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      A replication study separates polymorphisms behind migraine with and without depression

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          Abstract

          The largest migraine genome-wide association study identified 38 candidate loci. In this study we assessed whether these results replicate on a gene level in our European cohort and whether effects are altered by lifetime depression. We tested SNPs of the loci and their vicinity with or without interaction with depression in regression models. Advanced analysis methods such as Bayesian relevance analysis and a neural network based classifier were used to confirm findings. Main effects were found for rs2455107 of PRDM16 (OR = 1.304, p = 0.007) and five intergenic polymorphisms in 1p31.1 region: two of them showed risk effect (OR = 1.277, p = 0.003 for both rs11209657 and rs6686879), while the other three variants were protective factors (OR = 0.4956, p = 0.006 for both rs12090642 and rs72948266; OR = 0.4756, p = 0.005 for rs77864828). Additionally, 26 polymorphisms within ADGRL2, 2 in REST, 1 in HPSE2 and 33 mostly intergenic SNPs from 1p31.1 showed interaction effects. Among clumped results representing these significant regions, only rs11163394 of ADGRL2 showed a protective effect (OR = 0.607, p = 0.002), all other variants were risk factors (rs1043215 of REST with the strongest effect: OR = 6.596, p = 0.003). Bayesian relevance analysis confirmed the relevance of intergenic rs6660757 and rs12128399 (p31.1), rs1043215 ( REST), rs1889974 ( HPSE2) and rs11163394 ( ADGRL2) from depression interaction results, and the moderate relevance of rs77864828 and rs2455107 of PRDM16 from main effect analysis. Both main and interaction effect SNPs could enhance predictive power with the neural network based classifier. In summary, we replicated p31.1, PRDM16, REST, HPSE2 and ADGRL2 genes with classic genetic and advanced analysis methods. While the p31.1 region and PRDM16 are worthy of further investigations in migraine in general, REST, HPSE2 and ADGRL2 may be prime candidates behind migraine pathophysiology in patients with comorbid depression.

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          Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression

          Major depressive disorder (MDD) is a common illness accompanied by considerable morbidity, mortality, costs, and heightened risk of suicide. We conducted a genome-wide association (GWA) meta-analysis based in 135,458 cases and 344,901 control, We identified 44 independent and significant loci. The genetic findings were associated with clinical features of major depression, and implicated brain regions exhibiting anatomical differences in cases. Targets of antidepressant medications and genes involved in gene splicing were enriched for smaller association signal. We found important relations of genetic risk for major depression with educational attainment, body mass, and schizophrenia: lower educational attainment and higher body mass were putatively causal whereas major depression and schizophrenia reflected a partly shared biological etiology. All humans carry lesser or greater numbers of genetic risk factors for major depression. These findings help refine and define the basis of major depression and imply a continuous measure of risk underlies the clinical phenotype.
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            Genome-wide meta-analysis of depression identifies 102 independent variants and highlights the importance of the prefrontal brain regions

            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.
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              Analysis of shared heritability in common disorders of the brain

              Disorders of the brain can exhibit considerable epidemiological comorbidity and often share symptoms, provoking debate about their etiologic overlap. We quantified the genetic sharing of 25 brain disorders from genome-wide association studies of 265,218 patients and 784,643 control participants and assessed their relationship to 17 phenotypes from 1,191,588 individuals. Psychiatric disorders share common variant risk, whereas neurological disorders appear more distinct from one another and from the psychiatric disorders. We also identified significant sharing between disorders and a number of brain phenotypes, including cognitive measures. Further, we conducted simulations to explore how statistical power, diagnostic misclassification, and phenotypic heterogeneity affect genetic correlations. These results highlight the importance of common genetic variation as a risk factor for brain disorders and the value of heritability-based methods in understanding their etiology.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: MethodologyRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: MethodologyRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: MethodologyRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: MethodologyRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: Writing – original draftRole: Writing – review & editing
                Role: Funding acquisitionRole: InvestigationRole: Writing – original draftRole: Writing – review & editing
                Role: Funding acquisitionRole: InvestigationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS One
                plos
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                31 December 2021
                2021
                : 16
                : 12
                : e0261477
                Affiliations
                [1 ] Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, Japan
                [2 ] Department of Pharmacodynamics, Faculty of Pharmacy, Semmelweis University, Budapest, Hungary
                [3 ] MTA-SE Neuropsychopharmacology and Neurochemistry Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary
                [4 ] SE-NAP2 Genetic Brain Imaging Migraine Research Group, Hungarian Brain Research Program, Semmelweis University, Budapest, Hungary
                [5 ] Department of Measurement and Information Systems, Budapest University of Technology and Economics, Budapest, Hungary
                [6 ] NAP-2-SE New Antidepressant Target Research Group, Semmelweis University, Budapest, Hungary
                [7 ] Neuroscience and Psychiatry Unit, Division of Neuroscience and Experimental Psychology, The University of Manchester and Manchester Academic Health Sciences Centre, Manchester, United Kingdom
                Illumina Inc, UNITED STATES
                Author notes

