Global integration of knowledgebases for clinical interpretation of cancer variants
Year: 2017
Type: other
Abstract: The paradigm of precision medicine envisions a future in which a cancer patient’s molecular information can be interpreted in the context of accumulated knowledge to inform diagnosis, prognosis and treatment options most likely to benefit that individual patient. Accordingly, many groups have created knowledgebases to annotate cancer genomic mutations associated with evidence of pathogenicity or relevant treatment options. Integration of the available knowledge is currently infeasible because each group (often redundantly) curates their own knowledgebase without adherence to any interoperability standards. There is a clear need to standardize and coordinate clinical-genomics curation efforts, and create a public community resource able to query the aggregated information. To this end we have formed the Variant Interpretation for Cancer Consortium (VICC) as part of the Global Alliance for Genomic Health (GA4GH) to bring together the leading institutions that are independently developing comprehensive cancer variant interpretation databases. VICC participants share a desire to coordinate efforts and thus enhance the value of each independent effort. Each participant has agreed to: (1) Sharing at least a minimal set of required data elements for cancer variant interpretations; (2) Protecting patient privacy by focusing on only clinical interpretations of variants derived from published findings, not variant-level observations from individual patients; (3) Sharing all or a significant proportion of interpretations accumulated by their ongoing curation efforts; (4) Releasing content under a permissive license (free and non-exclusive for research use); (5) Releasing software in public repositories with open source licenses; (6) Making data available through publicly accessible and documented APIs and cross-knowlegebase downloads; and (7) Using the existing schemas, APIs and demonstration implementations developed by GA4GH. Academic and commercial groups who have agreed to participate include those at Washington University (CIViC), MSKCC (OncoKB), Weill Cornell (PMKB), OHSU, DFCI, Institute for Research in Biomedicine, Illumina Inc, and others. Additional participants are welcome ( http://ga4gh.org/#/vicc ). We will present progress by the VICC to create a federated query service able to interrogate associations between cancer variants and clinical actions, for each cancer subtype, based on evidence amassed from all participating knowledgebases world-wide.
Language: English
Topic: Genomics and Rare Diseases
Subfield: Genetics
Domain: Life Sciences
Open Access status: gold
OpenAlex ID: W2735179487