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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

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

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
  1. 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
  2. bSimulations under alternatives used homogeneous populations