Table 2.
Comparison of haplotype risks for cleft phenotypic subsets, and haplotype effects odds ratios (OR), for specific rs642961 and rs2235371 (V274I) haplotypes, calculated in the proband nuclear families only
| Population | CL Haplotype V-A vs. V-G | CL Haplotype V-G vs. I-G | CLP Haplotype V-A vs. V-G | CLP Haplotype V-G vs. I-G | ||||
|---|---|---|---|---|---|---|---|---|
| LRT a P-value | V-A OR (95% CI) b [V-G reference] | LRT P-value | V-G OR (95% CI) [I-G reference] | LRT P-value | V-A OR (95% CI) [V-G reference] | LRT P-value | V-G OR (95% CI) [I-G reference] | |
| Norway (N) | 0.040 | 1.54 (1.01–2.35) | 0.237 | 2.51 (0.50–12.66) | 0.142 | 1.31 (0.91–1.88) | 0.402 | 1.54 (0.55–4.28) |
| Denmark (DK) | 0.008 | 1.58 (1.12–2.24) | 0.287 | 0.31 (0.03–3.15) | 0.002 | 1.77 (1.20–2.59) | 0.665 | 1.50 (0.24–9.45) |
| EUROCRAN | 0.001 | 1.72 (1.24–2.39) | 0.336 | 2.25 (0.20–25.22) | 0.301 | 1.16 (0.88–1.54) | 0.119 | 0.37 (0.10–1.40) |
| Europe | 3e-06 | 1.62 (1.32–2.00) | 0.413 | 1.47 (0.58–3.76) | 0.002 | 1.34 (1.11–1.62) | 0.849 | 0.93 (0.46–1.89) |
| Philippines | 0.002 | 1.50 (1.16–1.95) | 0.020 | 1.42 (1.05–1.92) | 0.618 | 1.07 (0.83–1.37) | 9e-04 | 1.55 (1.19–2.02) |
| TOTAL | 3e-08 | 1.57 (1.34–1.85) | 0.013 | 1.42 (1.07–1.88) | 0.005 | 1.24 (1.07–1.45) | 0.008 | 1.37 (1.08–1.73) |
| Population | CL/P (CL + CLP) Haplotype V-A vs. V-G | CL/P (CL + CLP) Haplotype V-G vs. I-G | PALATE Haplotype V-A vs. V-G | PALATE Haplotype V-G vs. I-G | ||||
| LRT P-value | V-A OR (95% CI) [V-G reference] | LRT P-value | V-G OR (95% CI) [I-G reference] | LRT P-value | V-A OR (95% CI) [V-G reference] | LRT P-value | V-G OR (95% CI) [I-G reference] | |
| Norway (N) | 0.013 | 1.41 (1.07–1.85) | 0.177 | 1.78 (0.75–4.20) | 0.683 | 0.91 (0.56–1.45) | 0.173 | 1.98 (0.72–5.40) |
| Denmark (DK) | 7e-05 | 1.65 (1.28–2.13) | 0.700 | 0.77 (0.20–2.91) | 0.512 | 0.86 (0.55–1.35) | 0.910 | 1.12 (0.16–7.94) |
| EUROCRAN | 0.003 | 1.38 (1.11–1.70) | 0.559 | 0.76 (0.30–1.93) | 0.469 | 1.15 (0.78–1.70) | 0.394 | 0.49 (0.09–2.67) |
| Europe | 5e-08 | 1.47 (1.28–1.69) | 0.728 | 1.10 (0.63–1.93) | 0.922 | 0.99 (0.77–1.27) | 0.517 | 1.29 (0.60–2.75) |
| Philippines | 0.009 | 1.27 (1.06–1.52) | 1e-04 | 1.47 (1.21–1.79) | 0.338 | 0.66 (0.28–1.57) | 0.493 | 0.75 (0.32–1.73) |
| TOTAL | 4e-09 | 1.39 (1.25–1.55) | 4e-04 | 1.38 (1.15–1.65) | 0.680 | 0.95 (0.75–1.21) | 0.802 | 0.93 (0.55–1.60) |
a
Likelihood Ratio Test (LRT) of risks of specified haplotypes: under the null, their risks are set to equal, under the alternative, the risks are assumed not equal (freely estimated), all other haplotype risks freely estimated under both null and alternative (background/nuisance parameters).
b
Odds Ratio of the estimated haplotype effects associated with the specified haplotype compared to the effects associated with the reference haplotype. CI, confidence interval.