In the effort to improve the potential of GWA studies for diverse human populations, African populations are not the only populations that pose significant challenges. Tag-SNP and imputation studies have found that indigenous populations genetically intermediate between reference groups are among those that require special consideration. In these cases, the challenges result largely from the way in which genomic resources have been developed, rather than from intrinsic population properties. A second form of intermediate population exists, however, in which the challenges are in fact intrinsic.
