Another limitation is that we did not account for the potential confounding effects of population stratification. However, odds ratios were essentially unchanged after adjusting for global European ancestry in a subset of African Americans (336 cases 397 controls) for whom ancestry markers were available, suggesting that effects due to population substructure were not substantial, at least in this group. We also noted that controlling for education, a proxy for SES which has been shown to be significantly associated with Native American ancestry in Latinos [23], had little effect on the associations with these risk alleles. Furthermore, the risk alleles were not generally more frequent in Latinos than in European Americans which would be likely if these alleles were proxies for more general ancestry differences. While population stratification is unlikely to fully explain these findings, it remains possible that at some loci, the causal alleles may be more correlated with ancestry than the index SNPs.
