Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria
- PMID: 28492532
- PMCID: PMC5632818
- DOI: 10.1038/gim.2017.37
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria
Erratum in
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Correction: Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9. Genet Med. 2020. PMID: 31346256 Free PMC article.
Abstract
PurposeThe 2015 American College of Medical Genetics and Genomics-Association for Molecular Pathology (ACMG-AMP) guidelines were a major step toward establishing a common framework for variant classification. In practice, however, several aspects of the guidelines lack specificity, are subject to varied interpretations, or fail to capture relevant aspects of clinical molecular genetics. A simple implementation of the guidelines in their current form is insufficient for consistent and comprehensive variant classification.MethodsWe undertook an iterative process of refining the ACMG-AMP guidelines. We used the guidelines to classify more than 40,000 clinically observed variants, assessed the outcome, and refined the classification criteria to capture exceptions and edge cases. During this process, the criteria evolved through eight major and minor revisions.ResultsOur implementation: (i) separated ambiguous ACMG-AMP criteria into a set of discrete but related rules with refined weights; (ii) grouped certain criteria to protect against the overcounting of conceptually related evidence; and (iii) replaced the "clinical criteria" style of the guidelines with additive, semiquantitative criteria.ConclusionSherloc builds on the strong framework of 33 rules established by the ACMG-AMP guidelines and introduces 108 detailed refinements, which support a more consistent and transparent approach to variant classification.
Conflict of interest statement
All of the authors are employees and shareholders of Invitae, a commercial laboratory performing diagnostic genetic testing.
Figures
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Comment in
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A new era in the interpretation of human genomic variation.Genet Med. 2017 Oct;19(10):1092-1095. doi: 10.1038/gim.2017.90. Epub 2017 Jul 13. Genet Med. 2017. PMID: 28703787 Free PMC article. No abstract available.
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