDHB ENST00000350669.5 JUNC00000053 NA HMMFNLSHY 1 HLA-A*29:02 48 None 15 6 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Pass Pending +DBN1.ENST00000292385.JUNC00000178.chr5:177460555-177460556.D 6 9 DBN1 ENST00000292385.9 JUNC00000178 NA SESEVEAAA 1 HLA-B*45:01 274 None 15 5 29.935 0.040 109.087 0.070 7.636 129.000 0.290 Pass Pending +DBN1.ENST00000309007.JUNC00000178.chr5:177460555-177460556.D 6 9 DBN1 ENST00000309007.9 JUNC00000178 NA SESEVEAAA 1 HLA-B*45:01 272 None 15 5 29.935 0.040 109.087 0.070 7.636 129.000 0.290 Pass Pending +LDHB.ENST00000350669.JUNC00000046.chr12:21654541-21654542.A 8 7 LDHB ENST00000350669.5 JUNC00000046 NA EEESLADELA 1 HLA-B*45:01 14 None 15 2 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Pass Pending +SEC24D.ENST00000280551.JUNC00000153.chr4:118740662-118740663.NDA 14 1 SEC24D ENST00000280551.11 JUNC00000153 Q TSTAFKAVLHQPLKV 1 DRB1*04:05 695 None 15 12 71.040 3.720 67.286 0.120 8.074 575.000 0.205 Pass Pending +SEC24D.ENST00000511481.JUNC00000153.chr4:118740662-118740663.NDA 14 1 SEC24D ENST00000511481.5 JUNC00000153 Q TSTAFKAVLHQPLKV 1 DRB1*04:05 326 None 15 12 71.040 3.720 67.286 0.120 8.074 575.000 0.205 Pass Pending +SEC24D.ENST00000280551.JUNC00000155.chr4:118740662-118740663.A 11 2 2 SEC24D ENST00000280551.11 JUNC00000155 Q VIESCAVLY 1 HLA-A*29:02 747 None 15 5 92.091 0.310 67.286 0.120 8.074 575.000 0.205 Pass Pending +SEC24D.ENST00000511481.JUNC00000155.chr4:118740662-118740663.A 11 2 2 SEC24D ENST00000511481.5 JUNC00000155 Q VIESCAVLY 1 HLA-A*29:02 378 None 15 5 92.091 0.310 67.286 0.120 8.074 575.000 0.205 Pass Pending +UBE2I.ENST00000397514.JUNC00000100.chr16:1320436-1320437.D 5 2 UBE2I ENST00000397514.8 JUNC00000100 NA DKDWRPAITIKQEYR 1 DRB1*04:05 100 None 7 4 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Pass Pending +UBE2I.ENST00000402301.JUNC00000100.chr16:1320436-1320437.D 5 2 UBE2I ENST00000402301.5 JUNC00000100 NA DKDWRPAITIKQEYR 1 DRB1*04:05 100 None 7 4 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Pass Pending +UBE2I.ENST00000567074.JUNC00000100.chr16:1320436-1320437.D 5 2 UBE2I ENST00000567074.6 JUNC00000100 NA DKDWRPAITIKQEYR 1 DRB1*04:05 100 None 7 4 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Pass Pending +TIPRL.ENST00000367830.JUNC00000028.chr1:168179177-168179178.D 12 TIPRL ENST00000367830.3 JUNC00000028 E/V SKTHIMKSADVVKQR 1 DRB1*04:05 23 None 12 1 442.135 20.000 55.746 0.332 18.508 927.000 0.273 Pass Pending +TIPRL.ENST00000367833.JUNC00000028.chr1:168179177-168179178.D 12 TIPRL ENST00000367833.7 JUNC00000028 E/V SKTHIMKSADVVKQR 1 DRB1*04:05 23 None 12 1 442.135 20.000 55.746 0.332 18.508 927.000 0.273 Pass Pending +DBN1.ENST00000292385.JUNC00000177.chr5:177460555-177460556.D 10 5 DBN1 ENST00000292385.9 JUNC00000177 NA KESHRPLRAA 1 HLA-B*45:01 298 None 15 1 311.785 0.570 109.087 0.070 7.636 129.000 0.290 Pass Pending +DBN1.ENST00000309007.JUNC00000177.chr5:177460555-177460556.D 10 5 DBN1 ENST00000309007.9 JUNC00000177 NA KESHRPLRAA 1 HLA-B*45:01 296 None 15 1 311.785 0.570 109.087 0.070 7.636 129.000 0.290 Pass Pending +TIPRL.ENST00000367830.JUNC00000027.chr1:168179177-168179178.D 2 TIPRL ENST00000367830.3 JUNC00000027 E/V ASKTHIMKSADVVNR 1 DRB1*04:05 22 None 2 1 485.250 21.000 55.746 0.332 18.508 927.000 0.273 Pass Pending +TIPRL.ENST00000367833.JUNC00000027.chr1:168179177-168179178.D 2 TIPRL ENST00000367833.7 JUNC00000027 E/V ASKTHIMKSADVVNR 1 DRB1*04:05 22 None 2 1 485.250 21.000 55.746 0.332 18.508 927.000 0.273 Pass Pending +DBN1.ENST00000292385.JUNC00000178.chr5:177460554-177460555.D 6 9 DBN1 ENST00000292385.9 JUNC00000178 E/K SESEVEAAA 1 HLA-B*45:01 274 None 15 5 29.935 0.040 109.087 0.009 0.982 1076.000 0.285 LowExpr Pending +DBN1.ENST00000309007.JUNC00000178.chr5:177460554-177460555.D 6 9 DBN1 ENST00000309007.9 JUNC00000178 E/K SESEVEAAA 1 HLA-B*45:01 272 None 15 5 29.935 0.040 109.087 0.009 0.982 1076.000 0.285 LowExpr Pending +DBN1.ENST00000292385.JUNC00000177.chr5:177460554-177460555.D 10 5 DBN1 ENST00000292385.9 JUNC00000177 E/K KESHRPLRAA 1 HLA-B*45:01 298 None 15 1 311.785 0.570 109.087 0.009 0.982 1076.000 0.285 LowExpr Pending +DBN1.ENST00000309007.JUNC00000177.chr5:177460554-177460555.D 10 5 DBN1 ENST00000309007.9 JUNC00000177 E/K KESHRPLRAA 1 HLA-B*45:01 296 None 15 1 311.785 0.570 109.087 0.009 0.982 1076.000 0.285 LowExpr Pending +LDHB.ENST00000396075.JUNC00000053.chr12:21654541-21654542.D 11 4 LDHB ENST00000396075.5 JUNC00000053 NA HMMFNLSHY 3 HLA-A*29:02 48 None 15 6 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396076.JUNC00000053.chr12:21654541-21654542.D 11 4 LDHB ENST00000396076.5 JUNC00000053 NA HMMFNLSHY 5 HLA-A*29:02 48 None 15 6 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000450584.JUNC00000053.chr12:21654541-21654542.D 11 4 LDHB ENST00000450584.5 JUNC00000053 NA HMMFNLSHY 3 HLA-A*29:02 48 None 15 6 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000539782.JUNC00000053.chr12:21654541-21654542.D 11 4 LDHB ENST00000539782.1 JUNC00000053 NA HMMFNLSHY 3 HLA-A*29:02 48 None 15 6 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000673047.JUNC00000053.chr12:21654541-21654542.D 11 4 LDHB ENST00000673047.2 JUNC00000053 NA HMMFNLSHY NA HLA-A*29:02 48 None 15 6 31.540 0.190 203.702 0.881 179.461 118.000 0.780 Poor Pending +DBN1.ENST00000393565.JUNC00000178.chr5:177460555-177460556.D 6 9 DBN1 ENST00000393565.6 JUNC00000178 NA SESEVEAAA 5 HLA-B*45:01 272 None 15 5 29.935 0.040 109.087 0.070 7.636 129.000 0.290 Poor Pending +DBN1.ENST00000477391.JUNC00000178.chr5:177460555-177460556.D 6 9 DBN1 ENST00000477391.6 JUNC00000178 NA SESEVEAAA 3 HLA-B*45:01 271 None 15 5 29.935 0.040 109.087 0.070 7.636 129.000 0.290 Poor Pending +DBN1.ENST00000512501.JUNC00000178.chr5:177460555-177460556.D 6 9 DBN1 ENST00000512501.1 JUNC00000178 NA SESEVEAAA 3 HLA-B*45:01 4 None 15 5 29.935 0.040 109.087 0.070 7.636 129.000 0.290 Poor Pending +LDHB.ENST00000396075.JUNC00000046.chr12:21654541-21654542.A 8 7 LDHB ENST00000396075.5 JUNC00000046 NA EEESLADELA 3 HLA-B*45:01 14 None 15 2 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396076.JUNC00000046.chr12:21654541-21654542.A 8 7 LDHB ENST00000396076.5 JUNC00000046 NA EEESLADELA 5 HLA-B*45:01 14 None 15 2 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000450584.JUNC00000046.chr12:21654541-21654542.A 8 7 LDHB ENST00000450584.5 JUNC00000046 NA EEESLADELA 3 HLA-B*45:01 14 None 15 2 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000539782.JUNC00000046.chr12:21654541-21654542.A 8 7 LDHB ENST00000539782.1 JUNC00000046 NA EEESLADELA 3 HLA-B*45:01 14 None 15 2 