Table 1.
Haplotype frequencies by population
| Disease | Population | Marker
|
Total | |
|---|---|---|---|---|
| Disease-associated allele + | Nonassociated allele − | |||
| Disease allele | Founders | Q | 0 | Q |
| + | Equilibrium | QR | Q (1 − R) | Q |
| Cohort | Qρ + QR (1 − ρ) | (1 − ρ) Q (1 − R) | Q | |
| Case-control | f11 = ωQ [ρ + R (1 − ρ)]/Σ | f12 = ω (1 − ρ) Q (1 − R)/Σ | ωQ/Σ | |
| Observed (counts) | a | b | ||
| Normal allele | Founders | R − Q | 1 − R | 1 − Q |
| − | Equilibrium | R (1 − Q) | (1 − R) (1 − Q) | 1 − Q |
| Cohort | (R − Q) ρ + R (1 − Q) ( 1 − ρ) | (1 − R) [ρ + (1 − Q) (1 − ρ)] | 1 − Q | |
| Case-control | f21 = [(R − Q) ρ + R (1 − Q) (1 − ρ)]/Σ | f22 = (1 − R) [ρ + (1 − Q) (1 − ρ)]/Σ | (1 − Q)/Σ | |
| Observed (counts) | c | d | ||
| Total (except case-control) | R | 1 − R | 1 | |
Σ = 1 + (ω − 1) Q
For the ith marker locus all parameters are subscripted by i. lnlk = a ln f11 + b ln f12 + c ln f21 + d ln f22; Q = disease gene frequency; R = disease-associated marker allele frequency; ω = sample enrichment factor; ρ = association.