Benchmarking of whole exome sequencing and ad hoc designed panels for genetic testing of hereditary cancer

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• dc.contributor.author Feliubadaló, Lídia
• dc.contributor.author Tonda, Raúl
• dc.contributor.author Trotta, Jean-Remi
• dc.contributor.author Gut, Marta
• dc.contributor.author Gut, Ivo Glynne
• dc.contributor.author Beltran, Sergi
• dc.contributor.author Lázaro García, Conxi
• dc.date.accessioned 2023-12-19T06:55:12Z
• dc.date.available 2023-12-19T06:55:12Z
• dc.date.issued 2017
• dc.description.abstract Next generation sequencing panels have been developed for hereditary cancer, although there is some debate about their cost-effectiveness compared to exome sequencing. The performance of two panels is compared to exome sequencing. Twenty-four patients were selected: ten with identified mutations (control set) and fourteen suspicious of hereditary cancer but with no mutation (discovery set). TruSight Cancer (94 genes) and a custom panel (122 genes) were assessed alongside exome sequencing. Eighty-three genes were targeted by the two panels and exome sequencing. More than 99% of bases had a read depth of over 30x in the panels, whereas exome sequencing covered 94%. Variant calling with standard settings identified the 10 mutations in the control set, with the exception of MSH6 c.255dupC using TruSight Cancer. In the discovery set, 240 unique non-silent coding and canonic splice-site variants were identified in the panel genes, 7 of them putatively pathogenic (in ATM, BARD1, CHEK2, ERCC3, FANCL, FANCM, MSH2). The three approaches identified a similar number of variants in the shared genes. Exomes were more expensive than panels but provided additional data. In terms of cost and depth, panels are a suitable option for genetic diagnostics, although exomes also identify variants in non-targeted genes.
• dc.format.mimetype application/pdf
• dc.identifier.citation Feliubadaló L, Tonda R, Gausachs M, Trotta JR, Castellanos E, López-Doriga A, et al. Benchmarking of whole exome sequencing and ad hoc designed panels for genetic testing of hereditary cancer. Sci Rep. 2017 Jan 4;7(1):37984. DOI: 10.1038/srep37984
• dc.identifier.doi http://dx.doi.org/10.1038/srep37984
• dc.identifier.issn 2045-2322
• dc.identifier.uri http://hdl.handle.net/10230/58578
• dc.language.iso eng
• dc.publisher Nature Research
• dc.relation.ispartof Scientific Reports. 2017 Jan 4;7(1):37984
• dc.rights © The Author(s) 2017. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.other Càncer
• dc.subject.other Càncer -- Aspectes genètics
• dc.subject.other Gens del càncer
• dc.title Benchmarking of whole exome sequencing and ad hoc designed panels for genetic testing of hereditary cancer
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion