[NO MERGE] TCGA + CPTAC Release v2

crdc/README.md

@@ -16,7 +16,7 @@ Supported programs:
 ### TCGA
 
 - **Cancer type mapping:** Each study corresponds to one TCGA project. The suffix of the TCGA project is taken and converted to an OncoTree code, which is used for the name of the study.
-    - **Example:** For the TCGA project `TCGA-LAML`, the `LAML` suffix is taken and converted to the Oncotree code `AML`. The resulting cBioPortal study is `aml_tcga_gdc`.
+    - **Example:** For the TCGA project `TCGA-LAML`, the `LAML` suffix is taken and converted to the OncoTree code `AML`. The resulting cBioPortal study is `aml_tcga_gdc`.
     - [Mapping file](https://github.com/cBioPortal/nci-crdc-pipeline/blob/main/resources/oncotree_mappings/tcga.txt)
 
 #### List of TCGA cBioPortal Studies
@@ -58,18 +58,18 @@ Supported programs:
 ### CPTAC
 
 - **Cancer type mapping:** CPTAC is comprised of the CPTAC-2 and CPTAC-3 projects, both of which encompass multiple cancer types. Each study corresponds to a subset of these projects with a particular OncoTree code. The code is determined by looking at `disease_type` and `primary_site` in the BigQuery tables.
-    - **Example:** The `luad_cptac` study is generated from all samples with primary site `Bronchus and lung` and disease type `Adenomas and Adenocarcinomas`.
+    - **Example:** The `luad_cptac3_gdc` study is a subset of CPTAC-3 generated from all samples with primary site `Bronchus and lung` and disease type `Adenomas and Adenocarcinomas`.
     - [Mapping file](https://github.com/cBioPortal/nci-crdc-pipeline/blob/main/resources/oncotree_mappings/cptac.txt)
 