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000673047.JUNC00000046.chr12:21654541-21654542.A 8 7 LDHB ENST00000673047.2 JUNC00000046 NA EEESLADELA NA HLA-B*45:01 14 None 15 2 136.611 0.320 203.702 0.881 179.461 118.000 0.780 Poor Pending +DBN1.ENST00000393565.JUNC00000178.chr5:177460554-177460555.D 6 9 DBN1 ENST00000393565.6 JUNC00000178 E/K SESEVEAAA 5 HLA-B*45:01 272 None 15 5 29.935 0.040 109.087 0.009 0.982 1076.000 0.285 Poor Pending +DBN1.ENST00000477391.JUNC00000178.chr5:177460554-177460555.D 6 9 DBN1 ENST00000477391.6 JUNC00000178 E/K SESEVEAAA 3 HLA-B*45:01 271 None 15 5 29.935 0.040 109.087 0.009 0.982 1076.000 0.285 Poor Pending +DBN1.ENST00000512501.JUNC00000178.chr5:177460554-177460555.D 6 9 DBN1 ENST00000512501.1 JUNC00000178 E/K SESEVEAAA 3 HLA-B*45:01 4 None 15 5 29.935 0.040 109.087 0.009 0.982 1076.000 0.285 Poor Pending +SEC24D.ENST00000419654.JUNC00000153.chr4:118740662-118740663.NDA 14 1 SEC24D ENST00000419654.6 JUNC00000153 Q TSTAFKAVLHQPLKV 5 DRB1*04:05 251 None 15 12 71.040 3.720 67.286 0.120 8.074 575.000 0.205 Poor Pending +SEC24D.ENST00000419654.JUNC00000155.chr4:118740662-118740663.A 11 2 2 SEC24D ENST00000419654.6 JUNC00000155 Q VIESCAVLY 5 HLA-A*29:02 303 None 15 5 92.091 0.310 67.286 0.120 8.074 575.000 0.205 Poor Pending +PRDM4.ENST00000228437.JUNC00000069.chr12:107746273-107746274.A 12 3 PRDM4 ENST00000228437.10 JUNC00000069 NA KQLVLRQSIVGAEVD 2 DRB1*04:05 412 None 15 4 298.575 15.000 13.577 1.000 13.577 71.000 0.980 Poor Pending +UBE2I.ENST00000325437.JUNC00000100.chr16:1320436-1320437.D 5 2 UBE2I ENST00000325437.9 JUNC00000100 NA DKDWRPAITIKQEYR 3 DRB1*04:05 100 None 7 4 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000355803.JUNC00000100.chr16:1320436-1320437.D 5 2 UBE2I ENST00000355803.8 JUNC00000100 NA DKDWRPAITIKQEYR 2 DRB1*04:05 100 None 7 4 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000397515.JUNC00000100.chr16:1320436-1320437.D 5 2 UBE2I ENST00000397515.6 JUNC00000100 NA DKDWRPAITIKQEYR 3 DRB1*04:05 100 None 7 4 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000403747.JUNC00000100.chr16:1320436-1320437.D 5 2 UBE2I ENST00000403747.6 JUNC00000100 NA DKDWRPAITIKQEYR 5 DRB1*04:05 100 None 7 4 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000406620.JUNC00000100.chr16:1320436-1320437.D 5 2 UBE2I ENST00000406620.6 JUNC00000100 NA DKDWRPAITIKQEYR 2 DRB1*04:05 100 None 7 4 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000562470.JUNC00000100.chr16:1320436-1320437.D 5 2 UBE2I ENST00000562470.3 JUNC00000100 NA DKDWRPAITIKQEYR 2 DRB1*04:05 100 None 7 4 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000566587.JUNC00000100.chr16:1320436-1320437.D 5 2 UBE2I ENST00000566587.5 JUNC00000100 NA DKDWRPAITIKQEYR 2 DRB1*04:05 100 None 7 4 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000567383.JUNC00000100.chr16:1320436-1320437.D 5 2 UBE2I ENST00000567383.6 JUNC00000100 NA DKDWRPAITIKQEYR 4 DRB1*04:05 100 None 7 4 332.835 8.200 58.799 0.385 22.638 26.000 0.602 Poor Pending +DBN1.ENST00000393565.JUNC00000177.chr5:177460555-177460556.D 8 7 DBN1 ENST00000393565.6 JUNC00000177 NA KESHRPLRAA 5 HLA-B*45:01 296 None 15 1 311.785 0.570 109.087 0.070 7.636 129.000 0.290 Poor Pending +DBN1.ENST00000477391.JUNC00000177.chr5:177460555-177460556.D 8 7 