Genotype imputation for genome-wide association studies
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Updated: Jun 12, 2026

Infinium Assay for Large-scale SNP Genotyping Applications
Published on: November 19, 2013
Jonathan Marchini1, Bryan Howie
1Department of Statistics, University of Oxford, Oxford, UK. marchini@stats.ox.ac.uk
Abstract:
In the past few years genome-wide association (GWA) studies have uncovered a large number of convincingly replicated associations for many complex human diseases. Genotype imputation has been used widely in the analysis of GWA studies to boost power, fine-map associations and facilitate the combination of results across studies using meta-analysis. This Review describes the details of several different statistical methods for imputing genotypes, illustrates and discusses the factors that influence imputation performance, and reviews methods that can be used to assess imputation performance and test association at imputed SNPs.
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