A mega-analysis of genome-wide association studies for major depressive disorder.
- Authors
- Major Depressive Disorder Working Group of the Psychiatric GWAS Consortium; Ripke, Stephan; Wray, Naomi R; Lewis, Cathryn M; Hamilton, Steven P; Weissman, Myrna M; Breen, Gerome; Byrne, Enda M; Blackwood, Douglas H R; Boomsma, Dorret I; Cichon, Sven; Heath, Andrew C; Holsboer, Florian; Lucae, Susanne; Madden, Pamela A F; Martin, Nicholas G; McGuffin, Peter; Muglia, Pierandrea; Noethen, Markus M; Penninx, Brenda P; Pergadia, Michele L; Potash, James B; Rietschel, Marcella; Lin, Danyu; MΓΌller-Myhsok, Bertram; Shi, Jianxin; Steinberg, Stacy; Grabe, Hans J; Lichtenstein, Paul; Magnusson, Patrik; Perlis, Roy H; Preisig, Martin; Smoller, Jordan W; Stefansson, Kari; Uher, Rudolf; Kutalik, Zoltan; Tansey, Katherine E; Teumer, Alexander; Viktorin, Alexander; Barnes, Michael R; Bettecken, Thomas; Binder, Elisabeth B; Breuer, RenΓ©; Castro, Victor M; Churchill, Susanne E; Coryell, William H; Craddock, Nick; Craig, Ian W; Czamara, Darina; De Geus, Eco J; Degenhardt, Franziska; Farmer, Anne E; Fava, Maurizio; Frank, Josef; Gainer, Vivian S; Gallagher, Patience J; Gordon, Scott D; Goryachev, Sergey; Gross, Magdalena; Guipponi, Michel; Henders, Anjali K; Herms, Stefan; Hickie, Ian B; Hoefels, Susanne; Hoogendijk, Witte; Hottenga, Jouke Jan; Iosifescu, Dan V; Ising, Marcus; Jones, Ian; Jones, Lisa; Jung-Ying, Tzeng; Knowles, James A; Kohane, Isaac S; Kohli, Martin A; Korszun, Ania; Landen, Mikael; Lawson, William B; Lewis, Glyn; Macintyre, Donald; Maier, Wolfgang; Mattheisen, Manuel; McGrath, Patrick J; McIntosh, Andrew; McLean, Alan; Middeldorp, Christel M; Middleton, Lefkos; Montgomery, Grant M; Murphy, Shawn N; Nauck, Matthias; Nolen, Willem A; Nyholt, Dale R; O'Donovan, Michael; Oskarsson, HΓΆgni; Pedersen, Nancy; Scheftner, William A; Schulz, Andrea; Schulze, Thomas G; Shyn, Stanley I; Sigurdsson, Engilbert; Slager, Susan L; Smit, Johannes H; Stefansson, Hreinn; Steffens, Michael; Thorgeirsson, Thorgeir; Tozzi, Federica; Treutlein, Jens; Uhr, Manfred; van den Oord, Edwin J C G; Van Grootheest, Gerard; VΓΆlzke, Henry; Weilburg, Jeffrey B; Willemsen, Gonneke; Zitman, Frans G; Neale, Benjamin; Daly, Mark; Levinson, Douglas F; Sullivan, Patrick F
- Year
- 2013
- Journal
- Molecular psychiatry
- PMID
- 22472876
- DOI
- 10.1038/mp.2012.21
- PMCID
- PMC3837431
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 18β759 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 50β695 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 Γ 10(-8)), and all were in a 248βkb interval of high LD on 3p21.1 (chr3:52β425β083-53β822β102, minimum P=5.9 Γ 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.
Overview of results from the discovery genome-wide association study mega-analysis for major depressive disorder. The inset shows the quantileβquantile plot (observed by expected P-values on the βlog10scale) showing conformity of the observed results to expectations under the null. The main part of the figure shows the Manhattan plot (βlog10 of the P-value by genomic location) of the association results in genomic context. No region exceeded genome-wide significance in the discovery sample.
