Table 3.

Most relevant databases and public data resources for interrogating tumour genomics and clinical actionability data

Resource	Declared aim	Focus alterations (if applicable)	Interface	Annotation process	URL
Cancer Genome Interpreter (CGI)	The CGI is a web platform dedicated to the interpretation of variants identified in patient’s tumours	Point mutations and structural variants	Browser, download, API Interactive reports are provided as a result of analysis of a patient’s tumour	Semi-automated annotation and manual curation of literature. Oncologists’ review of biomarkers. In house tools	cancergenome interpreter.org
cBioPortal	Resource collecting alterations observed across patients’ tumours (probed at whole-exome, whole-genome or gene panel level)	Point mutations and structural variants	Browser, download, API	Automated annotation and analysis of tumour alterations data	www.cbioportal.org/
Catalog of somatic mutation in cancer (COSMIC)	Resource collecting alterations observed across patients’ tumours (probed at whole-exome, whole-genome or gene panel level) and cancer cell lines	Point mutations and structural variants	Browser, download, API	Automated annotation and analysis of tumour alterations data	cancer.sanger.ac.uk/ cosmic
Clinical Interpretation of Variants in Cancer (CiVIC)	Clinical relevance of variants in cancer	Point mutations and structural variants	Browser and API	Community-driven annotation and curation. Experts review	civicdb.org/
Database of Curated Mutations(DoCM)	Database of known, disease-causing mutations with direct links to source citations	Point mutations (SNVs and short indels)	Browser, download	Manual curation of literature	http://docm.info/
Jackson Laboratory	Database cataloguing cancer alterations and biomarkers	Point mutations and structural variants	Browser	Semi-automated annotation and manual curation of literature	ckb.jax.org
MyCancerGenome	Database of validated driver alterations in a list of cancer genes and their influence on the response to a range of therapeutic agents, with links to clinical trials	Point mutations and structural variants	Browser	Manual curation of literature	www.mycancer genome.org
Precision medicine knowledgebase (PMKB)	Information (including clinical relevance) about cancer variants	Point mutations and structural variants	Browser	Community-driven annotation and curation. Review by cancer pathologists	pmkb.weill. cornell.edu/
OncoKB	Information about the effects and treatment implications of specific cancer gene alterations	Point mutations and structural variants	Browser, download, API	Manually curated by a network of clinical fellows, research fellows, and faculty members at MSK from resources and literature	oncokb.org/
T-Quest	Open source platform to link molecular abnormalities to potential therapies	Point mutations and structural variants	Browser, download, API	Automated text search of clinicaltials.gov database and public databases	http://tquest.us/