diff --git a/public/appendiceal_msk_2022/LICENSE b/public/appendiceal_msk_2022/LICENSE new file mode 100644 index 0000000000..d5f3c4b535 --- /dev/null +++ b/public/appendiceal_msk_2022/LICENSE @@ -0,0 +1 @@ +The data are available under the ODC Open Database License (ODbL)(http://opendatacommons.org/licenses/odbl/1.0/) (summary available here: http://www.opendatacommons.org/licenses/odbl/1-0/summary/): you are free to share and modify the data so long as you attribute any public use of the database, or works produced from the database; keep the resulting data-sets open; and offer your shared or adapted version of the data-set under the same ODbL license. diff --git a/public/appendiceal_msk_2022/Readme.txt b/public/appendiceal_msk_2022/Readme.txt new file mode 100644 index 0000000000..6202caf574 --- /dev/null +++ b/public/appendiceal_msk_2022/Readme.txt @@ -0,0 +1 @@ +Gene panels for this study can be found here: https://github.com/cBioPortal/datahub/tree/master/reference_data/gene_panels \ No newline at end of file diff --git a/public/appendiceal_msk_2022/case_lists/cases_all.txt b/public/appendiceal_msk_2022/case_lists/cases_all.txt new file mode 100644 index 0000000000..92a2dca84b --- /dev/null +++ b/public/appendiceal_msk_2022/case_lists/cases_all.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: appendiceal_msk_2022 +stable_id: appendiceal_msk_2022_all +case_list_name: All samples +case_list_description: All samples (273 samples) +case_list_category: all_cases_in_study +case_list_ids: P-0039302-T02-IM6 P-0045104-T01-IM6 P-0050969-T01-IM6 P-0032634-T01-IM6 P-0022517-T01-IM6 P-0032140-T01-IM6 P-0010408-T01-IM5 P-0007673-T01-IM5 P-0029091-T01-IM6 P-0010702-T01-IM5 P-0034626-T01-IM6 P-0011271-T01-IM5 P-0044815-T01-IM6 P-0001411-T01-IM3 P-0011350-T01-IM5 P-0008730-T01-IM5 P-0030739-T01-IM6 P-0015019-T01-IM6 P-0005296-T01-IM5 P-0017993-T01-IM6 P-0016610-T01-IM6 P-0040462-T01-IM6 P-0003638-T01-IM5 P-0026149-T01-IM6 P-0012739-T01-IM5 P-0003135-T04-IM5 P-0012187-T01-IM5 P-0009900-T01-IM5 P-0027188-T01-IM6 P-0039305-T01-IM6 P-0030703-T01-IM6 P-0047460-T01-IM6 P-0012269-T01-IM5 P-0004192-T01-IM5 P-0006765-T01-IM5 P-0019762-T01-IM6 P-0049625-T01-IM6 P-0008142-T02-IM5 P-0033011-T01-IM6 P-0014673-T01-IM6 P-0026747-T04-IM6 P-0002322-T01-IM3 P-0008692-T01-IM5 P-0033680-T01-IM6 P-0021404-T01-IM6 P-0044082-T01-IM6 P-0009519-T01-IM5 P-0051228-T01-IM6 P-0058081-T01-IM6 P-0032135-T01-IM6 P-0034466-T01-IM6 P-0028106-T01-IM6 P-0028785-T01-IM6 P-0046365-T01-IM6 P-0003705-T01-IM5 P-0023429-T01-IM6 P-0007923-T01-IM5 P-0033344-T01-IM6 P-0017912-T01-IM6 P-0020483-T01-IM6 P-0013832-T01-IM5 P-0052100-T01-IM6 P-0037278-T01-IM6 P-0010198-T01-IM5 P-0032176-T01-IM6 P-0005056-T01-IM5 P-0049746-T01-IM6 P-0001322-T01-IM3 P-0055805-T01-IM6 P-0023090-T01-IM6 P-0022792-T01-IM6 P-0020414-T01-IM6 P-0027295-T01-IM6 P-0038339-T01-IM6 P-0000927-T01-IM3 P-0028254-T01-IM6 P-0042371-T01-IM6 P-0038242-T01-IM6 P-0046597-T01-IM6 P-0004648-T01-IM5 P-0051021-T01-IM6 P-0048651-T01-IM6 P-0016369-T01-IM6 P-0036299-T01-IM6 P-0055267-T01-IM6 P-0050785-T01-IM6 P-0001857-T01-IM3 P-0029752-T01-IM6 P-0046994-T01-IM6 P-0053192-T01-IM6 P-0003074-T01-IM5 P-0012812-T01-IM5 P-0054872-T01-IM6 P-0046245-T01-IM6 P-0017741-T01-IM6 P-0037220-T01-IM6 P-0041603-T01-IM6 P-0018189-T01-IM6 P-0031497-T01-IM6 P-0011212-T01-IM5 P-0050062-T01-IM6 P-0044538-T01-IM6 P-0058199-T01-IM6 P-0007116-T01-IM5 P-0007030-T01-IM5 P-0052086-T01-IM6 P-0012868-T01-IM5 P-0037573-T01-IM6 P-0009173-T01-IM5 P-0031056-T01-IM6 P-0004188-T01-IM5 P-0004724-T01-IM5 P-0057460-T01-IM6 P-0001146-T01-IM3 P-0031776-T01-IM6 P-0025438-T01-IM6 P-0034770-T01-IM6 P-0035749-T01-IM6 P-0058404-T01-IM6 P-0009321-T01-IM5 P-0028267-T01-IM6 P-0044181-T01-IM6 P-0046487-T01-IM6 P-0009079-T01-IM5 P-0056938-T01-IM6 P-0044643-T01-IM6 P-0001581-T02-IM5 P-0002461-T02-IM5 P-0008038-T01-IM5 P-0016118-T01-IM6 P-0004624-T01-IM5 P-0025920-T01-IM6 P-0010042-T01-IM5 P-0010747-T01-IM5 P-0058864-T01-IM7 P-0014674-T01-IM6 P-0014337-T01-IM6 P-0003542-T01-IM5 P-0025688-T01-IM6 P-0044360-T01-IM6 P-0003334-T02-IM5 P-0023935-T01-IM6 P-0006841-T01-IM5 P-0019512-T01-IM6 P-0047789-T01-IM6 P-0042350-T01-IM6 P-0024739-T01-IM6 P-0014174-T01-IM5 P-0016486-T01-IM6 P-0019063-T01-IM6 P-0043941-T01-IM6 P-0039780-T01-IM6 P-0006478-T01-IM5 P-0008238-T02-IM6 P-0032498-T01-IM6 P-0056730-T01-IM6 P-0052966-T01-IM6 P-0007105-T01-IM5 P-0003143-T01-IM5 P-0003768-T01-IM5 P-0047213-T01-IM6 P-0040305-T01-IM6 P-0036335-T01-IM6 P-0019061-T01-IM6 P-0039265-T01-IM6 P-0048999-T01-IM6 P-0051904-T01-IM6 P-0046567-T01-IM6 P-0022171-T01-IM6 P-0058948-T01-IM7 P-0016693-T01-IM6 P-0010631-T01-IM5 P-0009693-T01-IM5 P-0032042-T01-IM6 P-0045716-T01-IM6 P-0004809-T01-IM5 P-0027806-T01-IM6 P-0034667-T01-IM6 P-0021557-T01-IM6 P-0004390-T01-IM5 P-0028346-T01-IM6 P-0004672-T01-IM5 P-0001161-T01-IM3 P-0021929-T01-IM6 P-0026210-T01-IM6 P-0039330-T01-IM6 P-0001098-T01-IM3 P-0012054-T01-IM5 P-0003251-T01-IM5 P-0012435-T01-IM5 P-0014041-T01-IM5 P-0046153-T01-IM6 P-0029369-T01-IM6 P-0010032-T02-IM5 P-0013952-T01-IM5 P-0045691-T01-IM6 P-0056785-T01-IM6 P-0055165-T01-IM6 P-0053788-T01-IM6 P-0007512-T01-IM5 P-0003371-T01-IM5 P-0017351-T01-IM6 P-0039008-T01-IM6 P-0050237-T01-IM6 P-0006302-T01-IM5 P-0057472-T01-IM6 P-0029641-T01-IM6 P-0011073-T01-IM5 P-0040296-T01-IM6 P-0042746-T01-IM6 P-0055292-T01-IM6 P-0031339-T02-IM6 P-0016389-T01-IM6 P-0008815-T01-IM5 P-0028756-T01-IM6 P-0014016-T01-IM5 P-0043490-T01-IM6 P-0003657-T01-IM5 P-0055980-T01-IM6 P-0013538-T01-IM5 P-0054224-T01-IM6 P-0041537-T01-IM6 P-0007094-T01-IM5 P-0011482-T01-IM5 P-0049859-T01-IM6 P-0029511-T01-IM6 P-0052029-T01-IM6 P-0051025-T01-IM6 P-0009794-T01-IM5 P-0019051-T01-IM6 P-0031799-T02-IM6 P-0031913-T01-IM6 P-0009899-T01-IM5 P-0032805-T01-IM6 P-0001402-T01-IM3 P-0052254-T01-IM6 P-0043236-T01-IM6 P-0005796-T01-IM5 P-0005363-T01-IM5 P-0029552-T01-IM6 P-0017685-T01-IM6 P-0010031-T01-IM5 P-0018729-T01-IM6 P-0012601-T01-IM5 P-0014233-T01-IM6 P-0029851-T01-IM6 P-0041585-T01-IM6 P-0027839-T01-IM6 P-0011083-T01-IM5 P-0009138-T01-IM5 P-0008568-T01-IM5 P-0048506-T01-IM6 P-0047945-T01-IM6 P-0005208-T01-IM5 P-0004356-T01-IM5 P-0024951-T01-IM6 P-0050742-T01-IM6 P-0055979-T01-IM6 P-0040179-T01-IM6 P-0047384-T01-IM6 P-0007217-T01-IM5 P-0006438-T01-IM5 P-0057160-T01-IM6 P-0014203-T01-IM6 P-0006817-T01-IM5 P-0011444-T01-IM5 P-0029410-T01-IM6 P-0016482-T01-IM6 P-0012896-T01-IM5 P-0009698-T01-IM5 P-0031417-T01-IM6 P-0038512-T01-IM6 P-0025220-T01-IM6 diff --git a/public/appendiceal_msk_2022/case_lists/cases_cna.txt b/public/appendiceal_msk_2022/case_lists/cases_cna.txt new file mode 100644 index 0000000000..877d3ed348 --- /dev/null +++ b/public/appendiceal_msk_2022/case_lists/cases_cna.