All study designs maintained power near levels obtained under negligible population stratification when the proportion of POP1 ancestry in public controls was within 0.05 of the proportion of POP1 ancestry in the study population regardless of the frequencies of the disease-susceptibility allele in the POP1 and POP2 ancestral populations (Table 3). Power for the one-stage design that only included public controls dropped noticeably when the proportion of POP1 ancestry in public controls was either 0.10 or 0.40. Under these two scenarios, the greatest decline in power was observed when the susceptibility allele was more (for proportion POP1 = 0.10) or less (for proportion POP1 = 0.40) frequent in the POP1 ancestral population. Power for the two-stage design with follow-up on 100 of the best SNPs dropped when the proportion of POP1 ancestry in public controls was equal to 0.40. Power for the one-stage design with both public and study controls and the remaining two-stage designs stayed relatively stable across the range of considered proportions of POP1 ancestry in public controls.
