From 438e7e4169200607196a8833a07a076224bc6d9d Mon Sep 17 00:00:00 2001 From: Ramya Madupuri <34350829+rmadupuri@users.noreply.github.com> Date: Fri, 15 Nov 2024 16:35:14 -0500 Subject: [PATCH] Add Tumor Break Load Scores for Pancan, PCAWG, CCLE studies (#2092) * add Tumor Break Load Scores for pancan studies * add TBL scores for pcawg, ccle study * initial commit * update meta data * update TBL Scores * add TBL documentation --- public/acc_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../acc_tcga_pan_can_atlas_2018/data_clinical_sample.txt | 4 ++-- public/acc_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/blca_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/blca_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/brca_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/brca_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/ccle_broad_2019/README.md | 7 +++++++ public/ccle_broad_2019/data_clinical_sample.txt | 4 ++-- public/cesc_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/cesc_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/chol_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/chol_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/coadread_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/coadread_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/dlbc_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/dlbc_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/esca_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/esca_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/gbm_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../gbm_tcga_pan_can_atlas_2018/data_clinical_sample.txt | 4 ++-- public/gbm_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/hnsc_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/hnsc_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/kich_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/kich_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/kirc_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/kirc_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/kirp_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/kirp_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/laml_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/laml_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/lgg_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../lgg_tcga_pan_can_atlas_2018/data_clinical_sample.txt | 4 ++-- public/lgg_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/lihc_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/lihc_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/luad_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/luad_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/lusc_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/lusc_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/meso_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/meso_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/ov_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../ov_tcga_pan_can_atlas_2018/data_clinical_sample.txt | 4 ++-- public/ov_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/paad_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/paad_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/pancan_pcawg_2020/README.md | 7 +++++++ public/pancan_pcawg_2020/data_clinical_sample.txt | 4 ++-- public/pancan_pcawg_2020/meta_resource_definition.txt | 3 +++ public/pancan_pcawg_2020/meta_study.txt | 2 +- public/pcpg_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/pcpg_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/prad_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/prad_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/sarc_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/sarc_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/skcm_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/skcm_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/stad_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/stad_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/tgct_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/tgct_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/thca_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/thca_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/thym_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/thym_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/ucec_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../data_clinical_sample.txt | 4 ++-- public/ucec_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/ucs_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../ucs_tcga_pan_can_atlas_2018/data_clinical_sample.txt | 4 ++-- public/ucs_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- public/uvm_tcga_pan_can_atlas_2018/README.md | 9 ++++++++- .../uvm_tcga_pan_can_atlas_2018/data_clinical_sample.txt | 4 ++-- public/uvm_tcga_pan_can_atlas_2018/meta_study.txt | 2 +- 102 files changed, 374 insertions(+), 133 deletions(-) create mode 100644 public/pancan_pcawg_2020/meta_resource_definition.txt diff --git a/public/acc_tcga_pan_can_atlas_2018/README.md b/public/acc_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/acc_tcga_pan_can_atlas_2018/README.md +++ b/public/acc_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/acc_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/acc_tcga_pan_can_atlas_2018/data_clinical_sample.txt index 21b3cce710..6c8b9572d0 100644 --- a/public/acc_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/acc_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:9a1d1c7f04017842c4d4dd0f082eab66887883acfdd0d1c46420c9e75021f0cd -size 21056 +oid sha256:902079901f973f6b1ca598ea60dcfdf8e09dcf46761ff9137d1bfc7618439395 +size 21521 diff --git a/public/acc_tcga_pan_can_atlas_2018/meta_study.txt b/public/acc_tcga_pan_can_atlas_2018/meta_study.txt index 69bbe861d8..5bcbbd1884 100644 --- a/public/acc_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/acc_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Adrenocortical Carcinoma (TCGA, PanCancer Atlas) short_name: ACC (TCGA PanCan 2018) description: Adrenocortical Carcinoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/blca_tcga_pan_can_atlas_2018/README.md b/public/blca_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/blca_tcga_pan_can_atlas_2018/README.md +++ b/public/blca_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/blca_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/blca_tcga_pan_can_atlas_2018/data_clinical_sample.txt index 84ac3d9ba1..8dc73445da 100644 --- a/public/blca_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/blca_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:bca3bebb7e373c62115de38f170d49714d056052ae1245f8e3a4a2dd6064e9b2 -size 92838 +oid sha256:0addd03ac8ed17879a8809f7dd1cd663765da559bd35be9414a84f95307db5c3 +size 94436 diff --git a/public/blca_tcga_pan_can_atlas_2018/meta_study.txt b/public/blca_tcga_pan_can_atlas_2018/meta_study.txt index 1f32501c4c..0c81a047a9 100644 --- a/public/blca_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/blca_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Bladder Urothelial Carcinoma (TCGA, PanCancer Atlas) short_name: Bladder (TCGA PanCan 2018) description: Bladder Urothelial Carcinoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/brca_tcga_pan_can_atlas_2018/README.md b/public/brca_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/brca_tcga_pan_can_atlas_2018/README.md +++ b/public/brca_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/brca_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/brca_tcga_pan_can_atlas_2018/data_clinical_sample.txt index 82c454b372..8895f2ed24 100644 --- a/public/brca_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/brca_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:33531fd2bb788f25bb494d737f850a19353c98283588936d72d151b4a144f9b7 -size 200366 +oid sha256:e96e6e4895a6ddcdb31d508a9e8f5676ca78ce396d2f82cd111a286a17e75ca6 +size 204137 diff --git a/public/brca_tcga_pan_can_atlas_2018/meta_study.txt b/public/brca_tcga_pan_can_atlas_2018/meta_study.txt index e36a2d424b..be24c3f5d9 100644 --- a/public/brca_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/brca_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Breast Invasive Carcinoma (TCGA, PanCancer Atlas) short_name: Breast Invasive Carcinoma Breast (TCGA PanCan 2018) description: Breast Invasive Carcinoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/ccle_broad_2019/README.md b/public/ccle_broad_2019/README.md index cf44bb657b..f9b3417c94 100644 --- a/public/ccle_broad_2019/README.md +++ b/public/ccle_broad_2019/README.md @@ -13,3 +13,10 @@ Proteomics data: https://gygi.hms.harvard.edu/data/ccle/protein_quant_current_no - 2130 (17%) of the proteins returned non-unique gene IDs, indicating that some proteins originated from the same gene. The duplicates were collapsed to per per-gene values by taking the average. - A matrix was generated containing Z-scores derived from the log2-ratios per-gene. This enables the user to select protein abundance values as a separate profile from the query-by-gene interface in cBioPortal. - Sample annotations were added to the clinical sample data indicating the 10-Plex ID and the TMT label. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/ccle_broad_2019/data_clinical_sample.txt b/public/ccle_broad_2019/data_clinical_sample.txt index da648d7e20..f3e0acc447 100644 --- a/public/ccle_broad_2019/data_clinical_sample.txt +++ b/public/ccle_broad_2019/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:aaff0fbb4b53cfbc4195040f65408bc19f577f43440560ff77f1a36e15658506 -size 579588 +oid sha256:7b72ace385c02d3c1037330749306dd86a7ecbb5983f55715416a5bbebffaa02 +size 582349 diff --git a/public/cesc_tcga_pan_can_atlas_2018/README.md b/public/cesc_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/cesc_tcga_pan_can_atlas_2018/README.md +++ b/public/cesc_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/cesc_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/cesc_tcga_pan_can_atlas_2018/data_clinical_sample.txt index 2b2762ea4a..38dc96091a 100644 --- a/public/cesc_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/cesc_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:69d099780dde9caaef881f35d0369beeb33130be94805ed0a97ce1ed27e25db7 -size 60695 +oid sha256:1ad7360fee3539eced5cd758bb4a2c7d0790b1dea38a26295be5f0085bdef161 +size 61778 diff --git a/public/cesc_tcga_pan_can_atlas_2018/meta_study.txt b/public/cesc_tcga_pan_can_atlas_2018/meta_study.txt index 86c869d7ca..ed1fbc737e 100644 --- a/public/cesc_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/cesc_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Cervical Squamous Cell Carcinoma (TCGA, PanCancer Atlas) short_name: Cervical (TCGA PanCan) description: Cervical Squamous Cell Carcinoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/chol_tcga_pan_can_atlas_2018/README.md b/public/chol_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/chol_tcga_pan_can_atlas_2018/README.md +++ b/public/chol_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/chol_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/chol_tcga_pan_can_atlas_2018/data_clinical_sample.txt index f1c0ad2e76..7f1b997191 100644 --- a/public/chol_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/chol_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:7b51c0c31e12ac22be1279143c8c2fb899a300bf66b2b794e9576d00d126827a -size 8969 +oid sha256:d9ef53317ee291ebc5ae757c7b9806cb945e6b6432cbd1c8c90db42e6aa3d1cf +size 9255 diff --git a/public/chol_tcga_pan_can_atlas_2018/meta_study.txt b/public/chol_tcga_pan_can_atlas_2018/meta_study.txt index 0566ac1a40..28e1776c93 100644 --- a/public/chol_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/chol_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Cholangiocarcinoma (TCGA, PanCancer Atlas) short_name: Cholangiocarcinoma (TCGA PanCan) description: Cholangiocarcinoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/coadread_tcga_pan_can_atlas_2018/README.md b/public/coadread_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/coadread_tcga_pan_can_atlas_2018/README.md +++ b/public/coadread_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/coadread_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/coadread_tcga_pan_can_atlas_2018/data_clinical_sample.txt index cc1debade6..5d02a481dc 100644 --- a/public/coadread_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/coadread_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:696dbd287e2d222105b341918f5fbe7e365773e28aa3302d30b1be4d0277684c -size 103825 +oid sha256:b9cbcc7cbc7471b44a3767aac48d4d0625001e3c07f8776c50f77364341f7817 +size 105858 diff --git a/public/coadread_tcga_pan_can_atlas_2018/meta_study.txt b/public/coadread_tcga_pan_can_atlas_2018/meta_study.txt index ae052f2c32..9b3416e0dc 100644 --- a/public/coadread_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/coadread_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Colorectal Adenocarcinoma (TCGA, PanCancer Atlas) short_name: Colorectal (TCGA PanCan) description: Colorectal Adenocarcinoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/dlbc_tcga_pan_can_atlas_2018/README.md b/public/dlbc_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/dlbc_tcga_pan_can_atlas_2018/README.md +++ b/public/dlbc_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/dlbc_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/dlbc_tcga_pan_can_atlas_2018/data_clinical_sample.txt index e248baef10..b5ac004d02 100644 --- a/public/dlbc_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/dlbc_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:02b22aad44a44deaa06d5fce35f3c271d507e6797c376bd407ba212d0bb2bcd9 -size 12312 +oid sha256:bf4388fc2859f652535f11bc14621f4e6d46b53563a000177c17214f923c133d +size 12633 diff --git a/public/dlbc_tcga_pan_can_atlas_2018/meta_study.txt b/public/dlbc_tcga_pan_can_atlas_2018/meta_study.txt index b6ae8f9e04..5324238fb0 100644 --- a/public/dlbc_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/dlbc_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Diffuse Large B-Cell Lymphoma (TCGA, PanCancer Atlas) short_name: DLBC (TCGA PanCan) description: Diffuse Large B-Cell Lymphoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/esca_tcga_pan_can_atlas_2018/README.md b/public/esca_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/esca_tcga_pan_can_atlas_2018/README.md +++ b/public/esca_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/esca_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/esca_tcga_pan_can_atlas_2018/data_clinical_sample.txt index b110fce96a..a7dcc80fd6 100644 --- a/public/esca_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/esca_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:3966037210f1c2080f796e0e7d77e6932604acc25d8b999bc61b0be106aa344d -size 38141 +oid sha256:0f868028bf50767bf742615bfb5bf25b17ef2bfe5a24647e4681a81315a4ce58 +size 38990 diff --git a/public/esca_tcga_pan_can_atlas_2018/meta_study.txt b/public/esca_tcga_pan_can_atlas_2018/meta_study.txt index 35e8952e9e..a74727d46c 100644 --- a/public/esca_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/esca_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Esophageal Adenocarcinoma (TCGA, PanCancer Atlas) short_name: Esophagus (TCGA PanCan) description: Esophageal Adenocarcinoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/gbm_tcga_pan_can_atlas_2018/README.md b/public/gbm_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/gbm_tcga_pan_can_atlas_2018/README.md +++ b/public/gbm_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/gbm_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/gbm_tcga_pan_can_atlas_2018/data_clinical_sample.txt index 1c06deaa42..3780915bb5 100644 --- a/public/gbm_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/gbm_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:d9a6af1a5f9d195fc04bbc25f2cb2c80157a4e40cb861994845a6582390b4e11 -size 104953 +oid sha256:d63bd951527a84616328ce3a71838f4d3815055e6db8bb7f0d1673932c780168 +size 106982 diff --git a/public/gbm_tcga_pan_can_atlas_2018/meta_study.txt b/public/gbm_tcga_pan_can_atlas_2018/meta_study.txt index d5f101f2c0..ef197f6dbc 100644 --- a/public/gbm_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/gbm_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Glioblastoma Multiforme (TCGA, PanCancer Atlas) short_name: GBM (TCGA PanCan) description: Glioblastoma Multiforme TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/hnsc_tcga_pan_can_atlas_2018/README.md b/public/hnsc_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/hnsc_tcga_pan_can_atlas_2018/README.md +++ b/public/hnsc_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/hnsc_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/hnsc_tcga_pan_can_atlas_2018/data_clinical_sample.txt index 9f0600e25e..f4b9828449 100644 --- a/public/hnsc_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/hnsc_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:368b08bff2a6bea440cbc2e496468a1a8e1a5dada2914e1f10624b48b37a67c4 -size 116818 +oid sha256:cb7beef2111e56636674f50af28d5653f416ea2ca5ccaa2704448c3e13864fcb +size 118661 diff --git a/public/hnsc_tcga_pan_can_atlas_2018/meta_study.txt b/public/hnsc_tcga_pan_can_atlas_2018/meta_study.txt index 5b9862ef0f..59f0051609 100644 --- a/public/hnsc_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/hnsc_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Head and Neck Squamous Cell Carcinoma (TCGA, PanCancer Atlas) short_name: Head & neck (TCGA PanCan) description: Head and Neck Squamous Cell Carcinoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/kich_tcga_pan_can_atlas_2018/README.md b/public/kich_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/kich_tcga_pan_can_atlas_2018/README.md +++ b/public/kich_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/kich_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/kich_tcga_pan_can_atlas_2018/data_clinical_sample.txt index a7d4b20c54..3dfda9bef1 100644 --- a/public/kich_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/kich_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:671c3bbee0b0323b520d309dfd201c33bc6b4b926998881743acb5cf14dbb8df -size 15559 +oid sha256:710f1e87d0cbed4f23f58fd623ecba66dfbb4e6b8fe57ddf95ffa96dfc87e8a3 +size 15886 diff --git a/public/kich_tcga_pan_can_atlas_2018/meta_study.txt b/public/kich_tcga_pan_can_atlas_2018/meta_study.txt index c69e9be4c4..3ea0f33eb3 100644 --- a/public/kich_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/kich_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Kidney Chromophobe (TCGA, PanCancer Atlas) short_name: chromophobe RCC (TCGA PanCan) description: Kidney Chromophobe TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/kirc_tcga_pan_can_atlas_2018/README.md b/public/kirc_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/kirc_tcga_pan_can_atlas_2018/README.md +++ b/public/kirc_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/kirc_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/kirc_tcga_pan_can_atlas_2018/data_clinical_sample.txt index bf2e6ab606..f989b43a6a 100644 --- a/public/kirc_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/kirc_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:b675f13c9c6d85aa2fb33b07e67298262ae7a2b220acbe7fb349c438c3c06eac -size 101321 +oid sha256:dc8353955113fb2927fc848539a88cdf631f0561e781df9c05b34605904d748c +size 102856 diff --git a/public/kirc_tcga_pan_can_atlas_2018/meta_study.txt b/public/kirc_tcga_pan_can_atlas_2018/meta_study.txt index ed1e06bac4..2eeb9efed3 100644 --- a/public/kirc_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/kirc_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Kidney Renal Clear Cell Carcinoma (TCGA, PanCancer Atlas) short_name: ccRCC (TCGA PanCan) description: Kidney Renal Clear Cell Carcinoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/kirp_tcga_pan_can_atlas_2018/README.md b/public/kirp_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/kirp_tcga_pan_can_atlas_2018/README.md +++ b/public/kirp_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/kirp_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/kirp_tcga_pan_can_atlas_2018/data_clinical_sample.txt index 7082f3fb53..5552559f7d 100644 --- a/public/kirp_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/kirp_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:afb3e6b227aef806b66ee954488344022dd5686ca566eadbd6f38e2f23fb40bb -size 62003 +oid sha256:b75e74a4c719d052bdb71517f094431dfe1aef7a336aa823a881b8a3e8572aa7 +size 62841 diff --git a/public/kirp_tcga_pan_can_atlas_2018/meta_study.txt b/public/kirp_tcga_pan_can_atlas_2018/meta_study.txt index 3dd068ce17..4042f492e7 100644 --- a/public/kirp_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/kirp_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Kidney Renal Papillary Cell Carcinoma (TCGA, PanCancer Atlas) short_name: pRCC (TCGA PanCan) description: Kidney Renal Papillary Cell Carcinoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/laml_tcga_pan_can_atlas_2018/README.md b/public/laml_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/laml_tcga_pan_can_atlas_2018/README.md +++ b/public/laml_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/laml_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/laml_tcga_pan_can_atlas_2018/data_clinical_sample.txt index 5d3e0659bf..6f2b01fb6a 100644 --- a/public/laml_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/laml_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:fe1056309650084909815659cdba7248561aecfcdd030aadc6f7233bc3c65999 -size 32499 +oid sha256:56bb2daa4aab210ce79557cfbd2021000d492c22296a2edbabda7168bf62f6cc +size 33119 diff --git a/public/laml_tcga_pan_can_atlas_2018/meta_study.txt b/public/laml_tcga_pan_can_atlas_2018/meta_study.txt index 02beecc92a..5d6a95c06f 100644 --- a/public/laml_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/laml_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Acute Myeloid Leukemia (TCGA, PanCancer Atlas) short_name: AML (TCGA PanCan) description: Acute Myeloid Leukemia TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/lgg_tcga_pan_can_atlas_2018/README.md b/public/lgg_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/lgg_tcga_pan_can_atlas_2018/README.md +++ b/public/lgg_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/lgg_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/lgg_tcga_pan_can_atlas_2018/data_clinical_sample.txt index bc54055cfa..6485648dcd 100644 --- a/public/lgg_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/lgg_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:efa37c1eb4953b215178b83979d93e9d0c673570f9b102cbbaed24a8741718d3 -size 78058 +oid sha256:d12e1546ad7fcd2cc724028127bcb93aee419f0c12a8b005ddb162c28a298254 +size 79602 diff --git a/public/lgg_tcga_pan_can_atlas_2018/meta_study.txt b/public/lgg_tcga_pan_can_atlas_2018/meta_study.txt index 4ae05482bf..19ce3a67b4 100644 --- a/public/lgg_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/lgg_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Brain Lower Grade Glioma (TCGA, PanCancer Atlas) short_name: LGG (TCGA PanCan) description: Brain Lower Grade Glioma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/lihc_tcga_pan_can_atlas_2018/README.md b/public/lihc_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/lihc_tcga_pan_can_atlas_2018/README.md +++ b/public/lihc_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/lihc_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/lihc_tcga_pan_can_atlas_2018/data_clinical_sample.txt index faed7ef93b..b5ee4f547b 100644 --- a/public/lihc_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/lihc_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:1c6ee90105d5fe6c1dd0f4c9afe53456133e66bc95b12a35ac2c2e8434cdf3ba -size 69355 +oid sha256:a078658d00505906dee1edf7fcd21202f3ddeb6bfd4a2645ecc66591a6d905de +size 70707 diff --git a/public/lihc_tcga_pan_can_atlas_2018/meta_study.txt b/public/lihc_tcga_pan_can_atlas_2018/meta_study.txt index e8474495da..68a477a8e2 100644 --- a/public/lihc_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/lihc_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Liver Hepatocellular Carcinoma (TCGA, PanCancer Atlas) short_name: Liver (TCGA PanCan) description: Liver Hepatocellular Carcinoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/luad_tcga_pan_can_atlas_2018/README.md b/public/luad_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/luad_tcga_pan_can_atlas_2018/README.md +++ b/public/luad_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/luad_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/luad_tcga_pan_can_atlas_2018/data_clinical_sample.txt index 6be64f3591..ff92995031 100644 --- a/public/luad_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/luad_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:22d4e9717a768b874e71a95f0caa7c5fbd8e66590b434b9c51d5adb87505db77 -size 109496 +oid sha256:b443896a6aed8256f3aa1b5e2f41e700392c76461be10936d2c344988bc5d84e +size 111469 diff --git a/public/luad_tcga_pan_can_atlas_2018/meta_study.txt b/public/luad_tcga_pan_can_atlas_2018/meta_study.txt index 59fef361b5..af4b5668ab 100644 --- a/public/luad_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/luad_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Lung Adenocarcinoma (TCGA, PanCancer Atlas) short_name: Lung adeno (TCGA PanCan) description: Lung Adenocarcinoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/lusc_tcga_pan_can_atlas_2018/README.md b/public/lusc_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/lusc_tcga_pan_can_atlas_2018/README.md +++ b/public/lusc_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/lusc_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/lusc_tcga_pan_can_atlas_2018/data_clinical_sample.txt index 8ad6a5b4ca..793a322756 100644 --- a/public/lusc_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/lusc_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:519fd5bf94f95c3ada9bd3e1093ddaae4b1c868ace8f0cea084d1e22be507ad0 -size 101440 +oid sha256:d30c4fe3655331d67411dda67cac8af08e8616070b213c998cf84c6453315aae +size 103338 diff --git a/public/lusc_tcga_pan_can_atlas_2018/meta_study.txt b/public/lusc_tcga_pan_can_atlas_2018/meta_study.txt index 730b817a56..6c5902d3cf 100644 --- a/public/lusc_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/lusc_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Lung Squamous Cell Carcinoma (TCGA, PanCancer Atlas) short_name: Lung squ (TCGA PanCan) description: Lung Squamous Cell Carcinoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/meso_tcga_pan_can_atlas_2018/README.md b/public/meso_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/meso_tcga_pan_can_atlas_2018/README.md +++ b/public/meso_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/meso_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/meso_tcga_pan_can_atlas_2018/data_clinical_sample.txt index 18b5933a2a..a58417a343 100644 --- a/public/meso_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/meso_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:d447b86600f1d94122b0188eb429868b86bda4abab5f53a2bccae2bc9c9e8d46 -size 19771 +oid sha256:6166fe9a8ed03310d0e1efd11bd44797c7ea5eef6252653debd2002fb83eb1c1 +size 20214 diff --git a/public/meso_tcga_pan_can_atlas_2018/meta_study.txt b/public/meso_tcga_pan_can_atlas_2018/meta_study.txt index f4982ea26e..9b403aa391 100644 --- a/public/meso_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/meso_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Mesothelioma (TCGA, PanCancer Atlas) short_name: Mesothelioma (TCGA PanCan 2018) description: Mesothelioma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/ov_tcga_pan_can_atlas_2018/README.md b/public/ov_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/ov_tcga_pan_can_atlas_2018/README.md +++ b/public/ov_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/ov_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/ov_tcga_pan_can_atlas_2018/data_clinical_sample.txt index c61ad2c400..741aead6db 100644 --- a/public/ov_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/ov_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:41dda2f14ad4f5f3b1c253baae4e1863cf6e596d06283e7b7c00805bab8f8613 -size 107183 +oid