deCODE data to the meta-analysis. This trend test is therefore independent of the primary case-control GWAS). Third, analysing the 1,235 parent-proband trios, we again found excess transmission of the schizophrenia-associated allele at 69% of the LD-independent SNPs with P <1×10−6 in the case-control GWAS. This is again unlikely to occur by chance (P = 1×10−9) and additionally excludes population stratification as fully explaining the associations that surpassed our threshold for seeking replication. Fourth, we used the trios trend data to estimate the expected proportion of true associations at P <1×10−6 in the discovery GWAS, allowing for the fact that half of the index SNPs are expected to show the same allelic trend in the trios by chance, and that some true associations will show opposite trends given the limited number of trio samples (Supplementary Material). Given the observed trend test results, around 67% (95% CI 64%-73%) or N = 176 of the associations in the scan at P <1×10−6 are expected to be true, and therefore the number of associations that will ultimately be validated from this set of SNPs will be considerably more than those that now meet genome-wide significance. Taken together, these analyses indicate that the observed deviation
