We have focused on diallelic markers and disease/no disease phenotypes. We have developed a model to simulate the effects of varying these parameters that has resulted in a program “Gene Detective”. We can use this approach (see Supplement for details) to simulate the ca 620,000 diallelic markers reported to date for samples with n = 400 case and n = 400 controls with nominal 0.05 α levels (Figure 4). We can observe effects of sample size, heterogeneity/penetrance ratios, marker minor allele frequencies and disease frequencies. Such effects are each relatively modest over a reasonable range of values for genome-wide distributions of linkage disequilibrium. However, there is a striking relationship between power and effect size. Power to detect effects that would produce odds ratios of less than 1.2 –fold is modest, while power to detect effects as high as 1.7 fold is relatively good.
