Table 4.
Odds Ratios and corresponding 95% confidence intervals for selected variants using maximum likelihood and pseudo-likelihood methods under different second stage model scenarios.
| Variant | SPM | MPM | Functional | GenoMEL | Polya | Odds Ratios (95% CI) |
||||
|---|---|---|---|---|---|---|---|---|---|---|
| MLE b | Model 1c | Model 2d | Model 3e | Model 4f | ||||||
| c.50+37G/C | 15 | 6 | no | 0 | 0.8 (0.3–2.1) | 0.9 (0.4–2.3) | 0.8 (0.3–2.1) | 0.8 (0.3–2.1) | 0.8 (0.3–2.1) | |
| (−)33G>C | 9 | 6 | no | 0 | 1.2 (0.4–3.6) | 1.3 (0.5–3.7) | 1.2 (0.4–3.3) | 1.1 (0.4–3.3) | 1.1 (0.4–3.3) | |
| (−)34G>T | 2 | 7 | no | 1 | 13.5 (2.7–67.3) | 7.6 (2.1–27.5) | 6.4 (1.8–23.3) | 7.5 (2.0–28.6) | 6.8 (1.8–25.3) | |
| c.301G>T | 1 | 5 | yes | 1 | 2.29 | 14.7 (1.6–132.3) | 6.3 (1.4–29) | 7.3 (1.5–35.4) | 8.8 (1.8–44.2) | 10.8 (2.0–57.8) |
| c.8_9ins | 6 | 0 | yes | 0 | 0.6 (0.1–3.5) | 0.7 (0.1–3.9) | 0.7 (0.1–3.7) | 0.5 (0.1–3.3) | ||
| c.123G>A | 4 | 1 | no | 0 | 0.4 (0.0–5.0) | 0.9 (0.2–4.5) | 0.6 (0.1–3.6) | 0.7 (0.1–3.7) | 0.6 (0.1–3.7) | |
| (−)14C>T | 2 | 1 | no | 0 | 1.2 (0.1–14.6) | 1.6 (0.2–14.3) | 0.8 (0.1–10.1) | 0.8 (0.1–6.7) | 0.8 (0.1–7.5) | |
| (−)25C>T | 2 | 0 | no | 0 | 1.1 (0.1–8.9) | 0.7 (0.1–6.8) | 0.7 (0.1–5.4) | 0.7 (0.1–5.9) | ||
| c.373G>C | 3 | 0 | yes | 0 | 1.99 | 0.9 (0.1–6.4) | 1.1 (0.2–7.6) | 1.0 (0.1–6.2) | 1.3 (0.2–9.0) | |
| c.87_89delG | 2 | 0 | yes | 1 | 0.9 (0.1–6.3) | 1.0 (0.1–7.6) | 2.2 (0.3–15.1) | 1.1 (0.1–10.0) | ||
| c.318G>A | 2 | 1 | yes | 0 | 2.0 (0.2–23.1) | 2.0 (0.3–12.5) | 2.4 (0.4–15.0) | 1.8 (0.3–10.7) | 1.3 (0.2–9.5) | |
| c.159G>A | 1 | 2 | yes | 1 | 2.52 | 2.3 (0.2–25.5) | 2.2 (0.4–13.0) | 2.6 (0.4–16.4) | 4.2 (0.6–28.1) | 6.1 (0.8–46.3) |
| c.159G>C | 1 | 1 | yes | 1 | 2.52 | 2.5 (0.1–41.4) | 2.2 (0.3–15.2) | 2.7 (0.4–19.3) | 4.5 (0.7–31.0) | 6.5 (0.8–50.4) |
| c.334C>G | 0 | 2 | yes | 1 | 1.99 | 6.3 (0.9–43.8) | 8.0 (1.1–59.6) | 10.2 (1.5–70.7) | 11.5 (1.6–85.5) | |
| c.170C>T | 0 | 2 | yes | 0 | 0.28 | 3.6 (0.5–28.3) | 4.7 (0.5–40.5) | 2.7 (0.4–18.1) | 1.6 (0.2–14.0) | |
| c.95T>C | 0 | 2 | yes | 1 | 2.32 | 7.1 (1.0–48.4) | 9.0 (1.2–65.3) | 11.0 (1.6–75.0) | 15.0 (2.0–111.9) | |
| (−)70G/A | 0 | 1 | no | 0 | 3.3 (0.4–28.0) | 2.0 (0.2–19.6) | 1.4 (0.2–11.3) | 1.6 (0.2–12.9) | ||
| c.146T>G | 0 | 1 | yes | 1 | 1.98 | 3.7 (0.4–31.6) | 4.9 (0.5–44.9) | 7.5 (1.0–58.9) | 8.5 (1.0–72.2) | |
| c.247C>T | 0 | 1 | yes | 0 | 2.67 | 4.5 (0.5–37.8) | 5.9 (0.7–53.2) | 3.0 (0.4–22.1) | 7.6 (0.8–74.0) | |
| c.67G>A | 0 | 1 | yes | 0 | 1.82 | 3.9 (0.5–32.5) | 5.1 (0.6–46.1) | 2.7 (0.4–19.8) | 4.0 (0.5–32.8) | |
| c.249C>A | 1 | 0 | yes | 0 | 3.12 | 1.3 (0.2–11.7) | 1.7 (0.2–15.5) | 1.3 (0.2–9.4) | 4.0 (0.3–46.6) | |
| c.370C>T | 1 | 0 | yes | 0 | 0.17 | 1.6 (0.2–14.1) | 2.0 (0.2–19.1) | 1.4 (0.2–10.5) | 0.6 (0.0–9.5) | |
| c.384G>A | 1 | 0 | no | 0 | 1.3 (0.2–11.7) | 0.8 (0.1–8.3) | 0.7 (0.1–6.1) | 0.8 (0.1–6.7) | ||
| c.67G>C | 1 | 0 | yes | 1 | 2.27 | 1.6 (0.2–14.4) | 2.0 (0.2–19.5) | 4.1 (0.5–31.8) | 5.3 (0.6–44.3) | |
A “ – “ indicates that the Polyphen score could not be computed
Variants without at least one case and one control do not have a finite MLE
Model 1 assumes exchangeability of the random effects β
Model 2 contains an intercept and the functional status as a 2nd stage covariate
Model 3 contains as 2nd stage covariates an intercept, the functional status, and an indicator whether the variant was observed in GenoMEL[14]
Model 4 contains the following 2nd stage covariates: intercept, functional status, an indicator whether the variant was observed in GenoMEL, and the Polyphen score