Table 1.

Type I error rates for different tests at a p-value threshold of 0.05. The simulation is based on real genotype data in the presence of LD. We simulated case-control status affected by main genetic effects only. The results with inflated type I error rates arc in bold. The fixed-effects test with no filtering is based on the test statistic ${\sum }_{j=1}^k{\left({\sum }_{s=1}^S{w}_s{Z}_{js}\right)}^2$.

MAF	gene size	fixed-effects test with no filtering	random-effects test with meta filtering	fixed-effects test with meta-filtering	ofGEM
0.05–0.5	5	0.092	0.035	0.055	0.040
	5–10	0.105	0.043	0.059	0.054
	5–15	0.112	0.043	0.063	0.057
0.005–0.025	5	0.042	0.030	0.043	0.041
	5–10	0.039	0.034	0.056	0.052
	5–15	0.039	0.030	0.051	0.046