Tumor type names are different across working groups (i.e. TCGA and ICGC)

[jkunisak]

Step 1a.2: Map clinical information (i.e. cancer type) to sample ids from both working group datasets

Generate consensus cancer type mapping file

• GOAL: Generate a consensus file to map ICGC's 'project_code' to MC3's 'project_id' to the same disease
• Use TCGA study abbreviations and ICGC study abbreviations to obtain consensus TCGA and ICGC cancer type name.
• The consensus cancer type name will be indicated in the 'Simplified Name' column...

TCGA Study Code	ICGC Project Code	ICGC Cancer Type	TCGA Cancer Type	Simplified Name	TCGA?	ICGC?
TCGA-BRCA	BRCA-CN	Breast Triple Negative Cancer	Breast invasive carcinoma	Breast invasive carcinoma	1	1
TCGA-BRCA	BRCA-EU	Breast ER+ and HER2	Breast invasive carcinoma	Breast invasive carcinoma	1	1
TCGA-BRCA	BRCA-FR	Breast Cancer	Breast invasive carcinoma	Breast invasive carcinoma	1	1
TCGA-BRCA	BRCA-KR	Breast Cancer	Breast invasive carcinoma	Breast invasive carcinoma	1	1
TCGA-BRCA	BRCA-UK	Breast Triple Negative/Lobular Cancer	Breast invasive carcinoma	Breast invasive carcinoma	1	1

• Some cancer type names are only found in ICGC --> see below for a few examples:

TCGA Study Code	ICGC Project Code	ICGC Cancer Type	TCGA Cancer Type	Simplified Name	TCGA?	ICGC?
NA	ALL-US	Acute Lymphoblastic Lymphoma	NA	Acute Lymphoblastic Lymphoma	0	1
NA	LIAD-US	Benign Liver Tumor	NA	Benign Liver Tumor	0	1
NA	CCSK-US	Clear Cell Sarcomas of the Kidney	NA	Clear Cell Sarcomas of the Kidney	0	1
NA	PEME-CA	Pediatric Medulloblastoma	NA	Pediatric Medulloblastoma	0	1
NA	RT-US	Rhabdoid Tumor	NA	Rhabdoid Tumor	0	1
NA	SKCA-BR	Skin Adenocarcinoma	NA	Skin Adenocarcinoma	0	1
NA	LMS-FR	Soft tissue cancer	NA	Soft tissue cancer	0	1
NA	WT-US	Wilms Tumor	NA	Wilms Tumor	0	1

• Some cancer type names are only found in TCGA --> see below for a few examples:

TCGA Study Code	ICGC Project Code	ICGC Cancer Type	TCGA Cancer Type	Simplified Name	TCGA?	ICGC?
TCGA-UVM	NA	NA	Uveal Melanoma	Uveal Melanoma	1	0
TCGA-MESO	NA	NA	Mesothelioma	Mesothelioma	1	0
TCGA-THYM	NA	NA	Thymoma	Thymoma	1	0