Abstract
Despite an estimated heritability of ~50%, genome-wide association studies of opioid use disorder (OUD) have revealed few genome-wide significant loci. We conducted a cross-ancestry meta-analysis of OUD in the Million Veteran Program (Nā=ā425,944). In addition to known exonic variants in OPRM1 and FURIN, we identified intronic variants in RABEPK, FBXW4, NCAM1 and KCNN1. A meta-analysis including other datasets identified a locus in TSNARE1. In total, we identified 14 loci for OUD, 12 of which are novel. Significant genetic correlations were identified for 127 traits, including psychiatric disorders and other substance use-related traits. The only significantly enriched cell-type group was CNS, with gene expression enrichment in brain regions previously associated with substance use disorders. These findings increase our understanding of the biological basis of OUD and provide further evidence that it is a brain disease, which may help to reduce stigma and inform efforts to address the opioid epidemic.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 /Ā 30Ā days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
Data availability
The full summary-level association data from the meta-analysis are available through dbGaP at https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001672.
Code availability
Imputation was performed using Minimac3 (https://genome.sph.umich.edu/wiki/Minimac3). GWAS was performed using PLINK2 (https://www.cog-genomics.org/plink2). Meta-analyses were performed using METAL (https://genome.sph.umich.edu/wiki/METAL_Documentation). GCTA (https://cnsgenomics.com/software/gcta/#Overview) was used for identification of independent loci (GCTA-COJO) and gene-based analysis (GCTA-fastBAT). FUMA (https://fuma.ctglab.nl/) was used for gene association, functional enrichment and gene-set enrichment analyses. Transcriptomic analyses were performed using S-PrediXcan and S-MultiXcan (https://github.com/hakyimlab/MetaXcan). LDSC (https://github.com/bulik/ldsc) was used for heritability estimation, genetic correlation analysis (also using the CTG-VL; https://genoma.io) and heritability enrichment analyses. Trans-ancestry genetic correlation was estimated using Popcorn (https://github.com/brielin/Popcorn). PRS analyses were performed using PRS-CS (https://github.com/getian107/PRScs). PheWAS analyses were run using the PheWAS R package (https://github.com/PheWAS/PheWAS). The MendelianRandomization R package (https://cran.r-project.org/web/packages/MendelianRandomization/index.html) was used for MR analyses. Genomic SEM was conducted using the GenomicsSEM R package (https://github.com/GenomicSEM/GenomicSEM).
References
American Psychiatric Association Diagnostic and Statistical Manual of Mental Disorders (American Psychiatric Association, 2013); https://doi.org/10.1176/appi.books.9780890425596
Strang, J. et al. Opioid use disorder. Nat. Rev. Dis. Primers 6, 3 (2020).
Vowles, K. E. et al. Rates of opioid misuse, abuse, and addiction in chronic pain: a systematic review and data synthesis. Pain 156, 569ā576 (2015).
Centers for Disease Control and Prevention Vital signs: overdoses of prescription opioid pain relievers and other drugs among womenāUnited States, 1999ā2010. MMWR Morb. Mortal. Wkly Rep. 62, 537ā542 (2013).
Key Substance Use and Mental Health Indicators in the United States: Results from the 2019 National Survey on Drug Use and Health (Substance Abuse and Mental Health Services Administration, 2020); https://www.samhsa.gov/data/sites/default/files/reports/rpt29393/2019NSDUHFFRPDFWHTML/2019NSDUHFFR090120.htm
Wilson, N. Drug and opioid-involved overdose deathsāUnited States, 2017ā2018. MMWR Morb. Mortal. Wkly Rep. 69, 290ā297 (2020).
Kendler, K. S., Jacobson, K. C., Prescott, C. A. & Neale, M. C. Specificity of genetic and environmental risk factors for use and abuse/dependence of cannabis, cocaine, hallucinogens, sedatives, stimulants, and opiates in male twins. Am. J. Psychiatry 160, 687ā695 (2003).
Gelernter, J. et al. Genome-wide association study of opioid dependence: multiple associations mapped to calcium and potassium pathways. Biol. Psychiatry 76, 66ā74 (2014).
Cheng, Z. et al. Genome-wide association study identifies a regulatory variant of rgma associated with opioid dependence in European Americans. Biol. Psychiatry 84, 762ā770 (2018).
Nelson, E. C. et al. Evidence of CNIH3 involvement in opioid dependence. Mol. Psychiatry 21, 608ā614 (2016).
Polimanti, R. et al. Leveraging genome-wide data to investigate differences between opioid use vs. opioid dependence in 41,176 individuals from the Psychiatric Genomics Consortium. Mol. Psychiatry 25, 1673ā1687 (2020).
Song, W. et al. Genome-wide association analysis of opioid use disorder: a novel approach using clinical data. Drug Alcohol Depend. 217, 108276 (2020).
Zhou, H. et al. Association of OPRM1 functional coding variant with opioid use disorder: a genome-wide association study. JAMA Psychiatry 77, 1072ā1080 (2020).
Deak, J. D. et al. Genome-wide association study and multi-trait analysis of opioid use disorder identifies novel associations in 639,709 individuals of European and African ancestry. Mol. Psychiatry https://doi.org/10.1038/s41380-022-01709-1 (2022).
Sanchez-Roige, S. et al. Genome-wide association study of problematic opioid prescription use in 132,113 23andMe research participants of European ancestry. Mol. Psychiatry https://doi.org/10.1038/s41380-021-01335-3 (2021).
Gaddis, N. et al. Multi-trait genome-wide association study of opioid addiction: OPRM1 and beyond. Preprint at medRxiv https://doi.org/10.1101/2021.09.13.21263503v1 (2021).
