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Harmonizing cancer variant knowledgebases

Wagner, A. H. et al. Nat. Genet. 52, 448–457 (2020).

Sequencing genomes from cancer samples reveals somatic mutational changes. While potentially informative, observed variants need to be carefully interpreted to assess biological and clinical significance. Knowledgebases collecting information about genomic variants, diseases and drugs from published literature are important resources. However, disparities between knowledgebases are not uncommon and can cause inconsistency. The Variant Interpretation for Cancer Consortium harmonized variant interpretations across six widely used somatic cancer variant knowledgebases. Different data types were mapped to established standards and ontologies describing genes, variants, diseases, drugs and evidence levels, generating a single meta-knowledgebase composed of 12,856 interpretations. Testing results using data from the GENIE cohort showed improved interpretation performance and efficiency after harmonization. The group developed a web interface for searching and exploring the meta-knowledgebase.

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Correspondence to Lin Tang.

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Tang, L. Harmonizing cancer variant knowledgebases. Nat Methods 17, 563 (2020). https://doi.org/10.1038/s41592-020-0871-3

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