|
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
|
|
penetrance
| | | | | |
| |
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
|
|
penetrance
| | | | | |
| | |
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
| |
- 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%