 #### List of CPTAC cBioPortal Studies
 
-- [`brain_cptac_gdc`](https://www.cbioportal.org/study/summary?id=brain_cptac_gdc): [CNS/Brain Cancer](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22brain%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D)
-- [`breast_cptac_gdc`](https://www.cbioportal.org/study/summary?id=breast_cptac_gdc): [Breast Cancer](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22breast%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D)
-- [`coad_cptac_gdc`](https://www.cbioportal.org/study/summary?id=coad_cptac_gdc): [Colon Adenocarcinoma](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22colon%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D)
-- [`luad_cptac_gdc`](https://www.cbioportal.org/study/summary?id=luad_cptac_gdc): [Lung Adenocarcinoma](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.disease_type%22%2C%22value%22%3A%5B%22adenomas%20and%20adenocarcinomas%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22bronchus%20and%20lung%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D)
-- [`lusc_cptac_gdc`](https://www.cbioportal.org/study/summary?id=lusc_cptac_gdc): [Lung Squamous Cell Carcinoma](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.disease_type%22%2C%22value%22%3A%5B%22squamous%20cell%20neoplasms%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22bronchus%20and%20lung%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D)
-- [`ohnca_cptac_gdc`](https://www.cbioportal.org/study/summary?id=ohnca_cptac_gdc): [Head and Neck Carcinoma, Other](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22other%20and%20ill-defined%20sites%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D)
-- [`ovary_cptac_gdc`](https://www.cbioportal.org/study/summary?id=ovary_cptac_gdc): [Ovarian Cancer](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22other%20and%20unspecified%20female%20genital%20organs%22%2C%22ovary%22%2C%22rectum%22%2C%22retroperitoneum%20and%20peritoneum%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D)
-- [`pancreas_cptac_gdc`](https://www.cbioportal.org/study/summary?id=pancreas_cptac_gdc): [Pancreatic Cancer](https://portal.gdc.cancer.gov/repository?facetTab=files&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22pancreas%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D)
-- [`rcc_cptac_gdc`](https://www.cbioportal.org/study/summary?id=rcc_cptac_gdc): [Renal Cell Carcinoma](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.disease_type%22%2C%22value%22%3A%5B%22Adenomas%20and%20Adenocarcinomas%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22Kidney%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D)
-- [`uec_cptac_gdc`](https://www.cbioportal.org/study/summary?id=uec_cptac_gdc): [Uterine Endometrioid Carcinoma](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.disease_type%22%2C%22value%22%3A%5B%22Adenomas%20and%20Adenocarcinomas%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22Uterus%2C%20NOS%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%7D%5D%7D)
+- [`brain_cptac3_gdc`](https://www.cbioportal.org/study/summary?id=brain_cptac3_gdc): CNS/Brain Cancer, [CPTAC-3](https://portal.gdc.cancer.gov/projects/CPTAC-3)
+- [`breast_cptac2_gdc`](https://www.cbioportal.org/study/summary?id=breast_cptac2_gdc): Breast Cancer, [CPTAC-2](https://portal.gdc.cancer.gov/projects/CPTAC-2)
+- [`coad_cptac2_gdc`](https://www.cbioportal.org/study/summary?id=coad_cptac2_gdc): Colon Adenocarcinoma, [CPTAC-2](https://portal.gdc.cancer.gov/projects/CPTAC-2)
+- [`luad_cptac3_gdc`](https://www.cbioportal.org/study/summary?id=luad_cptac3_gdc): Lung Adenocarcinoma, [CPTAC-3](https://portal.gdc.cancer.gov/projects/CPTAC-3)
+- [`lusc_cptac3_gdc`](https://www.cbioportal.org/study/summary?id=lusc_cptac3_gdc): Lung Squamous Cell Carcinoma, [CPTAC-3](https://portal.gdc.cancer.gov/projects/CPTAC-3)
+- [`ohnca_cptac3_gdc`](https://www.cbioportal.org/study/summary?id=ohnca_cptac3_gdc): Head and Neck Carcinoma, Other, [CPTAC-3](https://portal.gdc.cancer.gov/projects/CPTAC-3)
+- [`ovary_cptac2_gdc`](https://www.cbioportal.org/study/summary?id=ovary_cptac2_gdc): Ovarian Cancer, [CPTAC-2](https://portal.gdc.cancer.gov/projects/CPTAC-2)
+- [`pancreas_cptac3_gdc`](https://www.cbioportal.org/study/summary?id=pancreas_cptac3_gdc): Pancreatic Cancer, [CPTAC-3](https://portal.gdc.cancer.gov/projects/CPTAC-3)
+- [`rcc_cptac3_gdc`](https://www.cbioportal.org/study/summary?id=rcc_cptac3_gdc): Renal Cell Carcinoma, [CPTAC-3](https://portal.gdc.cancer.gov/projects/CPTAC-3)
+- [`uec_cptac3_gdc`](https://www.cbioportal.org/study/summary?id=uec_cptac3_gdc): Uterine Endometrioid Carcinoma, [CPTAC-3](https://portal.gdc.cancer.gov/projects/CPTAC-3)

crdc/gdc/acc_tcga_gdc/README.md

@@ -8,6 +8,7 @@
 - TCGA started using the hg38 genome as of GDC release 32. For more information, refer to the [GDC release notes](https://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#data-release-320).
 - This is the primary difference between this study and the legacy TCGA studies (PanCan / provisional), which use the hg19 genome. See [here](https://broadinstitute.atlassian.net/wiki/spaces/GDAC/pages/844334036/FAQ#FAQ-EndOfTCGAQ%3AIunderstandthatTCGAdatahasmigratedtotheGDC%2CbutwhydoIseediscrepanciesbetweenGDCandFireBrowse%3F) for more information.
 - Only tumor sample data is included (no normal samples)
+- [GDC project webpage](https://portal.gdc.cancer.gov/projects/TCGA-ACC)
 
 ## Clinical data
 
@@ -26,23 +27,30 @@ Survival fields are calculated from the clinical data and added as new columns i
 
 ### Timeline data
 
-- Timeline data is extracted from the clinical data and stored in a separate data file. After extraction, the corresponding BigQuery fields are removed from the clinical file. For example, a timeline status of `DEATH` corresponds to the BigQuery field `demo__days_to_death`.
+- Timeline data is extracted from the clinical data and stored in separate data files. After extraction, the corresponding BigQuery fields are removed from the clinical file. For example, a timeline status of `DEATH` corresponds to the BigQuery field `demo__days_to_death`.
 
-- For TCGA, the "time 0" anchor point is always the date of diagnosis. Not all patients have timeline data available, as indicated by a null `diag__days_to_diagnosis` (TCGA) or `index_date` (CPTAC) field.
+#### Patient status data
+
+- For TCGA, the "time 0" anchor point is always the date of diagnosis. Not all patients have timeline data available, as indicated by a null `diag__days_to_diagnosis` (TCGA) or `index_date` (CPTAC, TARGET) field.
 
