Meta-analysis of the 23andMe dataset with the previously reported Psychiatric Genomics Consortium (PGC) meta-analysis of MDD, which encompassed 9,240 cases and 9,519 controls of European descent, is presented in Figure 1a–b (Supplementary Table 2). From the PGC cohort only 1.22 million SNPs overlapped with the 23andMe MDD data (no results were reported for X or Y chromosomes)14 and only these SNPs were used for downstream analysis. As a result, several lead SNPs from the discovery 23andMe GWAS are absent including rs77741769 (SPPL3-HNF1A), rs144294997 (N6AMT1), rs1432639 (NEGR1), and rs67744457 (EP300-L3MBTL2). Each cohort was individually adjusted for inflation using LD score regression (as described in the Methods) and subsequently meta-analyzed using a standard fixed-effects, inverse-variance weighted approach15. Final results from the meta-analysis were further adjusted for the meta-analysis LD score regression intercept of 1.0025.
