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Population-specific genotype imputations using minimac or IMPUTE2.

Elisabeth M van Leeuwen1, Alexandros Kanterakis2, Patrick Deelen2

  • 1Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands.

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|July 31, 2015
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Summary
This summary is machine-generated.

Combining genome-wide association studies (GWASs) requires consistent single-nucleotide polymorphisms (SNPs). This protocol details imputation methods using minimac and IMPUTE2 for enhanced genetic variant analysis.

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Area of Science:

  • Genetics
  • Bioinformatics
  • Computational Biology

Background:

  • Genome-wide association studies (GWASs) require large sample sizes for robust analysis of common and rare genetic variants.
  • Meta-analysis of multiple cohorts increases statistical power but necessitates standardized genetic data, specifically identical single-nucleotide polymorphisms (SNPs).
  • Genotype imputation is a crucial method for harmonizing SNP data across diverse cohorts when direct genotyping is incomplete.

Purpose of the Study:

  • To provide comprehensive guidelines for performing genotype imputation using minimac and IMPUTE2.
  • To detail the application of these imputation methods within the Genome of the Netherlands (GoNL) consortium.
  • To identify factors influencing the quality of genetic imputation.

Main Methods:

  • The protocol outlines genotype imputation procedures using the minimac and IMPUTE2 software.
  • It incorporates the use of a population-specific reference panel developed by the Genome of the Netherlands (GoNL) consortium.
  • Guidelines are provided for imputing genotypes in large biobanks.

Main Results:

  • The protocol has been successfully applied by the Genome of the Netherlands (GoNL) consortium for imputing genetic data in Dutch biobanks.
  • The developed guidelines facilitate the harmonization of SNP data across different cohorts for meta-analysis.
  • Factors affecting imputation quality are discussed to optimize results.

Conclusions:

  • This protocol offers a standardized approach for genotype imputation, essential for powerful GWAS meta-analyses.
  • The use of population-specific reference panels, like the one from GoNL, enhances imputation accuracy.
  • The guidelines are practical for large-scale biobank imputation projects, requiring several days for completion.