Further complicating this situation is the fact that tag SNPs may differ across populations. Assume the simple scenario of a single causal SNP in an association region, with the same effect size β in two ancestral populations P1 and P2. Suppose that in the admixed population (ADM) the proportion of genomic intervals containing the causal variant inherited from populations P1 and P2 is α and (1 − α), respectively. This is demonstrated in Figure 1, which shows that even if the same tag SNPs were available in the two ancestral populations P1 and P2, and we knew which SNPs were the best tags in each population, it is not clear which is the best tag SNP in ADM. This becomes even more complicated when there are multiple ancestral populations, when SNP availability differs due to different genotyping platforms, and when effect sizes differ between ancestral populations.
