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Genome Med. 2019 Nov 29;11(1):76. doi: 10.1186/s13073-019-0687-x.

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

Author information

1
McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
2
Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
3
Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
4
Innovation Center for Biomedical Informatics, Georgetown University, Washington DC, USA.
5
Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA.
6
Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA.
7
Keck School of Medicine, University of Southern California, Los Angeles, California, USA.
8
Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, USA.
9
Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.
10
Fred A. Litwin Family Center in Genetic Medicine, University Health Network, Toronto, ON, Canada.
11
Georgetown Lombardi Comprehensive Cancer Center, Washington DC, USA.
12
McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA. mgriffit@wustl.edu.
13
Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA. mgriffit@wustl.edu.
14
Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA. mgriffit@wustl.edu.
15
Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA. mgriffit@wustl.edu.
16
McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA. obigriffith@wustl.edu.
17
Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA. obigriffith@wustl.edu.
18
Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA. obigriffith@wustl.edu.
19
Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA. obigriffith@wustl.edu.

Abstract

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.

KEYWORDS:

Cancer; Curation; Knowledgebase; Standard operating procedure; Variant

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