sha256:f2196f64c8f32eb69eb927d5c383fd2f69ac2c4406a4954f715cff80febfcb0a +size 109610 diff --git a/public/ov_tcga_pan_can_atlas_2018/meta_study.txt b/public/ov_tcga_pan_can_atlas_2018/meta_study.txt index 13bad11aa9..0294db6d0b 100644 --- a/public/ov_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/ov_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Ovarian Serous Cystadenocarcinoma (TCGA, PanCancer Atlas) short_name: Ovarian (TCGA PanCan 2018) description: Ovarian Serous Cystadenocarcinoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/paad_tcga_pan_can_atlas_2018/README.md b/public/paad_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/paad_tcga_pan_can_atlas_2018/README.md +++ b/public/paad_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/paad_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/paad_tcga_pan_can_atlas_2018/data_clinical_sample.txt index 15cfb1935a..3903eaf990 100644 --- a/public/paad_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/paad_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:d546561a8e101c537b4092a559554c8e2839ef042d4fd5f2796a53ec14e347e5 -size 38281 +oid sha256:557fdead8f0376156048947aac32cbfc92f7770be9ffb1aa2f0883ff677a457c +size 38978 diff --git a/public/paad_tcga_pan_can_atlas_2018/meta_study.txt b/public/paad_tcga_pan_can_atlas_2018/meta_study.txt index 48bf0b0f36..0f1721e3a8 100644 --- a/public/paad_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/paad_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Pancreatic Adenocarcinoma (TCGA, PanCancer Atlas) short_name: Pancreas (TCGA PanCan 2018) description: Pancreatic Adenocarcinoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/pancan_pcawg_2020/README.md b/public/pancan_pcawg_2020/README.md index 215f1418e4..3599ee583d 100644 --- a/public/pancan_pcawg_2020/README.md +++ b/public/pancan_pcawg_2020/README.md @@ -20,3 +20,10 @@ Only samples present in the cBioPortal study were included. The mutational matrix was extracted from the `data_mutations.txt` file using SigProfilerMatrixGenerator python package (v1.2.15) and the included reference genome GRCh37 (`SigProfilerMatrixGenerator.install.install('GRCh37')`). Only samples with contribution scores were included. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/pancan_pcawg_2020/data_clinical_sample.txt b/public/pancan_pcawg_2020/data_clinical_sample.txt index 217cba28f4..ce29e2e92f 100644 --- a/public/pancan_pcawg_2020/data_clinical_sample.txt +++ b/public/pancan_pcawg_2020/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:dde20c28b12c18c2c6a3eb4615acb623e500970f903f22be04edb296150b9569 -size 791335 +oid sha256:548380b7b008845aa2a077aa917ddb328af835b3bff7f08df5615f2b485dcaa0 +size 799763 diff --git a/public/pancan_pcawg_2020/meta_resource_definition.txt b/public/pancan_pcawg_2020/meta_resource_definition.txt new file mode 100644 index 0000000000..bf5aa3f0e1 --- /dev/null +++ b/public/pancan_pcawg_2020/meta_resource_definition.txt @@ -0,0 +1,3 @@ +cancer_study_identifier: pancan_pcawg_2020 +resource_type: DEFINITION +data_filename: data_resource_definition.txt \ No newline at end of file diff --git a/public/pancan_pcawg_2020/meta_study.txt b/public/pancan_pcawg_2020/meta_study.txt index 55d69e1ff9..977804f4ba 100644 --- a/public/pancan_pcawg_2020/meta_study.txt +++ b/public/pancan_pcawg_2020/meta_study.txt @@ -4,4 +4,4 @@ name: Pan-cancer analysis of whole genomes (ICGC/TCGA, Nature 2020) description: WGS changes cataloged in 2,583 whole-cancer genomes and their matched normal tissues across 38 tumor types. Source data from UCSC Xena and ICGC Data Portal. citation: Campbell et al. Nature 2020 short_name: PCAWG (ICGC/TCGA) -pmid: 32025007 \ No newline at end of file +pmid: 32025007 diff --git a/public/pcpg_tcga_pan_can_atlas_2018/README.md b/public/pcpg_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/pcpg_tcga_pan_can_atlas_2018/README.md +++ b/public/pcpg_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/pcpg_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/pcpg_tcga_pan_can_atlas_2018/data_clinical_sample.txt index b904e6b026..443e5147bb 100644 --- a/public/pcpg_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/pcpg_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:1a8b053dec51baf18163abbfdc07b29b6d1f874d3e3a813da3df35866d136402 -size 33225 +oid sha256:9f8752b15f36c94452849f88d5f22651fff38ebdb398f7ab4f556fd9f96e1e0c +size 33879 diff --git a/public/pcpg_tcga_pan_can_atlas_2018/meta_study.txt b/public/pcpg_tcga_pan_can_atlas_2018/meta_study.txt index cfff2d3825..8b0108cdc5 100644 --- a/public/pcpg_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/pcpg_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Pheochromocytoma and Paraganglioma (TCGA, PanCancer Atlas) short_name: PCPG (TCGA PanCan 2018) description: Pheochromocytoma and Paraganglioma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/prad_tcga_pan_can_atlas_2018/README.md b/public/prad_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/prad_tcga_pan_can_atlas_2018/README.md +++ b/public/prad_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/prad_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/prad_tcga_pan_can_atlas_2018/data_clinical_sample.txt index 3598ec8d5a..b1eaa9b0cc 100644 --- a/public/prad_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/prad_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:5746a4e33a0236cdac824c33e9480f4f5345cef13b28bc597452fa1fb0901e91 -size 98036 +oid sha256:f98d060c2ee54c54f2519d062473b78a3accad8c53dc6d8a58d1180aaaeff993 +size 99734 diff --git a/public/prad_tcga_pan_can_atlas_2018/meta_study.txt b/public/prad_tcga_pan_can_atlas_2018/meta_study.txt index 