Heterogeneity of admixture has posed a barrier to association mapping in admixed populations. These populations have instead been considered with other designs, such as admixture mapping, in which genomic segments with excess ancestry from a high-prevalence parental population are identified as potential locations for risk variants74,75,76,77. The utility of admixture mapping, which has had some success in mapping loci for traits with strong differences in phenotypic distribution between parental populations78,79,80,81, has relied on its relative efficiency. Whereas GWA has typically used tens to hundreds of thousands of markers, admixture mapping requires only a few thousand markers for estimating the ancestry of genomic segments82,83,84,85. However, as GWA designs have improved, the efficiency of GWA now exceeds that of admixture mapping over a broad range of possible values for model parameters86. Future analyses in admixed populations might rely on a combination of GWA and admixture-mapping principles, considering unusual local ancestry estimates jointly with association signals. In addition, because it requires fewer markers, admixture mapping might continue to be valuable in genomic regions poorly covered by typical GWA marker sets.
