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Table 2 Imposed genotype penetrance table and disease prevalence calculation in the general population with allele frequencies under assumption of Hardy-Weinberg equilibrium

From: Confounding of linkage disequilibrium patterns in large scale DNA based gene-gene interaction studies

Genotype   Penetrance of genotype Marginal
   −−−−−−−−−−−−−−−− penetrance
   AA Aa aa  
   (1−p)2 2p(1−p) p 2  
BB (1−p)2 p(D|G1) p(D|G2) p(D|G3) Mx(x=1)
Bb 2p(1−p) p(D|G4) p(D|G5) p(D|G6) Mx(x=2)
bb p 2 p(D|G7) p(D|G8) p(D|G9) Mx(x=3)
Marginal   My(y=1) My(y=2) My(y=3) p(D)=K
  DSL 1 AA=TT Aa=TA aa=AA  
DSL 2 A   0.9025 0.095 0.0025  
BB=AA 0.36 0.0067 0.0911 0.0911 0.015
Bb=CA 0.48 0.0067 0.0392 0.0392 0.010
bb=CC 0.16 0.0067 0.0163 0.0163 0.008
Marginal   0.0067 0.054 0.054 p(D)=0.0113
   Odds ratio as compared to double homozygous CC/TT as baseline  
   AA=TT Aa=TA aa=AA  
BB=AA   1.00 14.88 14.88  
Bb=CA   1.00 6.05 6.05  
bb=CC   1.00 2.46 2.46  
  1. In all settings, the minor allele frequency for DSL 1 is p=0.05 and for DSL 2 is p=0.40. Upper part: probabilities of disease given the genotype, values for simulated datasets in setting A (DSL 1 and DSL 2 A) with epistasis effect size β3=0.90 (see text). Lower part : odds ratio with major homozygous (TT) as baseline in setting A with epistasis effect size β3=0.90. The prevalence in the general population with this setting is around 1%