                Competing Interests: J. F. William Deakin has share options in P1vital and Gyorgy Bagdy is a member of the Board of directors at Gedeon Richter. The other authors declare no competing interests exist.

                Author information
                https://orcid.org/0000-0002-7826-9179
                https://orcid.org/0000-0002-5975-4267
                Article
                PONE-D-21-17017
                10.1371/journal.pone.0261477
                8719675
                34972135
                da55be75-6ae6-4db8-bb7c-fb87250a0ad8
                © 2021 Petschner et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 23 May 2021
                : 3 December 2021
                Page count
                Figures: 0, Tables: 5, Pages: 21
                Funding
                Funded by: Ministry of Human Capacities, Hungary
                Award ID: BME FIKP-BIO
                Award Recipient :
                Funded by: Hungarian Brain Research Program, National Development Agency
                Award ID: 2017-1.2.1-NKP-2017-00002; KTIA_13_NAPA-II/14; KTIA_NAP_13-1-2013-0001
                Award Recipient :
                Funded by: Hungarian Academy of Sciences, Semmelweis University and the Hungarian Brain Research Program
                Award ID: KTIA_NAP_13-2-2015-0001
                Award Recipient :
                Funded by: Sixth Framework Program of the European Union, NewMood
                Award ID: LSHM-CT-2004-503474
                Award Recipient :
                Funded by: National Institute for Health Research Manchester Biomedical Research Centre
                Award Recipient :
                Funded by: Hungarian Academy of Sciences (MTA-SE Neuropsychopharmacology and Neurochemistry Research Group)
                Award Recipient :
                Funded by: National Research, Development and Innovation Office, Hungary under the frame of ERA PerMed
                Award ID: 2019-2.1.7-ERA-NET-2020-00005; ERAPERMED2019-108
                Award Recipient :
                Funded by: New National Excellence Program of Ministry of Human Capacities
                Award ID: UNKP-17-4-I-SE-8
                Award Recipient :
                Funded by: New National Excellence Program of Ministry of Human Capacities
                Award ID: UNKP-19-4-BME-344
                Award Recipient :
                Funded by: New National Excellence Program of the Ministry for Innovation and Technology from the source of the National Research, Development and Innovation Fund
                Award ID: ÚNKP-20-3-II-SE-51
                Award Recipient :
                Funded by: New National Excellence Program of the Ministry for Innovation and Technology from the source of the National Research, Development and Innovation Fund
                Award ID: ÚNKP-20-5-BME-92
                Award Recipient :
                Funded by: Thematic Excellence Programme (Tématerületi Kiválósági Program) of the Ministry for Innovation and Technology in Hungary, within the framework of the Neurology and Translational Biotechnology thematic programmes of the Semmelweis University
                Award ID: 2020-4.1.1.-TKP2020
                Award Recipient :
                Funded by: OTKA
                Award ID: 119866
                Award Recipient :
                Funded by: NRDI Fund based on the charter of bolster issued by the NRDI Office under the auspices of the Ministry for Innovation and Technology
                Award ID: BME NC TKP2020, BME IE-BIO TKP2020
                Award Recipient :
                Funded by: Janos Bolyai Research Scholarship of the Hungarian Academy of Sciences
                Award Recipient :
                Funded by: Japan Society for the Promotion of Science (Postdoctoral Fellowships for Research in Japan, standard program)
                Award ID: P20809
                Award Recipient :
                Funded by: New National Excellence Program of the Ministry for Innovation and Technology from the source of the National Research, Development and Innovation Fund
                Award ID: ÚNKP-21-5-BME-362
                Award Recipient :
                Funded by: New National Excellence Program of the Ministry for Innovation and Technology from the source of the National Research, Development and Innovation Fund
                Award ID: ÚNKP-21-4-I-SE-15
                Award Recipient :
