To understand the financial impact of the different genotyping sampling strategies, we estimated the relative total experimental cost of each genotype sampling design for a GWA study based on M = 500,000 SNPs using NA = 2,000 study cases, NU = 2,000 screened study controls and NPU = 5,000 public controls. We assumed a multiplicative trait with a prevalence K = 0.1, GRR = 1.3 and fD = 0.3 (Model 1). We calculated the relative total costs of performing the three single-stage studies that used either study or public controls or both. For these single-stage sampling designs, all study samples were assumed to be genotyped on all 500,000 SNPs; genotype data for public controls were assumed to be available at no expense. In addition, we calculated the relative total cost of the optimal (highest power) replication-based two-stage study design for each follow-up platform. For the purpose of our calculations, we assumed the Illumina Human660W-Quad platform would be used for genotyping 500,000 viable SNPs in stage 1 and Illumina’s GoldenGate 96, 384 and 1,536 SNP panels and Illumina’s Custom iSelect Infinium
