Table 5.

Statistical power calculations for replication-based two-stage design accounting for batch genotype effects between study samples and public controls. Calculations assume 2,000 study cases (spread across stages 1 and 2), 5,000 public controls (stage 1), 2,000 public controls (stage 2) and M = 500,000 markers in stage 1. Power was calculated for a multiplicative genetic model with susceptibility minor allele frequency = 0.3, K = 0.10 and GRR = 1.3 across different combinations of error rates for the three genotyping platforms both before and after adjustment for mean systematic inflation in test statistics for SNPs across the genome due to batch effects. Power was calculated for each replication-based two-stage follow-up study design.

			Power
Error Rate Public Controls	Error Rate Stage 1	Error Rate Stage 2	No Systematic Inflation Across Genome Due to Batch Effects (μ = 1.0)				Systematic Inflation Across Genome Due to Batch Effects*
			16,500	7,500	1,500	100	16,500	7,500	1,500	100
+ 0.01	+ 0.01	+ 0.01	0.81	0.83	0.85	0.87	0.81	0.82	0.84	0.86
		0.00	0.83	0.84	0.86	0.88	0.83	0.84	0.86	0.87
		− 0.01	0.82	0.83	0.86	0.88	0.82	0.83	0.85	0.86
	0.00	+ 0.01	0.77	0.78	0.79	0.78	0.77	0.77	0.78	0.76
		0.00	0.79	0.80	0.80	0.79	0.79	0.79	0.79	0.77
		− 0.01	0.78	0.79	0.79	0.79	0.78	0.78	0.78	0.76
	− 0.01	+ 0.01	0.74	0.74	0.74	0.70	0.74	0.74	0.72	0.68
		0.00	0.76	0.76	0.75	0.72	0.76	0.76	0.74	0.69
		− 0.01	0.75	0.75	0.75	0.71	0.75	0.75	0.73	0.68
0.00	+ 0.01	+ 0.01	0.84	0.86	0.89	0.93	0.84	0.86	0.89	0.92
		0.00	0.86	0.88	0.90	0.93	0.86	0.87	0.90	0.93
		− 0.01	0.85	0.87	0.90	0.93	0.85	0.87	0.89	0.92
	0.00	+ 0.01	0.82	0.83	0.85	0.88	0.81	0.83	0.85	0.87
		0.00	0.84	0.85	0.87	0.89	0.83	0.84	0.86	0.88
		− 0.01	0.83	0.84	0.86	0.89	0.82	0.84	0.86	0.87
	− 0.01	+ 0.01	0.80	0.81	0.83	0.84	0.80	0.80	0.82	0.82
		0.00	0.82	0.83	0.84	0.85	0.81	0.82	0.83	0.83
		− 0.01	0.81	0.82	0.83	0.84	0.81	0.81	0.83	0.83
− 0.01	+ 0.01	+ 0.01	0.85	0.87	0.90	0.94	0.85	0.87	0.90	0.94
		0.00	0.87	0.89	0.92	0.95	0.87	0.88	0.91	0.94
		− 0.01	0.86	0.88	0.91	0.95	0.86	0.88	0.91	0.94
	0.00	+ 0.01	0.83	0.85	0.87	0.91	0.83	0.84	0.87	0.90
		0.00	0.85	0.86	0.89	0.92	0.85	0.86	0.88	0.91
		− 0.01	0.84	0.86	0.88	0.91	0.84	0.85	0.88	0.90
	− 0.01	+ 0.01	0.82	0.83	0.85	0.88	0.81	0.83	0.85	0.86
		0.00	0.83	0.85	0.87	0.89	0.83	0.84	0.86	0.87
		− 0.01	0.83	0.84	0.86	0.88	0.82	0.83	0.85	0.87

^*μ = 1.063, 1.048, 1.039, and 1.034 for the first stage of replication-based two-stage studies with follow-up on 100, 1500, 7500, and 16500 SNPs, respectively. For the second stage, μ = 1.000 for all follow-up studies.