In the PGC samples, (Table S1), individual genotypes were assembled, processed through a central quality control pipeline and imputed using the CEU and TSI HapMap3 reference panels. Quality control procedures were extensive (7). In the CHARGE cohorts, genotype quality control and imputation were conducted in each study separately. The imputation reference was the HapMap2 Central EUrope (CEU) panel (14). In the MDD replication cohorts (Table S3), imputation was performed using IMPUTE2 / SHAPEIT (chunk size of 3 Mb and default parameters). The imputation reference set consisted of 2,186 phased haplotypes from the 1000 Genomes Project. In the Health and Retirement Study, imputation was performed using the HapMap2 CEU reference panel.
