As in a meta-analysis, the focus is on combining estimates of association parameters, it seems prudent to base QC on post-analysis information measures that also cover the strength of association, such as SNPTEST info or RT2. These measures can be used to obtain homogeneity and to increase the comparability between the studies.9 Marchini et al10 showed that based on a simulated data set of 1000 cases and 1000 controls the MACH and IMPUTE preanalysis information measures were highly correlated, and that there was a good agreement between the IMPUTE preanalysis information measure and the SNPTEST post-analysis information measure when testing an additive genetic model. In this paper we investigate whether good agreement holds for strongly associated SNPs between the pre- and postanalysis information measures, and whether the post-analysis information measures such as SNPTEST info and RT2 can have an important role as an inclusion criterion of candidate SNPs.
