unclear. Combining the three HapMap panels is also a good choice for genotype imputation in admixed populations [Mathias et al., 2010] where, depending on the ancestry of each stretch of the genome, the best matching haplotype will likely originate from a different HapMap reference panel. Our conclusion that the combined panel is a sensible reference for all populations facilitates practical decision making on the choice of reference panel. The conclusion is also supported by Huang et al. [Huang et al., 2009]. Although their aim was to find an optimal population-specific reference panel for each HGDP sample, their Figure 6 shows that a combined panel, including all HapMap haplotypes is the best compromise choice, in the sense that it performs almost optimally in each of the 39 HGDP populations examined. In the future, we expect that imputation methods that weigh the different reference panels could further improve imputation quality.