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: appendiceal_msk_2022 +stable_id: appendiceal_msk_2022_cna +case_list_name: Samples with CNA data +case_list_description: Samples with CNA data (273 samples) +case_list_category: all_cases_with_cna_data +case_list_ids: P-0039302-T02-IM6 P-0045104-T01-IM6 P-0050969-T01-IM6 P-0032634-T01-IM6 P-0022517-T01-IM6 P-0032140-T01-IM6 P-0010408-T01-IM5 P-0007673-T01-IM5 P-0029091-T01-IM6 P-0010702-T01-IM5 P-0034626-T01-IM6 P-0011271-T01-IM5 P-0044815-T01-IM6 P-0001411-T01-IM3 P-0011350-T01-IM5 P-0008730-T01-IM5 P-0030739-T01-IM6 P-0005296-T01-IM5 P-0017993-T01-IM6 P-0016610-T01-IM6 P-0034667-T01-IM6 P-0003638-T01-IM5 P-0012739-T01-IM5 P-0003135-T04-IM5 P-0012187-T01-IM5 P-0009900-T01-IM5 P-0027188-T01-IM6 P-0008038-T01-IM5 P-0030703-T01-IM6 P-0047460-T01-IM6 P-0012269-T01-IM5 P-0004192-T01-IM5 P-0006765-T01-IM5 P-0019762-T01-IM6 P-0049625-T01-IM6 P-0008142-T02-IM5 P-0033011-T01-IM6 P-0014673-T01-IM6 P-0026747-T04-IM6 P-0002322-T01-IM3 P-0008692-T01-IM5 P-0033680-T01-IM6 P-0021404-T01-IM6 P-0044082-T01-IM6 P-0009519-T01-IM5 P-0051228-T01-IM6 P-0032135-T01-IM6 P-0058081-T01-IM6 P-0034466-T01-IM6 P-0028106-T01-IM6 P-0028785-T01-IM6 P-0037220-T01-IM6 P-0003705-T01-IM5 P-0044181-T01-IM6 P-0023429-T01-IM6 P-0007923-T01-IM5 P-0033344-T01-IM6 P-0017912-T01-IM6 P-0020483-T01-IM6 P-0013832-T01-IM5 P-0052100-T01-IM6 P-0037278-T01-IM6 P-0010198-T01-IM5 P-0032176-T01-IM6 P-0005056-T01-IM5 P-0049746-T01-IM6 P-0001322-T01-IM3 P-0055805-T01-IM6 P-0023090-T01-IM6 P-0022792-T01-IM6 P-0020414-T01-IM6 P-0027295-T01-IM6 P-0038339-T01-IM6 P-0044360-T01-IM6 P-0003334-T02-IM5 P-0042371-T01-IM6 P-0012054-T01-IM5 P-0046597-T01-IM6 P-0004648-T01-IM5 P-0051021-T01-IM6 P-0048651-T01-IM6 P-0016369-T01-IM6 P-0036299-T01-IM6 P-0050062-T01-IM6 P-0025920-T01-IM6 P-0050785-T01-IM6 P-0001857-T01-IM3 P-0029752-T01-IM6 P-0053192-T01-IM6 P-0003074-T01-IM5 P-0012812-T01-IM5 P-0005363-T01-IM5 P-0054872-T01-IM6 P-0046245-T01-IM6 P-0052086-T01-IM6 P-0017741-T01-IM6 P-0046365-T01-IM6 P-0041603-T01-IM6 P-0018189-T01-IM6 P-0044538-T01-IM6 P-0011212-T01-IM5 P-0055267-T01-IM6 P-0031497-T01-IM6 P-0058199-T01-IM6 P-0007116-T01-IM5 P-0007030-T01-IM5 P-0029552-T01-IM6 P-0001402-T01-IM3 P-0012868-T01-IM5 P-0037573-T01-IM6 P-0009173-T01-IM5 P-0031056-T01-IM6 P-0004188-T01-IM5 P-0004724-T01-IM5 P-0057460-T01-IM6 P-0001146-T01-IM3 P-0031776-T01-IM6 P-0025438-T01-IM6 P-0034770-T01-IM6 P-0035749-T01-IM6 P-0058404-T01-IM6 P-0009321-T01-IM5 P-0028267-T01-IM6 P-0031417-T01-IM6 P-0046487-T01-IM6 P-0009079-T01-IM5 P-0056938-T01-IM6 P-0044643-T01-IM6 P-0001581-T02-IM5 P-0002461-T02-IM5 P-0039305-T01-IM6 P-0016118-T01-IM6 P-0004624-T01-IM5 P-0014674-T01-IM6 P-0010042-T01-IM5 P-0010747-T01-IM5 P-0007512-T01-IM5 P-0014337-T01-IM6 P-0003542-T01-IM5 P-0025688-T01-IM6 P-0000927-T01-IM3 P-0028254-T01-IM6 P-0023935-T01-IM6 P-0006841-T01-IM5 P-0019512-T01-IM6 P-0047789-T01-IM6 P-0042350-T01-IM6 P-0024739-T01-IM6 P-0052966-T01-IM6 P-0016486-T01-IM6 P-0019063-T01-IM6 P-0043941-T01-IM6 P-0027839-T01-IM6 P-0006478-T01-IM5 P-0039008-T01-IM6 P-0032498-T01-IM6 P-0056730-T01-IM6 P-0014174-T01-IM5 P-0007105-T01-IM5 P-0003143-T01-IM5 P-0003768-T01-IM5 P-0047213-T01-IM6 P-0040305-T01-IM6 P-0036335-T01-IM6 P-0019061-T01-IM6 P-0039265-T01-IM6 P-0048999-T01-IM6 P-0051904-T01-IM6 P-0046567-T01-IM6 P-0022171-T01-IM6 P-0003657-T01-IM5 P-0058948-T01-IM7 P-0016693-T01-IM6 P-0010631-T01-IM5 P-0009693-T01-IM5 P-0032042-T01-IM6 P-0045716-T01-IM6 P-0004809-T01-IM5 P-0027806-T01-IM6 P-0040462-T01-IM6 P-0021557-T01-IM6 P-0004390-T01-IM5 P-0028346-T01-IM6 P-0004672-T01-IM5 P-0001161-T01-IM3 P-0021929-T01-IM6 P-0026210-T01-IM6 P-0039330-T01-IM6 P-0001098-T01-IM3 P-0038242-T01-IM6 P-0003251-T01-IM5 P-0012435-T01-IM5 P-0014041-T01-IM5 P-0046153-T01-IM6 P-0029369-T01-IM6 P-0010032-T02-IM5 P-0013952-T01-IM5 P-0045691-T01-IM6 P-0056785-T01-IM6 P-0055165-T01-IM6 P-0053788-T01-IM6 P-0058864-T01-IM7 P-0003371-T01-IM5 P-0017351-T01-IM6 P-0008238-T02-IM6 P-0050237-T01-IM6 P-0006302-T01-IM5 P-0057472-T01-IM6 P-0029641-T01-IM6 P-0011073-T01-IM5 P-0042746-T01-IM6 P-0055292-T01-IM6 P-0031339-T02-IM6 P-0016389-T01-IM6 P-0008815-T01-IM5 P-0028756-T01-IM6 P-0014016-T01-IM5 P-0043490-T01-IM6 P-0015019-T01-IM6 P-0055980-T01-IM6 P-0013538-T01-IM5 P-0054224-T01-IM6 P-0041537-T01-IM6 P-0007094-T01-IM5 P-0011482-T01-IM5 P-0049859-T01-IM6 P-0029511-T01-IM6 P-0052029-T01-IM6 P-0051025-T01-IM6 P-0009794-T01-IM5 P-0009899-T01-IM5 P-0019051-T01-IM6 P-0031799-T02-IM6 P-0031913-T01-IM6 P-0026149-T01-IM6 P-0006438-T01-IM5 P-0046994-T01-IM6 P-0052254-T01-IM6 P-0043236-T01-IM6 P-0005796-T01-IM5 P-0040296-T01-IM6 P-0017685-T01-IM6 P-0010031-T01-IM5 P-0018729-T01-IM6 P-0012601-T01-IM5 P-0014233-T01-IM6 P-0029851-T01-IM6 P-0041585-T01-IM6 P-0039780-T01-IM6 P-0011083-T01-IM5 P-0009138-T01-IM5 P-0008568-T01-IM5 P-0048506-T01-IM6 P-0047945-T01-IM6 P-0005208-T01-IM5 P-0004356-T01-IM5 P-0024951-T01-IM6 P-0050742-T01-IM6 P-0055979-T01-IM6 P-0040179-T01-IM6 P-0047384-T01-IM6 P-0032805-T01-IM6 P-0057160-T01-IM6 P-0014203-T01-IM6 P-0006817-T01-IM5 P-0011444-T01-IM5 P-0029410-T01-IM6 P-0016482-T01-IM6 P-0012896-T01-IM5 P-0009698-T01-IM5 P-0007217-T01-IM5 P-0038512-T01-IM6 P-0025220-T01-IM6 diff --git a/public/appendiceal_msk_2022/case_lists/cases_cnaseq.txt b/public/appendiceal_msk_2022/case_lists/cases_cnaseq.txt new file mode 100644 index 0000000000..33d1359674 --- /dev/null +++ b/public/appendiceal_msk_2022/case_lists/cases_cnaseq.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: appendiceal_msk_2022 +stable_id: appendiceal_msk_2022_cnaseq +case_list_name: Samples with mutation and CNA data +case_list_description: Samples with mutation and CNA data (273 samples) +case_list_category: all_cases_with_mutation_and_cna_data +case_list_ids: P-0039302-T02-IM6 P-0045104-T01-IM6 P-0050969-T01-IM6 P-0032634-T01-IM6 P-0022517-T01-IM6 P-0032140-T01-IM6 P-0010408-T01-IM5 P-0007673-T01-IM5 P-0029091-T01-IM6 P-0010702-T01-IM5 P-0034626-T01-IM6 P-0011271-T01-IM5 P-0044815-T01-IM6 P-0001411-T01-IM3 P-0011350-T01-IM5 P-0008730-T01-IM5 P-0030739-T01-IM6 P-0005296-T01-IM5 P-0017993-T01-IM6 P-0016610-T01-IM6 P-0034667-T01-IM6 P-0003638-T01-IM5 P-0012739-T01-IM5 P-0003135-T04-IM5 P-0012187-T01-IM5 P-0009900-T01-IM5 P-0027188-T01-IM6 P-0008038-T01-IM5 P-0030703-T01-IM6 P-0047460-T01-IM6 P-0012269-T01-IM5 P-0004192-T01-IM5 P-0006765-T01-IM5 P-0019762-T01-IM6 P-0049625-T01-IM6 P-0008142-T02-IM5 P-0033011-T01-IM6 P-0014673-T01-IM6 P-0026747-T04-IM6 P-0002322-T01-IM3 P-0008692-T01-IM5 P-0033680-T01-IM6 P-0021404-T01-IM6 P-0044082-T01-IM6 P-0009519-T01-IM5 P-0051228-T01-IM6 P-0032135-T01-IM6 P-0058081-T01-IM6 P-0034466-T01-IM6 P-0028106-T01-IM6 P-0028785-T01-IM6 P-0037220-T01-IM6 P-0003705-T01-IM5 P-0044181-T01-IM6 P-0023429-T01-IM6 P-0007923-T01-IM5 P-0033344-T01-IM6 P-0017912-T01-IM6 P-0020483-T01-IM6 P-0013832-T01-IM5 P-0052100-T01-IM6 P-0037278-T01-IM6 P-0010198-T01-IM5 P-0032176-T01-IM6 P-0005056-T01-IM5 P-0049746-T01-IM6 P-0001322-T01-IM3 P-0055805-T01-IM6 P-0023090-T01-IM6 P-0022792-T01-IM6 P-0020414-T01-IM6 P-0027295-T01-IM6 P-0038339-T01-IM6 P-0044360-T01-IM6 P-0003334-T02-IM5 P-0042371-T01-IM6 P-0012054-T01-IM5 P-0046597-T01-IM6 P-0004648-T01-IM5 P-0051021-T01-IM6 P-0048651-T01-IM6 P-0016369-T01-IM6 P-0036299-T01-IM6 P-0050062-T01-IM6 P-0025920-T01-IM6 P-0050785-T01-IM6 P-0001857-T01-IM3 P-0029752-T01-IM6 P-0053192-T01-IM6 P-0003074-T01-IM5 P-0012812-T01-IM5 P-0005363-T01-IM5 P-0054872-T01-IM6 P-0046245-T01-IM6 P-0052086-T01-IM6 P-0017741-T01-IM6 P-0046365-T01-IM6 P-0041603-T01-IM6 P-0018189-T01-IM6 P-0044538-T01-IM6 P-0011212-T01-IM5 P-0055267-T01-IM6 P-0031497-T01-IM6 P-0058199-T01-IM6 P-0007116-T01-IM5 P-0007030-T01-IM5 P-0029552-T01-IM6 P-0001402-T01-IM3 P-0012868-T01-IM5 P-0037573-T01-IM6 P-0009173-T01-IM5 P-0031056-T01-IM6 P-0004188-T01-IM5 P-0004724-T01-IM5 P-0057460-T01-IM6 P-0001146-T01-IM3 P-0031776-T01-IM6 P-0025438-T01-IM6 P-0034770-T01-IM6 P-0035749-T01-IM6 P-0058404-T01-IM6 P-0009321-T01-IM5 P-0028267-T01-IM6 P-0031417-T01-IM6 P-0046487-T01-IM6 P-0009079-T01-IM5 P-0056938-T01-IM6 P-0044643-T01-IM6 P-0001581-T02-IM5 P-0002461-T02-IM5 P-0039305-T01-IM6 P-0016118-T01-IM6 P-0004624-T01-IM5 P-0014674-T01-IM6 P-0010042-T01-IM5 P-0010747-T01-IM5 P-0007512-T01-IM5 P-0014337-T01-IM6 P-0003542-T01-IM5 P-0025688-T01-IM6 P-0000927-T01-IM3 P-0028254-T01-IM6 P-0023935-T01-IM6 P-0006841-T01-IM5 P-0019512-T01-IM6 P-0047789-T01-IM6 P-0042350-T01-IM6 P-0024739-T01-IM6 P-0052966-T01-IM6 P-0016486-T01-IM6 P-0019063-T01-IM6 P-0043941-T01-IM6 P-0027839-T01-IM6 P-0006478-T01-IM5 P-0039008-T01-IM6 