Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community‐driven standards
Year: 2018
Type: article
Abstract: Harmonization of cancer variant representation, efficient communication, and free distribution of clinical variant-associated knowledge are central problems that arise with increased usage of clinical next-generation sequencing. The Clinical Genome Resource (ClinGen) Somatic Working Group (WG) developed a minimal variant level data (MVLD) representation of cancer variants, and has an ongoing collaboration with Clinical Interpretations of Variants in Cancer (CIViC), an open-source platform supporting crowdsourced and expert-moderated cancer variant curation. Harmonization between MVLD and CIViC variant formats was assessed by formal field-by-field analysis. Adjustments to the CIViC format were made to harmonize with MVLD and support ClinGen Somatic WG curation activities, including four new features in CIViC: (1) introduction of an assertions feature for clinical variant assessment following the Association of Molecular Pathologists (AMP) guidelines, (2) group-level curation tracking for organizations, enabling member transparency, and curation effort summaries, (3) introduction of ClinGen Allele Registry IDs to CIViC, and (4) mapping of CIViC assertions into ClinVar submission with automated submissions. A generalizable workflow utilizing MVLD and new CIViC features is outlined for use by ClinGen Somatic WG task teams for curation and submission to ClinVar, and provides a model for promoting harmonization of cancer variant representation and efficient distribution of this information.
Source: Human Mutation
DOI: 10.1002/humu.23651
Authors: Arpad M. Danos, Deborah I. Ritter, Alex H. Wagner, Kilannin Krysiak, Dmitriy Sonkin, Christine Micheel, Matthew McCoy, Shruti Rao, Gordana Raca, Simina M. Boca, Angshumoy Roy, Erica K. Barnell, Joshua F. McMichael, Susanna Kiwala, Adam C. Coffman, Lynzey Kujan, Shashikant Kulkarni, Malachi Griffith, Subha Madhavan, Obi L. Griffith
Institutions: Washington University in St. Louis, Baylor College of Medicine, National Cancer Institute, Vanderbilt University, Vanderbilt-Ingram Cancer Center, Georgetown Lombardi Comprehensive Cancer Center, University of Southern California, Baylor Genetics, Dan L Duncan Comprehensive Cancer Center
Language: English
Topic: Genomics and Rare Diseases
Subfield: Genetics
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $2,740
Awards: G1515700839, G154717235, G1773452051, G2813239719, CGDnet: Cancer Gene Drug Network: Using patient-specific drug-gene networks for recommending targeted cancer therapies., G3902167863, The Clinical Genome Resource - Expert Curation and EHR Integration, G5171270215, G5310623310, G5841304809, G8989167464
OpenAlex ID: W2895954017