{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,10,17]],"date-time":"2024-10-17T04:16:36Z","timestamp":1729138596895,"version":"3.27.0"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,3,14]],"date-time":"2023-03-14T00:00:00Z","timestamp":1678752000000},"content-version":"vor","delay-in-days":13,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Carlos III National Health Institute"},{"DOI":"10.13039\/501100004837","name":"Ministerio de Ciencia e Innovaci\u00f3n","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002924","name":"FEDER","doi-asserted-by":"publisher","award":["PI19\/00553"],"id":[{"id":"10.13039\/501100002924","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100014139","name":"CIBERONC","doi-asserted-by":"publisher","award":["CB16\/12\/00234"],"id":[{"id":"10.13039\/501100014139","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002809","name":"Government of Catalonia","doi-asserted-by":"publisher","award":["2017SGR1282","2017SGR496","2021SGR01112"],"id":[{"id":"10.13039\/501100002809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010552","name":"Departament de Salut de la Generalitat de Catalunya","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100010552","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,3,1]]},"abstract":"Abstract<\/jats:title>Motivation<\/jats:title>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.<\/jats:p><\/jats:sec>Results<\/jats:title>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.<\/jats:p><\/jats:sec>Availability and implementation<\/jats:title>The source code can be consulted in the GitHub repository (https:\/\/github.com\/emunte\/vaRHC) Additionally, it will be submitted to CRAN soon.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad128","type":"journal-article","created":{"date-parts":[[2023,3,14]],"date-time":"2023-03-14T12:26:36Z","timestamp":1678796796000},"source":"Crossref","is-referenced-by-count":3,"title":["vaRHC: an R package for semi-automation of variant classification in hereditary cancer genes according to ACMG\/AMP and gene-specific ClinGen guidelines"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"http:\/\/orcid.org\/0000-0001-8396-8284","authenticated-orcid":false,"given":"Elisabet","family":"Munt\u00e9","sequence":"first","affiliation":[{"name":"Hereditary 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C\u00e1ncer (CIBERONC) , Madrid, Spain"}]},{"given":"Eva","family":"Tornero","sequence":"additional","affiliation":[{"name":"Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Catalan Institute of Oncology , L\u2019Hospitalet de Llobregat 08908, Spain"}]},{"given":"Maribel","family":"Gonzalez","sequence":"additional","affiliation":[{"name":"Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Catalan Institute of Oncology , L\u2019Hospitalet de Llobregat 08908, Spain"}]},{"ORCID":"http:\/\/orcid.org\/0000-0001-8570-0345","authenticated-orcid":false,"given":"Jos\u00e9 Marcos","family":"Moreno-Cabrera","sequence":"additional","affiliation":[{"name":"Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Catalan Institute of Oncology , L\u2019Hospitalet de Llobregat 08908, 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