ScoreInvHap: inversion genotyping for genome-wide association studies
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- dc.contributor.author Ruiz-Arenas, Carlos
- dc.contributor.author Cáceres, Alejandro
- dc.contributor.author López Sánchez, Marcos, 1986-
- dc.contributor.author Tolosana, Ignacio
- dc.contributor.author Pérez Jurado, Luis Alberto
- dc.contributor.author González Ruiz, Juan Ramón
- dc.date.accessioned 2020-03-26T07:41:07Z
- dc.date.available 2020-03-26T07:41:07Z
- dc.date.issued 2019
- dc.description.abstract Polymorphic inversions contribute to adaptation and phenotypic variation. However, large multi-centric association studies of inversions remain challenging. We present scoreInvHap, a method to genotype inversions from SNP data for genome-wide association studies (GWASs), overcoming important limitations of current methods and outperforming them in accuracy and applicability. scoreInvHap calls individual inversion-genotypes from a similarity score to the SNPs of experimentally validated references. It can be used on different sources of SNP data, including those with low SNP coverage such as exome sequencing, and is easily adaptable to genotype new inversions, either in humans or in other species. We present 20 human inversions that can be reliably and easily genotyped with scoreInvHap to discover their role in complex human traits, and illustrate a first genome-wide association study of experimentally-validated human inversions. scoreInvHap is implemented in R and it is freely available from Bioconductor.
- dc.description.sponsorship This work was supported by the Spanish Ministry of Economy and Competitiveness (RTI2018-100-789-B-I00) (http://www.mineco.gob.es/) by a project awarded to JRG. CR-A was supported by a FI fellowship from Catalan Government (http://agaur.gencat.cat/es/inici/) (#016FI_B 00272). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
- dc.format.mimetype application/pdf
- dc.identifier.citation Ruiz-Arenas C, Cáceres A, López-Sánchez M, Tolosana I, Pérez-Jurado L, González JR. ScoreInvHap: inversion genotyping for genome-wide association studies. PLoS Genet. 2019 Jul 3; 15(7):e1008203. DOI: 10.1371/journal.pgen.1008203
- dc.identifier.doi http://dx.doi.org/10.1371/journal.pgen.1008203
- dc.identifier.issn 1553-7390
- dc.identifier.uri http://hdl.handle.net/10230/44030
- dc.language.iso eng
- dc.publisher Public Library of Science (PLoS)
- dc.relation.ispartof PLoS Genetics. 2019 Jul 3;15(7):e1008203
- dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/RTI2018-100-789-B-I00
- dc.rights © 2019 Ruiz-Arenas et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, https://creativecommons.org/licenses/by/4.0/ which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.rights.uri https://creativecommons.org/licenses/by/4.0/
- dc.subject.other Genotip
- dc.subject.other Genètica
- dc.title ScoreInvHap: inversion genotyping for genome-wide association studies
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion