Lab Publication - Human Mutation

As knowledge of the tumor genome expands, efficient representation, communication and distribution of clinical information on cancer variants becomes a more complicated problem of increasing importance. For example successful automated transfer of knowledge accumulated in one clinical datastore to another is highly dependent on proper harmonization of structured variant representation and clinical annotations. In this work we demonstrate harmonization of CIViC database (www.civicdb.org) with ClinGen Minimum Variant Level Data (MVLD). We discuss alterations in the CIViC data format which allow for intuitive mappings of data from the MVLD format and introduce the CIViC Clinical Assertion to make state of the field valuations on cancer variant, disease, and drug combinations using AMP Tier and Level. A method for automated transformation of this data into a format for ClinVar submission is also mapped out. The work demonstrates harmonization across multiple cancer variant databases and curation efforts, and is part of the Human Mutation Special Issue ClinGen and ClinVar: Enabling Genomics in Precision Medicine

Read the article: [PubMed] [Human Mutation]