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
cBioPortal · Nov 15, 2024 · 438e7e4 · 438e7e4
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diff --git 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.
+ - 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
diff --git 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 <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
 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
diff --git 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.
+ - 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
diff --git 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 <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
 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
diff --git 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.
+ - 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
diff --git 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 <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
 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
diff --git 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
diff --git 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.
+ - 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
diff --git 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 <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
 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
diff --git 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.
+ - 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
diff --git 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 <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
 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
diff --git 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.
+ - 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
diff --git 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 <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
 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
diff --git 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.
+ - 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
diff --git 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 <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
 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
diff --git 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.
+ - 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
diff --git 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 <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
 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
diff --git 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.
+ - 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
diff --git 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 <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
 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
diff --git 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.
+ - 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
diff --git 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 <a href="https://gdc.cancer.gov/about-data/publications/pancanatlas">here</a>. The publications are <a href="https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html">here</a>.
 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
diff --git 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.
+ - 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