Table 6.

Estimated relative total cost^* (power/proportion of total study samples genotyped in stage 1) of GWA study (M = 500,000 SNPs) for one- and two-stage study designs that include only study controls (n = 2,000), only public controls (n = 5,000) or both. Relative cost estimates assume 2,000 cases, a multiplicative genetic model with susceptibility minor allele frequency = 0.3, K = 0.10 and GRR = 1.3. The relative costs of genotyping 16,000, 7,500, 1,500, and 100 SNPs was assumed to be 1/2, 1/3, 1/5, and 1/12 of the cost of genotyping all 500,000 SNPs on GWA panel, respectively.

One–Stage Genotype Design(All Samples Genotyped on GWA Panel)	Study Controls Only		Public Controls Only	Study + Public Controls
	$1.00 (0.78/1.00)		$0.50 (0.90/1.00)	$1.00 (0.97/1.00)
Two-Stage Genotype Design	Joint-Analysis Study Controls Onlya	Joint-Analysis Public Controls Onlyb	Joint-Analysis Public + Study Controlsc	Replication- Based Public + Study Controlsc
Follow-up Platform
100 SNPs	$0.725 (0.78/0.70)	$0.317 (0.89/0.60)	$0.395 (0.95/0.68)	$0.335 (0.89/0.55)
1,500 SNPs	$0.640 (0.78/0.55)	$0.280 (0.89/0.45)	$0.400 (0.95/0.50)	$0.360 (0.87/0.40)
7,500 SNPs	$0.640 (0.78/0.46)	$0.287 (0.89/0.36)	$0.448 (0.95/0.39)	$0.437 (0.85/0.31)
16,500 SNPs	$0.700 (0.78/0.40)	$0.328 (0.89/0.31)	$0.585 (0.95/0.34)	$0.568 (0.84/0.27)

^*Costs are calculated relative to the cost of genotyping 2,000 study cases and 2,000 study controls on GWA marker panel

^aFor joint-analysis two-stage design, proportion of samples genotyped in stage 1 represents proportion of cases and study controls (both included in stage 1 genotyping)

^bFor joint-analysis two-stage design, proportion of samples genotyped in stage 1 represents proportion of cases genotyped in stage 1. No study controls are genotyped in stage 1 or stage 2.

^cFor joint-analysis and replication-based two-stage designs, proportion of samples genotyped in stage 1 represents proportion of cases genotyped in stage 1. All study controls are genotyped in stage 2.