scoreInvHap: Inversion genotyping for genome-wide association studies

PLoS Genet. 2019 Jul 3;15(7):e1008203. doi: 10.1371/journal.pgen.1008203. eCollection 2019 Jul.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Genome-Wide Association Study / methods*
  • Genotyping Techniques
  • Humans
  • Polymorphism, Single Nucleotide
  • Sequence Inversion*
  • Software

Grants and funding

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.