Imputation accuracy relies on having an appropriate reference panel that includes haplotypes from the population studied. Matching alleles and allele frequencies in the study cohort with reference panels as part of pre-imputation QC also relies on using reference data from a matched ancestral background. Reference panels with better coverage of haplotypes from the population of the genotyped cohort will yield a greater number of well-imputed variants for GWAS, especially among lower frequency variants (Ahmad et al., 2017; Howie et al., 2012). Table 1 lists major imputation panels that are currently publicly available. We note that although many ongoing projects are aiming at more diverse populations (Supplemental Table S3), additional efforts in more populations are needed to expand the diversity of imputation reference panels (Kelleher et al., 2018).
