the susceptibility allele to be fD = 0.30 in the study population, but varied fD between 0.00 and 0.60 in POP1 (in both the study and public control populations). Finally, we assumed that any extreme outliers, such as individuals with misreported ethnicity, would be identified and removed prior to testing for association. Simulated data sets (n = 10,000) were analyzed using logistic regression models, with covariate adjustment for the proportion of POP1 descent of each subject to control for population stratification as would be routinely done in a GWA study using analytic methods such as principal components, for the one- and two-stage designs under the null model (GRR = 1.0) and the alternative model described above.