P-0032498-T01-IM6 P-0056730-T01-IM6 P-0014174-T01-IM5 P-0007105-T01-IM5 P-0003143-T01-IM5 P-0003768-T01-IM5 P-0047213-T01-IM6 P-0040305-T01-IM6 P-0036335-T01-IM6 P-0019061-T01-IM6 P-0039265-T01-IM6 P-0048999-T01-IM6 P-0051904-T01-IM6 P-0046567-T01-IM6 P-0022171-T01-IM6 P-0003657-T01-IM5 P-0058948-T01-IM7 P-0016693-T01-IM6 P-0010631-T01-IM5 P-0009693-T01-IM5 P-0032042-T01-IM6 P-0045716-T01-IM6 P-0004809-T01-IM5 P-0027806-T01-IM6 P-0040462-T01-IM6 P-0021557-T01-IM6 P-0004390-T01-IM5 P-0028346-T01-IM6 P-0004672-T01-IM5 P-0001161-T01-IM3 P-0021929-T01-IM6 P-0026210-T01-IM6 P-0039330-T01-IM6 P-0001098-T01-IM3 P-0038242-T01-IM6 P-0003251-T01-IM5 P-0012435-T01-IM5 P-0014041-T01-IM5 P-0046153-T01-IM6 P-0029369-T01-IM6 P-0010032-T02-IM5 P-0013952-T01-IM5 P-0045691-T01-IM6 P-0056785-T01-IM6 P-0055165-T01-IM6 P-0053788-T01-IM6 P-0058864-T01-IM7 P-0003371-T01-IM5 P-0017351-T01-IM6 P-0008238-T02-IM6 P-0050237-T01-IM6 P-0006302-T01-IM5 P-0057472-T01-IM6 P-0029641-T01-IM6 P-0011073-T01-IM5 P-0042746-T01-IM6 P-0055292-T01-IM6 P-0031339-T02-IM6 P-0016389-T01-IM6 P-0008815-T01-IM5 P-0028756-T01-IM6 P-0014016-T01-IM5 P-0043490-T01-IM6 P-0015019-T01-IM6 P-0055980-T01-IM6 P-0013538-T01-IM5 P-0054224-T01-IM6 P-0041537-T01-IM6 P-0007094-T01-IM5 P-0011482-T01-IM5 P-0049859-T01-IM6 P-0029511-T01-IM6 P-0052029-T01-IM6 P-0051025-T01-IM6 P-0009794-T01-IM5 P-0009899-T01-IM5 P-0019051-T01-IM6 P-0031799-T02-IM6 P-0031913-T01-IM6 P-0026149-T01-IM6 P-0006438-T01-IM5 P-0046994-T01-IM6 P-0052254-T01-IM6 P-0043236-T01-IM6 P-0005796-T01-IM5 P-0040296-T01-IM6 P-0017685-T01-IM6 P-0010031-T01-IM5 P-0018729-T01-IM6 P-0012601-T01-IM5 P-0014233-T01-IM6 P-0029851-T01-IM6 P-0041585-T01-IM6 P-0039780-T01-IM6 P-0011083-T01-IM5 P-0009138-T01-IM5 P-0008568-T01-IM5 P-0048506-T01-IM6 P-0047945-T01-IM6 P-0005208-T01-IM5 P-0004356-T01-IM5 P-0024951-T01-IM6 P-0050742-T01-IM6 P-0055979-T01-IM6 P-0040179-T01-IM6 P-0047384-T01-IM6 P-0032805-T01-IM6 P-0057160-T01-IM6 P-0014203-T01-IM6 P-0006817-T01-IM5 P-0011444-T01-IM5 P-0029410-T01-IM6 P-0016482-T01-IM6 P-0012896-T01-IM5 P-0009698-T01-IM5 P-0007217-T01-IM5 P-0038512-T01-IM6 P-0025220-T01-IM6 \ No newline at end of file diff --git a/public/appendiceal_msk_2022/case_lists/cases_sequenced.txt b/public/appendiceal_msk_2022/case_lists/cases_sequenced.txt new file mode 100644 index 0000000000..6496012083 --- /dev/null +++ b/public/appendiceal_msk_2022/case_lists/cases_sequenced.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: appendiceal_msk_2022 +stable_id: appendiceal_msk_2022_sequenced +case_list_name: Samples with mutation data +case_list_description: Samples with mutation data (273 samples) +case_list_category: all_cases_with_mutation_data +case_list_ids: P-0039302-T02-IM6 P-0045104-T01-IM6 P-0050969-T01-IM6 P-0032634-T01-IM6 P-0022517-T01-IM6 P-0032140-T01-IM6 P-0010408-T01-IM5 P-0007673-T01-IM5 P-0029091-T01-IM6 P-0010702-T01-IM5 P-0034626-T01-IM6 P-0011271-T01-IM5 P-0044815-T01-IM6 P-0001411-T01-IM3 P-0011350-T01-IM5 P-0008730-T01-IM5 P-0030739-T01-IM6 P-0005296-T01-IM5 P-0017993-T01-IM6 P-0016610-T01-IM6 P-0034667-T01-IM6 P-0003638-T01-IM5 P-0012739-T01-IM5 P-0003135-T04-IM5 P-0012187-T01-IM5 P-0009900-T01-IM5 P-0027188-T01-IM6 P-0008038-T01-IM5 P-0030703-T01-IM6 P-0047460-T01-IM6 P-0012269-T01-IM5 P-0004192-T01-IM5 P-0006765-T01-IM5 P-0019762-T01-IM6 P-0049625-T01-IM6 P-0008142-T02-IM5 P-0033011-T01-IM6 P-0014673-T01-IM6 P-0026747-T04-IM6 P-0002322-T01-IM3 P-0008692-T01-IM5 P-0033680-T01-IM6 P-0021404-T01-IM6 P-0044082-T01-IM6 P-0009519-T01-IM5 P-0051228-T01-IM6 P-0032135-T01-IM6 P-0058081-T01-IM6 P-0034466-T01-IM6 P-0028106-T01-IM6 P-0028785-T01-IM6 P-0037220-T01-IM6 P-0003705-T01-IM5 P-0044181-T01-IM6 P-0023429-T01-IM6 P-0007923-T01-IM5 P-0033344-T01-IM6 P-0017912-T01-IM6 P-0020483-T01-IM6 P-0013832-T01-IM5 P-0052100-T01-IM6 P-0037278-T01-IM6 P-0010198-T01-IM5 P-0032176-T01-IM6 P-0005056-T01-IM5 P-0049746-T01-IM6 P-0001322-T01-IM3 P-0055805-T01-IM6 P-0023090-T01-IM6 P-0022792-T01-IM6 P-0020414-T01-IM6 P-0027295-T01-IM6 P-0038339-T01-IM6 P-0044360-T01-IM6 P-0003334-T02-IM5 P-0042371-T01-IM6 P-0012054-T01-IM5 P-0046597-T01-IM6 P-0004648-T01-IM5 P-0051021-T01-IM6 P-0048651-T01-IM6 P-0016369-T01-IM6 P-0036299-T01-IM6 P-0050062-T01-IM6 P-0025920-T01-IM6 P-0050785-T01-IM6 P-0001857-T01-IM3 P-0029752-T01-IM6 P-0053192-T01-IM6 P-0003074-T01-IM5 P-0012812-T01-IM5 P-0005363-T01-IM5 P-0054872-T01-IM6 P-0046245-T01-IM6 P-0052086-T01-IM6 P-0017741-T01-IM6 P-0046365-T01-IM6 P-0041603-T01-IM6 P-0018189-T01-IM6 P-0044538-T01-IM6 P-0011212-T01-IM5 P-0055267-T01-IM6 P-0031497-T01-IM6 P-0058199-T01-IM6 P-0007116-T01-IM5 P-0007030-T01-IM5 P-0029552-T01-IM6 P-0001402-T01-IM3 P-0012868-T01-IM5 P-0037573-T01-IM6 P-0009173-T01-IM5 P-0031056-T01-IM6 P-0004188-T01-IM5 P-0004724-T01-IM5 P-0057460-T01-IM6 P-0001146-T01-IM3 P-0031776-T01-IM6 P-0025438-T01-IM6 P-0034770-T01-IM6 P-0035749-T01-IM6 P-0058404-T01-IM6 P-0009321-T01-IM5 P-0028267-T01-IM6 P-0031417-T01-IM6 P-0046487-T01-IM6 P-0009079-T01-IM5 P-0056938-T01-IM6 P-0044643-T01-IM6 P-0001581-T02-IM5 P-0002461-T02-IM5 P-0039305-T01-IM6 P-0016118-T01-IM6 P-0004624-T01-IM5 P-0014674-T01-IM6 P-0010042-T01-IM5 P-0010747-T01-IM5 P-0007512-T01-IM5 P-0014337-T01-IM6 P-0003542-T01-IM5 P-0025688-T01-IM6 P-0000927-T01-IM3 P-0028254-T01-IM6 P-0023935-T01-IM6 P-0006841-T01-IM5 P-0019512-T01-IM6 P-0047789-T01-IM6 P-0042350-T01-IM6 P-0024739-T01-IM6 P-0052966-T01-IM6 P-0016486-T01-IM6 P-0019063-T01-IM6 P-0043941-T01-IM6 P-0027839-T01-IM6 P-0006478-T01-IM5 P-0039008-T01-IM6 P-0032498-T01-IM6 P-0056730-T01-IM6 P-0014174-T01-IM5 P-0007105-T01-IM5 P-0003143-T01-IM5 P-0003768-T01-IM5 P-0047213-T01-IM6 P-0040305-T01-IM6 P-0036335-T01-IM6 P-0019061-T01-IM6 P-0039265-T01-IM6 P-0048999-T01-IM6 P-0051904-T01-IM6 P-0046567-T01-IM6 P-0022171-T01-IM6 P-0003657-T01-IM5 P-0058948-T01-IM7 P-0016693-T01-IM6 P-0010631-T01-IM5 P-0009693-T01-IM5 P-0032042-T01-IM6 P-0045716-T01-IM6 P-0004809-T01-IM5 P-0027806-T01-IM6 P-0040462-T01-IM6 P-0021557-T01-IM6 P-0004390-T01-IM5 P-0028346-T01-IM6 P-0004672-T01-IM5 P-0001161-T01-IM3 P-0021929-T01-IM6 P-0026210-T01-IM6 P-0039330-T01-IM6 P-0001098-T01-IM3 P-0038242-T01-IM6 P-0003251-T01-IM5 P-0012435-T01-IM5 P-0014041-T01-IM5 P-0046153-T01-IM6 P-0029369-T01-IM6 P-0010032-T02-IM5 P-0013952-T01-IM5 P-0045691-T01-IM6 P-0056785-T01-IM6 P-0055165-T01-IM6 P-0053788-T01-IM6 P-0058864-T01-IM7 P-0003371-T01-IM5 P-0017351-T01-IM6 P-0008238-T02-IM6 P-0050237-T01-IM6 P-0006302-T01-IM5 P-0057472-T01-IM6 P-0029641-T01-IM6 P-0011073-T01-IM5 P-0042746-T01-IM6 P-0055292-T01-IM6 P-0031339-T02-IM6 P-0016389-T01-IM6 P-0008815-T01-IM5 P-0028756-T01-IM6 P-0014016-T01-IM5 P-0043490-T01-IM6 P-0015019-T01-IM6 P-0055980-T01-IM6 P-0013538-T01-IM5 P-0054224-T01-IM6 P-0041537-T01-IM6 P-0007094-T01-IM5 P-0011482-T01-IM5 P-0049859-T01-IM6 P-0029511-T01-IM6 P-0052029-T01-IM6 P-0051025-T01-IM6 P-0009794-T01-IM5 P-0009899-T01-IM5 P-0019051-T01-IM6 P-0031799-T02-IM6 P-0031913-T01-IM6 P-0026149-T01-IM6 P-0006438-T01-IM5 P-0046994-T01-IM6 P-0052254-T01-IM6 P-0043236-T01-IM6 P-0005796-T01-IM5 P-0040296-T01-IM6 P-0017685-T01-IM6 P-0010031-T01-IM5 P-0018729-T01-IM6 P-0012601-T01-IM5 P-0014233-T01-IM6 P-0029851-T01-IM6 P-0041585-T01-IM6 P-0039780-T01-IM6 P-0011083-T01-IM5 P-0009138-T01-IM5 P-0008568-T01-IM5 P-0048506-T01-IM6 P-0047945-T01-IM6 P-0005208-T01-IM5 P-0004356-T01-IM5 P-0024951-T01-IM6 P-0050742-T01-IM6 P-0055979-T01-IM6 P-0040179-T01-IM6 P-0047384-T01-IM6 P-0032805-T01-IM6 P-0057160-T01-IM6 P-0014203-T01-IM6 P-0006817-T01-IM5 P-0011444-T01-IM5 P-0029410-T01-IM6 P-0016482-T01-IM6 P-0012896-T01-IM5 P-0009698-T01-IM5 P-0007217-T01-IM5 P-0038512-T01-IM6 P-0025220-T01-IM6 \ No newline at end of file diff --git a/public/appendiceal_msk_2022/case_lists/cases_sv.txt b/public/appendiceal_msk_2022/case_lists/cases_sv.txt new file mode 100644 index 0000000000..d6ccb6212b --- /dev/null +++ b/public/appendiceal_msk_2022/case_lists/cases_sv.