Available CHASMplus models

CHASMplus can perform predictions either using a cancer type-specific model or in a “pan-cancer” manner by consider multiple cancer types together. Pan-cancer is a useful default if a matching cancer type is not available from The Cancer Genome Atlas (TCGA). We have made the following results available through OpenCRAVAT:

Annotator name Data source Cancer type
chasmplus TCGA Pan-cancer (multiple cancer types)
chasmplus_LAML TCGA Acute Myeloid Leukemia
chasmplus_ACC TCGA Adrenocortical carcinoma
chasmplus_BLCA TCGA Bladder Urothelial Carcinoma
chasmplus_LGG TCGA Brain Lower Grade Glioma
chasmplus_BRCA TCGA Breast invasive carcinoma
chasmplus_CESC TCGA Cervical squamous cell carcinoma and endocervical adenocarcinoma
chasmplus_CHOL TCGA Cholangiocarcinoma
chasmplus_COAD TCGA Colon adenocarcinoma
chasmplus_ESCA TCGA Esophageal carcinoma
chasmplus_GBM TCGA Glioblastoma multiforme
chasmplus_HNSC TCGA Head and Neck squamous cell carcinoma
chasmplus_KICH TCGA Kidney Chromophobe
chasmplus_KIRC TCGA Kidney renal clear cell carcinoma
chasmplus_KIRP TCGA Kidney renal papillary cell carcinoma
chasmplus_LIHC TCGA Liver hepatocellular carcinoma
chasmplus_LUAD TCGA Lung adenocarcinoma
chasmplus_LUSC TCGA Lung squamous cell carcinoma
chasmplus_DLBC TCGA Lymphoid Neoplasm Diffuse Large B-cell Lymphoma
chasmplus_MESO TCGA Mesothelioma
chasmplus_OV TCGA Ovarian serous cystadenocarcinoma
chasmplus_PAAD TCGA Pancreatic adenocarcinoma
chasmplus_PCPG TCGA Pheochromocytoma and Paraganglioma
chasmplus_PRAD TCGA Prostate adenocarcinoma
chasmplus_READ TCGA Rectum adenocarcinoma
chasmplus_SARC TCGA Sarcoma
chasmplus_SKCM TCGA Skin Cutaneous Melanoma
chasmplus_STAD TCGA Stomach adenocarcinoma
chasmplus_TGCT TCGA Testicular Germ Cell Tumors
chasmplus_THYM TCGA Thymoma
chasmplus_THCA TCGA Thyroid carcinoma
chasmplus_UCS TCGA Uterine Carcinosarcoma
chasmplus_UCEC TCGA Uterine Corpus Endometrial Carcinoma
chasmplus_UVM TCGA Uveal Melanoma