Thus far power calculations were based on simulations restricted to 1:1 matching of probands to unrelated controls. Next we examined what would happen to the power if we increased the ratio of controls matched to the trio proband within each stratum. For instance in Figure 1 each HapMap trio could be matched to many POPRES controls. Therefore, we decided to vary the ratio of unrelated controls to each trio proband for three levels of relative risk (ψ = 1.3, 1.4, 1.5). To make the simulations more realistic we used features of the POPRES database [29]. In the European sample of POPRES we identified C = 6 large, genetically homogeneous clusters [12]. Within each of these six clusters we computed the allele frequencies for 10 000 randomly selected SNPs, each with minor allele frequency greater than 0.05. Using these allele frequencies we generated 50 trios from each of the six subpopulations. Next, we generated unrelated controls from these six subpopulations to obtain, on average, a matching ratio of R. We vary R from 0 to 20. From Figure 6(b) we can
