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

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)

M_x(x=1)

Bb

2p(1−p)

p(D|G₄)

p(D|G₅)

p(D|G₆)

M_x(x=2)

bb

p ²

p(D|G₇)

p(D|G₈)

p(D|G₉)

M_x(x=3)

Marginal

M_y(y=1)

M_y(y=2)

M_y(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