Evaluating the accuracy of imputation methods in a five-way admixed population

Schurz, Haiko ; Muller, Stephanie J. ; Van Helden, Paul David ; Tromp, Gerard ; Hoal, Eileen G. ; Kinnear, Craig J. ; Moller, Marlo (2019)

CITATION: Schurz, H., et al. 2019. Evaluating the accuracy of imputation methods in a five-way admixed population. Frontiers in Genetics, 10:34, doi:10.3389/fgene.2019.00034.

The original publication is available at https://www.frontiersin.org

Publication of this article was funded by the Stellenbosch University Open Access Fund.


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.

Please refer to this item in SUNScholar by using the following persistent URL: http://hdl.handle.net/10019.1/105467
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