Evaluating the Accuracy of Imputation Methods in a Five-Way Admixed Population

Frontiers in Genetics
Haiko SchurzMarlo Möller

Abstract

Genotype imputation is a powerful tool for increasing statistical power in an association analysis. Meta-analysis of multiple study datasets also requires a substantial overlap of SNPs for a successful association analysis, which can be achieved by imputation. Quality of imputed datasets is largely dependent on the software used, as well as the reference populations chosen. The accuracy of imputation of available reference populations has not been tested for the five-way admixed South African Colored (SAC) population. In this study, imputation results obtained using three freely-accessible methods were evaluated for accuracy and quality. We show that the African Genome Resource is the best reference panel for imputation of missing genotypes in samples from the SAC population, implemented via the freely accessible Sanger Imputation Server.

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Citations

May 23, 2020·Molecular Genetics and Genomics : MGG·Yolandi SwartMarlo Möller
Mar 7, 2020·NPJ Genomic Medicine·Amy R BentleyCharles N Rotimi
Feb 27, 2021·Pediatric Nephrology : Journal of the International Pediatric Nephrology Association·Moumita Barua, Andrew D Paterson
Feb 14, 2021·NPJ Genomic Medicine·Amy R BentleyCharles N Rotimi
Mar 20, 2021·Scientific Reports·Céline CharonJean-François Deleuze
Mar 30, 2021·JACC. Basic to Translational Science·Robert RobertsTrevor Hadley
May 28, 2021·Human Genetics·Milda Aleknonytė-ReschMichael Krawczak
Aug 4, 2021·Nature Reviews. Genetics·Aaron K WongOlga G Troyanskaya
Oct 12, 2021·Frontiers in Genetics·Katharina StahlInke R König

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Methods Mentioned

BETA
genotyping

Software Mentioned

Affymetrix
Beagle
Minimac3
Genotype Harmoniser
PLINK
Impute2
Minimac
R
SHAPEIT
Genotype Harmonizer

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