Table 1 TCGA cohorts used in the study. Patient numbers include those who passed filtering criteria and had complete datasets (somatic alteration, gene expression, genotyping data) available. Only cancer types with at least 200 patients were used in downsampling analyses
From: Contribution and clinical relevance of germline variation to the cancer transcriptome
Code | Cancer types | Number of patients | Included in downsampling |
|---|---|---|---|
BLCA | Bladder carcinoma | 320 | Y |
ERPOS | ER + breast carcinoma | 659 | Y |
ERNEG | ER- breast carcinoma | 203 | Y |
CESC | Cervical squamous cell carcinoma | 246 | Y |
COAD | Colorectal adenocarcinoma | 334 | Y |
ESCA | Esophageal carcinoma | 143 | N |
HNSC | Head and neck squamous cell carcinoma | 438 | Y |
KIRC | Kidney renal clear cell carcinoma | 279 | Y |
KIRP | Kidney renal papillary cell carcinoma | 230 | Y |
LGG | Low-grade glioma | 88 | N |
LIHC | Liver hepatocellular carcinoma | 308 | Y |
LUAD | Lung adenocarcinoma | 443 | Y |
LUSC | Lung squamous cell carcinoma | 355 | Y |
OV | Ovarian serous cystadenocarcinoma | 168 | N |
PAAD | Pancreatic adenocarcinoma | 139 | N |
PRAD | Prostate adenocarcinoma | 443 | Y |
READ | Rectal adenocarcinoma | 112 | N |
STAD | Stomach adenocarcinoma | 293 | Y |
SKCM | Skin cutaneous melanoma | 433 | Y |
TGCT | Testicular germ cell tumors | 122 | N |
THCA | Thyroid carcinoma | 448 | Y |
THYM | Thymoma | 113 | N |
UCEC | Uterine corpus endometrial carcinoma | 458 | Y |
UVM | Uveal melanoma | 78 | N |