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scoreInvHap: Inversion genotyping for genome-wide association studies.

Carlos Ruiz-Arenas1,2,3, Alejandro Cáceres1,3, Marcos López-Sánchez4,5

  • 1ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain.

Plos Genetics
|July 4, 2019
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Summary
This summary is machine-generated.

We developed scoreInvHap, a new method for genotyping polymorphic inversions using SNP data. This tool enables accurate genome-wide association studies (GWASs) for complex human traits, overcoming previous limitations.

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Area of Science:

  • Genetics
  • Genomics
  • Bioinformatics

Background:

  • Polymorphic inversions are crucial for adaptation and phenotypic variation.
  • Large-scale association studies of inversions are hindered by current methodological challenges.

Purpose of the Study:

  • To introduce scoreInvHap, a novel method for genotyping inversions from SNP data.
  • To enable accurate genome-wide association studies (GWASs) for inversions.
  • To overcome limitations of existing inversion genotyping methods.

Main Methods:

  • scoreInvHap genotypes inversions by calculating a similarity score between individual SNP data and experimentally validated reference inversions.
  • The method is applicable to various SNP data sources, including low-coverage exome sequencing.
  • It is adaptable for genotyping new inversions across species.

Main Results:

  • scoreInvHap accurately genotypes 20 human inversions.
  • The method demonstrates superior accuracy and applicability compared to existing approaches.
  • A first genome-wide association study using experimentally validated human inversions is presented.

Conclusions:

  • scoreInvHap provides a reliable and accessible tool for inversion genotyping in GWASs.
  • This method facilitates the discovery of inversion roles in complex human traits.
  • The R-implemented tool is freely available via Bioconductor.