Table 3.

Simulation results for power of the joint- and interaction-tests for different procedures under various scenarios. For MAF=0.3, power is shown for nominal significance levels of 0.0001 and 0.001 for the joint- and interaction- tests, respectively. For MAF as 0.05, power is shown for the nominal significance level of 0.05 for both types of tests. In all settings, power was evaluated under an interaction odds-ratio=1.2. Results are shown when causal SNP is typed (bottom panels) or imputed (top panels). Variance is estimated based on information matrix.

Untyped SNPs
MAF	βx	βg	PT-joint	RT-joint	EB-joint	PT-int	RT-int	EB-int
0.3	log(1.5)	log(1)	0.419	0.713	0.518	0.243	0.574	0.406
0.05	log(1.5)	log(1)	0.342	0.498	0.404	0.231	0.389	0.309
0.3	log(1.5)	log(1.05)	0.822	0.948	0.873	0.233	0.565	0.415
0.05	log(1.5)	log(1.05)	0.558	0.692	0.603	0.220	0.411	0.302
0.3	log(2)	log(1)	0.446	0.744	0.568	0.234	0.498	0.376
0.05	log(2)	log(1)	0.366	0.517	0.430	0.223	0.356	0.307
0.3	log(2)	log(1.05)	0.818	0.952	0.871	0.212	0.483	0.367
0.05	log(2)	log(1.05)	0.599	0.733	0.643	0.230	0.392	0.312
Typed SNPs
MAF	βx	βg	PT-joint	RT-joint	EB-joint	PT-int	RT-int	EB-int
0.3	log(1.5)	log(1)	0.604	0.874	0.724	0.349	0.728	0.559
0.05	log(1.5)	log(1)	0.443	0.613	0.521	0.271	0.491	0.4
0.3	log(1.5)	log(1.05)	0.943	0.987	0.954	0.335	0.724	0.551
0.05	log(1.5)	log(1.05)	0.694	0.804	0.709	0.286	0.495	0.360
0.3	log(2)	log(1)	0.647	0.887	0.731	0.321	0.645	0.499
0.05	log(2)	log(1)	0.469	0.645	0.54	0.286	0.443	0.373
0.3	log(2)	log(1.05)	0.942	0.992	0.955	0.333	0.662	0.531
0.05	log(2)	log(1.05)	0.707	0.83	0.744	0.284	0.466	0.379

PT-joint, prospective joint test; RT- joint, retrospective joint test; EB-joint, empirical Bayes joint test; PT-int, prospective interaction test; RT-int, retrospective interaction test; EB-int, empirical Bayes interaction test; SNP, single nucleotide polymorphism; MAF, minor allele frequency.