excluded. We estimated statistical power using Quanto (57) (assumptions: log-additive genetic model, MDD lifetime risk 0.15, MAF=0.45 (similar to rs2522833), a genotypic relative risk of 1.14 (“shrunk” down from the observed GRR of 1.26 for rs2522833 to account for the “Winner's Curse” phenomenon) (79), and a conservative two-tailed type 1 error rate of 0.00167 (=0.05/30 replication SNPs). Statistical power was 97.2% for replication for the two SNPs genotyped in all samples (N=11,972) and 90.4% for the remaining SNPs (N=9,278). Five replication samples were genotyped for 30 SNPs using the same Sequenom iPlex SNP pool (15 SNPs were in the primary GWAS and 15 were selected to tag common variation in Europeans) (80) and one sample was successfully genotyped for two SNPs using TaqMan. The SNP selection strategy effectively cast a broad net over the region showing association in Figure 2. For the NESDA/NTR samples, agreement between the initial Perlegen genotypes in this region and independent re-genotyping was high (0.9987).
