Genome-wide meta-analysis of depression identifies 102 independent variants and highlights the importance of the prefrontal brain regions.
- Authors
- Howard, David M; Adams, Mark J; Clarke, Toni-Kim; Hafferty, Jonathan D; Gibson, Jude; Shirali, Masoud; Coleman, Jonathan R I; Hagenaars, Saskia P; Ward, Joey; Wigmore, Eleanor M; Alloza, Clara; Shen, Xueyi; Barbu, Miruna C; Xu, Eileen Y; Whalley, Heather C; Marioni, Riccardo E; Porteous, David J; Davies, Gail; Deary, Ian J; Hemani, Gibran; Berger, Klaus; Teismann, Henning; Rawal, Rajesh; Arolt, Volker; Baune, Bernhard T; Dannlowski, Udo; Domschke, Katharina; Tian, Chao; Hinds, David A; 23andMe Research Team; Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium; Trzaskowski, Maciej; Byrne, Enda M; Ripke, Stephan; Smith, Daniel J; Sullivan, Patrick F; Wray, Naomi R; Breen, Gerome; Lewis, Cathryn M; McIntosh, Andrew M
- Year
- 2019
- Journal
- Nature neuroscience
- PMID
- 30718901
- DOI
- 10.1038/s41593-018-0326-7
- PMCID
- PMC6522363
Major depression is a debilitating psychiatric illness that is typically associated with low mood and anhedonia. Depression has a heritable component that has remained difficult to elucidate with current sample sizes due to the polygenic nature of the disorder. To maximize sample size, we meta-analyzed data on 807,553 individuals (246,363 cases and 561,190 controls) from the three largest genome-wide association studies of depression. We identified 102 independent variants, 269 genes, and 15 genesets associated with depression, including both genes and gene pathways associated with synaptic structure and neurotransmission. An enrichment analysis provided further evidence of the importance of prefrontal brain regions. In an independent replication sample of 1,306,354 individuals (414,055 cases and 892,299 controls), 87 of the 102 associated variants were significant after multiple testing correction. These findings advance our understanding of the complex genetic architecture of depression and provide several future avenues for understanding etiology and developing new treatment approaches.
(A) Manhattan plot of the observed –log10 P-values of each variant for an association with depression in the meta-analysis (n = 807,553; 246,363 cases and 561,190 controls). Variants are positioned according to the GRCh37 assembly
(A) Significance of cell type enrichment using a partitioned heritability approach. The dashed line represents statistical significance after Bonferroni correction (-log10P = 2.36) and * indicates significant enrichment for that cell type(B) Significance of enrichment estimates, based on genetic summary statistics, for brain regions using GTEx. The dashed line represents the Bonferroni cut-off for statistical significance (-log10P = 2.41) and * indicates significant enrichment for that brain region(C) Significant enrichment P-values, based on genetic summary statistics, for brain cell regions using GTEx overlaid on a physical representation of brain anatomyThe pseudo-coloring used in Figure 2C highlights the P-values of the regions of the brain in red that were significantly enriched (P < 0.05) for depression variants
Chord diagram of genes significantly associated (P < 2.80 × 10-6) with depression and the second level Anatomical Therapeutic Chemical classifications to which interacting drugs have been assigned. The width of each line is determined by the number of drugs known to interact with each gene. The genes are ordered by significance with depression with those most significantly associated located at the top of the diagramThe second level Anatomical Therapeutic Chemical classifications identified were: Stomatological preparations (A01), Drugs for acid related disorders (A02), Drugs for functional gastrointestinal disorders (A03), Bile and liver therapy (A05), Drugs for constipation (A06), Drugs used in diabetes (A10), Vitamins (A11), Mineral Supplements (A12), Anabolic agents for systemic use (A14), Blood substitutes and perfusion solutions (B05), Other hematological agents (B06), Cardiac therapy (C01), Diuretics (C03), Peripheral vasodilators (C04), Vasoprotectives (C05), Beta blocking agents (C07), Calcium channel blockers (C08), Corticosteroids, dermatological preparations (D07), Anti-acne preparations (D10), Other dermatological preparations (D11), Other gynecologicals (G02), Sex hormones and modulators of the genital system (G03), Urologicals (G04), Pituitary and hypothalamic hormones and analogues (H01), Corticosteroids for systemic use (H02), Antibacterials for systemic use (J01), Antivirals for systemic use (J05), Vaccines (J07), Antineoplastic agents (L01), Endocrine therapy (L02), Immunostimulants (L03), Immunosuppressants (L04), Anti-inflammatory and antirheumatic products (M01), Muscle relaxants (M03), Antigout preparations (M04), Drugs for treatment of bone diseases (M05), Anesthetics (N01), Analgesics (N02), Antiepileptics (N03), Anti-Parkinson drugs (N04), Psycholeptics (N05), Psychoanaleptics (N06), Other nervous system drugs (N07), Antiprotozoals (P01), Ectoparasiticides, incl. scabicides, insecticides and repellents (P03), Nasal preparations (R01), Drugs for obstructive airway diseases (R03), Antihistamines for systemic use (R06), Ophthalmologicals (S01), Otologicals (S02), Ophthalmological and otological preparations (S03), All other therapeutic products (V03), Diagnostic agents (V04), and Diagnostic radiopharmaceuticals (V09)
