We used the Armitage trend test (1df) to generate SNP association p-values. In the bipolar and schizophrenia datasets, the association test statistics for the markers we used here are respectively inflated as estimated by the genomic control22 metric λ by 1.11 and 1.08. In neither dataset does this appear attributable to population structure since analyses conditional on the principal components derived from multi dimensional scaling had negligible impact3,20. Nevertheless, to address our aims conservatively, all SNP p-values in the true datasets are corrected for λ. The corrected p-values were then in turn used to generate three types of gene-wide tests. The first was based on the smallest SNP p-value per gene, and the second and third were respectively the threshold truncated23 product of all SNP p-values within a gene where the truncation thresholds were p≤0.01 and p≤0.001. Product analyses were restricted to those genes which had more than 1 SNP.
