In addition to increased power, in Table 6 we illustrate that substantial cost savings can be achieved for a GWA study when including public controls. We compared the relative cost of one- and two-stage study designs that include study controls, public controls or both. We required the power of the joint-analysis two-stage study designs to be within 0.01 of the corresponding one-stage designs. As expected, the most expensive study designs were the one-stage study designs that genotyped all samples (excluding public controls – which provide genotype data at no expense) on all SNPs. Significant cost savings were observed when using the joint-analysis two-stage design described by Skol et al. (Skol et al., 2006). For example, when utilizing the joint-analysis two-stage design following-up the top 1,500 SNPs (corresponding to the 1,536 SNP Illumina GoldenGate custom panel) in stage 2, a 36%, 44% and 60% cost savings was achieved relative to the corresponding one-stage designs that included only study controls, only public controls and both public and study controls, respectively. The total cost of our proposed replication-based two-stage design was consistently less