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| Genome-wide analyses reveal novel opioid use disorder loci and genetic overlap with schizophrenia, bipolar disorder, and major depression. | Holen B et al. | — | 2023 | → |
| Genome-wide association studies and cross-population meta-analyses investigating short and long sleep duration. | Austin-Zimmerman I et al. | — | 2023 | → |
| Genome-wide association study of antisocial personality disorder diagnostic criteria provides evidence for shared risk factors across disorders. | Li W et al. | — | 2023 | → |
| Genome-wide multi-trait analysis of irritable bowel syndrome and related mental conditions identifies 38 new independent variants. | Alemany S et al. | — | 2023 | → |
| Glycoprotein acetyls and depression: Testing for directionality and potential causality using longitudinal data and Mendelian randomization analyses. | Crick DCP et al. | — | 2023 | → |
| GWAS Meta-Analysis of Suicide Attempt: Identification of 12 Genome-Wide Significant Loci and Implication of Genetic Risks for Specific Health Factors. | Docherty AR et al. | — | 2023 | → |
| High genetic risk for depression as an independent risk factor for mortality in patients referred for coronary angiography. | Krämer RM et al. | — | 2023 | → |
| High-throughput screening of glucocorticoid-induced enhancer activity reveals mechanisms of stress-related psychiatric disorders. | Penner-Goeke S et al. | — | 2023 | → |
| Hofbauer cell function in the term placenta associates with adult cardiovascular and depressive outcomes. | Fitzgerald E et al. | — | 2023 | → |
| Identification of four novel loci associated with psychotropic drug-induced weight gain in a Swiss psychiatric longitudinal study: A GWAS analysis. | Sjaarda J et al. | — | 2023 | → |
| Identification of region-specific splicing QTLs in human hippocampal tissue and its distinctive role in brain disorders. | Li X et al. | — | 2023 | → |
| Identifying causal associations between early sexual intercourse or number of sexual partners and major depressive disorders: A bidirectional two-sample Mendelian randomization analysis. | Lu Z et al. | — | 2023 | → |
| Identifying potential risk genes and pathways for neuropsychiatric and substance use disorders using intermediate molecular mediator information. | Gedik H et al. | — | 2023 | → |
| Immune System and Brain/Intestinal Barrier Functions in Psychiatric Diseases: Is Sphingosine-1-Phosphate at the Helm? | Martín-Hernández D et al. | — | 2023 | → |
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| Inferring cell-type-specific causal gene regulatory networks during human neurogenesis. | Aygün N et al. | — | 2023 | → |
| Integrating genetics and transcriptomics to study major depressive disorder: a conceptual framework, bioinformatic approaches, and recent findings. | Hicks EM et al. | — | 2023 | → |
| Interplay of Metabolome and Gut Microbiome in Individuals With Major Depressive Disorder vs Control Individuals. | Amin N et al. | — | 2023 | → |
| Investigating the relationship between depression and breast cancer: observational and genetic analyses. | Wu X et al. | — | 2023 | → |
| Investigating the role of the relaxin-3/RXFP3 system in neuropsychiatric disorders and metabolic phenotypes: A candidate gene approach. | Wong WLE et al. | — | 2023 | → |
| Isoform-level transcriptome-wide association uncovers genetic risk mechanisms for neuropsychiatric disorders in the human brain. | Bhattacharya A et al. | — | 2023 | → |
| Leveraging genetic overlap between irritability and psychiatric disorders to identify genetic variants of major psychiatric disorders. | Jung K et al. | — | 2023 | → |
| Linking neuropsychiatric disease to neuronal metabolism. | Schmidt MV | — | 2023 | → |
| Local genetic correlations exist among neurodegenerative and neuropsychiatric diseases. | Reynolds RH et al. | — | 2023 | → |
| Major depression disorder may causally associate with the increased atrial fibrillation risk: evidence from two-sample mendelian randomization analyses. | Wang L et al. | — | 2023 | → |
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| Major depressive disorder and chronic gastritis: A bidirectional two-sample Mendelian randomization study. | Li J et al. | — | 2023 | → |
| Major depressive disorder plays a vital role in the pathway from gastroesophageal reflux disease to chronic obstructive pulmonary disease: a Mendelian randomization study. | Zou M et al. | — | 2023 | → |
