the presence of population stratification (Figure 5). When Fst =0.05, the combined association analysis produced unacceptably high Type I errors at every level of q. Even when the two populations are quite similar genetically (Fst = 0.001), the combined association analysis produced false positives at a rate above the threshold value of α = 0.05 when sampling ratios are substantially unbalanced. Epstein et al. [26] recommends testing whether the data should be combined prior to performing the analysis. If that test were successful, it would prevent inflated Type I errors, but would also fail to capture the information in the unrelated controls samples.
