Table 1.

Cancer-Specific Knowledge Bases to Assist in Clinical Interpretation of Tumor Variants

Knowledge Base or Database	Description	Types of Relationships	Clinical Domains	Size of Database (2012)
Catalogue of Somatic Mutations in Cancer (COSMIC)57	COSMIC is a database of somatic mutations in cancers derived from curation of case reports in the literature	Tumor variant–disease	All cancer diagnoses	> 700,000 tumors cases with > 280,000 mutations
Genomics of Drug Sensitivity in Cancer79	The Genomics of Drug Sensitivity in Cancer database contains information on the drug sensitivity of cancer cell lines	Tumor gene–drug	Cancer cell lines	Screen of several hundred cancer cell lines with 130 cancer drugs
The Cancer Genome Atlas (TCGA) data portal80	The TCGA data portal contains cases of tumor with extensive molecular annotations and more limited clinical annotations	Tumor variant–disease–drug–outcome	21 cancer types	21 cancer diagnoses with > 6,000 tumor samples with genome and clinical annotations
DNA-Mutation Inventory to Refine and Enhance Cancer Treatment (DIRECT)81	DIRECT is a database of cases of non–small-cell lung cancer reported in the literature with tumor variant(s), drug exposure, and clinical outcome annotations25	Tumor variant-disease-drug-outcome	Non–small-cell lung cancer	> 1,800 patient cases, 150 EGFR variants
My Cancer Genome82	My Cancer Genome is a knowledge base describing the clinical significance of common tumor gene mutations and their relationships to disease and drugs. It includes annotations of gene directed cancer clinical trials27	Tumor variant-disease-drug-outcome	All cancers	> 10,000 active cancer trials annotated with over 400 cancer genes. Detailed reviews for 17 cancer types, 25 cancer genes, over 280 tumor variant-disease relationships
Atlas Genetics Oncology83	Atlas Genetics Oncology is a peer reviewed on-line journal and database in free access on internet devoted to genes, cytogenetics, and clinical entities in cancer, and cancer-prone diseases. It presents concise and updated reviews (cards) or longer texts (deep insights)29	Tumor variant–disease relationships	All cancer diagnoses with a focus on hematologic malignancies	Tumor cytogenetic aberrations in all 24 chromosomes. Not currently up to date in all topics
cBio Cancer Genomics Portal84	This portal contains data from multiple large-scale cancer genomic data sets and allows for explorative analysis	Tumor variant–pathway–disease relationships	19 cancer types	The portal data includes 7,848 tumor samples from 26 cancer studies