DBN1 ENST00000477391.6 JUNC00000177 NA KESHRPLRAA 3 HLA-B*45:01 295 None 15 1 311.785 0.570 109.087 0.070 7.636 129.000 0.290 Poor Pending +DBN1.ENST00000512501.JUNC00000177.chr5:177460555-177460556.D 10 5 DBN1 ENST00000512501.1 JUNC00000177 NA KESHRPLRAA 3 HLA-B*45:01 28 None 15 1 311.785 0.570 109.087 0.070 7.636 129.000 0.290 Poor Pending +TIPRL.ENST00000367830.JUNC00000025.chr1:168179177-168179178.D 7 TIPRL ENST00000367830.3 JUNC00000025 E/V SKTHIMKSADVVKVK 1 DRB1*04:05 23 None 7 0 512.505 23.000 55.746 0.332 18.508 927.000 0.273 Poor Pending +TIPRL.ENST00000367833.JUNC00000025.chr1:168179177-168179178.D 7 TIPRL ENST00000367833.7 JUNC00000025 E/V SKTHIMKSADVVKVK 1 DRB1*04:05 23 None 7 0 512.505 23.000 55.746 0.332 18.508 927.000 0.273 Poor Pending +LDHB.ENST00000350669.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000350669.5 JUNC00000045 NA VSLADELALVDVLED 1 DRB1*04:05 26 None 12 0 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396075.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000396075.5 JUNC00000045 NA VSLADELALVDVLED 3 DRB1*04:05 26 None 12 0 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396076.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000396076.5 JUNC00000045 NA VSLADELALVDVLED 5 DRB1*04:05 26 None 12 0 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000450584.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000450584.5 JUNC00000045 NA VSLADELALVDVLED 3 DRB1*04:05 26 None 12 0 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000539782.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000539782.1 JUNC00000045 NA VSLADELALVDVLED 3 DRB1*04:05 26 None 12 0 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000673047.JUNC00000045.chr12:21654541-21654542.A 12 LDHB ENST00000673047.2 JUNC00000045 NA VSLADELALVDVLED NA DRB1*04:05 26 None 12 0 670.720 23.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +PODXL.ENST00000322985.JUNC00000200.chr7:131504507-131504508.D 12 3 PODXL ENST00000322985.9 JUNC00000200 Q/* SEMQEKKVV 1 HLA-B*45:01 487 None 15 11 256.275 0.410 0.630 0.455 0.287 11.000 0.124 Poor Pending +PODXL.ENST00000378555.JUNC00000200.chr7:131504507-131504508.D 12 3 PODXL ENST00000378555.8 JUNC00000200 Q/* SEMQEKKVV 1 HLA-B*45:01 519 None 15 11 256.275 0.410 0.630 0.455 0.287 11.000 0.124 Poor Pending +UBE2I.ENST00000325437.JUNC00000102.chr16:1320436-1320437.NDA 6 1 UBE2I ENST00000325437.9 JUNC00000102 NA KDWRPAITIKQPKQS 3 DRB1*04:05 101 None 7 0 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000355803.JUNC00000102.chr16:1320436-1320437.NDA 6 1 UBE2I ENST00000355803.8 JUNC00000102 NA KDWRPAITIKQPKQS 2 DRB1*04:05 101 None 7 0 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000397514.JUNC00000102.chr16:1320436-1320437.NDA 6 1 UBE2I ENST00000397514.8 JUNC00000102 NA KDWRPAITIKQPKQS 1 DRB1*04:05 101 None 7 0 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000397515.JUNC00000102.chr16:1320436-1320437.NDA 6 1 UBE2I ENST00000397515.6 JUNC00000102 NA KDWRPAITIKQPKQS 3 DRB1*04:05 101 None 7 0 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000403747.JUNC00000102.chr16:1320436-1320437.NDA 6 1 UBE2I ENST00000403747.6 JUNC00000102 NA KDWRPAITIKQPKQS 5 DRB1*04:05 101 None 7 0 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000406620.JUNC00000102.chr16:1320436-1320437.NDA 