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).
Document Type
Article
Publication Date
5-1-2022
Publication Title
Genetics in medicine : official journal of the American College of Medical Genetics
Keywords
JGM, Genetic Testing, Genetic Variation, Genome, Human, Genomics, Humans, Neoplasms, Virulence
JAX Source
Genet Med 2022 May; 24(5):986-998
Volume
24
Issue
5
First Page
986
Last Page
998
ISSN
1530-0366
PMID
35101336
DOI
https://doi.org/10.1016/j.gim.2022.01.001
Abstract
PURPOSE: 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.
METHODS: 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.
RESULTS: 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.
CONCLUSION: The comprehensive SOP is now available for classification of oncogenicity of somatic variants.
Recommended Citation
Horak P,
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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). Genet Med 2022 May; 24(5):986-998