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

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 (co...

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Detalhes bibliográficos
Autores: Feliubadaló, Lídia, Tonda, Raúl, Trotta, Jean-Remi, Gut, Marta, Gut, Ivo Glynne, Beltran, Sergi, Lázaro García, Conxi
Formato: artículo
Estado:Versión publicada
Fecha de publicación:2017
País:España
Recursos:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/58578
Acesso em linha:http://hdl.handle.net/10230/58578
http://dx.doi.org/10.1038/srep37984
Access Level:acceso abierto
Palavra-chave:Càncer
Càncer -- Aspectes genètics
Gens del càncer
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spelling Benchmarking of whole exome sequencing and ad hoc designed panels for genetic testing of hereditary cancerFeliubadaló, LídiaTonda, RaúlTrotta, Jean-RemiGut, MartaGut, Ivo GlynneBeltran, SergiLázaro García, ConxiCàncerCàncer -- Aspectes genèticsGens del càncerNext 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.Nature Research202320232017info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/58578http://dx.doi.org/10.1038/srep37984reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésScientific Reports. 2017 Jan 4;7(1):37984© 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/http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/585782026-05-29T05:05:01Z
dc.title.none.fl_str_mv Benchmarking of whole exome sequencing and ad hoc designed panels for genetic testing of hereditary cancer
title Benchmarking of whole exome sequencing and ad hoc designed panels for genetic testing of hereditary cancer
spellingShingle Benchmarking of whole exome sequencing and ad hoc designed panels for genetic testing of hereditary cancer
Feliubadaló, Lídia
Càncer
Càncer -- Aspectes genètics
Gens del càncer
title_short Benchmarking of whole exome sequencing and ad hoc designed panels for genetic testing of hereditary cancer
title_full Benchmarking of whole exome sequencing and ad hoc designed panels for genetic testing of hereditary cancer
title_fullStr Benchmarking of whole exome sequencing and ad hoc designed panels for genetic testing of hereditary cancer
title_full_unstemmed Benchmarking of whole exome sequencing and ad hoc designed panels for genetic testing of hereditary cancer
title_sort Benchmarking of whole exome sequencing and ad hoc designed panels for genetic testing of hereditary cancer
dc.creator.none.fl_str_mv Feliubadaló, Lídia
Tonda, Raúl
Trotta, Jean-Remi
Gut, Marta
Gut, Ivo Glynne
Beltran, Sergi
Lázaro García, Conxi
author Feliubadaló, Lídia
author_facet Feliubadaló, Lídia
Tonda, Raúl
Trotta, Jean-Remi
Gut, Marta
Gut, Ivo Glynne
Beltran, Sergi
Lázaro García, Conxi
author_role author
author2 Tonda, Raúl
Trotta, Jean-Remi
Gut, Marta
Gut, Ivo Glynne
Beltran, Sergi
Lázaro García, Conxi
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv Càncer
Càncer -- Aspectes genètics
Gens del càncer
topic Càncer
Càncer -- Aspectes genètics
Gens del càncer
description 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.
publishDate 2017
dc.date.none.fl_str_mv 2017
2023
2023
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/58578
http://dx.doi.org/10.1038/srep37984
url http://hdl.handle.net/10230/58578
http://dx.doi.org/10.1038/srep37984
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Scientific Reports. 2017 Jan 4;7(1):37984
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Nature Research
publisher.none.fl_str_mv Nature Research
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.811543

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