In the imputation context, it has been largely unclear whether genotypes in an admixed population can be most accurately imputed using a mixture of reference panels from the parental populations, or using a comparable reference panel from the admixed population itself. Numerous techniques are now available for inferring ancestry blocks along the genome87,88,89,90,91, and one recent approach uses imputation accuracy as a basis for evaluating inference of ancestry blocks92. This set of developments now offers the possibility of improving imputation in admixed populations by integrating the inference of admixture and missing genotypes93, either by locally imputing from parental reference panels along the genome (Fig. 5), or by concurrently imputing genotypes and inferring ancestry. Although evaluations in admixed populations of the performance of different imputation approaches have not yet utilized local ancestry94, these advances suggest that the intrinsic challenges of working with admixed populations in GWA studies can be surmounted or at least reduced.
