We used the Cochran-Armitage trend test to test for association of the 435,291 SNPs in the GWAS dataset with case/control status. The estimated lambda (69) was 1.046 (similar p-value minima and lambdas were obtained using logistic regression with 10 principal components and using a stratified Cochran-Mantel-Haenszel tests based on identity-by-state clusters) (43, 44). The minimum q-value was 0.28 (i.e., if these tests were called significant, over the long-term, a minimum false discovery rate of ∼28% would be incurred). As the pre-specified q-value threshold was 0.10, no SNP reached genomewide significance. The proportion of all SNPs without true effects (p0) (54) was conservatively estimated to be p0=0.9999954, consistent with the presence of ∼2 SNPs with true effects in these GWAS data. The results of this MDD GWAS are included as a Supplemental File (“results.txt”) to facilitate comparisons with other studies.
