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btad128.pdf (3.94 MB)

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2023-03-14

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cc-by (c) Munté, Elisabet et al., 2023
Si us plau utilitzeu sempre aquest identificador per citar o enllaçar aquest document: https://hdl.handle.net/2445/224336

VaRHC: an R package for semi-automation of variant classification in hereditary cancer genes according to ACMG/AMP and gene-specific ClinGen guidelines

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https://doi.org/10.1093/bioinformatics/btad128

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Motivation: Germline variant classification allows accurate genetic diagnosis and risk assessment. However, it is a tedious iterative process integrating information from several sources and types of evidence. It should follow gene-specific (if available) or general updated international guidelines. Thus, it is the main burden of the incorporation of next-generation sequencing into the clinical setting.Results: We created the vaRiants in HC (vaRHC) R package to assist the process of variant classification in hereditary cancer by: (i) collecting information from diverse databases; (ii) assigning or denying different types of evidence according to updated American College of Molecular Genetics and Genomics/Association of Molecular Pathologist gene-specific criteria for ATM, CDH1, CHEK2, MLH1, MSH2, MSH6, PMS2, PTEN, and TP53 and general criteria for other genes; (iii) providing an automated classification of variants using a Bayesian metastructure and considering CanVIG-UK recommendations; and (iv) optionally printing the output to an .xlsx file. A validation using 659 classified variants demonstrated the robustness of vaRHC, presenting a better criteria assignment than Cancer SIGVAR, an available similar tool.Availability and implementation: The source code can be consulted in the GitHub repository () Additionally, it will be submitted to CRAN soon.

Matèries

Patologia molecular, Genètica mèdica, Proteïnes supressores de tumors

Matèries (anglès)

Molecular pathology, Medical genetics, Tumor suppressor protein

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Articles publicats en revistes (Institut d'lnvestigació Biomèdica de Bellvitge (IDIBELL))

Citació

MUNTÉ, Elisabet, et al. VaRHC: an R package for semi-automation of variant classification in hereditary cancer genes according to ACMG/AMP and gene-specific ClinGen guidelines. Bioinformatics. 2023. Vol. 39, num. 3. ISSN 1367-4811. [consulted: 8 of September of 2026]. Available at: https://hdl.handle.net/2445/224336

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