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The CIViC knowledge model and standard operating procedures for curation and clinical interpretation of variants in cancer

View ORCID ProfileArpad M. Danos, View ORCID ProfileKilannin Krysiak, View ORCID ProfileErica K. Barnell, Adam C. Coffman, Joshua F. McMichael, View ORCID ProfileSusanna Kiwala, View ORCID ProfileNicholas C. Spies, View ORCID ProfileLana M. Sheta, View ORCID ProfileShahil P. Pema, View ORCID ProfileLynzey Kujan, Kaitlin A. Clark, View ORCID ProfileAmber Z. Wollam, View ORCID ProfileShruti Rao, Deborah I. Ritter, View ORCID ProfileDmitriy Sonkin, View ORCID ProfileGordana Raca, Raymond H. Kim, View ORCID ProfileAlex H. Wagner, View ORCID ProfileSubha Madhavan, View ORCID ProfileMalachi Griffith, View ORCID ProfileObi L. Griffith
doi: https://doi.org/10.1101/700179
Arpad M. Danos
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Kilannin Krysiak
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
2Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
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Erica K. Barnell
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
3Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
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Adam C. Coffman
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Joshua F. McMichael
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Susanna Kiwala
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Nicholas C. Spies
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Lana M. Sheta
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Shahil P. Pema
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Lynzey Kujan
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Kaitlin A. Clark
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Amber Z. Wollam
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Shruti Rao
4Innovation Center for Biomedical Informatics, Georgetown University, Washington D.C., USA
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Deborah I. Ritter
5Department of Pediatrics, Texas Children’s Hospital, Baylor College of Medicine, Houston, Texas, USA
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Dmitriy Sonkin
6Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, Maryland, USA
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Gordana Raca
7Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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Raymond H. Kim
8Fred A. Litwin Family Center in Genetic Medicine, University Health Network, Toronto, ON, Canada
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Alex H. Wagner
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
2Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
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Subha Madhavan
4Innovation Center for Biomedical Informatics, Georgetown University, Washington D.C., USA
9Georgetown Lombardi Comprehensive Cancer Center, Washington, District of Columbia, USA
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Malachi Griffith
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
2Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
3Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
10Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
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  • For correspondence: mgriffit@wustl.edu obigriffith@wustl.edu
Obi L. Griffith
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
2Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
3Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
10Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
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  • For correspondence: mgriffit@wustl.edu obigriffith@wustl.edu
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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 Interpretations 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. Currently, the CIViC knowledge model consists of four main components: Genes, Variants, Evidence Items, and Assertions. Each component has an associated knowledge model and methods for curation. Gene and Variant data contextualize the genomic region(s) involved in the clinical statement. Evidence Items provide structured associations between variants and their clinically predictive/therapeutic, prognostic, diagnostic, predisposing, and functional implications. Finally, CIViC Assertions summarize collections of CIViC Evidence Items for a specific Disease, Variant, and Clinical Significance with incorporation of clinical and technical guidelines. Here we present the CIViC knowledge model, curation standard operating procedures, and detailed examples to support community-driven curation of cancer variants.

Footnotes

  • https://civicdb.org/

  • List of Abbreviations

    API
    Application Programming Interface
    ACMG
    American College of Medical Genetics
    AID
    CIViC Assertion identifier
    AMP
    Association for Molecular Pathology
    ASCO
    American Society of Clinical Oncology
    CIViC
    Clinical Interpretations of Variants In Cancer
    DGIdb
    Drug Gene Interaction database
    DOID
    Disease Ontology identifiers
    EID
    CIViC Evidence Item identifier
    FDA
    Food and Drug Administration
    HGNC
    Human Gene Nomenclature Committee
    HPO
    Human Phenotype Ontology
    NCI
    National Cancer Institute
    NCCN
    National Comprehensive Cancer Network
    SOP
    Standard Operating Procedure
    SOID
    Sequence Ontology identifier
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    The CIViC knowledge model and standard operating procedures for curation and clinical interpretation of variants in cancer
    Arpad M. Danos, Kilannin Krysiak, Erica K. Barnell, Adam C. Coffman, Joshua F. McMichael, Susanna Kiwala, Nicholas C. Spies, Lana M. Sheta, Shahil P. Pema, Lynzey Kujan, Kaitlin A. Clark, Amber Z. Wollam, Shruti Rao, Deborah I. Ritter, Dmitriy Sonkin, Gordana Raca, Raymond H. Kim, Alex H. Wagner, Subha Madhavan, Malachi Griffith, Obi L. Griffith
    bioRxiv 700179; doi: https://doi.org/10.1101/700179
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    The CIViC knowledge model and standard operating procedures for curation and clinical interpretation of variants in cancer
    Arpad M. Danos, Kilannin Krysiak, Erica K. Barnell, Adam C. Coffman, Joshua F. McMichael, Susanna Kiwala, Nicholas C. Spies, Lana M. Sheta, Shahil P. Pema, Lynzey Kujan, Kaitlin A. Clark, Amber Z. Wollam, Shruti Rao, Deborah I. Ritter, Dmitriy Sonkin, Gordana Raca, Raymond H. Kim, Alex H. Wagner, Subha Madhavan, Malachi Griffith, Obi L. Griffith
    bioRxiv 700179; doi: https://doi.org/10.1101/700179

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