 - Birth timeline events are removed, as they (1) push other events to the far right of the graph and (2) can potentially be used to identify the patient.
 
 The following status values are supported in `data_timeline_status.txt`:
 
-- `__time0__`
-- `demo__days_to_death`
-- `diag__days_to_last_follow_up`
+- (time 0) → `Initial Diagnosis`
+- `demo__days_to_death` → `DECEASED`
+- `diag__days_to_last_follow_up` → `Last Follow Up`
+#### Sample acquisition data
+
+- The `days_to_sample_procurement` field is converted to the `Sample Acquisition` event.
+- TCGA sample IDs are stripped of their trailing 'A' to remain consistent with the sample IDs after they have been imported to the portal.
+  - While TCGA studies sourced from GDC do have a trailing 'A', the importer [automatically strips them](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/util/StableIdUtil.java) from the sample ID.
 ### Other transformations
 
 - `"not reported"` values are replaced with blanks.
 - If a clinical field is missing for the entire study, the column is removed from the data file.
 - `RACE`, `ETHNICITY`, and `SEX` are capitalized.
-- `AGE` is clipped from 18 to 89 to protect patient confidentiality.
+- `AGE` is converted from days to years. It is also clipped from 18 to 89 in order to protect patient confidentiality.
 
 ## CNA data
 
@@ -93,6 +101,7 @@ Only amplifications (GISTIC = 2) and deep deletions (GISTIC = -2) are shown on t
 
   - Samples that lack any genomic data are removed from the clinical sample file.
   - Metadata headers are added to the clinical patient and sample files using a curation-provided script.
+  - TMB scores are calculated and added to the clinical sample file using a curation-provided script.
   - Case lists are generated under `case_lists/` using a curation-provided script.
   - The validator script is run and the HTML report is saved under `validation_reports/`.
 