19623ddfdd..081d49a535 100644 --- a/public/prad_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/prad_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Prostate Adenocarcinoma (TCGA, PanCancer Atlas) short_name: Prostate (TCGA PanCan 2018) description: Prostate Adenocarcinoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/sarc_tcga_pan_can_atlas_2018/README.md b/public/sarc_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/sarc_tcga_pan_can_atlas_2018/README.md +++ b/public/sarc_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/sarc_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/sarc_tcga_pan_can_atlas_2018/data_clinical_sample.txt index 58505e2ec7..d0837af67b 100644 --- a/public/sarc_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/sarc_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:eea7a4d9b6b63a7cb2bec182f3548a54ab841b2028d398dc0de666d412558e6c -size 51451 +oid sha256:ef919038bd6bd6803fe84e67b4a966e60301e7fd421ed10e3ea767245cce6c44 +size 52542 diff --git a/public/sarc_tcga_pan_can_atlas_2018/meta_study.txt b/public/sarc_tcga_pan_can_atlas_2018/meta_study.txt index b0e3b722ac..9de6bafbf8 100644 --- a/public/sarc_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/sarc_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Sarcoma (TCGA, PanCancer Atlas) short_name: Sarcoma (TCGA PanCan 2018) description: Sarcoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/skcm_tcga_pan_can_atlas_2018/README.md b/public/skcm_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/skcm_tcga_pan_can_atlas_2018/README.md +++ b/public/skcm_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/skcm_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/skcm_tcga_pan_can_atlas_2018/data_clinical_sample.txt index cdb8f08385..2dcc42edc8 100644 --- a/public/skcm_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/skcm_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:20469ab8a19295f2c5f3fce0ebbb5ccfc3ee8955b0ef3a8773f5e064bad509b2 -size 82192 +oid sha256:1da0e866ba04db38a3efc98da78bff1ffb6204558859c7546683f791995fc90d +size 82995 diff --git a/public/skcm_tcga_pan_can_atlas_2018/meta_study.txt b/public/skcm_tcga_pan_can_atlas_2018/meta_study.txt index ea373fa350..f68dd083d2 100644 --- a/public/skcm_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/skcm_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Skin Cutaneous Melanoma (TCGA, PanCancer Atlas) short_name: Melanoma (TCGA PanCan 2018) description: Skin Cutaneous Melanoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/stad_tcga_pan_can_atlas_2018/README.md b/public/stad_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/stad_tcga_pan_can_atlas_2018/README.md +++ b/public/stad_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/stad_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/stad_tcga_pan_can_atlas_2018/data_clinical_sample.txt index be17702a7c..ab552a4817 100644 --- a/public/stad_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/stad_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:26ce81cc94aa402d93f7f09733b80c3220c7aa75c5c14d022dafcae5c6241cd4 -size 91514 +oid sha256:e082f706bbbb5ff1104389b93cdc852f9dd31019b0bcf4afcbf7d7654cb2ace1 +size 93194 diff --git a/public/stad_tcga_pan_can_atlas_2018/meta_study.txt b/public/stad_tcga_pan_can_atlas_2018/meta_study.txt index 0faf00e01f..599453ccee 100644 --- a/public/stad_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/stad_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Stomach Adenocarcinoma (TCGA, PanCancer Atlas) short_name: Stomach (TCGA PanCan 2018) description: Stomach Adenocarcinoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/tgct_tcga_pan_can_atlas_2018/README.md b/public/tgct_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/tgct_tcga_pan_can_atlas_2018/README.md +++ b/public/tgct_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/tgct_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/tgct_tcga_pan_can_atlas_2018/data_clinical_sample.txt index ea3d16678c..fc43baf5a9 100644 --- a/public/tgct_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/tgct_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:f2469fcc4ed9b55066e4197c9fe697b9cbd0c8cfae4b8b7b38483544aab9a17b -size 30743 +oid sha256:a1f9831e0806ddf4672928037c215032b6ac6461ff34fd445c2e4c9ce387627a +size 31359 diff --git a/public/tgct_tcga_pan_can_atlas_2018/meta_study.txt b/public/tgct_tcga_pan_can_atlas_2018/meta_study.txt index 087f6b5cf9..a880d81bec 100644 --- a/public/tgct_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/tgct_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Testicular Germ Cell Tumors (TCGA, PanCancer Atlas) short_name: Testicular germ cell (TCGA PanCan 2018) description: Testicular Germ Cell Tumors TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/thca_tcga_pan_can_atlas_2018/README.md b/public/thca_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/thca_tcga_pan_can_atlas_2018/README.md +++ b/public/thca_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/thca_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/thca_tcga_pan_can_atlas_2018/data_clinical_sample.txt index 1bfd90e7a2..f928a73829 100644 --- a/public/thca_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/thca_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:818be6bebac78ca1f0958a74144195382e06af3b990750fbb532f8e2f5f5f773 -size 105082 +oid sha256:10fd8a0f4a0272c479007ea1869383ccab474d0c011d64d6ae935b0884712727 +size 106275 diff --git a/public/thca_tcga_pan_can_atlas_2018/meta_study.txt b/public/thca_tcga_pan_can_atlas_2018/meta_study.txt index 4c07c28b22..6da7f6f852 100644 --- a/public/thca_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/thca_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Thyroid Carcinoma (TCGA, PanCancer Atlas) short_name: Thyroid (TCGA PanCan 2018) description: Thyroid Carcinoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/thym_tcga_pan_can_atlas_2018/README.md b/public/thym_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/thym_tcga_pan_can_atlas_2018/README.md +++ b/public/thym_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/thym_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/thym_tcga_pan_can_atlas_2018/data_clinical_sample.txt index 8b913c4911..39dff0f960 100644 --- a/public/thym_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/thym_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:054398bac4ced6b8cde9999608a04ae266a7154a4690bddcf5d9e11efa4a82e2 -size 21374 +oid sha256:924a652da15705672d4dba11f7fb9a040d39fd42d63cfcce6cdc4008d6c20a71 +size 21821 diff --git a/public/thym_tcga_pan_can_atlas_2018/meta_study.txt b/public/thym_tcga_pan_can_atlas_2018/meta_study.txt index ffccf796f0..7d92c97de9 100644 --- a/public/thym_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/thym_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Thymoma (TCGA, PanCancer Atlas) short_name: Thymoma (TCGA PanCan 2018) description: Thymoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/ucec_tcga_pan_can_atlas_2018/README.md b/public/ucec_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/ucec_tcga_pan_can_atlas_2018/README.md +++ b/public/ucec_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/ucec_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/ucec_tcga_pan_can_atlas_2018/data_clinical_sample.txt index de8862b8c0..81848d6ef4 100644 --- a/public/ucec_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/ucec_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:c234eccf5cf3e6056accc6f04f30fa2504e15dfadaa5df98102cc6ba478e11be -size 110843 +oid sha256:205a1081c4d51441b4ee6d4302d9c42dac1320b9f51c87137090d41a6b00cf0d +size 112480 diff --git a/public/ucec_tcga_pan_can_atlas_2018/meta_study.txt b/public/ucec_tcga_pan_can_atlas_2018/meta_study.txt index 27cc0dea1b..7d2aeb1462 100644 --- a/public/ucec_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/ucec_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Uterine Corpus Endometrial Carcinoma (TCGA, PanCancer Atlas) short_name: Uterine (TCGA PanCan 2018) description: Uterine Corpus Endometrial Carcinoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,30643250,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/ucs_tcga_pan_can_atlas_2018/README.md b/public/ucs_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/ucs_tcga_pan_can_atlas_2018/README.md +++ b/public/ucs_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/ucs_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/ucs_tcga_pan_can_atlas_2018/data_clinical_sample.txt index 9db632577c..16efa357a4 100644 --- a/public/ucs_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/ucs_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:824525ec03f62fa850884f895a0b42e8a15dc54ff09f13f47622afaac7b74bc4 -size 15280 +oid sha256:8ee834031c86d7ac0ea987cca8c55975b988354e59b05ee6f38e321354aa91c2 +size 15671 diff --git a/public/ucs_tcga_pan_can_atlas_2018/meta_study.txt b/public/ucs_tcga_pan_can_atlas_2018/meta_study.txt index b40458ecca..f021ac1565 100644 --- a/public/ucs_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/ucs_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Uterine Carcinosarcoma (TCGA, PanCancer Atlas) short_name: Uterine CS (TCGA PanCan 2018) description: Uterine Carcinosarcoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file diff --git a/public/uvm_tcga_pan_can_atlas_2018/README.md b/public/uvm_tcga_pan_can_atlas_2018/README.md index 4372ea260f..b72ab066fd 100644 --- a/public/uvm_tcga_pan_can_atlas_2018/README.md +++ b/public/uvm_tcga_pan_can_atlas_2018/README.md @@ -25,4 +25,11 @@ **Data Transformation** - The detailed transformation steps are listed in the Pull Request [here](https://github.com/cBioPortal/datahub/pull/1597) - - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. \ No newline at end of file + - The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina. + +### Tumor Break Load (TBL): + +**Data Source** + - TBL scores based on Lakbir et al., 2024 (Manuscript in progress) + - Overview of TBL calculation for TCGA, from [Lakbir et al., Eur J Cancer 2024](https://pubmed.ncbi.nlm.nih.gov/36334560/) + - Data is provided as a sample-level clinical attribute labeled `Tumor Break Load` diff --git a/public/uvm_tcga_pan_can_atlas_2018/data_clinical_sample.txt b/public/uvm_tcga_pan_can_atlas_2018/data_clinical_sample.txt index 9805ff0d67..4e225791b8 100644 --- a/public/uvm_tcga_pan_can_atlas_2018/data_clinical_sample.txt +++ b/public/uvm_tcga_pan_can_atlas_2018/data_clinical_sample.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:c6cd941411d0cb6dbf7a4fe2b72bd68b88c4c91e353a2a9fca2dca2c6974ed85 -size 13777 +oid sha256:bef30b57a0087c9f3180b053da095dfb400faba2fda0d5ca25661165f6001733 +size 14145 diff --git a/public/uvm_tcga_pan_can_atlas_2018/meta_study.txt b/public/uvm_tcga_pan_can_atlas_2018/meta_study.txt index c388c7d7c1..535c839389 100644 --- a/public/uvm_tcga_pan_can_atlas_2018/meta_study.txt +++ b/public/uvm_tcga_pan_can_atlas_2018/meta_study.txt @@ -4,5 +4,5 @@ name: Uveal Melanoma (TCGA, PanCancer Atlas) short_name: Uveal melanoma (TCGA PanCan 2018) description: Uveal melanoma TCGA PanCancer data. The original data is here. The publications are here. groups: PUBLIC;PANCAN -pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653,36334560 citation: TCGA, Cell 2018 \ No newline at end of file