AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data

Detalhes bibliográficos
Autor(a) principal: Quinodoz, Mathieu
Data de Publicação: 2021
Outros Autores: Peter, Virginie G, Bedoni, Nicola, Royer Bertrand, Béryl, Cisarova, Katarina, Salmaninejad, Arash, Sepahi, Neda, Rodrigues, Raquel, Piran, Mehran, Mojarrad, Majid, Pasdar, Alireza, Ghanbari Asad, Ali, Sousa, Ana Berta, Santos, Maria Luisa, Superti-Furga, Andrea, Rivolta, Carlo
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10451/46213
Resumo: © The Author(s) 2021. Open AccessThis article is licensed under a Creative CommonsAttribution 4.0 International License, which permits use, sharing,adaptation, distribution and reproduction in any medium or format, as long as you giveappropriate credit to the original author(s) and the source, provide a link to the CreativeCommons license, and indicate if changes were made. The images or other third partymaterial in this article are included in the article’s Creative Commons license, unlessindicated otherwise in a credit line to the material. If material is not included in thearticle’s Creative Commons license and your intended use is not permitted by statutoryregulation or exceeds the permitted use, you will need to obtain permission directly fromthe copyright holder. To view a copy of this license, visithttp://creativecommons.org/licenses/by/4.0/.
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spelling AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data© The Author(s) 2021. Open AccessThis article is licensed under a Creative CommonsAttribution 4.0 International License, which permits use, sharing,adaptation, distribution and reproduction in any medium or format, as long as you giveappropriate credit to the original author(s) and the source, provide a link to the CreativeCommons license, and indicate if changes were made. The images or other third partymaterial in this article are included in the article’s Creative Commons license, unlessindicated otherwise in a credit line to the material. If material is not included in thearticle’s Creative Commons license and your intended use is not permitted by statutoryregulation or exceeds the permitted use, you will need to obtain permission directly fromthe copyright holder. To view a copy of this license, visithttp://creativecommons.org/licenses/by/4.0/.Homozygosity mapping is a powerful method for identifying mutations in patients with recessive conditions, especially in consanguineous families or isolated populations. Historically, it has been used in conjunction with genotypes from highly polymorphic markers, such as DNA microsatellites or common SNPs. Traditional software performs rather poorly with data from Whole Exome Sequencing (WES) and Whole Genome Sequencing (WGS), which are now extensively used in medical genetics. We develop AutoMap, a tool that is both web-based or downloadable, to allow performing homozygosity mapping directly on VCF (Variant Call Format) calls from WES or WGS projects. Following a training step on WES data from 26 consanguineous families and a validation procedure on a matched cohort, our method shows higher overall performances when compared with eight existing tools. Most importantly, when tested on real cases with negative molecular diagnosis from an internal set, AutoMap detects three gene-disease and multiple variant-disease associations that were previously unrecognized, projecting clear benefits for both molecular diagnosis and research activities in medical genetics.Springer NatureRepositório da Universidade de LisboaQuinodoz, MathieuPeter, Virginie GBedoni, NicolaRoyer Bertrand, BérylCisarova, KatarinaSalmaninejad, ArashSepahi, NedaRodrigues, RaquelPiran, MehranMojarrad, MajidPasdar, AlirezaGhanbari Asad, AliSousa, Ana BertaSantos, Maria LuisaSuperti-Furga, AndreaRivolta, Carlo2021-02-05T17:34:03Z20212021-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10451/46213engNat Commun. 2021 Jan 22;12(1):51810.1038/s41467-020-20584-42041-1723info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-11-08T16:48:25Zoai:repositorio.ul.pt:10451/46213Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T21:58:28.034161Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data
title AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data
spellingShingle AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data
Quinodoz, Mathieu
title_short AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data
title_full AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data
title_fullStr AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data
title_full_unstemmed AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data
title_sort AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data
author Quinodoz, Mathieu
author_facet Quinodoz, Mathieu
Peter, Virginie G
Bedoni, Nicola
Royer Bertrand, Béryl
Cisarova, Katarina
Salmaninejad, Arash
Sepahi, Neda
Rodrigues, Raquel
Piran, Mehran
Mojarrad, Majid
Pasdar, Alireza
Ghanbari Asad, Ali
Sousa, Ana Berta
Santos, Maria Luisa
Superti-Furga, Andrea
Rivolta, Carlo
author_role author
author2 Peter, Virginie G
Bedoni, Nicola
Royer Bertrand, Béryl
Cisarova, Katarina
Salmaninejad, Arash
Sepahi, Neda
Rodrigues, Raquel
Piran, Mehran
Mojarrad, Majid
Pasdar, Alireza
Ghanbari Asad, Ali
Sousa, Ana Berta
Santos, Maria Luisa
Superti-Furga, Andrea
Rivolta, Carlo
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Repositório da Universidade de Lisboa
dc.contributor.author.fl_str_mv Quinodoz, Mathieu
Peter, Virginie G
Bedoni, Nicola
Royer Bertrand, Béryl
Cisarova, Katarina
Salmaninejad, Arash
Sepahi, Neda
Rodrigues, Raquel
Piran, Mehran
Mojarrad, Majid
Pasdar, Alireza
Ghanbari Asad, Ali
Sousa, Ana Berta
Santos, Maria Luisa
Superti-Furga, Andrea
Rivolta, Carlo
description © The Author(s) 2021. Open AccessThis article is licensed under a Creative CommonsAttribution 4.0 International License, which permits use, sharing,adaptation, distribution and reproduction in any medium or format, as long as you giveappropriate credit to the original author(s) and the source, provide a link to the CreativeCommons license, and indicate if changes were made. The images or other third partymaterial in this article are included in the article’s Creative Commons license, unlessindicated otherwise in a credit line to the material. If material is not included in thearticle’s Creative Commons license and your intended use is not permitted by statutoryregulation or exceeds the permitted use, you will need to obtain permission directly fromthe copyright holder. To view a copy of this license, visithttp://creativecommons.org/licenses/by/4.0/.
publishDate 2021
dc.date.none.fl_str_mv 2021-02-05T17:34:03Z
2021
2021-01-01T00:00:00Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10451/46213
url http://hdl.handle.net/10451/46213
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Nat Commun. 2021 Jan 22;12(1):518
10.1038/s41467-020-20584-4
2041-1723
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Springer Nature
publisher.none.fl_str_mv Springer Nature
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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