A three-stage approach for genome-wide association studies with family data for quantitative traits

BMC Genomic Data

Table 1 Type I error estimate at alpha = 0.05 with 10,000 replicates for quantitative phenotype and single SNP genotype data with MAF = 0.1.

Phenotype Distribution	Polygenic Variance	LM	LME	FBAT	LM-LME 1	LM-LME 2
Normal	0.3	0.084	0.051	0.050	0.049	0.051
Normal	0.6	0.115	0.052	0.049	0.046	0.050
Abs Normal	0.3	0.055	0.053	0.049	0.053	0.053
Abs Normal	0.6	0.064	0.050	0.049	0.050	0.050
Chi-square(1)	0.3	0.076	0.052	0.050	0.052	0.052
Chi-square(1)	0.6	0.104	0.049	0.051	0.045	0.047
Lognormal	0.3	0.059	0.054	0.046	0.054	0.054
Lognormal	0.6	0.066	0.049	0.047	0.049	0.049

The SNP explains 0% phenotype variation.
Normal: marginal phenotype follows the standard normal distribution
Abs Normal: marginal phenotype follows the absolute standard normal distribution
Chi-square(1): marginal phenotype follows a Chi-square distribution with 1 degree of freedom
Lognormal: marginal phenotype follows a Lognormal distribution
LM_LME1: two-stage approach with LM (p-value cut-off 0.1) at first stage
LM_LME2: two-stage approach with LM (p-value cut-off 0.2) at first stage

ISSN: 2730-6844