crdc/gdc/acc_tcga_gdc/case_lists/cases_all.txt

@@ -3,4 +3,4 @@ stable_id: acc_tcga_gdc_all
 case_list_name: All samples
 case_list_description: All samples (92 samples)
 case_list_category: all_cases_in_study
-case_list_ids: TCGA-OR-A5JD-01A	TCGA-OR-A5K4-01A	TCGA-OR-A5LS-01A	TCGA-P6-A5OH-01A	TCGA-OR-A5KO-01A	TCGA-OR-A5JF-01A	TCGA-OR-A5K8-01A	TCGA-OR-A5LG-01A	TCGA-OR-A5J4-01A	TCGA-OR-A5L5-01A	TCGA-OR-A5KS-01A	TCGA-OR-A5L8-01A	TCGA-OR-A5JX-01A	TCGA-OR-A5J2-01A	TCGA-OR-A5JE-01A	TCGA-OR-A5L6-01A	TCGA-OR-A5JW-01A	TCGA-OR-A5L3-01A	TCGA-OR-A5LR-01A	TCGA-OR-A5JZ-01A	TCGA-OR-A5JH-01A	TCGA-OR-A5J5-01A	TCGA-OR-A5KW-01A	TCGA-OR-A5LC-01A	TCGA-OR-A5K3-01A	TCGA-OR-A5JC-01A	TCGA-OR-A5LN-01A	TCGA-OR-A5KU-01A	TCGA-OR-A5JY-01A	TCGA-OR-A5J8-01A	TCGA-OR-A5KQ-01A	TCGA-OR-A5J7-01A	TCGA-OR-A5K0-01A	TCGA-OR-A5LP-01A	TCGA-OR-A5LB-01A	TCGA-OR-A5K5-01A	TCGA-OR-A5KT-01A	TCGA-OR-A5LA-01A	TCGA-OR-A5JS-01A	TCGA-OR-A5KY-01A	TCGA-OR-A5LM-01A	TCGA-OR-A5KX-01A	TCGA-OR-A5LF-01A	TCGA-OR-A5JG-01A	TCGA-OR-A5JJ-01A	TCGA-OR-A5LO-01A	TCGA-OR-A5JO-01A	TCGA-OR-A5LD-01A	TCGA-OR-A5KZ-01A	TCGA-PK-A5H8-01A	TCGA-OR-A5JA-01A	TCGA-OR-A5J3-01A	TCGA-OR-A5K9-01A	TCGA-OR-A5JM-01A	TCGA-OR-A5LT-01A	TCGA-OR-A5JU-01A	TCGA-OR-A5K2-01A	TCGA-PA-A5YG-01A	TCGA-OR-A5J6-01A	TCGA-OR-A5LJ-01A	TCGA-OR-A5L9-01A	TCGA-OR-A5LE-01A	TCGA-OR-A5KP-01A	TCGA-OR-A5LH-01A	TCGA-OR-A5L4-01A	TCGA-OR-A5LI-01A	TCGA-OR-A5JQ-01A	TCGA-PK-A5HA-01A	TCGA-OR-A5LK-01A	TCGA-OR-A5LL-01A	TCGA-OR-A5KB-01A	TCGA-OR-A5L2-01A	TCGA-OR-A5JL-01A	TCGA-OU-A5PI-01A	TCGA-OR-A5JI-01A	TCGA-PK-A5HB-01A	TCGA-OR-A5JB-01A	TCGA-OR-A5KV-01A	TCGA-OR-A5J1-01A	TCGA-OR-A5JP-01A	TCGA-OR-A5L1-01A	TCGA-OR-A5J9-01A	TCGA-OR-A5K1-01A	TCGA-PK-A5H9-01A	TCGA-PK-A5HC-01A	TCGA-OR-A5K6-01A	TCGA-OR-A5JT-01A	TCGA-OR-A5JK-01A	TCGA-P6-A5OF-01A	TCGA-OR-A5JV-01A	TCGA-P6-A5OG-01A	TCGA-OR-A5JR-01A
