Prior genome-wide association studies (GWAS) of major depressive disorder
(MDD) have met with limited success. We sought to increase statistical power to
detect disease loci by conducting a GWAS mega-analysis for MDD. In the MDD
discovery phase, we analyzed more than 1.2 million autosomal and X chromosome
single-nucleotide polymorphisms (SNPs) in 18 759 independent and unrelated
subjects of recent European ancestry (9240 MDD cases and 9519 controls). In the
MDD replication phase, we evaluated 554 SNPs in independent samples (6783 MDD
cases and 50 695 controls). We also conducted a cross-disorder meta-analysis
using 819 autosomal SNPs with P< 0.0001 for either MDD or
the Psychiatric GWAS Consortium bipolar disorder (BIP) mega-analysis (9238 MDD
cases/8039 controls and 6998 BIP cases/7775 controls). No SNPs achieved
genome-wide significance in the MDD discovery phase, the MDD replication phase
or in pre-planned secondary analyses (by sex, recurrent MDD, recurrent
early-onset MDD, age of onset, pre-pubertal onset MDD or typical-like MDD from a
latent class analyses of the MDD criteria). In the MDD-bipolar cross-disorder
analysis, 15 SNPs exceeded genome-wide significance
(P<5×10−8), and all were in a
248 kb interval of high LD on 3p21.1 (chr3:52 425 083–53 822 102,
minimum P= 5.9×10−9 at
rs2535629). Although this is the largest genome-wide analysis of MDD yet
conducted, its high prevalence means that the sample is still underpowered to
detect genetic effects typical for complex traits. Therefore, we were unable to
identify robust and replicable findings. We discuss what this means for genetic
research for MDD. The 3p21.1 MDD-BIP finding should be interpreted with caution
as the most significant SNP did not replicate in MDD samples, and genotyping in
independent samples will be needed to resolve its status.