Skol et al. (Skol et al., 2006) demonstrated that a joint-analysis two-stage study design could effectively achieve equivalent power to a single-stage study for a fraction of the cost. Consequently, for the three single-stage sampling designs, we also estimated the relative cost of performing a joint-analysis two-stage association study for each follow-up platform. For each combination of sampling design and follow-up platform, we performed a series of simulations to identify the least expensive joint-analysis two-stage sampling design that obtained an estimated power within 0.01 of the power obtained from the corresponding single-stage study. For the sampling design that used only public controls, cases were divided between stages 1 and 2 while all public controls were assumed to be available in stage 1. For the sampling design that included both study and public controls, all study controls were assumed to be genotyped in stage 2, and all public controls were assumed to be available in stage 1. Cases were divided between stages 1 and 2.
