(a) Although statistical power has been systematically underestimated in psychiatric genetics, when we began this study in Q3 2006, it was believed that statistical power would be reasonable to detect realistic genetic effects. However, the definition of “realistic” has shifted considerably since 2006 and it may be important to design studies that can detect genotypic relative risks <1.10. (b) When this study began, the coverage and performance of the Perlegen GWAS platform were among the better options available (19). The technology and pricing have evolved rapidly and superior platforms are now available. A key limitation of the Perlegen platform is its inability to assess copy number variation (106) that may be particularly salient for psychiatric disorders (107, 108). More generally, the GWAS platform might not be sufficiently “genomewide” and unbiased: the platform may have had inadequate coverage in an etiologically important region of the genome, SNPs are only one type of genetic variation, and important non-SNP genetic variation might not have been sufficiently well captured. (c) There was an imbalance in the proportion of males in cases and controls. Although
