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Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC)

  1. Author:
    Horak, Peter
    Griffith, Malachi
    Danos, Arpad M
    Pitel, Beth A
    Madhavan, Subha
    Liu, Xuelu
    Chow, Cynthia
    Williams, Heather
    Carmody, Leigh
    Barrow-Laing, Lisa
    Rieke, Damian
    Kreutzfeldt, Simon
    Stenzinger, Albrecht
    Tamborero, David
    Benary, Manuela
    Rajagopal, Padma Sheila
    Ida, Cristiane M
    Lesmana, Harry
    Satgunaseelan, Laveniya
    Merker, Jason D
    Tolstorukov, Michael Y
    Campregher, Paulo Vidal
    Warner, Jeremy L
    Rao, Shruti
    Natesan, Maya
    Shen, Haolin
    Venstrom, Jeffrey
    Roy, Somak
    Tao, Kayoko
    Kanagal-Shamanna, Rashmi
    Xu, Xinjie
    Ritter, Deborah I
    Pagel, Kym
    Krysiak, Kilannin
    Dubuc, Adrian
    Akkari, Yassmine M
    Li, Xuan Shirley
    Lee, Jennifer
    King, Ian
    Raca, Gordana
    Wagner, Alex H
    Li, Marylin M
    Plon, Sharon E
    Kulkarni, Shashikant
    Griffith, Obi L
    Chakravarty, Debyani
    Sonkin, Dmitriy

  2. Author Address

    National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany. Electronic address: peter.horak@nct-heidelberg.de., Washington University School of Medicine in St. Louis, St. Louis, MO., Mayo Clinic, Rochester, MN., Georgetown University Medical Center, Washington, DC., Dana-Farber Cancer Institute, Boston, MA., BC Cancer Agency, Vancouver, British Columbia, Canada., Columbia University, New York, NY., The Jackson Laboratory for Genomic Medicine, Farmington, CT., QIAGEN Inc, Redwood City, CA., Charit 233;-Universit 228;tsmedizin Berlin, Berlin, Germany., Institute of Pathology, University of Heidelberg, Heidelberg, Germany., Karolinska Institute, Stockholm, Sweden., Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD., Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH., Royal Prince Alfred Hospital, Sydney, New South Wales, Australia., UNC School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC., Hospital Israelita Albert Einstein, S 227;o Paulo, S 227;o Paulo, Brazil., Vanderbilt University, Nashville, TN., Foundation Medicine, Inc, Cambridge, MA., Cincinnati Children 39;s Hospital Medical Center, Cincinnati, OH., National Cancer Center Hospital, Tokyo, Japan., The University of Texas MD Anderson Cancer Center, Houston, TX., Baylor College of Medicine, Houston, TX., Johns Hopkins University, Baltimore, MD., Brigham and Women 39;s Hospital, Harvard Medical School, Boston, MA., Legacy Health, Portland, OR., Congenica Ltd, Cambridge, United Kingdom., Frederick National Laboratory for Cancer Research, National Cancer Institute, Rockville, MD., University Health Network, Toronto, Ontario, Canada., University of Southern California, Los Angeles, CA., Nationwide Children 39;s Hospital, Columbus, OH; The Ohio State University College of Medicine, Columbus, OH., Children 39;s Hospital of Philadelphia, Philadelphia, PA., Memorial Sloan Kettering Cancer Center, New York, NY. Electronic address: chakravd@mskcc.org., National Cancer Institute, Rockville, MD. Electronic address: dmitriy.sonkin@nih.gov.,
    1. Year: 2022
    2. Date: Jan 28
  2. Journal: Genetics in Medicine : Official Journal of the American College of Medical Genetics
  4. Type of Article: Article
  1. Abstract:

    Several professional societies have published guidelines for the clinical interpretation of somatic variants, which specifically address diagnostic, prognostic, and therapeutic implications. Although these guidelines for the clinical interpretation of variants include data types that may be used to determine the oncogenicity of a variant (eg, population frequency, functional, and in silico data or somatic frequency), they do not provide a direct, systematic, and comprehensive set of standards and rules to classify the oncogenicity of a somatic variant. This insufficient guidance leads to inconsistent classification of rare somatic variants in cancer, generates variability in their clinical interpretation, and, importantly, affects patient care. Therefore, it is essential to address this unmet need. Clinical Genome Resource (ClinGen) Somatic Cancer Clinical Domain Working Group and ClinGen Germline/Somatic Variant Subcommittee, the Cancer Genomics Consortium, and the Variant Interpretation for Cancer Consortium used a consensus approach to develop a standard operating procedure (SOP) for the classification of oncogenicity of somatic variants. This comprehensive SOP has been developed to improve consistency in somatic variant classification and has been validated on 94 somatic variants in 10 common cancer-related genes. The comprehensive SOP is now available for classification of oncogenicity of somatic variants. Copyright © 2022. Published by Elsevier Inc.

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External Sources

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  2. DOI: 10.1016/j.gim.2022.01.001
  3. PMID: 35101336
  4. PII : S1098-3600(22)00001-6

Library Notes

  1. Fiscal Year: FY2021-2022
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