GS is a family and population-based cohort of 20,195 participants genotyped on the Illumina OmniExpress BeadChip (706,786 SNPs). The raw genotype data in GS underwent quality control so that individuals with a call rate < 98%, SNPs with a genotyping rate < 98%, a minor allele frequency < 1% and a Hardy-Weinberg equilibrium P-value < 10-6 were removed from the dataset and then imputed 62, leaving a total of 19,997 GS individuals and 8,633,288 SNPs. Participants underwent a clinical diagnosis of MDD using the Structured Clinical Interview for the Diagnostic and Statistical Manual of Mental Disorders 63 with further information on the phenotype used provided in Fernandez-Pujals, et al. 64. An unrelated sample was selected by removing one individual from each pair that shared a genomic relationship > 0.025, leaving a total of 975 cases and 5,971 controls. To calculate the PRS, GS was removed from the current meta-analysis and the Wray PRS prior to calculated single nucleotide polymorphism (SNP) weights which were filtered so that they only contained SNPs that overlapped between the current meta-analysis PRS and the Wray