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: appendiceal_msk_2022 +stable_id: appendiceal_msk_2022_sv +case_list_name: Samples with SV data +case_list_description: All samples (273 samples) +case_list_category: all_cases_with_sv_data +case_list_ids: P-0039302-T02-IM6 P-0045104-T01-IM6 P-0050969-T01-IM6 P-0032634-T01-IM6 P-0022517-T01-IM6 P-0032140-T01-IM6 P-0010408-T01-IM5 P-0007673-T01-IM5 P-0029091-T01-IM6 P-0010702-T01-IM5 P-0034626-T01-IM6 P-0011271-T01-IM5 P-0044815-T01-IM6 P-0001411-T01-IM3 P-0011350-T01-IM5 P-0008730-T01-IM5 P-0030739-T01-IM6 P-0005296-T01-IM5 P-0017993-T01-IM6 P-0016610-T01-IM6 P-0034667-T01-IM6 P-0003638-T01-IM5 P-0012739-T01-IM5 P-0003135-T04-IM5 P-0012187-T01-IM5 P-0009900-T01-IM5 P-0027188-T01-IM6 P-0008038-T01-IM5 P-0030703-T01-IM6 P-0047460-T01-IM6 P-0012269-T01-IM5 P-0004192-T01-IM5 P-0006765-T01-IM5 P-0019762-T01-IM6 P-0049625-T01-IM6 P-0008142-T02-IM5 P-0033011-T01-IM6 P-0014673-T01-IM6 P-0026747-T04-IM6 P-0002322-T01-IM3 P-0008692-T01-IM5 P-0033680-T01-IM6 P-0021404-T01-IM6 P-0044082-T01-IM6 P-0009519-T01-IM5 P-0051228-T01-IM6 P-0032135-T01-IM6 P-0058081-T01-IM6 P-0034466-T01-IM6 P-0028106-T01-IM6 P-0028785-T01-IM6 P-0037220-T01-IM6 P-0003705-T01-IM5 P-0044181-T01-IM6 P-0023429-T01-IM6 P-0007923-T01-IM5 P-0033344-T01-IM6 P-0017912-T01-IM6 P-0020483-T01-IM6 P-0013832-T01-IM5 P-0052100-T01-IM6 P-0037278-T01-IM6 P-0010198-T01-IM5 P-0032176-T01-IM6 P-0005056-T01-IM5 P-0049746-T01-IM6 P-0001322-T01-IM3 P-0055805-T01-IM6 P-0023090-T01-IM6 P-0022792-T01-IM6 P-0020414-T01-IM6 P-0027295-T01-IM6 P-0038339-T01-IM6 P-0044360-T01-IM6 P-0003334-T02-IM5 P-0042371-T01-IM6 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diff --git a/public/appendiceal_msk_2022/data_clinical_sample.txt b/public/appendiceal_msk_2022/data_clinical_sample.txt new file mode 100644 index 0000000000..68a9ce9879 --- /dev/null +++ b/public/appendiceal_msk_2022/data_clinical_sample.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:07b42bd26015664b0a94b43e2b960050292024350032432d3407236117d58fec +size 45626 diff --git a/public/appendiceal_msk_2022/data_cna.txt b/public/appendiceal_msk_2022/data_cna.txt new file mode 100644 index 0000000000..0bc99d499b --- /dev/null +++ b/public/appendiceal_msk_2022/data_cna.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9565e177da8eb343d47b1d549b91bfc300b41e91bcd25968a1067c458275ab1e +size 303565 diff --git a/public/appendiceal_msk_2022/data_cna_hg19.seg b/public/appendiceal_msk_2022/data_cna_hg19.seg new file mode 100644 index 0000000000..e1a858604b --- /dev/null +++ b/public/appendiceal_msk_2022/data_cna_hg19.seg @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7c3efd3e7f2271d7cb731c920bf28547e10c6792a0660d9b49ab9e87df9b14f4 +size 582989 diff --git a/public/appendiceal_msk_2022/data_gene_panel_matrix.txt b/public/appendiceal_msk_2022/data_gene_panel_matrix.txt new file mode 100644 index 0000000000..bd3391c7da --- /dev/null +++ b/public/appendiceal_msk_2022/data_gene_panel_matrix.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:35f5a5827253fa385f4970c232b7fcb55e3a4f224b831d8df53a3239a66ec95e +size 13147 diff --git a/public/appendiceal_msk_2022/data_mutations.txt b/public/appendiceal_msk_2022/data_mutations.txt new file mode 100644 index 0000000000..e474a7c965 --- /dev/null +++ b/public/appendiceal_msk_2022/data_mutations.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8b946c3f060a9d4e802792be963b9ab2a1296617821c7aa1f8ea3d5b8e0b7c10 +size 370156 diff --git a/public/appendiceal_msk_2022/data_sv.txt b/public/appendiceal_msk_2022/data_sv.txt new file mode 100644 index 0000000000..d6e6f1499e --- /dev/null +++ b/public/appendiceal_msk_2022/data_sv.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:13cc3cbfb126f1ce3b21d3fac1690d0caab0dfc33bf9df788f314d0a759ce41c +size 10180 diff --git a/public/appendiceal_msk_2022/meta_clinical_patient.txt b/public/appendiceal_msk_2022/meta_clinical_patient.txt new file mode 100644 index 0000000000..a4a7655f86 --- /dev/null +++ b/public/appendiceal_msk_2022/meta_clinical_patient.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: appendiceal_msk_2022 +genetic_alteration_type: CLINICAL +datatype: PATIENT_ATTRIBUTES +data_filename: data_clinical_patient.txt diff --git a/public/appendiceal_msk_2022/meta_clinical_sample.txt b/public/appendiceal_msk_2022/meta_clinical_sample.txt new file mode 100644 index 0000000000..0b123abdcf --- /dev/null +++ b/public/appendiceal_msk_2022/meta_clinical_sample.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: appendiceal_msk_2022 +genetic_alteration_type: CLINICAL +datatype: SAMPLE_ATTRIBUTES +data_filename: data_clinical_sample.txt diff --git a/public/appendiceal_msk_2022/meta_cna.txt b/public/appendiceal_msk_2022/meta_cna.txt new file mode 100644 index 0000000000..d130ae6172 --- /dev/null +++ b/public/appendiceal_msk_2022/meta_cna.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: appendiceal_msk_2022 +genetic_alteration_type: COPY_NUMBER_ALTERATION +stable_id: cna +show_profile_in_analysis_tab: true +profile_name: Copy Number Alterations. +profile_description: Copy number alterations from targeted sequencing via MK-IMPACT on Illumina HiSeq sequencers. +datatype: DISCRETE +data_filename: data_cna.txt \ No newline at end of file diff --git a/public/appendiceal_msk_2022/meta_cna_hg19_seg.txt b/public/appendiceal_msk_2022/meta_cna_hg19_seg.txt new file mode 100644 index 0000000000..7c99385896 --- /dev/null +++ b/public/appendiceal_msk_2022/meta_cna_hg19_seg.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: appendiceal_msk_2022 +genetic_alteration_type: COPY_NUMBER_ALTERATION +datatype: SEG +reference_genome_id: hg19 +description: Somatic CNA data (copy number ratio from tumor samples minus ratio from matched normals) from TCGA. +data_filename: data_cna_hg19.seg \ No newline at end of file diff --git a/public/appendiceal_msk_2022/meta_gene_panel_matrix.txt b/public/appendiceal_msk_2022/meta_gene_panel_matrix.txt new file mode 100644 index 0000000000..0d8c624380 --- /dev/null +++ b/public/appendiceal_msk_2022/meta_gene_panel_matrix.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: appendiceal_msk_2022 +genetic_alteration_type: GENE_PANEL_MATRIX +datatype: GENE_PANEL_MATRIX +data_filename: data_gene_panel_matrix.txt diff --git a/public/appendiceal_msk_2022/meta_mutations.txt b/public/appendiceal_msk_2022/meta_mutations.txt new file mode 100644 index 0000000000..3a16a90f92 --- /dev/null +++ b/public/appendiceal_msk_2022/meta_mutations.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: appendiceal_msk_2022 +stable_id: mutations +profile_name: Mutations +profile_description: Targeted sequencing via MSK-IMPACT on Illumina HiSeq sequencers. +genetic_alteration_type: MUTATION_EXTENDED +datatype: MAF +data_filename: data_mutations.txt +show_profile_in_analysis_tab: true \ No newline at end of file diff --git a/public/appendiceal_msk_2022/meta_study.txt b/public/appendiceal_msk_2022/meta_study.txt new file mode 100644 index 0000000000..38f8c17f05 --- /dev/null +++ b/public/appendiceal_msk_2022/meta_study.txt @@ -0,0 +1,8 @@ +type_of_cancer: apad +cancer_study_identifier: appendiceal_msk_2022 +name: Appendiceal Cancer (MSK, J Clin Oncol 2022) +short_name: Appendiceal Cancer (MSK , 2022) +description: Targeted sequencing of 273 appendiceal tumor/normal pairs via MSK-IMPACT platform. +citation: Michael B et al. J Clin Oncol 2022 +pmid: 36493333 +groups: PUBLIC \ No newline at end of file diff --git a/public/appendiceal_msk_2022/meta_sv.txt b/public/appendiceal_msk_2022/meta_sv.txt new file mode 100644 index 0000000000..9fd05b739e --- /dev/null +++ b/public/appendiceal_msk_2022/meta_sv.