We also performed simulations in which Latino phenotypes were explicitly correlated to ancestry (population stratification). In these simulations, we added a constant multiple of PC1 (representing European vs. Native American ancestry, with positive values representing higher European ancestry) to the Latino phenotypes such that the correlation between phenotype and PC1 was equal to −0.11, which is the correlation between the T2D phenotype and PC1 in the SIGMA data set.
