Solved – How to calculate confidence intervals for pooled odd ratios in meta-analysis

confidence intervalgeneticsmeta-analysisodds-ratio

I have two datasets from genome-wide association studies. The only information available are the odd ratios and their confidence intervals (95%) for each genotyped SNP.
My want to generate a forest plot comparing these two odds ratios, but I can't find the way to calculate the combined confidence intervals to visualize the summary effects. I used the program PLINK to perform the meta-analysis using fixed effects, but the program did not show these confidence intervals.

  • How can I calculate such confidence intervals?

The data available is:

  • Odd ratios for each study,
  • 95% confidence intervals and
  • Standard errors.

Best Answer

In most meta-analysis of odds ratios, the standard errors $se_i$ are based on the log odds ratios $log(OR_i)$. So, do you happen to know how your $se_i$ have been estimated (and what metric they reflect? $OR$ or $log(OR)$)? Given that the $se_i$ are based on $log(OR_i)$, then the pooled standard error (under a fixed effect model) can be easily computed. First, let's compute the weights for each effect size: $w_i = \frac{1}{se_i^2}$. Second, the pooled standard error is $se_{FEM} = \sqrt{\frac{1}{\sum w}}$. Furthermore, let $log(OR_{FEM})$ be the common effect (fixed effect model). Then, the ("pooled") 95% confidence interval is $log(OR_{FEM}) \pm 1.96 \cdot se_{FEM}$.

Update

Since BIBB kindly provided the data, I am able to run the 'full' meta-analysis in R.

library(meta)
or <- c(0.75, 0.85)
se <- c(0.0937, 0.1029)
logor <- log(or)
(or.fem <- metagen(logor, se, sm = "OR"))

> (or.fem <- metagen(logor, se, sm = "OR"))
    OR            95%-CI %W(fixed) %W(random)
1 0.75  [0.6242; 0.9012]     54.67      54.67
2 0.85  [0.6948; 1.0399]     45.33      45.33

Number of trials combined: 2 

                         OR           95%-CI       z  p.value
Fixed effect model   0.7938  [0.693; 0.9092] -3.3335   0.0009
Random effects model 0.7938  [0.693; 0.9092] -3.3335   0.0009

Quantifying heterogeneity:
tau^2 < 0.0001; H = 1; I^2 = 0%

Test of heterogeneity:
    Q d.f.  p.value
 0.81    1   0.3685

Method: Inverse variance method

References

See, e.g., Lipsey/Wilson (2001: 114)