Table 2.

Power of identifying a specific interaction, associated with the parameter β₃ in model (7) where both involved SNPs have at least one variant allele for 40% or 20% of the samples (corresponding to a minor allele frequency of 0.225 and 0.106, respectively) for a case-control study with 5000 cases and 5000 controls, measuring 500,000 SNPs, for a variety of two-stage procedures, allowing 3 false positives.

β3	Odds ratio	First stage significance level α1
		0.0001	0.001	0.002	0.005	0.01	0.02	0.05	1
P(SNP > 0) = 0.4 ⇒ minor allele frequency 0.225
0.4	1.49	0.41	0.52	0.49	0.41	0.34	0.27	0.18	0.03
0.5	1.65	0.89	0.94	0.92	0.87	0.81	0.74	0.62	0.27
0.6	1.82	0.99	1.00	1.00	0.99	0.98	0.97	0.94	0.72
0.7	2.01	1.00	1.00	1.00	1.00	1.00	1.00	1.00	0.96
P(SNP > 0) = 0.2 ⇒ minor allele frequency 0.106
0.6	1.82	0.02	0.09	0.12	0.15	0.17	0.18	0.16	0.05
0.7	2.01	0.11	0.30	0.38	0.46	0.50	0.51	0.49	0.21
0.8	2.23	0.32	0.60	0.68	0.77	0.82	0.83	0.81	0.52
0.9	2.46	0.61	0.84	0.89	0.94	0.96	0.97	0.96	0.82
1.0	2.72	0.85	0.96	0.97	0.99	0.99	1.00	1.00	0.96