Table 3.
Odds Ratios and corresponding 95% confidence intervals for the higher level covariates under pseudo-likelihood methods
| 2nd stage | Model 1a,b | Model 2c | Model 3d | Model 4e |
|---|---|---|---|---|
| Functional | – | 2.8 (1.4–5.9) | 1.6 (0.7–3.9) | 1.0 (0.3–4.2) |
| GenoMEL | – | – | 3.6 (1.0–12.5) | 2.3 (0.6–9.1) |
| Polyphen | – | – | – | 2.2 (0.7–6.5) |
| Polyphen exist | – | – | – | 0.6 (0.04–8.1) |
| τ̂ | 1.16 | 1.19 | 0.94 | 0.98 |
a
A “ – “ indicates that the corresponding variable was not included in the model
b
Model 1 assumes exchangeability of the random effects β
c
Model 2 contains an intercept and functional status as 2nd stage covariates
d
Model 3 contains as 2nd stage covariates an intercept, the functional status and an indicator whether the variant was observed in GenoMEL [14]
e
Model 4 contains the following 2nd stage covariates: intercept, functional status, an indicator whether the variant was observed in GenoMEL, the Polyphen score, and an indicator whether the Polyphen score is missing or not