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: appendiceal_msk_2022 +genetic_alteration_type: STRUCTURAL_VARIANT +datatype: SV +stable_id: structural_variants +show_profile_in_analysis_tab: true +profile_name: Structural variants +profile_description: Structural Variant Data. +data_filename: data_sv.txt diff --git a/public/coadread_mskresistance_2022/LICENSE b/public/coadread_mskresistance_2022/LICENSE new file mode 100644 index 0000000000..d5f3c4b535 --- /dev/null +++ b/public/coadread_mskresistance_2022/LICENSE @@ -0,0 +1 @@ +The data are available under the ODC Open Database License (ODbL)(http://opendatacommons.org/licenses/odbl/1.0/) (summary available here: http://www.opendatacommons.org/licenses/odbl/1-0/summary/): you are free to share and modify the data so long as you attribute any public use of the database, or works produced from the database; keep the resulting data-sets open; and offer your shared or adapted version of the data-set under the same ODbL license. diff --git a/public/coadread_mskresistance_2022/Readme.txt b/public/coadread_mskresistance_2022/Readme.txt new file mode 100644 index 0000000000..6202caf574 --- /dev/null +++ b/public/coadread_mskresistance_2022/Readme.txt @@ -0,0 +1 @@ +Gene panels for this study can be found here: https://github.com/cBioPortal/datahub/tree/master/reference_data/gene_panels \ No newline at end of file diff --git a/public/coadread_mskresistance_2022/case_lists/cases_all.txt b/public/coadread_mskresistance_2022/case_lists/cases_all.txt new file mode 100644 index 0000000000..1b6c1368c3 --- /dev/null +++ b/public/coadread_mskresistance_2022/case_lists/cases_all.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: coadread_mskresistance_2022 +stable_id: coadread_mskresistance_2022_all +case_list_name: All samples +case_list_description: All samples (22 samples) +case_list_category: all_cases_in_study +case_list_ids: s_RW7213_R_V1_04609AI s_RW7213_resistant_04609AB s_RW7213_R_V3_04609AI s_C106_resistant_04609AB P-0063407-T01-IM7 s_RW7213_R_D3_04609AI s_C106_parental_04609AB s_RW7213_R_D1_04609AI P-0070822-T01-IM7 s_RW7213_parental_04609AB s_C_E2UFRP_X008_d P-0069572-T02-IM7 s_RW7213_R_V2_04609AI s_RW7213_R_V4_04609AI P-0064340-T01-IM7 P-0018488-T07-IM7 s_RW7213_R_D4_04609AI s_RW7213_R_D2_04609AI P-0018488-T01-IM6 s_C_E2UFRP_X007_d P-0032505-T01-IM6 P-0038647-T01-IM6 diff --git a/public/coadread_mskresistance_2022/case_lists/cases_cna.txt b/public/coadread_mskresistance_2022/case_lists/cases_cna.txt new file mode 100644 index 0000000000..dbbf952db8 --- /dev/null +++ b/public/coadread_mskresistance_2022/case_lists/cases_cna.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: coadread_mskresistance_2022 +stable_id: coadread_mskresistance_2022_cna +case_list_name: Samples with CNA data +case_list_description: Samples with CNA data (22 samples) +case_list_category: all_cases_with_cna_data +case_list_ids: s_RW7213_R_V1_04609AI s_RW7213_R_V3_04609AI s_C106_resistant_04609AB P-0063407-T01-IM7 P-0038647-T01-IM6 s_RW7213_R_D3_04609AI s_RW7213_R_D1_04609AI P-0070822-T01-IM7 s_C106_parental_04609AB s_RW7213_parental_04609AB s_C_E2UFRP_X008_d P-0069572-T02-IM7 s_RW7213_R_V2_04609AI s_RW7213_R_V4_04609AI P-0064340-T01-IM7 P-0018488-T07-IM7 s_RW7213_R_D4_04609AI s_RW7213_resistant_04609AB P-0018488-T01-IM6 s_C_E2UFRP_X007_d P-0032505-T01-IM6 s_RW7213_R_D2_04609AI diff --git a/public/coadread_mskresistance_2022/case_lists/cases_cnaseq.txt b/public/coadread_mskresistance_2022/case_lists/cases_cnaseq.txt new file mode 100644 index 0000000000..34cfffd700 --- /dev/null +++ b/public/coadread_mskresistance_2022/case_lists/cases_cnaseq.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: coadread_mskresistance_2022 +stable_id: coadread_mskresistance_2022_cnaseq +case_list_name: Samples with mutation and CNA data +case_list_description: Samples with mutation and CNA data (22 samples) +case_list_category: all_cases_with_mutation_and_cna_data +case_list_ids: s_RW7213_R_V1_04609AI s_RW7213_R_V3_04609AI P-0063407-T01-IM7 s_RW7213_R_D3_04609AI s_RW7213_R_D1_04609AI s_RW7213_parental_04609AB P-0018488-T07-IM7 P-0069572-T02-IM7 s_C_E2UFRP_X008_d s_RW7213_resistant_04609AB P-0018488-T01-IM6 s_RW7213_R_D2_04609AI s_C106_resistant_04609AB P-0038647-T01-IM6 s_C106_parental_04609AB P-0070822-T01-IM7 s_RW7213_R_V2_04609AI s_RW7213_R_V4_04609AI P-0064340-T01-IM7 s_RW7213_R_D4_04609AI s_C_E2UFRP_X007_d P-0032505-T01-IM6 diff --git a/public/coadread_mskresistance_2022/case_lists/cases_sequenced.txt b/public/coadread_mskresistance_2022/case_lists/cases_sequenced.txt new file mode 100644 index 0000000000..96e08853ba --- /dev/null +++ b/public/coadread_mskresistance_2022/case_lists/cases_sequenced.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: coadread_mskresistance_2022 +stable_id: coadread_mskresistance_2022_sequenced +case_list_name: Samples with mutation data +case_list_description: Samples with mutation data (22 samples) +case_list_category: all_cases_with_mutation_data +case_list_ids: s_RW7213_R_V1_04609AI s_RW7213_R_V3_04609AI P-0063407-T01-IM7 s_RW7213_R_D3_04609AI s_RW7213_R_D1_04609AI s_RW7213_parental_04609AB P-0018488-T07-IM7 P-0069572-T02-IM7 s_C_E2UFRP_X008_d s_RW7213_resistant_04609AB P-0018488-T01-IM6 s_RW7213_R_D2_04609AI s_C106_resistant_04609AB P-0038647-T01-IM6 s_C106_parental_04609AB P-0070822-T01-IM7 s_RW7213_R_V2_04609AI s_RW7213_R_V4_04609AI P-0064340-T01-IM7 s_RW7213_R_D4_04609AI s_C_E2UFRP_X007_d P-0032505-T01-IM6 diff --git a/public/coadread_mskresistance_2022/case_lists/cases_sv.txt b/public/coadread_mskresistance_2022/case_lists/cases_sv.txt new file mode 100644 index 0000000000..1fbc564e88 --- /dev/null +++ b/public/coadread_mskresistance_2022/case_lists/cases_sv.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: coadread_mskresistance_2022 +stable_id: coadread_mskresistance_2022_sv +case_list_name: Samples with SV data +case_list_description: All samples with SV data (22 samples) +case_list_category: all_cases_with_sv_data +case_list_ids: s_RW7213_R_V1_04609AI s_RW7213_R_V3_04609AI P-0063407-T01-IM7 s_RW7213_R_D3_04609AI s_RW7213_R_D1_04609AI s_RW7213_parental_04609AB P-0018488-T07-IM7 P-0069572-T02-IM7 s_C_E2UFRP_X008_d s_RW7213_resistant_04609AB P-0018488-T01-IM6 s_RW7213_R_D2_04609AI s_C106_resistant_04609AB P-0038647-T01-IM6 s_C106_parental_04609AB P-0070822-T01-IM7 s_RW7213_R_V2_04609AI s_RW7213_R_V4_04609AI P-0064340-T01-IM7 s_RW7213_R_D4_04609AI s_C_E2UFRP_X007_d P-0032505-T01-IM6 \ No newline at end of file diff --git a/public/coadread_mskresistance_2022/data_clinical_patient.txt b/public/coadread_mskresistance_2022/data_clinical_patient.txt new file mode 100644 index 0000000000..5065c0de5b --- /dev/null +++ b/public/coadread_mskresistance_2022/data_clinical_patient.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8548ea382f442c78ff90ba6d8add41275d2c8603c073331aca4295664c9505d0 +size 1127 diff --git a/public/coadread_mskresistance_2022/data_clinical_sample.txt b/public/coadread_mskresistance_2022/data_clinical_sample.txt new file mode 100644 index 0000000000..e9ed52d48c --- /dev/null +++ b/public/coadread_mskresistance_2022/data_clinical_sample.