Table 4.

Statistical power calculations for one-stage study designs accounting for batch genotype effects between study samples and public controls. Calculations assume 2,000 study cases, 2,000 study controls and 5,000 public controls and M = 500,000 markers. Power 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 two genotyping platforms both before and after adjustment for mean systematic inflation in test statistics for SNPs across the genome due to batch genotype effects.

		Power
Error Rate Public Controls	Error Rate Study Samples	No Systematic Inflation Across Genome Due to Batch Effects (μ =1.0)	Systematic Inflation Across Genome Due to Batch Effects*
Single Stage Design with Study Controls Only
n.a.	+ 0.01	0.76	0.76
n.a.	0.00	0.79	0.79
n.a.	− 0.01	0.77	0.77
Single Stage Design with Public Controls Only
+ 0.01	+ 0.01	0.89	0.83
	0.00	0.68	0.59
	− 0.01	0.53	0.43
0.00	+ 0.01	0.98	0.96
	0.00	0.90	0.85
	− 0.01	0.82	0.74
− 0.01	+ 0.01	0.99	0.98
	0.00	0.95	0.92
	− 0.01	0.90	0.84
Single Stage Design with Study and Public Controls
+ 0.01	+ 0.01	0.96	0.94
	0.00	0.89	0.86
	− 0.01	0.83	0.78
0.00	+ 0.01	0.99	0.99
	0.00	0.97	0.96
	− 0.01	0.94	0.92
− 0.01	+ 0.01	1.00	0.99
	0.00	0.98	0.98
	− 0.01	0.96	0.95

^*μ = 1.000, 1.100 and 1.056 for Study Controls Only, Public Controls Only, and Public and Study Controls, respectively.