| Name | Type |
|---|---|
| 1000 Genomes Project | cohort |
| 5-HTTLPR | variant |
| ADCY9 | gene |
| ADHD | phenotype |
| age of onset | phenotype |
| Age of onset of MDD local | phenotype |
| age-related macular degeneration | phenotype |
| all samples local | cohort |
| antipsychotics | drug |
| attention deficit hyperactivity disorder | phenotype |
| autism | phenotype |
| autosomal SNPs | cohort |
| BiP | phenotype |
| BIP66 local | cohort |
| BIP discovery phase local | cohort |
| bipolar disorder | phenotype |
| BIP sample local | cohort |
| body weight | phenotype |
| breast cancer | phenotype |
| Broad mood disorder phenotype local | phenotype |
| CEU+TSI HapMap3 local | cohort |
| Christchurch longitudinal study local | cohort |
| chrX SNPs local | variant |
| Clinically Ascertained Major Depressive Disorder local | phenotype |
| Combined BIP-schizophrenia phenotype local | phenotype |
| Combined MDD-BIP phenotype local | phenotype |
| common variation | variant |
| copy number variation | variant |
| Crohnβs disease | phenotype |
| cross-disorder analyses local | cohort |
| discovery and replication samples local | cohort |
| Discovery mega-analysis local | cohort |
| Discovery phase local | cohort |
| discovery samples local | cohort |
| Dunedin longitudinal study local | cohort |
| DVL3 local | gene |
| Early-onset MDD | phenotype |
| European ancestry | cohort |
| European population | cohort |
| external samples local | cohort |
| Female MDD cases and controls local | cohort |
| female-only analysis local | cohort |
| GLT8D1 | gene |
| GNL3 | gene |
| GRM7 | gene |
| HapMap | cohort |
| Hap-Map2 local | cohort |
| HapMap3 | cohort |
| HapMap3 CEU+TSI local | cohort |
| height | phenotype |
| HTR3C local | gene |
| HTR3D local | gene |
| HTR3E local | gene |
| Htr7 | gene |
| hypersomnia | phenotype |
| hypersomnia class local | cohort |
| independent samples | cohort |
| inflammatory bowel disease | phenotype |
| insomnia | phenotype |
| ITIH1 | gene |
| ITIH3 | gene |
| ITIH4 | gene |
| lung cancer | phenotype |
| major depressive disorder | phenotype |
| male cases and controls local | cohort |
| Male MDD cases and controls local | cohort |
| MDD-BIP cross-disorder cohort local | cohort |
| MDD cases | cohort |
| MDD controls | cohort |
| MDD discovery phase local | cohort |
| MDD discovery phase samples local | cohort |
| MDD replication phase local | cohort |
| MDD sample local | cohort |
| mood disorders | phenotype |
| Multiple cancers local | phenotype |
| multiple sclerosis | phenotype |
| NEK4 | gene |
| NHGRI-EBI GWAS catalog | cohort |
| NIMH Human Genetics Initiative Repository local | cohort |
| nine primary samples local | cohort |
| nucleus accumbens | anatomy |
| Parkinsonβs disease | phenotype |
| PBRM1 | gene |
| PDLIM5 | gene |
| PGC | cohort |
| PGC analyses local | cohort |
| PGC BIP mega-analysis local | cohort |
| PGC BIP megaanalysis local | cohort |
| PGC BIP study local | cohort |
| PGC discovery local | cohort |
| PGC schizophrenia study local | cohort |
| PGC SCZ study local | cohort |
| Pre-pubertal onset MDD local | phenotype |
| Primary MDD samples local | cohort |
| Psychiatric Genomics Consortium | cohort |
| recurrence | phenotype |
| Recurrent Early-Onset Major Depressive Disorder local | phenotype |
| recurrent major depressive disorder | phenotype |
| Reln | gene |
| replication sample | cohort |
| rs1042779 local | variant |
| rs11579964 local | variant |
| rs12837650 local | variant |
| rs1969253 local | variant |
| rs2239547 | variant |
| rs2251219 | variant |
| rs2498828 local | variant |
| rs2535629 local | variant |
| rs2668193 local | variant |
| rs2878628 local | variant |
| rs3773729 local | variant |
| rs3774609 local | variant |
| rs736408 local | variant |
| rs7647854 local | variant |
| schizophrenia | phenotype |
| SCZ | phenotype |
| secondary phenotypes local | phenotype |
| seven independent MDD samples local | cohort |
| sex | phenotype |
| Sklar et al.36 local | cohort |
| SLC6A4 | gene |
| SNP | cohort |
| SPCS1 local | gene |
| study cohort | cohort |
| systemic lupus erythematosus | phenotype |
| type 2 diabetes | phenotype |
| typicality | phenotype |
| typical MDD local | phenotype |
| uncommon variation local | variant |
| weight gain | phenotype |
| Weight gain/insomnia local | phenotype |
| weight gain/insomnia class local | cohort |
| weight loss | phenotype |
| Weight loss/insomnia local | phenotype |
| weight loss/insomnia class local | cohort |
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| Association of Genetic Variation at <i>AQP4</i> Locus with Vascular Depression. | Westermair AL et al. | β | 2018 | β |
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| Commentary for Special Issue of Prevention Science "Using Genetics in Prevention: Science Fiction or Science Fact?" | Dick DM | β | 2018 | β |
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