NA cases apportioned between stages 1 and 2. We assumed an underlying multiplicative genetic mode-of-inheritance risk model for a bi-allelic locus with alleles D and d and corresponding allele frequencies of fD and fd, respectively. For each alternative model, we set the population frequency of the susceptibility allele D in the general population, the prevalence (K) of the disease in the population, and the locus specific genetic relative risk (GRR) = Pen(DD)/Pen(Dd) = Pen(Dd)/Pen(dd), where Pen(dd), Pen(Dd), and Pen(DD) were the penetrances for the dd, Dd, and DD genotypes, respectively. Consistent with many genetic power calculators, our power calculations are for the main effects of a directly genotyped locus and, as such, do not rely on additional assumptions regarding the extent of linkage disequilibrium between this locus and an untyped causal locus. All power analyses were programmed into the freely available statistical software R version 2.4.1 (R Development Core Team, 2006).
