This study has several potential limitations. The use of shared controls genotyped previously on different Illumina platforms creates the possibility of a systematic technical bias. To address this concern, we employed stringent, iterative individual platform QC procedures, tests of cross-platform concordance using sample duplicates, and additional extensive testing for differential missing data between platforms. We also excluded SNPs known to perform differentially across Illumina platforms that can cause spurious results if not recognized (N. Cox, personal communication).46 The minimal inflation of the median test statistic in the primary meta-analysis (λGC= 0.996), as well as the nominal enrichment of the top signals for SNPs with known functional significance in brain, argues that these efforts effectively mitigated this potential confound.