| Mapping microRNA expression quantitative trait loci in the prenatal human brain implicates miR-1908-5p expression in bipolar disorder and other brain-related traits. | Toste CC et al. | — | 2023 | → |
| Mendelian randomization analyses identify bidirectional causal relationships of obesity with psychiatric disorders. | Chen W et al. | — | 2023 | → |
| Mendelian randomization shows depression increases the risk of type 2 diabetes. | Jin H et al. | — | 2023 | → |
| Mendelian Randomization Using the Druggable Genome Reveals Genetically Supported Drug Targets for Psychiatric Disorders. | Li X et al. | — | 2023 | → |
| Meta-Analyses of Genome-Wide Association Studies for Postpartum Depression. | Guintivano J et al. | — | 2023 | → |
| Methylome-wide association study of anxiety disorders. | Hettema JM et al. | — | 2023 | → |
| Multimodal Data Integration Advances Longitudinal Prediction of the Naturalistic Course of Depression and Reveals a Multimodal Signature of Remission During 2-Year Follow-up. | Habets PC et al. | — | 2023 | → |
| Multi-PGS enhances polygenic prediction by combining 937 polygenic scores. | Albiñana C et al. | — | 2023 | → |
| Multiple genes in a single GWAS risk locus synergistically mediate aberrant synaptic development and function in human neurons. | Zhang S et al. | — | 2023 | → |
| Multiple psychiatric polygenic risk scores predict associations between childhood adversity and bipolar disorder. | Yao K et al. | — | 2023 | → |
| Multi-trait genome-wide association analyses leveraging alcohol use disorder findings identify novel loci for smoking behaviors in the Million Veteran Program. | Cheng Y et al. | — | 2023 | → |
| Multivariate GWAS of Alzheimer's disease CSF biomarker profiles implies GRIN2D in synaptic functioning. | Neumann A et al. | — | 2023 | → |
| Neurobiological mechanisms of ECT and TMS treatment in depression: study protocol of a multimodal magnetic resonance investigation. | Frid LM et al. | — | 2023 | → |
| Nomogram model for predicting the risk of post-stroke depression based on clinical characteristics and DNA methylation. | Luo S et al. | — | 2023 | → |
| Novel synergistic treatment for depression: involvement of GSK3β-regulated AMPA receptors in the prefrontal cortex of mice. | Guo L et al. | — | 2023 | → |
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| Phenotype integration improves power and preserves specificity in biobank-based genetic studies of major depressive disorder. | Dahl A et al. | — | 2023 | → |
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| Polygenic risk prediction: why and when out-of-sample prediction R<sup>2</sup> can exceed SNP-based heritability. | Wang X et al. | — | 2023 | → |
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| Potential Causal Association between Depression and Oral Diseases: A Mendelian Randomization Study. | Zhang X et al. | — | 2023 | → |
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| Proteome-wide Mendelian randomization reveals the causal effects of immune-related plasma proteins on psychiatric disorders. | Dang X et al. | — | 2023 | → |
| Psychiatric polygenic risk as a predictor of COVID-19 risk and severity: insight into the genetic overlap between schizophrenia and COVID-19. | Alemany-Navarro M et al. | — | 2023 | → |
| Psychological, endocrine and polygenic predictors of emotional well-being during the COVID-19 pandemic in a longitudinal birth cohort. | Nguyen T et al. | — | 2023 | → |
| Reduced Vrk2 expression is associated with higher risk of depression in humans and mediates depressive-like behaviors in mice. | Yin MY et al. | — | 2023 | → |
| Relationship Between the Ovarian Cyst and Depression: A Two-Sample Mendelian Randomization Study. | Wen J et al. | — | 2023 | → |
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| Serum Extracellular Vesicle-Derived hsa-miR-2277-3p and hsa-miR-6813-3p Are Potential Biomarkers for Major Depression: A Preliminary Study. | Seki I et al. | — | 2023 | → |
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| Single-Nucleus Transcriptional Profiling of GAD2-Positive Neurons From Mouse Lateral Habenula Reveals Distinct Expression of Neurotransmission- and Depression-Related Genes. | Green MV et al. | — | 2023 | → |
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| Social isolation-induced transcriptomic changes in mouse hippocampus impact the synapse and show convergence with human genetic risk for neurodevelopmental phenotypes. | Laighneach A et al. | — | 2023 | → |
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| The Role of IgLON Cell Adhesion Molecules in Neurodegenerative Diseases. | Salluzzo M et al. | — | 2023 | → |
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| Variation along P2RX7 interacts with early traumas on severity of anxiety suggesting a role for neuroinflammation. | Kristof Z et al. | — | 2023 | → |
| Verbascoside: A neuroprotective phenylethanoid glycosides with anti-depressive properties. | Zhao Y et al. | — | 2023 | → |