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

BMC Genomic Data

Table 6 Type I error and power estimates in the presence of population admixture at alpha = 1e-6 using 100 replicates.

	Phenotype data	LM	LME	FBAT	LM-LME 1	Three-stage
Type I error (r2 = 0)	original phenotypes	0.63	0.08	0.02	0.08	0.02
	residuals (1)	0.59	0.07	-	0.07	-
	residuals (2)	0.13	0.01	-	0.01	-
Power r2 = 0.5	original phenotypes	0.43	0.39	0	0.39	0.31
	residuals (1)	0.45	0.37	-	0.37	-
	residuals (2)	0.17	0.14	-	0.14
Power r2 = 0.8	original phenotypes	0.66	0.63	0.05	0.63	0.56
	residuals (1)	0.66	0.63	-	0.63	-
	residuals (2)	0.57	0.47	-	0.47	-
Power QTL	original phenotypes	0.81	0.85	0.11	0.85	0.83
	residuals (1)	0.82	0.84	-	0.84	-
	residuals (2)	0.81	0.67	-	0.67	-

Marginal phenotype distribution follows a normal distribution with variance 1. The additive genetic effect in assessing power is sqrt(0.005/2/0.3/0.7) = 0.109.
LM_LME1: two-stage approach with LM at first stage with p-value cut-off 0.1 and LME at second stage with p-value cut-off 1e-6.
Three-stage: LM at first stage with p-value cut-off 0.1, LME at second stage with p-value cut-off 1e-6 and FBAT at third stage with p-value cut-off 0.05/n, where n is the number of SNPs entering the third stage.
The original simulated phenotypes and the residuals adjusted for 10 PC obtained from all 34,625 SNPs on chromosome 1 and 100 admixture SNPs (1), and from 100 admixture SNPs (2) are analyzed. The 100 admixture simulated SNPs have expected allele frequency 0.3, F_ST= 0.025, the offset value δ = 0.25, QTL variance is 0.005, and the polygenic variation is 0.3. When estimating power, 34,265 SNPs are not used.

ISSN: 2730-6844