TCGA Germline

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These annotations provide allele frequencies calculated from joint calling WES of normal samples from >11k subjects in TCGA:

  • TCGAGermline_All.AlleleFrequency count of Alternative allele across all 11,111 subjects
  • TCGAGermline_All.AlleleCount frequency of Alternative allele in all 11,111 subjects
  • Counts and Frequencies in 33 cancer types
    • ACC - Adrenocortical Carcinoma
    • BLCA - Bladder Urothelial Carcinoma
    • BRCA - Breast Invasive Carcinoma
    • CESC - Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma
    • CHOL - Cholangiocarcinoma
    • COAD - Colon Adenocarcinoma
    • DLBC - Lymphoid Neoplasm Diffuse Large B-cell Lymphoma
    • ESCA - Esophageal Carcinoma
    • GBM - Glioblastoma Multiforme
    • HNSC - Head and Neck Squamous Cell Carcinoma
    • KICH - Kidney Chromophobe
    • KIRC - Kidney Renal Clear Cell Carcinoma
    • KIRP - Kidney Renal Papillary Cell Carcinoma
    • LAML - Acute Myeloid Leukemia
    • LGG - Brain Lower Grade Glioma
    • LIHC - Liver Hepatocellular Carcinoma
    • LUAD - Lung Adenocarcinoma
    • LUSC - Lung Squamous Cell Carcinoma
    • MESO - Mesothelioma
    • OV - Ovarian Serous Cystadenocarcinoma
    • PAAD - Pancreatic Adenocarcinoma
    • PCPG - Pheochromocytoma and Paraganglioma
    • PRAD - Prostate Adenocarcinoma
    • READ - Rectum Adenocarcinoma
    • SARC - Sarcoma
    • SKCM - Skin Cutaneous Melanoma
    • STAD - Stomach Adenocarcinoma
    • TGCT - Testicular Germ Cell Tumors
    • THCA - Thyroid Carcinoma
    • THYM - Thymoma
    • UCEC - Uterine Corpus Endometrial Carcinoma
    • UCS - Uterine Carcinosarcoma
    • UVM - Uveal Melanoma

TCGAGermline.png

The current classifier versions (for specifying in Land.cfg) are:

TCGAGermline_All
TCGAGermline_ACC
TCGAGermline_BLCA
TCGAGermline_BRCA
TCGAGermline_CESC
TCGAGermline_CHOL
TCGAGermline_COAD
TCGAGermline_DLBC
TCGAGermline_ESCA
TCGAGermline_GBM
TCGAGermline_HNSC
TCGAGermline_KICH
TCGAGermline_KIRC
TCGAGermline_KIRP
TCGAGermline_LAML
TCGAGermline_LGG
TCGAGermline_LIHC
TCGAGermline_LUAD
TCGAGermline_LUSC
TCGAGermline_MESO
TCGAGermline_OV
TCGAGermline_PAAD
TCGAGermline_PCPG
TCGAGermline_PRAD
TCGAGermline_READ
TCGAGermline_SARC
TCGAGermline_SKCM
TCGAGermline_STAD
TCGAGermline_TGCT
TCGAGermline_THCA
TCGAGermline_THYM
TCGAGermline_UCEC
TCGAGermline_UCS
TCGAGermline_UVM