Journal Article

Standard operating procedure for curation and clinical interpretation of variants in cancer

Griffith, Obi L., Krysiak, Kilannin, Madhavan, Subha, Barnell, Erica K., Kujan, Lynzey, Spies, Nicholas C., Ritter, Deborah I., Clark, Kaitlin A., Rao, Shruti, Griffith, Malachi, Danos, Arpad M., Grisdale, Cameron J., Coffman, Adam C., Wagner, Alex H., Wollam, Amber Z., Raca, Gordana, Lin, Wan-Hsin, Sheta, Lana M., Sonkin, Dmitriy, McMichael, Joshua F., Pema, Shahil P., Kiwala, Susanna, Kim, Raymond H.

2019

Overview

Manually curated variant knowledgebases and their associated knowledge models are serving an increasingly important role in distributing and interpreting variants in cancer. These knowledgebases vary in their level of public accessibility, and the complexity of the models used to capture clinical knowledge. CIViC (Clinical Interpretation of Variants in Cancer - www.civicdb.org ) is a fully open, free-to-use cancer variant interpretation knowledgebase that incorporates highly detailed curation of evidence obtained from peer-reviewed publications and meeting abstracts, and currently holds over 6300 Evidence Items for over 2300 variants derived from over 400 genes. CIViC has seen increased adoption by, and also undertaken collaboration with, a wide range of users and organizations involved in research. To enhance CIViC’s clinical value, regular submission to the ClinVar database and pursuit of other regulatory approvals is necessary. For this reason, a formal peer reviewed curation guideline and discussion of the underlying principles of curation is needed. We present here the CIViC knowledge model, standard operating procedures (SOP) for variant curation, and detailed examples to support community-driven curation of cancer variants.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Application programming interface / Bioinformatics / Biomedical and Life Sciences / Biomedicine / Cancer / Cancer Research / Clinical Competence / Clinical interpretation of genome variation / Correspondence / Curation / Disease Management / Disease Susceptibility / Genes / Human Genetics / Humans / Knowledge / Knowledge Bases / Knowledgebase / Medicine/Public Health / Metabolomics / Models, Theoretical / Neoplasms - diagnosis / Neoplasms - etiology / Neoplasms - therapy / Peer review / Practice Patterns, Physicians / Regulatory approval / Reviews / Revisions / Standard operating procedure / Systems Biology / Variant