+case_list_ids: TCGA-PK-A5HA-01A	TCGA-OR-A5L8-01A	TCGA-OR-A5K2-01A	TCGA-OR-A5JG-01A	TCGA-OR-A5LF-01A	TCGA-OR-A5J1-01A	TCGA-OR-A5J9-01A	TCGA-OR-A5KU-01A	TCGA-OR-A5LS-01A	TCGA-OR-A5LB-01A	TCGA-OR-A5K6-01A	TCGA-OR-A5JY-01A	TCGA-OR-A5LI-01A	TCGA-OR-A5LC-01A	TCGA-OR-A5LL-01A	TCGA-OR-A5JO-01A	TCGA-P6-A5OG-01A	TCGA-OR-A5JL-01A	TCGA-OR-A5J4-01A	TCGA-PK-A5H8-01A	TCGA-PK-A5HB-01A	TCGA-OR-A5KW-01A	TCGA-OR-A5LA-01A	TCGA-OR-A5JA-01A	TCGA-OR-A5JT-01A	TCGA-P6-A5OH-01A	TCGA-OR-A5L2-01A	TCGA-OR-A5LT-01A	TCGA-OR-A5JM-01A	TCGA-OR-A5L1-01A	TCGA-OR-A5K3-01A	TCGA-OR-A5LJ-01A	TCGA-P6-A5OF-01A	TCGA-OR-A5LG-01A	TCGA-PK-A5HC-01A	TCGA-OR-A5JK-01A	TCGA-OR-A5JC-01A	TCGA-OR-A5LO-01A	TCGA-OR-A5J8-01A	TCGA-OR-A5K8-01A	TCGA-OR-A5LN-01A	TCGA-OR-A5L6-01A	TCGA-OR-A5JD-01A	TCGA-OR-A5L3-01A	TCGA-OR-A5KS-01A	TCGA-OR-A5LE-01A	TCGA-OR-A5LM-01A	TCGA-OR-A5LH-01A	TCGA-OR-A5J6-01A	TCGA-PA-A5YG-01A	TCGA-OR-A5J7-01A	TCGA-OR-A5J5-01A	TCGA-OR-A5KB-01A	TCGA-OR-A5KX-01A	TCGA-OR-A5JU-01A	TCGA-OR-A5KY-01A	TCGA-OR-A5K9-01A	TCGA-OR-A5JH-01A	TCGA-OR-A5JZ-01A	TCGA-OR-A5L5-01A	TCGA-OR-A5JX-01A	TCGA-OR-A5KT-01A	TCGA-OR-A5LR-01A	TCGA-OR-A5K5-01A	TCGA-OR-A5KZ-01A	TCGA-OR-A5JB-01A	TCGA-OR-A5JF-01A	TCGA-OU-A5PI-01A	TCGA-OR-A5KV-01A	TCGA-OR-A5KP-01A	TCGA-OR-A5LP-01A	TCGA-OR-A5KO-01A	TCGA-OR-A5L4-01A	TCGA-OR-A5JR-01A	TCGA-OR-A5JJ-01A	TCGA-OR-A5JP-01A	TCGA-OR-A5JQ-01A	TCGA-OR-A5JW-01A	TCGA-OR-A5K0-01A	TCGA-OR-A5J3-01A	TCGA-PK-A5H9-01A	TCGA-OR-A5KQ-01A	TCGA-OR-A5JI-01A	TCGA-OR-A5K1-01A	TCGA-OR-A5JE-01A	TCGA-OR-A5L9-01A	TCGA-OR-A5LK-01A	TCGA-OR-A5LD-01A	TCGA-OR-A5K4-01A	TCGA-OR-A5JS-01A	TCGA-OR-A5J2-01A	TCGA-OR-A5JV-01A

