Simulating autosomal genotypes with realistic linkage disequilibrium and a spiked-in genetic effect

BMC Bioinformatics

Table 2 Analytic recovery of pathway genetic effects for a dichotomous trait, based on 1000 (under alternatives) or 2000 (under the null) simulated studies of 1000 triads

Simulation Setup				Simulation Results
Scenario	Allele Frequency for each of the 4 SNPs in each pathway	True Relative Risk		Average Estimated Relative Risk (95% CI for the mean)		Estimated Coverage of Nominal 95% CIs
		Pathway 1	Pathway 2	Pathway 1	Pathway 2	Pathway 1	Pathway 2
Stratified null	a	1	1	1.00 (0.99,1.01)	1.00 (0.99,1.01)	0.948	0.952
Alternative ^b	0.3	1.65	2.71	1.65 (1.63,1.66)	2.73 (2.71,2.75)	0.948	0.959
Alternative ^b	0.2	1.65	2.71	1.64 (1.61,1.67)	2.72 (2.67,2.77)	0.963	0.964

^aBy design, the allele frequency for each of the 4 SNPs in each tested pathway in subpopulation one was close to 0.15 while that in subpopulation two was close to 0.5
^bSimulations under alternatives used homogeneous populations

ISSN: 1471-2105