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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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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.
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MUNTÉ, Elisabet, FELIUBADALÓ, Lidia, PINEDA, Marta, TORNERO, Eva, GONZALEZ, Maribel, MORENO-CABRERA, José marcos, ROCA, Carla, BALES RUBIO, Joan, ARNALDO, Laura, CAPELLÁ, Gabriel, LUIS MOSQUERA, Jose, LÁZARO, Conxi. 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, núm. 3. [consulta: 24 de novembre de 2025]. [Disponible a: https://hdl.handle.net/2445/224336]