A new association test based on disease allele selection for case–control genome-wide association studies

BMC Genomics

Table 2 Empirical type I error rates and powers for each method from 1000 replicates at significance level 0.05 when the sample sizes are 1000 for cases and controls and HWE holds for controls with minor allele is the disease allele and MAF equals 0.3

Λ ₁ Λ ₂	(1,1)	(1, 1.4) RM*	(1.1, 1.4)	(1.2, 1.4) AM*	(1.3, 1.4)	(1.4, 1.4) DM*	(1.5,1.4) ODM*	(0.9, 1.4) UDM*
ChiSQ	0.053	0.927	0.759	0.528	0.395	0.428	0.524	0.992
MAX3	0.051	0.941	0.794	0.568	0.438	0.445	0.484	0.994
GMS	0.05	0.933	0.772	0.577	0.431	0.432	0.459	0.993
CATT	0.05	0.934	0.807	0.644	0.427	0.25	0.136	0.986
MERT	0.051	0.879	0.744	0.642	0.479	0.377	0.261	0.938
GGM	0.053	0.944	0.793	0.598	0.447	0.432	0.412	0.995
New	0.049	0.927	0.761	0.574	0.455	0.46	0.512	0.982

*RM: Recessive Model; AM: Additive Model; DM: Dominant Model; ODM: Over-dominant Model; UDM: Under-dominant Model.

ISSN: 1471-2164