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A cautionary tale! The hazards of genotype imputation.
13 October 2021
Professor Dallas Swallow and Professor Nik Maniatis coauthor a joint paper on the 'hazards of genotype imputation in chromosomal regions under selection: a case study using the Lactase gene region'
Although imputation of missing SNP results has been widely used in genetic studies,听claims about the quality and usefulness of imputation have outnumbered the few studies that have听 questioned its limitations. We studied the 听imputation of 听variants that have become frequent 听due to selection,听听and compared imputed genotypes with directly genotyped data, then examined听the haplotype pairs of all 听individuals with discrepant and missing genotypes. 听 The errors are non random. Most incorrect and missing imputations result from听long听haplotypes that are evolutionarily closely related to those carrying the derived alleles, while some relate to听rare and听recombinant haplotypes. This is a cautionary tale.
"The hazards of genotype imputation in chromosomal regions under selection: a case study using the Lactase gene region" Ann Hum Genet 2021.听听Aminah T Ali, Anke Liebert, Winston Lau, Nikolas Maniatis听and Dallas M Swallow. ()