AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data
Autor(a) principal: | |
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Data de Publicação: | 2021 |
Outros Autores: | , , , , , , , , , , , , , , |
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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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 |
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info:eu-repo/semantics/openAccess |
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openAccess |
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application/pdf |
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Springer Nature |
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Springer Nature |
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reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
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RCAAP |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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