Huang and Tseng [2013] identified the cosmopolitan reference panel containing all population samples from the 1kGP to be optimal, in terms of having both high genotype imputation accuracy and low missing genotype call rates, for genotype imputation in GAW18 with the IMPUTE2 software. They also found that a larger-sized reference panel can reduce imputation error and missing genotype, but the improvement can be limited. Indeed, when comparing the cosmopolitan reference panel consisting of all 1,094 1kGP samples to the panel consisting of 181 sample individuals from the Americas, genotype imputation error rates and missing genotype call rates were comparable. They also found that reference panels from 1kGP that did not include samples from the Americas resulted in substantially higher imputation error rates compared to the two reference panels that included these samples. Using reference panels from 1kGP consisting of single ancestral populations, e.g., the African, European, and Asian reference panels, resulted in poor genotype imputation quality for the admixed GAW18 samples. Interestingly, the reference panel consisting of admixed individuals from GAW18 that closely matched the ancestry of the sample individuals
