scoreInvHap: Inversion genotyping for genome-wide association studies

Carlos Ruiz-Arenas, Alejandro Cáceres, Marcos López-Sánchez, Ignacio Tolosana, Luis Perez-Jurado, Juan R. González

Research output: Contribution to journalArticle

1 Citation (Scopus)

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.

LanguageEnglish
Article numbere1008203
JournalPLoS genetics
Volume15
Issue number7
DOIs
Publication statusPublished - 1 Jul 2019

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Genetics(clinical)
  • Cancer Research

Cite this

Ruiz-Arenas, C., Cáceres, A., López-Sánchez, M., Tolosana, I., Perez-Jurado, L., & González, J. R. (2019). scoreInvHap: Inversion genotyping for genome-wide association studies. PLoS genetics, 15(7), [e1008203]. https://doi.org/10.1371/journal.pgen.1008203
Ruiz-Arenas, Carlos ; Cáceres, Alejandro ; López-Sánchez, Marcos ; Tolosana, Ignacio ; Perez-Jurado, Luis ; González, Juan R. / scoreInvHap : Inversion genotyping for genome-wide association studies. In: PLoS genetics. 2019 ; Vol. 15, No. 7.
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Ruiz-Arenas, C, Cáceres, A, López-Sánchez, M, Tolosana, I, Perez-Jurado, L & González, JR 2019, 'scoreInvHap: Inversion genotyping for genome-wide association studies', PLoS genetics, vol. 15, no. 7, e1008203. https://doi.org/10.1371/journal.pgen.1008203

scoreInvHap : Inversion genotyping for genome-wide association studies. / Ruiz-Arenas, Carlos; Cáceres, Alejandro; López-Sánchez, Marcos; Tolosana, Ignacio; Perez-Jurado, Luis; González, Juan R.

In: PLoS genetics, Vol. 15, No. 7, e1008203, 01.07.2019.

Research output: Contribution to journalArticle

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Ruiz-Arenas C, Cáceres A, López-Sánchez M, Tolosana I, Perez-Jurado L, González JR. scoreInvHap: Inversion genotyping for genome-wide association studies. PLoS genetics. 2019 Jul 1;15(7). e1008203. https://doi.org/10.1371/journal.pgen.1008203