significant loci were selected from each meta-analysis. Power for replication in the excluded samples was estimated at different P-value thresholds and the deficit in replications (number of replications expected minus number observed) was calculated. The contribution of the winner’s curse to the deficit in replications was estimated as the average deficit across the three sets of random non-family-based cohorts. By subtracting this from the deficit observed for the family-based cohorts, we estimated the lack of replication that could be attributed to stratification (either inflation of effect size for true associations, or false positive associations).