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:06df005607bebc0559cdbdffb6955ab4972dc03d85f642448e1c03852ef8a0b2 +size 4868 diff --git a/public/coadread_mskresistance_2022/data_cna.txt b/public/coadread_mskresistance_2022/data_cna.txt new file mode 100644 index 0000000000..99f365dfbb --- /dev/null +++ b/public/coadread_mskresistance_2022/data_cna.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9a5181373fb00396e042169e3b16ff3e52df9184d5faaaafcee567f410c1a00b +size 126787 diff --git a/public/coadread_mskresistance_2022/data_cna_hg19.seg b/public/coadread_mskresistance_2022/data_cna_hg19.seg new file mode 100644 index 0000000000..3cc9411d7c --- /dev/null +++ b/public/coadread_mskresistance_2022/data_cna_hg19.seg @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:752812292e449f343888fa4ceffc2d669efcf56687f88486cbf869b488b6f077 +size 77992 diff --git a/public/coadread_mskresistance_2022/data_gene_panel_matrix.txt b/public/coadread_mskresistance_2022/data_gene_panel_matrix.txt new file mode 100644 index 0000000000..d9efecbb5d --- /dev/null +++ b/public/coadread_mskresistance_2022/data_gene_panel_matrix.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9b9f1350a4be298815468641a606439747201b40f2b6536d53caf39dd40734b8 +size 1162 diff --git a/public/coadread_mskresistance_2022/data_mutations.txt b/public/coadread_mskresistance_2022/data_mutations.txt new file mode 100644 index 0000000000..beee807c6e --- /dev/null +++ b/public/coadread_mskresistance_2022/data_mutations.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:832cd9a82420bd3af32699766798b37fe2aa6110c6264e44c0ce35ad826af3ca +size 4577769 diff --git a/public/coadread_mskresistance_2022/data_sv.txt b/public/coadread_mskresistance_2022/data_sv.txt new file mode 100644 index 0000000000..bf14a94cc2 --- /dev/null +++ b/public/coadread_mskresistance_2022/data_sv.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a1df237d5e8aebe0911ba138940b892f4beb5c6a9639291360d9e76954622345 +size 634 diff --git a/public/coadread_mskresistance_2022/meta_clinical_patient.txt b/public/coadread_mskresistance_2022/meta_clinical_patient.txt new file mode 100644 index 0000000000..bb8cde6b62 --- /dev/null +++ b/public/coadread_mskresistance_2022/meta_clinical_patient.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: coadread_mskresistance_2022 +genetic_alteration_type: CLINICAL +datatype: PATIENT_ATTRIBUTES +data_filename: data_clinical_patient.txt diff --git a/public/coadread_mskresistance_2022/meta_clinical_sample.txt b/public/coadread_mskresistance_2022/meta_clinical_sample.txt new file mode 100644 index 0000000000..7f48683471 --- /dev/null +++ b/public/coadread_mskresistance_2022/meta_clinical_sample.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: coadread_mskresistance_2022 +genetic_alteration_type: CLINICAL +datatype: SAMPLE_ATTRIBUTES +data_filename: data_clinical_sample.txt diff --git a/public/coadread_mskresistance_2022/meta_cna.txt b/public/coadread_mskresistance_2022/meta_cna.txt new file mode 100644 index 0000000000..63d045b25f --- /dev/null +++ b/public/coadread_mskresistance_2022/meta_cna.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: coadread_mskresistance_2022 +stable_id: cna +profile_name: Putative copy-number alterations +profile_description: Putative copy-number calls. Values: -2 = homozygous deletion; -1 = hemizygous deletion; 0 = neutral / no change; 1 = gain; 2 = high level amplification. +genetic_alteration_type: COPY_NUMBER_ALTERATION +datatype: DISCRETE +show_profile_in_analysis_tab: TRUE +data_filename: data_cna.txt diff --git a/public/coadread_mskresistance_2022/meta_cna_hg19_seg.txt b/public/coadread_mskresistance_2022/meta_cna_hg19_seg.txt new file mode 100644 index 0000000000..ee453dbe7b --- /dev/null +++ b/public/coadread_mskresistance_2022/meta_cna_hg19_seg.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: coadread_mskresistance_2022 +data_filename: data_cna_hg19.seg +datatype: SEG +description: Segmented Data +genetic_alteration_type: COPY_NUMBER_ALTERATION +reference_genome_id: hg19 \ No newline at end of file diff --git a/public/coadread_mskresistance_2022/meta_gene_panel_matrix.txt b/public/coadread_mskresistance_2022/meta_gene_panel_matrix.txt new file mode 100755 index 0000000000..dd5cfac596 --- /dev/null +++ b/public/coadread_mskresistance_2022/meta_gene_panel_matrix.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: coadread_mskresistance_2022 +genetic_alteration_type: GENE_PANEL_MATRIX +datatype: GENE_PANEL_MATRIX +data_filename: data_gene_panel_matrix.txt diff --git a/public/coadread_mskresistance_2022/meta_mutations.txt b/public/coadread_mskresistance_2022/meta_mutations.txt new file mode 100644 index 0000000000..49723ec94f --- /dev/null +++ b/public/coadread_mskresistance_2022/meta_mutations.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: coadread_mskresistance_2022 +genetic_alteration_type: MUTATION_EXTENDED +datatype: MAF +stable_id: mutations +show_profile_in_analysis_tab: true +profile_description: Targeted sequencing of colorectal tumor normal pairs via MSK-IMPACT. +profile_name: Mutations +data_filename: data_mutations.txt diff --git a/public/coadread_mskresistance_2022/meta_study.txt b/public/coadread_mskresistance_2022/meta_study.txt new file mode 100644 index 0000000000..4c2da566c0 --- /dev/null +++ b/public/coadread_mskresistance_2022/meta_study.txt @@ -0,0 +1,7 @@ +type_of_cancer: coadread +cancer_study_identifier: coadread_mskresistance_2022 +name: Colorectal Cancer (MSK, Cancer Discovery 2022) +description: Targeted sequencing of patient-derived xenografts, cell lines, tumors and their matched normals from 22 colorectal samples via MSK-IMPACT. +short_name: COADREAD (MSK, 2022) +pmid: 36355783 +citation: Yaeger et al. Cancer Discovery 2022 \ No newline at end of file diff --git a/public/coadread_mskresistance_2022/meta_sv.txt b/public/coadread_mskresistance_2022/meta_sv.txt new file mode 100755 index 0000000000..5568e78352 --- /dev/null +++ b/public/coadread_mskresistance_2022/meta_sv.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: coadread_mskresistance_2022 +genetic_alteration_type: STRUCTURAL_VARIANT +datatype: SV +stable_id: structural_variants +show_profile_in_analysis_tab: true +profile_name: Structural variants +profile_description: Structural Variant Data. +data_filename: data_sv.txt \ No newline at end of file diff --git a/public/gist_msk_2022/case_lists/cases_all.txt b/public/gist_msk_2022/case_lists/cases_all.txt index 0570ad8618..00497d98d9 100644 --- a/public/gist_msk_2022/case_lists/cases_all.txt +++ b/public/gist_msk_2022/case_lists/cases_all.txt @@ -1,6 +1,6 @@ cancer_study_identifier: gist_msk_2022 stable_id: gist_msk_2022_all case_list_name: All samples -case_list_description: All samples (669 samples) +case_list_description: All samples (499 samples) case_list_category: all_cases_in_study -case_list_ids: P-0018973-T01-IM6 P-0013114-T03-IM6 P-0024888-T02-IM6 P-0025754-T02-IM6 P-0024288-T01-IM6 P-0039417-T01-IM6 P-0004937-T01-IM5 P-0043479-T01-IM6 P-0008084-T03-IM6 P-0066631-T01-IM7 P-0048138-T01-IM6 P-0013789-T01-IM5 P-0057812-T01-IM6 P-0052061-T04-IM7 P-0018677-T02-IM7 P-0054913-T01-IM6 P-0044076-T01-IM6 P-0038669-T01-IM6 P-0028553-T02-IM6 P-0067881-T01-IM7 P-0014521-T01-IM6 P-0017729-T01-IM6 P-0014330-T01-IM6 P-0004760-T03-IM7 P-0017387-T01-IM6 P-0048280-T02-IM6 P-0001692-T02-IM3 P-0004937-T03-IM6 P-0052582-T01-IM6 P-0025989-T03-IM7 P-0016868-T01-IM6 P-0031480-T01-IM6 P-0006638-T01-IM5 P-0025653-T01-IM6 P-0031415-T01-IM6 P-0049663-T01-IM6 P-0015145-T01-IM6 P-0059848-T02-IM7 P-0014184-T03-IM6 P-0035634-T01-IM6 P-0004760-T01-IM5 P-0050110-T01-IM6 P-0044681-T03-IH3 P-0037156-T01-IM6 P-0044303-T01-IM6 P-0014933-T01-IM6 