6 1 UBE2I ENST00000406620.6 JUNC00000102 NA KDWRPAITIKQPKQS 2 DRB1*04:05 101 None 7 0 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000562470.JUNC00000102.chr16:1320436-1320437.NDA 6 1 UBE2I ENST00000562470.3 JUNC00000102 NA KDWRPAITIKQPKQS 2 DRB1*04:05 101 None 7 0 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000566587.JUNC00000102.chr16:1320436-1320437.NDA 6 1 UBE2I ENST00000566587.5 JUNC00000102 NA KDWRPAITIKQPKQS 2 DRB1*04:05 101 None 7 0 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000567074.JUNC00000102.chr16:1320436-1320437.NDA 6 1 UBE2I ENST00000567074.6 JUNC00000102 NA KDWRPAITIKQPKQS 1 DRB1*04:05 101 None 7 0 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending +UBE2I.ENST00000567383.JUNC00000102.chr16:1320436-1320437.NDA 6 1 UBE2I ENST00000567383.6 JUNC00000102 NA KDWRPAITIKQPKQS 4 DRB1*04:05 101 None 7 0 544.490 13.000 58.799 0.385 22.638 26.000 0.602 Poor Pending +DBN1.ENST00000393565.JUNC00000177.chr5:177460554-177460555.D 8 7 DBN1 ENST00000393565.6 JUNC00000177 E/K KESHRPLRAA 5 HLA-B*45:01 296 None 15 1 311.785 0.570 109.087 0.009 0.982 1076.000 0.285 Poor Pending +DBN1.ENST00000477391.JUNC00000177.chr5:177460554-177460555.D 8 7 DBN1 ENST00000477391.6 JUNC00000177 E/K KESHRPLRAA 3 HLA-B*45:01 295 None 15 1 311.785 0.570 109.087 0.009 0.982 1076.000 0.285 Poor Pending +DBN1.ENST00000512501.JUNC00000177.chr5:177460554-177460555.D 10 5 DBN1 ENST00000512501.1 JUNC00000177 E/K KESHRPLRAA 3 HLA-B*45:01 28 None 15 1 311.785 0.570 109.087 0.009 0.982 1076.000 0.285 Poor Pending +LDHB.ENST00000350669.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000350669.5 JUNC00000044 NA QSLADELALVDVLED 1 DRB1*04:05 31 None 14 0 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396075.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000396075.5 JUNC00000044 NA QSLADELALVDVLED 3 DRB1*04:05 31 None 14 0 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396076.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000396076.5 JUNC00000044 NA QSLADELALVDVLED 5 DRB1*04:05 31 None 14 0 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000450584.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000450584.5 JUNC00000044 NA QSLADELALVDVLED 3 DRB1*04:05 31 None 14 0 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000539782.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000539782.1 JUNC00000044 NA QSLADELALVDVLED 3 DRB1*04:05 31 None 14 0 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000673047.JUNC00000044.chr12:21654541-21654542.A 14 LDHB ENST00000673047.2 JUNC00000044 NA QSLADELALVDVLED NA DRB1*04:05 31 None 14 0 678.730 23.020 203.702 0.881 179.461 118.000 0.780 Poor Pending +CCDC18.ENST00000343253.JUNC00000006.chr1:93226448-93226449.NDA 11 1 3 CCDC18 ENST00000343253.11 JUNC00000006 E EETIKVYCL 5 HLA-B*45:01 720 None 15 0 520.055 1.400 18.750 0.300 5.625 20.000 0.628 Poor Pending +CCDC18.ENST00000370276.JUNC00000006.chr1:93226448-93226449.NDA 11 1 3 CCDC18 ENST00000370276.6 JUNC00000006 E EETIKVYCL 5 HLA-B*45:01 720 None 15 0 520.055 1.400 18.750 0.300 5.625 20.000 0.628 Poor Pending +CCDC18.ENST00000401026.JUNC00000006.chr1:93226448-93226449.NDA 11 1 3 CCDC18 ENST00000401026.7 JUNC00000006 E EETIKVYCL 1 HLA-B*45:01 721 None 15 0 520.055 