Finally, we developed a framework to assess how informative our negative genome-wide association study is about the cumulative contribution of common SNPs to schizophrenia. To mimic our study design, we assumed that for a SNP to be detected it must both obtain p<0.0003 in the initial GWAS and obtain a joint p<1.6×10−7 when combined over the initial GWAS and the first subsequent replication stage (see Methods for details of power calculations). We find that it is possible for a single causal SNP, tagged at r 2 = 0.8 with a GWAS SNP and with MAF = 0.2, to be undetected with a 20% probability if the allelic odds ratio is less than 1.58. This means, not unexpectedly, that a single SNP with a relatively large odds ratio could easily have been missed in our study. But it is important to note that while one such SNP might easily be missed, many such SNPs could not be missed, and alone, such a SNP would contribute a locus specific to λS of only 1.04, which amounts to only a tiny fraction of
