Genotype imputation is often conducted in genome-wide association studies (GWAS) as an efficient approach to expand coverage of single nucleotide polymorphisms (SNPs), enabling meta-analysis of GWAS from different genotyping platforms [1] and fine-mapping in regions of interest to identify potentially causal variants [2]. To infer untyped SNP genotypes, imputation uses reference haplotype panels genotyped at a dense set of SNPs, historically from the original HapMap [3], [4] populations of Yorubas from West Africa (YRI), European Americans (CEU), northern Chinese (CHB), and Japanese (JPT). CEU serves as a good reference for genotype imputation in European or European American studies, and CHB and JPT serve as good references for East Asian studies [5].