                Our study was part of NewMood (New Molecules in Mood Disorders, 2004-2009) research program funded by the European Union and was supported by the Hungarian Brain Research Program (KTIA_13_NAP-A-II/14, 2017-1.2.1-NKP-2017-00002); by the National Development Agency (KTIA_NAP_13-1-2013-0001); by the Sixth Framework Program of the European Union, NewMood (Grant No. LSHM-CT-2004-503474); by the Hungarian Academy of Sciences, Semmelweis University and the Hungarian Brain Research Program (MTA-SE-NAP B Genetic Brain Imaging Migraine Research Group, Grant KTIA_NAP_13-2-2015-0001); by the National Institute for Health Research Manchester Biomedical Research Centre; by the Hungarian Academy of Sciences (MTA-SE Neuropsychopharmacology and Neurochemistry Research Group); by the National Research, Development and Innovation Office, Hungary (2019-2.1.7-ERA-NET-2020-00005), under the frame of ERA PerMed (ERAPERMED2019-108); by the New National Excellence Program of Ministry of Human Capacities (UNKP-17-4-I-SE-8, UNKP-19-4-BME-344); by the New National Excellence Program of the Ministry for Innovation and Technology from the source of the National Research, Development and Innovation Fund (ÚNKP-20-3-II-SE-51, ÚNKP-20-5-BME-92, ÚNKP-21-5-BME-362, ÚNKP-21-4-I-SE-15); by the BME-Biotechnology FIKP grant of EMMI (BME FIKP-BIO); by the Thematic Excellence Programme (Tématerületi Kiválósági Program, 2020-4.1.1.-TKP2020) of the Ministry for Innovation and Technology in Hungary, within the framework of the Neurology and Translational Biotechnology thematic programmes of the Semmelweis University; by OTKA 119866; and by the NRDI Fund (BME NC TKP2020, BME IE-BIO TKP2020, Artificial Intelligence National Laboratory Programme) based on the charter of bolster issued by the NRDI Office under the auspices of the Ministry for Innovation and Technology. GH is a recipient of the Janos Bolyai Research Scholarship of the Hungarian Academy of Sciences. PP is an international research fellow of Japan Society for the Promotion of Science (Postdoctoral Fellowships for Research in Japan, standard program, P20809). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Medicine and Health Sciences
                Clinical Medicine
                Signs and Symptoms
                Headaches
                Migraine
                Medicine and Health Sciences
                Mental Health and Psychiatry
                Mood Disorders
                Depression
                Biology and Life Sciences
                Genetics
                Single Nucleotide Polymorphisms
                Medicine and Health Sciences
                Epidemiology
                Medical Risk Factors
                Computer and Information Sciences
                Neural Networks
                Biology and Life Sciences
                Neuroscience
                Neural Networks
                Biology and Life Sciences
                Genetics
                Biology and Life Sciences
                Computational Biology
                Genome Analysis
                Biology and Life Sciences
                Genetics
                Genomics
                Genome Analysis
                Biology and Life Sciences
                Computational Biology
                Genome Analysis
                Genome-Wide Association Studies
                Biology and Life Sciences
                Genetics
                Genomics
                Genome Analysis
                Genome-Wide Association Studies
                Biology and Life Sciences
                Genetics
                Human Genetics
                Genome-Wide Association Studies
                Custom metadata
                Our study was approved by Scientific and Research Ethics Committee of the Medical Re-search Council (Budapest, Hungary) and North Manchester Local Research Ethics Commit-tee, Manchester. At the time the DNA samples were collected, our participant consent form did not include a paragraph regarding open access data availability. Since our participants were not in a position to give or refuse permission for public data sharing, the authors are not allowed to share individual data publicly (all group-level, summarized data are available in the manuscript and in Supplementary Information). However, reasonable data access re-quests can be made to the corresponding author ( petschnerp@ 123456yahoo.com ) or to Dr. Xenia Gonda ( gonda.xenia@ 123456med.semmelweis-univ.hu ) at the Department of Psychiatry and Psychotherapy, Semmelweis University, a key member of the NewMood (New Molecules in Mood Disorders, 2004-2009) research program who took part in data collection and can be considered as a completely independent data manager regarding this paper.

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