P-0061177-T01-IM7 P-0013188-T01-IM5 P-0027598-T01-IM6 P-0053921-T03-IM7 P-0064686-T01-IM7 P-0030194-T01-IM6 P-0024909-T01-IM6 P-0025633-T01-IM6 P-0026071-T01-IM6 P-0044039-T01-IM6 P-0064216-T01-IM7 P-0028138-T01-IM6 P-0033478-T01-IM6 P-0006932-T01-IM5 P-0060670-T01-IM7 P-0045969-T02-IM7 P-0052059-T01-IM6 P-0025754-T04-IM6 P-0042544-T01-IM6 P-0021560-T01-IM6 P-0036220-T01-IM6 P-0057514-T02-IM6 P-0027730-T01-IM6 P-0007910-T01-IM5 P-0028773-T01-IM6 P-0044681-T09-IH3 P-0063511-T01-IM7 P-0038762-T02-IM6 P-0029072-T03-IM7 P-0010183-T01-IM5 P-0025934-T01-IM6 P-0037672-T02-XS1 P-0006875-T01-IM5 P-0005605-T01-IM5 P-0013433-T01-IM5 P-0007702-T02-IM6 P-0026349-T01-IM6 P-0054241-T01-IM6 P-0066506-T01-IM7 P-0014184-T08-XS1 P-0006293-T01-IM5 P-0053723-T01-IM6 P-0047565-T01-IM6 P-0025602-T01-IM6 P-0024492-T01-IM6 P-0006664-T01-IM5 P-0064040-T01-IM7 P-0046231-T01-IM6 P-0015826-T01-IM6 P-0027089-T02-IM6 P-0026918-T01-IM6 P-0017819-T01-IM6 P-0009195-T01-IM5 P-0068099-T01-IM7 P-0011070-T01-IM5 P-0012403-T03-IM6 P-0046084-T01-IM6 P-0034094-T01-IM6 P-0005891-T01-IM5 P-0002680-T01-IM3 P-0052033-T01-IM6 P-0040924-T01-IM6 P-0040359-T01-IM6 P-0004776-T01-IM5 P-0058047-T01-IM6 P-0015913-T01-IM6 P-0014184-T07-XS1 P-0021978-T01-IM6 P-0060670-T02-IM7 P-0025989-T02-IM6 P-0043409-T01-IM6 P-0013447-T01-IM5 P-0015969-T01-IM6 P-0002525-T01-IM3 P-0029524-T01-IM6 P-0061964-T01-IM7 P-0025989-T01-IM6 P-0014247-T01-IM6 P-0038101-T02-IM7 P-0038980-T01-IM6 P-0008084-T02-IM5 P-0025989-T04-IM7 P-0054860-T02-IM6 P-0037697-T01-IM6 P-0019006-T01-IM6 P-0029467-T01-IM6 P-0032950-T01-IM6 P-0017255-T01-IM6 P-0000309-T03-IM5 P-0001692-T01-IM3 P-0006755-T01-IM5 P-0032213-T01-IM6 P-0052570-T01-IM6 P-0047159-T01-IM6 P-0054008-T01-IM6 P-0013393-T01-IM5 P-0044681-T01-IH3 P-0048983-T01-IM6 P-0066467-T01-IM7 P-0000501-T01-IM3 P-0007985-T01-IM5 P-0037727-T01-IM6 P-0010175-T02-IM5 P-0001315-T02-IM5 P-0018913-T01-IM6 P-0016970-T01-IM6 P-0006343-T02-IM6 P-0002868-T02-IM5 P-0026329-T01-IM6 P-0064129-T01-IM7 P-0028553-T01-IM6 P-0024129-T02-IM7 P-0054654-T01-IM6 P-0005737-T02-IM5 P-0007268-T02-IM5 P-0027195-T01-IM6 P-0008391-T02-IM5 P-0068042-T01-IM7 P-0061392-T01-IM7 P-0004305-T01-IM5 P-0023175-T01-IM6 P-0006343-T01-IM5 P-0050110-T02-IM6 P-0012403-T01-IM5 P-0045145-T02-IM7 P-0003927-T01-IM3 P-0006712-T01-IM5 P-0013110-T01-IM5 P-0030330-T01-IM6 P-0035321-T01-IM6 P-0062514-T01-IM7 P-0056963-T01-IM6 P-0018677-T01-IM6 P-0005066-T01-IM5 P-0005379-T01-IM5 P-0051982-T01-IM6 P-0018225-T01-IM6 P-0059137-T02-IM7 P-0006501-T01-IM5 P-0015447-T01-IM6 P-0053921-T02-IM7 P-0001517-T01-IM3 P-0021758-T01-IM6 P-0023543-T02-IM6 P-0042549-T01-IM6 P-0055232-T01-IM6 P-0038341-T01-IM6 P-0020415-T04-IM7 P-0008468-T01-IM5 P-0032359-T01-IM6 P-0005986-T01-IM5 P-0044681-T08-IH3 P-0037522-T01-IM6 P-0052033-T02-IM7 P-0064725-T01-IM7 P-0014433-T01-IM6 P-0032636-T01-IM6 P-0000309-T01-IM3 P-0002409-T01-IM3 P-0035173-T01-IM6 P-0026733-T02-IM6 P-0037918-T01-IM6 P-0004883-T01-IM5 P-0043343-T01-IM6 P-0022451-T01-IM6 P-0022727-T01-IM6 P-0009156-T01-IM5 P-0049899-T02-IM7 P-0052126-T01-IM6 P-0008084-T01-IM5 P-0029072-T04-XS1 P-0026342-T01-IM6 P-0003416-T02-IM5 P-0024904-T01-IM6 P-0045969-T01-IM6 P-0004883-T03-IM6 P-0050865-T03-IM6 P-0044681-T06-IH3 P-0005330-T02-IM5 P-0046251-T01-IM6 P-0002477-T01-IM3 P-0001512-T01-IM3 P-0024888-T01-IM6 P-0010941-T01-IM5 P-0034471-T01-IM6 P-0063559-T01-IM7 P-0040351-T02-IM6 P-0050211-T01-IM6 P-0006104-T02-IM6 P-0016894-T02-IM6 P-0051984-T01-IM6 P-0014074-T01-IM5 P-0059434-T01-IM7 P-0045947-T02-IM6 P-0007513-T02-IM5 P-0026754-T02-IM6 P-0044291-T01-IM6 P-0025143-T01-IM6 P-0045947-T01-IM6 P-0057804-T01-IM6 P-0051271-T02-XS1 P-0029072-T06-XS1 P-0029072-T05-XS1 P-0051271-T01-IM6 P-0014411-T01-IM6 P-0014241-T01-IM6 P-0035022-T01-IM6 P-0003471-T01-IM5 P-0016532-T01-IM6 P-0014452-T01-IM6 P-0013007-T01-IM5 P-0056376-T01-IM6 P-0023447-T01-IM6 P-0013039-T01-IM5 P-0033833-T01-IM6 P-0014592-T01-IM6 P-0004509-T01-IM5 P-0053496-T01-IM6 P-0031004-T01-IM6 P-0026664-T02-IM6 P-0020389-T03-IM7 P-0010949-T02-IM7 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P-0062837-T01-IM7 P-0026260-T01-IM6 P-0050450-T01-IM6 P-0019993-T02-IM6 P-0033188-T01-IM6 P-0017851-T01-IM6 P-0029524-T01-IM6 P-0017729-T02-IM6 P-0062533-T01-IM7 P-0036219-T01-IM6 P-0057636-T01-IM6 P-0059137-T01-IM7 P-0059657-T01-IM7 P-0001254-T02-IM3 P-0046483-T01-IM6 P-0064072-T01-IM7 P-0015041-T01-IM6 P-0004225-T01-IM5 P-0013024-T01-IM5 P-0018913-T02-IM6 P-0064900-T01-IM7 P-0044481-T01-IM6 P-0046440-T01-IM6 P-0015065-T01-IM6 P-0007890-T01-IM5 P-0005379-T02-IM6 P-0032539-T01-IM6 P-0042490-T01-IM6 P-0065847-T01-IM7 P-0012178-T01-IM5 P-0051981-T01-IM6 P-0014433-T04-IM6 P-0048953-T01-IM6 P-0013114-T05-IM6 P-0042260-T02-IM6 P-0004784-T01-IM5 P-0046896-T01-IM6 P-0007967-T01-IM5 P-0040551-T01-IM6 P-0004235-T01-IM5 P-0026845-T01-IM6 P-0066645-T01-IM7 P-0064526-T01-IM7 P-0040191-T01-IM6 P-0007501-T01-IM5 P-0066404-T01-IM7 P-0006712-T02-IM7 P-0007513-T03-IM5 P-0039747-T01-IM6 P-0004677-T01-IM5 P-0032636-T01-IM6 P-0017811-T01-IM6 P-0030447-T01-IM6 P-0044022-T01-IM6 P-0029134-T01-IM6 P-0005737-T02-IM5 P-0006473-T01-IM5 P-0014722-T01-IM6 P-0024161-T01-IM6 P-0000134-T02-IM3 P-0023549-T01-IM6 P-0027918-T02-IM6 P-0002293-T01-IM3 P-0031415-T02-IM7 P-0017859-T01-IM6 P-0054241-T02-IM6 P-0026214-T03-IM6 P-0035576-T01-IM6 P-0015826-T03-IM6 P-0056816-T01-IM6 P-0065408-T01-IM7 P-0002726-T02-IM6 P-0063404-T01-IM7 P-0060395-T01-IM7 P-0012459-T02-IM6 P-0002594-T02-IM5 diff --git a/public/gist_msk_2022/case_lists/cases_cna.txt b/public/gist_msk_2022/case_lists/cases_cna.txt index 69f7a01e26..d7992141a0 100644 --- a/public/gist_msk_2022/case_lists/cases_cna.txt +++ b/public/gist_msk_2022/case_lists/cases_cna.txt @@ -1,6 +1,6 @@ cancer_study_identifier: gist_msk_2022 stable_id: gist_msk_2022_cna case_list_name: Samples with CNA data -case_list_description: Samples with CNA data (669 samples) +case_list_description: Samples with CNA data (499 samples) case_list_category: all_cases_with_cna_data -case_list_ids: P-0018973-T01-IM6 P-0062962-T01-IM7 P-0024888-T02-IM6 P-0025754-T02-IM6 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P-0014247-T01-IM6 P-0045969-T02-IM7 P-0052059-T01-IM6 P-0025754-T04-IM6 P-0042544-T01-IM6 P-0021560-T01-IM6 P-0036220-T01-IM6 P-0057514-T02-IM6 P-0006449-T01-IM5 P-0038101-T02-IM7 P-0007910-T01-IM5 P-0028773-T01-IM6 P-0044681-T09-IH3 P-0063511-T01-IM7 P-0038762-T02-IM6 P-0029072-T03-IM7 P-0010183-T01-IM5 P-0029150-T01-IM6 P-0025934-T01-IM6 P-0037672-T02-XS1 P-0000134-T02-IM3 P-0006875-T01-IM5 P-0005605-T01-IM5 P-0013433-T01-IM5 P-0007702-T02-IM6 P-0026349-T01-IM6 P-0054241-T01-IM6 P-0066506-T01-IM7 P-0014184-T08-XS1 P-0006293-T01-IM5 P-0053723-T01-IM6 P-0047565-T01-IM6 P-0001461-T01-IM3 P-0024492-T01-IM6 P-0006664-T01-IM5 P-0064040-T01-IM7 P-0046231-T01-IM6 P-0015826-T01-IM6 P-0027089-T02-IM6 P-0026918-T01-IM6 P-0009195-T01-IM5 P-0068099-T01-IM7 P-0054860-T02-IM6 P-0039196-T02-IM7 P-0046084-T01-IM6 P-0034094-T01-IM6 P-0005891-T01-IM5 P-0002680-T01-IM3 P-0052033-T01-IM6 P-0040924-T01-IM6 P-0040359-T01-IM6 P-0004776-T01-IM5 P-0058047-T01-IM6 P-0015913-T01-IM6 P-0014184-T07-XS1 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P-0026214-T03-IM6 P-0035576-T01-IM6 P-0015826-T03-IM6 P-0056816-T01-IM6 P-0065408-T01-IM7 P-0002726-T02-IM6 P-0063404-T01-IM7 P-0060395-T01-IM7 P-0012459-T02-IM6 P-0002594-T02-IM5 diff --git a/public/gist_msk_2022/case_lists/cases_cnaseq.txt b/public/gist_msk_2022/case_lists/cases_cnaseq.txt index cd66a410bf..aab272cf11 100755 --- a/public/gist_msk_2022/case_lists/cases_cnaseq.txt +++ b/public/gist_msk_2022/case_lists/cases_cnaseq.txt @@ -1,6 +1,6 @@ cancer_study_identifier: gist_msk_2022 stable_id: gist_msk_2022_cnaseq case_list_name: Samples with mutation and CNA data -case_list_description: Samples with mutation and CNA data (669 samples) +case_list_description: Samples with mutation and CNA data (499 samples) case_list_category: all_cases_with_mutation_and_cna_data -case_list_ids: P-0018973-T01-IM6 P-0062962-T01-IM7 P-0024888-T02-IM6 P-0025754-T02-IM6 P-0024288-T01-IM6 P-0039417-T01-IM6 P-0004937-T01-IM5 P-0043479-T01-IM6 P-0008084-T03-IM6 P-0066631-T01-IM7 P-0048138-T01-IM6 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P-0007230-T01-IM5 P-0015260-T01-IM6 P-0023543-T02-IM6 P-0042549-T01-IM6 P-0049529-T01-IM6 P-0007976-T01-IM5 P-0055232-T01-IM6 P-0038341-T01-IM6 P-0031080-T01-IM6 P-0008468-T01-IM5 P-0032359-T01-IM6 P-0005986-T01-IM5 P-0037522-T01-IM6 P-0052033-T02-IM7 P-0064725-T01-IM7 P-0007646-T01-IM5 P-0008247-T01-IM5 P-0019415-T01-IM6 P-0002409-T01-IM3 P-0026167-T01-IM6 P-0035173-T01-IM6 P-0005505-T01-IM5 P-0000501-T02-IM3 P-0038910-T01-IM6 P-0026343-T01-IM6 P-0026733-T02-IM6 P-0037918-T01-IM6 P-0054555-T01-IM6 P-0052126-T01-IM6 P-0021758-T01-IM6 P-0062194-T01-IM7 P-0043343-T01-IM6 P-0048547-T01-IM6 P-0022451-T01-IM6 P-0022727-T01-IM6 P-0054654-T01-IM6 P-0009156-T01-IM5 P-0020162-T01-IM6 P-0027089-T02-IM6 P-0037280-T02-IM6 P-0005626-T02-IM5 P-0012403-T05-IM6 P-0022831-T01-IM6 P-0014678-T01-IM6 P-0051670-T01-IM6 P-0014731-T01-IM6 P-0026342-T01-IM6 P-0003416-T02-IM5 P-0024904-T01-IM6 P-0003760-T01-IM5 P-0019004-T01-IM6 P-0013795-T01-IM5 P-0034265-T01-IM6 P-0028614-T01-IM6 P-0004883-T03-IM6 P-0044370-T01-IM6 P-0048138-T03-IM6 P-0031934-T01-IM6 P-0005330-T02-IM5 P-0046251-T01-IM6 P-0002477-T01-IM3 P-0015956-T01-IM6 P-0003384-T02-IM6 P-0001512-T01-IM3 P-0019438-T01-IM6 P-0026906-T03-IM6 P-0014683-T01-IM6 P-0034471-T01-IM6 P-0022237-T01-IM6 P-0063559-T01-IM7 P-0048006-T01-IM6 P-0040351-T02-IM6 P-0008486-T01-IM5 P-0006449-T01-IM5 P-0010629-T01-IM5 P-0050211-T01-IM6 P-0006104-T02-IM6 P-0016894-T02-IM6 P-0037285-T01-IM6 P-0006295-T01-IM5 P-0001461-T01-IM3 P-0028954-T01-IM6 P-0051984-T01-IM6 P-0014074-T01-IM5 P-0018583-T03-IM6 P-0059434-T01-IM7 P-0003490-T01-IM5 P-0010941-T01-IM5 P-0045947-T02-IM6 P-0014184-T04-IM6 P-0026754-T02-IM6 P-0011381-T01-IM5 P-0044291-T01-IM6 P-0061964-T01-IM7 P-0013410-T01-IM5 P-0025143-T01-IM6 P-0059436-T01-IM7 P-0008865-T01-IM5 P-0039414-T01-IM6 P-0001431-T02-IM6 P-0021667-T01-IM6 P-0051271-T01-IM6 P-0001157-T02-IM5 P-0014241-T01-IM6 P-0014295-T01-IM6 P-0050110-T02-IM6 P-0028553-T03-IM6 P-0014452-T01-IM6 P-0012411-T01-IM5 P-0008548-T03-IM6 P-0013007-T01-IM5 P-0023447-T01-IM6 P-0013039-T01-IM5 P-0026679-T02-IM6 P-0033833-T01-IM6 P-0049899-T02-IM7 P-0014592-T01-IM6 P-0028773-T02-IM6 P-0004509-T01-IM5 P-0028447-T02-IM6 P-0006991-T01-IM5 P-0031004-T01-IM6 P-0026664-T02-IM6 P-0010183-T02-IM6 P-0032950-T01-IM6 P-0049934-T01-IM6 P-0015279-T01-IM6 P-0028383-T01-IM6 P-0005923-T01-IM5 P-0063562-T01-IM7 P-0006325-T01-IM5 P-0026110-T01-IM6 P-0023107-T01-IM6 P-0047600-T01-IM6 P-0011178-T01-IM5 P-0010485-T01-IM5 P-0004639-T01-IM5 P-0007519-T01-IM5 P-0056963-T01-IM6 P-0053496-T02-IM7 P-0058185-T01-IM6 P-0000306-T01-IM3 P-0012007-T01-IM5 P-0004645-T01-IM5 P-0020724-T01-IM6 P-0038595-T01-IM6 P-0020389-T03-IM7 P-0061982-T01-IM7 P-0062837-T01-IM7 P-0026260-T01-IM6 P-0050450-T01-IM6 P-0019993-T02-IM6 P-0033188-T01-IM6 P-0017851-T01-IM6 P-0029524-T01-IM6 P-0017729-T02-IM6 P-0062533-T01-IM7 P-0036219-T01-IM6 P-0057636-T01-IM6 P-0059137-T01-IM7 P-0059657-T01-IM7 P-0001254-T02-IM3 P-0046483-T01-IM6 P-0064072-T01-IM7 P-0015041-T01-IM6 P-0004225-T01-IM5 P-0013024-T01-IM5 P-0018913-T02-IM6 P-0064900-T01-IM7 P-0044481-T01-IM6 P-0046440-T01-IM6 P-0015065-T01-IM6 P-0007890-T01-IM5 P-0005379-T02-IM6 P-0032539-T01-IM6 P-0042490-T01-IM6 P-0065847-T01-IM7 P-0012178-T01-IM5 P-0051981-T01-IM6 P-0014433-T04-IM6 P-0048953-T01-IM6 P-0013114-T05-IM6 P-0042260-T02-IM6 P-0004784-T01-IM5 P-0046896-T01-IM6 P-0007967-T01-IM5 P-0040551-T01-IM6 P-0004235-T01-IM5 P-0026845-T01-IM6 P-0066645-T01-IM7 P-0064526-T01-IM7 P-0040191-T01-IM6 P-0007501-T01-IM5 P-0066404-T01-IM7 P-0006712-T02-IM7 P-0007513-T03-IM5 P-0039747-T01-IM6 P-0004677-T01-IM5 P-0032636-T01-IM6 P-0017811-T01-IM6 P-0030447-T01-IM6 P-0044022-T01-IM6 P-0029134-T01-IM6 P-0005737-T02-IM5 P-0006473-T01-IM5 P-0014722-T01-IM6 P-0024161-T01-IM6 P-0000134-T02-IM3 P-0023549-T01-IM6 P-0027918-T02-IM6 P-0002293-T01-IM3 P-0031415-T02-IM7 P-0017859-T01-IM6 P-0054241-T02-IM6 P-0026214-T03-IM6 P-0035576-T01-IM6 P-0015826-T03-IM6 P-0056816-T01-IM6 P-0065408-T01-IM7 P-0002726-T02-IM6 P-0063404-T01-IM7 P-0060395-T01-IM7 P-0012459-T02-IM6 P-0002594-T02-IM5 \ No newline at end of file diff --git a/public/gist_msk_2022/case_lists/cases_sequenced.txt b/public/gist_msk_2022/case_lists/cases_sequenced.txt index cf38d9f90b..9e9f01e7c7 100755 --- a/public/gist_msk_2022/case_lists/cases_sequenced.txt +++ b/public/gist_msk_2022/case_lists/cases_sequenced.txt @@ -1,6 +1,6 @@ cancer_study_identifier: gist_msk_2022 stable_id: gist_msk_2022_sequenced case_list_name: Samples with mutation data -case_list_description: Samples with mutation data (669 samples) +case_list_description: Samples with mutation data (499 samples) case_list_category: all_cases_with_mutation_data -case_list_ids: P-0018973-T01-IM6 P-0062962-T01-IM7 P-0024888-T02-IM6 P-0025754-T02-IM6 P-0024288-T01-IM6 P-0039417-T01-IM6 P-0004937-T01-IM5 P-0043479-T01-IM6 P-0008084-T03-IM6 P-0066631-T01-IM7 P-0048138-T01-IM6 P-0013789-T01-IM5 P-0057812-T01-IM6 P-0052061-T04-IM7 P-0018677-T02-IM7 P-0054913-T01-IM6 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a/public/gist_msk_2022/case_lists/cases_sv.txt b/public/gist_msk_2022/case_lists/cases_sv.txt index c1af774795..b61b7477ed 100755 --- a/public/gist_msk_2022/case_lists/cases_sv.txt +++ b/public/gist_msk_2022/case_lists/cases_sv.txt @@ -1,6 +1,6 @@ cancer_study_identifier: gist_msk_2022 stable_id: gist_msk_2022_sv case_list_name: Samples with SV data -case_list_description: All samples (669 samples) +case_list_description: All samples with SV data (499 samples) case_list_category: all_cases_with_sv_data -case_list_ids: P-0018973-T01-IM6 P-0062962-T01-IM7 P-0024888-T02-IM6 P-0025754-T02-IM6 P-0024288-T01-IM6 P-0039417-T01-IM6 P-0004937-T01-IM5 P-0043479-T01-IM6 P-0008084-T03-IM6 P-0066631-T01-IM7 P-0048138-T01-IM6 P-0013789-T01-IM5 P-0057812-T01-IM6 P-0052061-T04-IM7 P-0018677-T02-IM7 P-0054913-T01-IM6 P-0044076-T01-IM6 P-0038669-T01-IM6 P-0028553-T02-IM6 P-0067881-T01-IM7 P-0014521-T01-IM6 P-0017729-T01-IM6 P-0014330-T01-IM6 P-0004760-T03-IM7 P-0017387-T01-IM6 P-0048280-T02-IM6 P-0001692-T02-IM3 P-0004937-T03-IM6 P-0052582-T01-IM6 P-0001512-T01-IM3 P-0016868-T01-IM6 P-0031480-T01-IM6 P-0006638-T01-IM5 P-0025653-T01-IM6 P-0022363-T01-IM6 P-0049663-T01-IM6 P-0015145-T01-IM6 P-0014184-T03-IM6 P-0035634-T01-IM6 P-0004760-T01-IM5 P-0044681-T03-IH3 P-0037156-T01-IM6 P-0044303-T01-IM6 P-0014933-T01-IM6 P-0061177-T01-IM7 P-0013188-T01-IM5 P-0002525-T01-IM3 P-0053921-T03-IM7 P-0064686-T01-IM7 P-0030194-T01-IM6 P-0024909-T01-IM6 P-0025633-T01-IM6 P-0044039-T01-IM6 P-0064216-T01-IM7 P-0028138-T01-IM6 P-0033352-T01-IM6 P-0012185-T01-IM5 P-0033478-T01-IM6 P-0006932-T01-IM5 P-0014247-T01-IM6 P-0045969-T02-IM7 P-0052059-T01-IM6 P-0025754-T04-IM6 P-0042544-T01-IM6 P-0021560-T01-IM6 P-0036220-T01-IM6 P-0057514-T02-IM6 P-0006449-T01-IM5 P-0038101-T02-IM7 P-0007910-T01-IM5 P-0028773-T01-IM6 P-0044681-T09-IH3 P-0063511-T01-IM7 P-0038762-T02-IM6 P-0029072-T03-IM7 P-0010183-T01-IM5 P-0029150-T01-IM6 P-0025934-T01-IM6 P-0037672-T02-XS1 P-0000134-T02-IM3 P-0006875-T01-IM5 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