1.400 18.750 0.300 5.625 20.000 0.628 Poor Pending +CCDC18.ENST00000690025.JUNC00000006.chr1:93226448-93226449.NDA 11 1 3 CCDC18 ENST00000690025.1 JUNC00000006 E EETIKVYCL NA HLA-B*45:01 721 None 15 0 520.055 1.400 18.750 0.300 5.625 20.000 0.628 Poor Pending +PRDM4.ENST00000228437.JUNC00000071.chr12:107746273-107746274.NDA 15 PRDM4 ENST00000228437.10 JUNC00000071 NA LFTICVWTGETIPVR 2 DRB1*04:05 372 None 15 0 715.145 32.000 13.577 1.000 13.577 71.000 0.980 Poor Pending +LDHB.ENST00000350669.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000350669.5 JUNC00000043 NA NNKITVVGVGQVVSG 1 DRB1*04:05 21 None 3 0 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396075.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000396075.5 JUNC00000043 NA NNKITVVGVGQVVSG 3 DRB1*04:05 21 None 3 0 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000396076.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000396076.5 JUNC00000043 NA NNKITVVGVGQVVSG 5 DRB1*04:05 21 None 3 0 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000450584.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000450584.5 JUNC00000043 NA NNKITVVGVGQVVSG 3 DRB1*04:05 21 None 3 0 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000539782.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000539782.1 JUNC00000043 NA NNKITVVGVGQVVSG 3 DRB1*04:05 21 None 3 0 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +LDHB.ENST00000673047.JUNC00000043.chr12:21654541-21654542.A 3 LDHB ENST00000673047.2 JUNC00000043 NA NNKITVVGVGQVVSG NA DRB1*04:05 21 None 3 0 2464.130 45.000 203.702 0.881 179.461 118.000 0.780 Poor Pending +EPS15L1.ENST00000455140.JUNC00000110.chr19:16361781-16361782.NDA 12 1 EPS15L1 ENST00000455140.7 JUNC00000110 T DFSQMSKFGNEEQQL 2 DRB1*04:05 743 None 13 0 1108.365 37.000 21.206 0.311 6.595 90.000 0.199 Poor Pending +CCDC18.ENST00000343253.JUNC00000011.chr1:93226448-93226449.D 4 1 CCDC18 ENST00000343253.11 JUNC00000011 E EKELKIKNHSLQETS 5 DRB1*04:05 763 None 5 0 1786.600 36.000 18.750 0.300 5.625 20.000 0.628 Poor Pending +CCDC18.ENST00000370276.JUNC00000011.chr1:93226448-93226449.D 4 1 CCDC18 ENST00000370276.6 JUNC00000011 E EKELKIKNHSLQETS 5 DRB1*04:05 763 None 5 0 1786.600 36.000 18.750 0.300 5.625 20.000 0.628 Poor Pending +CCDC18.ENST00000401026.JUNC00000011.chr1:93226448-93226449.D 4 1 CCDC18 ENST00000401026.7 JUNC00000011 E EKELKIKNHSLQETS 1 DRB1*04:05 764 None 5 0 1786.600 36.000 18.750 0.300 5.625 20.000 0.628 Poor Pending +CCDC18.ENST00000690025.JUNC00000011.chr1:93226448-93226449.D 4 1 CCDC18 ENST00000690025.1 JUNC00000011 E EKELKIKNHSLQETS NA DRB1*04:05 764 None 5 0 1786.600 36.000 18.750 0.300 5.625 20.000 0.628 Poor Pending +EPS15L1.ENST00000455140.JUNC00000108.chr19:16361781-16361782.A 1 EPS15L1 ENST00000455140.7 JUNC00000108 T KSTPFGNEEQQLAWA 2 DRB1*04:05 795 None 1 0 5252.645 75.000 21.206 0.311 6.595 90.000 0.199 Poor Pending +EPS15L1.ENST00000455140.JUNC00000109.chr19:16361781-16361782.NDA 1 EPS15L1 ENST00000455140.7 JUNC00000109 T PKKPAPPRPKPPSVW 2 DRB1*04:05 781 None 1 0 27220.365 100.000 21.206 0.311 6.595 90.000 0.199 Poor Pending +WASHC5.ENST00000318410.JUNC00000207.chr8:125067719-125067720.A 15 WASHC5 ENST00000318410.12 JUNC00000207 NA TLRIRTYFTMQSGLA 1 DRB1*04:05 399 None 15 15 42.905 2.100 65.088 0.000 0.000 