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

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dc.contributor.authorQuinodoz, Mathieu
dc.contributor.authorPeter, Virginie G
dc.contributor.authorBedoni, Nicola
dc.contributor.authorRoyer Bertrand, Béryl
dc.contributor.authorCisarova, Katarina
dc.contributor.authorSalmaninejad, Arash
dc.contributor.authorSepahi, Neda
dc.contributor.authorRodrigues, Raquel
dc.contributor.authorPiran, Mehran
dc.contributor.authorMojarrad, Majid
dc.contributor.authorPasdar, Alireza
dc.contributor.authorGhanbari Asad, Ali
dc.contributor.authorSousa, Ana Berta
dc.contributor.authorSantos, Maria Luisa
dc.contributor.authorSuperti-Furga, Andrea
dc.contributor.authorRivolta, Carlo
dc.date.accessioned2021-02-05T17:34:03Z
dc.date.available2021-02-05T17:34:03Z
dc.date.issued2021
dc.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/.pt_PT
dc.description.abstractHomozygosity 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.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationNat Commun. 2021 Jan 22;12(1):518pt_PT
dc.identifier.doi10.1038/s41467-020-20584-4pt_PT
dc.identifier.eissn2041-1723
dc.identifier.urihttp://hdl.handle.net/10451/46213
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherSpringer Naturept_PT
dc.relation.publisherversionhttps://www.nature.com/ncomms/pt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.titleAutoMap is a high performance homozygosity mapping tool using next-generation sequencing datapt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.citation.issue1pt_PT
oaire.citation.startPage518pt_PT
oaire.citation.titleNature Communicationspt_PT
oaire.citation.volume12pt_PT
person.familyNameRodrigues
person.familyNameFonseca Vieira Álvares Sousa Ferrand Almeida
person.familyNameSantos
person.givenNameRaquel
person.givenNameAna Berta
person.givenNameMaria Luisa
person.identifier.ciencia-id031D-CFAD-116A
person.identifier.orcid0000-0002-7557-1815
person.identifier.orcid0000-0001-5889-2492
person.identifier.orcid0000-0002-6181-4505
person.identifier.scopus-author-id39862203700
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
relation.isAuthorOfPublication447b4847-539c-4693-b0ce-3f279fda08db
relation.isAuthorOfPublication7763033e-aa1b-4f2b-ab30-3eba5815b1ee
relation.isAuthorOfPublication8eb61593-a4e5-4880-a527-6d8bb3802187
relation.isAuthorOfPublication.latestForDiscovery7763033e-aa1b-4f2b-ab30-3eba5815b1ee

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