WEScover: selection between clinical whole exome sequencing and gene panel testing

Background: Whole exome sequencing (WES) is widely adopted in clinical and research settings; however, one of the practical concerns is the potential false negatives due to incomplete breadth and depth of coverage for several exons in clinically implicated genes. In some cases, a targeted gene panel...

Descripción completa

Detalles Bibliográficos
Autores: Lee, In-Hee, Lin, Yufei, Jefferson Alvarez, William, Hernandez-Ferrer, Carles, 1987-, Mandl, Kenneth D., Kong, Sek Won
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2021
País:España
Institución: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:10230/48281
Acceso en línea:http://hdl.handle.net/10230/48281
http://dx.doi.org/10.1186/s12859-021-04178-5
Access Level:acceso abierto
Palabra clave:Seqüenciació total del genoma
Cromosomes humans -- Anomalies -- Diagnòstic
Gens
Fenotip
Exons
id ES_085cb08cb8a60e342d666561e43bb68d
oai_identifier_str oai:recercat.cat:10230/48281
network_acronym_str ES
network_name_str España
repository_id_str
spelling WEScover: selection between clinical whole exome sequencing and gene panel testingLee, In-HeeLin, YufeiJefferson Alvarez, WilliamHernandez-Ferrer, Carles, 1987-Mandl, Kenneth D.Kong, Sek WonSeqüenciació total del genomaCromosomes humans -- Anomalies -- DiagnòsticGensFenotipExonsBackground: Whole exome sequencing (WES) is widely adopted in clinical and research settings; however, one of the practical concerns is the potential false negatives due to incomplete breadth and depth of coverage for several exons in clinically implicated genes. In some cases, a targeted gene panel testing may be a dependable option to ascertain true negatives for genomic variants in known disease-associated genes. We developed a web-based tool to quickly gauge whether all genes of interest would be reliably covered by WES or whether targeted gene panel testing should be considered instead to minimize false negatives in candidate genes. Results: WEScover is a novel web application that provides an intuitive user interface for discovering breadth and depth of coverage across population-scale WES datasets, searching either by phenotype, by targeted gene panel(s) or by gene(s). Moreover, the application shows metrics from the Genome Aggregation Database to provide gene-centric view on breadth of coverage. Conclusions: WEScover allows users to efficiently query genes and phenotypes for the coverage of associated exons by WES and recommends use of panel tests for the genes with potential incomplete coverage by WES.The design of WEScover, data collection, analysis, interpretation and writing of the manuscript were supported by grants from the Boston Children’s Hospital Precision Link Biobank and from the National Institutes of Health (R01MH107205, R24OD024622, U01TR002623 and U01HG007530)BioMed Central202120212021info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/48281http://dx.doi.org/10.1186/s12859-021-04178-5reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)Inglés© In-Hee Lee et al. 2021. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were madehttps://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/482812026-05-29T05:05:01Z
dc.title.none.fl_str_mv WEScover: selection between clinical whole exome sequencing and gene panel testing
title WEScover: selection between clinical whole exome sequencing and gene panel testing
spellingShingle WEScover: selection between clinical whole exome sequencing and gene panel testing
Lee, In-Hee
Seqüenciació total del genoma
Cromosomes humans -- Anomalies -- Diagnòstic
Gens
Fenotip
Exons
title_short WEScover: selection between clinical whole exome sequencing and gene panel testing
title_full WEScover: selection between clinical whole exome sequencing and gene panel testing
title_fullStr WEScover: selection between clinical whole exome sequencing and gene panel testing
title_full_unstemmed WEScover: selection between clinical whole exome sequencing and gene panel testing
title_sort WEScover: selection between clinical whole exome sequencing and gene panel testing
dc.creator.none.fl_str_mv Lee, In-Hee
Lin, Yufei
Jefferson Alvarez, William
Hernandez-Ferrer, Carles, 1987-
Mandl, Kenneth D.
Kong, Sek Won
author Lee, In-Hee
author_facet Lee, In-Hee
Lin, Yufei
Jefferson Alvarez, William
Hernandez-Ferrer, Carles, 1987-
Mandl, Kenneth D.
Kong, Sek Won
author_role author
author2 Lin, Yufei
Jefferson Alvarez, William
Hernandez-Ferrer, Carles, 1987-
Mandl, Kenneth D.
Kong, Sek Won
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Seqüenciació total del genoma
Cromosomes humans -- Anomalies -- Diagnòstic
Gens
Fenotip
Exons
topic Seqüenciació total del genoma
Cromosomes humans -- Anomalies -- Diagnòstic
Gens
Fenotip
Exons
description Background: Whole exome sequencing (WES) is widely adopted in clinical and research settings; however, one of the practical concerns is the potential false negatives due to incomplete breadth and depth of coverage for several exons in clinically implicated genes. In some cases, a targeted gene panel testing may be a dependable option to ascertain true negatives for genomic variants in known disease-associated genes. We developed a web-based tool to quickly gauge whether all genes of interest would be reliably covered by WES or whether targeted gene panel testing should be considered instead to minimize false negatives in candidate genes. Results: WEScover is a novel web application that provides an intuitive user interface for discovering breadth and depth of coverage across population-scale WES datasets, searching either by phenotype, by targeted gene panel(s) or by gene(s). Moreover, the application shows metrics from the Genome Aggregation Database to provide gene-centric view on breadth of coverage. Conclusions: WEScover allows users to efficiently query genes and phenotypes for the coverage of associated exons by WES and recommends use of panel tests for the genes with potential incomplete coverage by WES.
publishDate 2021
dc.date.none.fl_str_mv 2021
2021
2021
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/10230/48281
http://dx.doi.org/10.1186/s12859-021-04178-5
url http://hdl.handle.net/10230/48281
http://dx.doi.org/10.1186/s12859-021-04178-5
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.rights.none.fl_str_mv https://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv https://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 BioMed Central
publisher.none.fl_str_mv BioMed Central
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
_version_ 1869403038259609600
score 15,812429

Similares en LA Referencia