25.000 0.062 NoExpr Pending +WASHC5.ENST00000517845.JUNC00000207.chr8:125067719-125067720.A 15 WASHC5 ENST00000517845.5 JUNC00000207 NA TLRIRTYFTMQSGLA 2 DRB1*04:05 251 None 15 15 42.905 2.100 65.088 0.000 0.000 25.000 0.062 NoExpr Pending +WASHC5.ENST00000318410.JUNC00000205.chr8:125067719-125067720.NDA 14 1 WASHC5 ENST00000318410.12 JUNC00000205 NA AIRWLMLHTADSDVQ 1 DRB1*04:05 372 None 15 5 47.320 1.800 65.088 0.000 0.000 25.000 0.062 NoExpr Pending +WASHC5.ENST00000517845.JUNC00000205.chr8:125067719-125067720.NDA 14 1 WASHC5 ENST00000517845.5 JUNC00000205 NA AIRWLMLHTADSDVQ 2 DRB1*04:05 224 None 15 5 47.320 1.800 65.088 0.000 0.000 25.000 0.062 NoExpr Pending +WASHC5.ENST00000318410.JUNC00000210.chr8:125067719-125067720.D 13 2 WASHC5 ENST00000318410.12 JUNC00000210 NA AIRWLMLHTADSDIF 1 DRB1*04:05 372 None 15 15 47.575 1.900 65.088 0.000 0.000 25.000 0.062 NoExpr Pending +WASHC5.ENST00000517845.JUNC00000210.chr8:125067719-125067720.D 13 2 WASHC5 ENST00000517845.5 JUNC00000210 NA AIRWLMLHTADSDIF 2 DRB1*04:05 224 None 15 15 47.575 1.900 65.088 0.000 0.000 25.000 0.062 NoExpr Pending +CUL9.ENST00000252050.JUNC00000183.chr6:43187095-43187096.NDA 15 CUL9 ENST00000252050.9 JUNC00000183 NA GCTLCRTSSPNLRRM 5 DRB1*04:05 429 None 15 0 928.575 37.000 16.683 0.000 0.000 6.000 0.252 NoExpr Pending +CUL9.ENST00000372647.JUNC00000183.chr6:43187095-43187096.NDA 15 CUL9 ENST00000372647.6 JUNC00000183 NA GCTLCRTSSPNLRRM 1 DRB1*04:05 429 None 15 0 928.575 37.000 16.683 0.000 0.000 6.000 0.252 NoExpr Pending +AGPS.ENST00000264167.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000264167.11 JUNC00000129 NA LGESFETSAPWDRSL 1 DRB1*04:05 524 None 2 0 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000637633.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000637633.2 JUNC00000129 NA LGESFETSAPWDRSL 5 DRB1*04:05 524 None 2 0 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000642466.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000642466.2 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 524 None 2 0 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000679459.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000679459.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 524 None 2 0 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000679478.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000679478.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 434 None 2 0 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000679994.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000679994.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 434 None 2 0 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000680155.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000680155.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 434 None 2 0 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000680770.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000680770.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 524 None 2 0 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending +AGPS.ENST00000681449.JUNC00000129.chr2:177513816-177513817.D 2 AGPS ENST00000681449.1 JUNC00000129 NA LGESFETSAPWDRSL NA DRB1*04:05 434 None 2 0 2217.885 46.000 38.437 0.000 0.000 9.000 0.237 NoExpr Pending