Huang and Tseng [2013] compared the genotype imputation results for the GAW18 admixed samples with the IMPUTE2 software using different reference panels. They identified the cosmopolitan reference panel consisting of all sample individuals in 1kGP to be optimal, where imputation with this reference panel resulted in both high genotype imputation accuracy and low missing genotype call rates for the GAW18 samples. They also found that using a reference panel consisting of GAW18 individuals that closely matched the admixed ancestry of the sample individuals had the highest genotype imputation accuracy among all reference panels considered, but it also resulted in higher missing genotype call rates compared to the composite 1kGP reference panel. A number of factors can impact genotype imputation quality in admixed populations [Hancock et al., 2012], in addition to the choice of reference panels, and a more extensive study investigating genotype imputation accuracy of rare versus common variants in GAW18 as well as comparing the imputation performance of different software programs will provide greater insight.
