The genotyping chips used by the primary studies had good coverage of common variation across the genome. It is possible that genetic variation important in the etiology of MDD was missed if LD was insufficient with genotyped variants. In particular, we had suboptimal or poor coverage of uncommon variation (MAF 0.005–0.05), and we have not yet analyzed copy number variation (PGC analyses of copy number variants are underway). In addition, the discovery studies used eight genotyping platforms, and it is possible that causal common variation was missed because not all platforms had good coverage in the same regions. However, these caveats should be interpreted in the context of the many successful GWAS meta-analyses that faced similar limitations.
