The sets of SNPs with P-values below 0.1, 0.2, 0.3, 0.4 and 0.5 based on the results in the discovery sample included the number of SNPs as expected for these P-values, that is, ∼200 k, 400 k, 600 k, 800 k and 1 million SNPs, respectively. The overlap with SNPs used to calculate polygenic scores in the target samples was 100% for the GAIN-MDD sample, 40% for the MDD2000+ sample, 20% for the WTCCC sample and 90% for the STEP-BD sample. The lower overlap is due to the use of HapMap 3 as a reference set in the MDD2000+ sample and to the use of observed genotypes only in the WTCCC sample.
