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Table 3 Analytic recovery of pathway genetic effects for a continuous trait, based on 1000 (under alternatives) or 2000 (under the null) simulated studies of 1000 offspring

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

Simulation Setup Simulation Results
  True Shift in mean Average Estimated Shift in Mean (95% CI for the Mean Shift in Mean) Estimated Coverage of Nominal 95% CIs
Scenario Allele Frequency for each of the 4 SNPs in each pathway Pathway 1 Pathway 2 Pathway 1 Pathway 2 Pathway 1 Pathway 2
Stratified null a 0 0 0.00 (−0.02,0.03) −0.01 (−0.03,0.02) 0.949 0.958
Alternative b 0.3 0.1 0.15 0.10 (0.09,0.11) 0.15 (0.14,0.15) 0.949 0.95
Alternative b 0.2 0.1 0.15 0.10 (0.09,0.12) 0.14 (0.13,0.16) 0.949 0.96
  1. aBy design, the allele frequency for each of the 4 SNPs in each 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