crdc/gdc/acc_tcga_gdc/case_lists/cases_cna.txt

@@ -3,4 +3,4 @@ stable_id: acc_tcga_gdc_cna
 case_list_name: Samples with CNA data
 case_list_description: Samples with CNA data (90 samples)
 case_list_category: all_cases_with_cna_data
-case_list_ids: TCGA-OR-A5JD-01A	TCGA-OR-A5K4-01A	TCGA-OR-A5LS-01A	TCGA-P6-A5OH-01A	TCGA-OR-A5KO-01A	TCGA-OR-A5JF-01A	TCGA-OR-A5K8-01A	TCGA-OR-A5LG-01A	TCGA-OR-A5J4-01A	TCGA-OR-A5L5-01A	TCGA-OR-A5KS-01A	TCGA-OR-A5L8-01A	TCGA-OR-A5JX-01A	TCGA-OR-A5J2-01A	TCGA-OR-A5JE-01A	TCGA-OR-A5L6-01A	TCGA-OR-A5JW-01A	TCGA-OR-A5L3-01A	TCGA-OR-A5LR-01A	TCGA-OR-A5JZ-01A	TCGA-OR-A5JH-01A	TCGA-OR-A5J5-01A	TCGA-OR-A5KW-01A	TCGA-OR-A5LC-01A	TCGA-OR-A5K3-01A	TCGA-OR-A5JC-01A	TCGA-OR-A5LN-01A	TCGA-OR-A5KU-01A	TCGA-OR-A5JY-01A	TCGA-OR-A5J8-01A	TCGA-OR-A5KQ-01A	TCGA-OR-A5J7-01A	TCGA-OR-A5K0-01A	TCGA-OR-A5LP-01A	TCGA-OR-A5LB-01A	TCGA-OR-A5K5-01A	TCGA-OR-A5KT-01A	TCGA-OR-A5LA-01A	TCGA-OR-A5JS-01A	TCGA-OR-A5KY-01A	TCGA-OR-A5LM-01A	TCGA-OR-A5KX-01A	TCGA-OR-A5LF-01A	TCGA-OR-A5JG-01A	TCGA-OR-A5LO-01A	TCGA-OR-A5JO-01A	TCGA-OR-A5LD-01A	TCGA-OR-A5KZ-01A	TCGA-OR-A5JA-01A	TCGA-OR-A5J3-01A	TCGA-OR-A5K9-01A	TCGA-OR-A5JM-01A	TCGA-OR-A5LT-01A	TCGA-OR-A5JU-01A	TCGA-OR-A5K2-01A	TCGA-PA-A5YG-01A	TCGA-OR-A5J6-01A	TCGA-OR-A5LJ-01A	TCGA-OR-A5L9-01A	TCGA-OR-A5LE-01A	TCGA-OR-A5KP-01A	TCGA-OR-A5LH-01A	TCGA-OR-A5L4-01A	TCGA-OR-A5LI-01A	TCGA-OR-A5JQ-01A	TCGA-PK-A5HA-01A	TCGA-OR-A5LK-01A	TCGA-OR-A5LL-01A	TCGA-OR-A5KB-01A	TCGA-OR-A5L2-01A	TCGA-OR-A5JL-01A	TCGA-OU-A5PI-01A	TCGA-OR-A5JI-01A	TCGA-PK-A5HB-01A	TCGA-OR-A5JB-01A	TCGA-OR-A5KV-01A	TCGA-OR-A5J1-01A	TCGA-OR-A5JP-01A	TCGA-OR-A5L1-01A	TCGA-OR-A5J9-01A	TCGA-OR-A5K1-01A	TCGA-PK-A5H9-01A	TCGA-PK-A5HC-01A	TCGA-OR-A5K6-01A	TCGA-OR-A5JT-01A	TCGA-OR-A5JK-01A	TCGA-OR-A5JJ-01A	TCGA-OR-A5JV-01A	TCGA-P6-A5OG-01A	TCGA-OR-A5JR-01A
+case_list_ids: TCGA-PK-A5HA-01A	TCGA-OR-A5L8-01A	TCGA-OR-A5K2-01A	TCGA-OR-A5JG-01A	TCGA-OR-A5LF-01A	TCGA-OR-A5J1-01A	TCGA-OR-A5J9-01A	TCGA-OR-A5KU-01A	TCGA-OR-A5LS-01A	TCGA-OR-A5LB-01A	TCGA-OR-A5K6-01A	TCGA-OR-A5JY-01A	TCGA-OR-A5LI-01A	TCGA-OR-A5LC-01A	TCGA-OR-A5LL-01A	TCGA-OR-A5JO-01A	TCGA-P6-A5OG-01A	TCGA-OR-A5JL-01A	TCGA-OR-A5J4-01A	TCGA-PK-A5HB-01A	TCGA-OR-A5KW-01A	TCGA-OR-A5LA-01A	TCGA-OR-A5JA-01A	TCGA-OR-A5JT-01A	TCGA-P6-A5OH-01A	TCGA-OR-A5L2-01A	TCGA-OR-A5LT-01A	TCGA-OR-A5JM-01A	TCGA-OR-A5L1-01A	TCGA-OR-A5K3-01A	TCGA-OR-A5LJ-01A	TCGA-OR-A5LG-01A	TCGA-PK-A5HC-01A	TCGA-OR-A5JK-01A	TCGA-OR-A5JC-01A	TCGA-OR-A5LO-01A	TCGA-OR-A5J8-01A	TCGA-OR-A5K8-01A	TCGA-OR-A5LN-01A	TCGA-OR-A5L6-01A	TCGA-OR-A5JD-01A	TCGA-OR-A5L3-01A	TCGA-OR-A5KS-01A	TCGA-OR-A5LE-01A	TCGA-OR-A5LM-01A	TCGA-OR-A5LH-01A	TCGA-OR-A5J6-01A	TCGA-PA-A5YG-01A	TCGA-OR-A5J7-01A	TCGA-OR-A5J5-01A	TCGA-OR-A5KB-01A	TCGA-OR-A5KX-01A	TCGA-OR-A5JU-01A	TCGA-OR-A5KY-01A	TCGA-OR-A5K9-01A	TCGA-OR-A5JH-01A	TCGA-OR-A5JZ-01A	TCGA-OR-A5L5-01A	TCGA-OR-A5JX-01A	TCGA-OR-A5KT-01A	TCGA-OR-A5LR-01A	TCGA-OR-A5K5-01A	TCGA-OR-A5KZ-01A	TCGA-OR-A5JB-01A	TCGA-OR-A5JF-01A	TCGA-OU-A5PI-01A	TCGA-OR-A5KV-01A	TCGA-OR-A5KP-01A	TCGA-OR-A5LP-01A	TCGA-OR-A5KO-01A	TCGA-OR-A5L4-01A	TCGA-OR-A5JR-01A	TCGA-OR-A5JJ-01A	TCGA-OR-A5JP-01A	TCGA-OR-A5JQ-01A	TCGA-OR-A5JW-01A	TCGA-OR-A5K0-01A	TCGA-OR-A5J3-01A	TCGA-PK-A5H9-01A	TCGA-OR-A5KQ-01A	TCGA-OR-A5JI-01A	TCGA-OR-A5K1-01A	TCGA-OR-A5JE-01A	TCGA-OR-A5L9-01A	TCGA-OR-A5LK-01A	TCGA-OR-A5LD-01A	TCGA-OR-A5K4-01A	TCGA-OR-A5JS-01A	TCGA-OR-A5J2-01A	TCGA-OR-A5JV-01A