Finucane, H. K. et al. Partitioning heritability by functional annotation using genome-wide association summary statistics. Nat. Genet. 47, 1228ā1235 (2015).
The GTEx Consortium. The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science 369, 1318ā1330 (2020).
Davydov, E. V. et al. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput. Biol. 6, e1001025 (2010).
Barbeira, A. N. et al. Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics. Nat. Commun. 9, 1825 (2018).
Barbeira, A. N. et al. Integrating predicted transcriptome from multiple tissues improves association detection. PLoS Genet. 15, e1007889 (2019).
Qi, T. et al. Identifying gene targets for brain-related traits using transcriptomic and methylomic data from blood. Nat. Commun. 9, 2282 (2018).
Bulik-Sullivan, B. K. et al. LD score regression distinguishes confounding from polygenicity in genome-wide association studies. Nat. Genet. 47, 291ā295 (2015).
Cuellar-Partida, G. et al. Complex-Trait Genetics Virtual Lab: a community-driven web platform for post-GWAS analyses. Preprint at bioRxiv https://doi.org/10.1101/518027 (2019).
Crist, R. C. & Berrettini, W. H. Pharmacogenetics of OPRM1. Pharmacol. Biochem. Behav. 123, 25ā33 (2014).
Crist, R. C., Reiner, B. C. & Berrettini, W. H. A review of opioid addiction genetics. Curr. Opin. Psychol. 27, 31ā35 (2019).
Moningka, H., Lichenstein, S. & Yip, S. W. Current understanding of the neurobiology of opioid use disorder: an overview. Curr. Behav. Neurosci. Rep. 6, 1ā11 (2019).
Gelernter, J., Kranzler, H. & Cubells, J. Genetics of two mu opioid receptor gene (OPRM1) exon I polymorphisms: population studies, and allele frequencies in alcohol- and drug-dependent subjects. Mol. Psychiatry 4, 476ā483 (1999).
Howe, K. L. et al. Ensembl 2021. Nucleic Acids Res. 49, D884āD891 (2021).
Zhang, H. et al. Association between two Āµ-opioid receptor gene (OPRM1) haplotype blocks and drug or alcohol dependence. Hum. Mol. Genet. 15, 807ā819 (2006).
Breslin, M. B. et al. Differential processing of proenkephalin by prohormone convertases 1(3) and 2 and furin. J. Biol. Chem. 268, 27084ā27093 (1993).
Christakoudi, S., Evangelou, E., Riboli, E. & Tsilidis, K. K. GWAS of allometric body-shape indices in UK Biobank identifies loci suggesting associations with morphogenesis, organogenesis, adrenal cell renewal and cancer. Sci. Rep. 11, 10688 (2021).
Liu, M. et al. Association studies of up to 1.2 million individuals yield new insights into the genetic etiology of tobacco and alcohol use. Nat. Genet. 51, 237ā244 (2019).
Grice, D. E. et al. Transcriptional profiling of C57 and DBA strains of mice in the absence and presence of morphine. BMC Genomics 8, 76 (2007).
Yu, L. et al. Activity in projection neurons from prelimbic cortex to the PVT is necessary for retrieval of morphine withdrawal memory. Cell Rep. 35, 108958 (2021).
Fujita-Hamabe, W., Nakamoto, K. & Tokuyama, S. Involvement of NCAM and FGF receptor signaling in the development of analgesic tolerance to morphine. Eur. J. Pharmacol. 672, 77ā82 (2011).
Yang, B.-Z. et al. Association of haplotypic variants in DRD2, ANKK1, TTC12 and NCAM1 to alcohol dependence in independent case control and family samples. Hum. Mol. Genet. 16, 2844ā2853 (2007).
Yang, B.-Z. et al. Haplotypic variants in DRD2, ANKK1, TTC12 and NCAM1 are associated with comorbid alcohol and drug dependence. Alcohol. Clin. Exp. Res. 32, 2117ā2127 (2008).
Pasman, J. A. et al. GWAS of lifetime cannabis use reveals new risk loci, genetic overlap with psychiatric traits, and a causal influence of schizophrenia. Nat. Neurosci. 21, 1161ā1170 (2018).
Vujkovic, M. et al. Discovery of 318 new risk loci for type 2 diabetes and related vascular outcomes among 1.4 million participants in a multi-ancestry meta-analysis. Nat. Genet. 52, 680ā691 (2020).
Lee, J. J. et al. Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals. Nat. Genet. 50, 1112ā1121 (2018).
Amare, A. T. et al. Bivariate genome-wide association analyses of the broad depression phenotype combined with major depressive disorder, bipolar disorder or schizophrenia reveal eight novel genetic loci for depression. Mol. Psychiatry 25, 1420ā1429 (2020).
Koob, G. F. Neurobiology of opioid addiction: opponent process, hyperkatifeia and negative reinforcement. Biol. Psychiatry 87, 44ā53 (2020).
Leshner, A. I. Addiction is a brain disease, and it matters. Science 278, 45ā47 (1997).
Karlsson LinnĆ©r, R. et al. Multivariate analysis of 1.5 million people identifies genetic associations with traits related to self-regulation and addiction. Nat. Neurosci. 24, 1367ā1376 (2021).
Vanyukov, M. M. et al. Common liability to addiction and āgateway hypothesisā: Theoretical, empirical and evolutionary perspective. Drug Alcohol Depend. 123, S3āS17 (2012).
Cross-Disorder Group of the Psychiatric Genomics Consortium. Genomic relationships, novel loci and pleiotropic mechanisms across eight psychiatric disorders. Cell 179, 1469ā1482 (2019).
Howell, B. A. et al. Validity of incident opioid use disorder (OUD) diagnoses in administrative data: a chart verification study. J. Gen. Intern. Med. 36, 1264ā1270 (2021).
Gaziano, J. M. et al. Million Veteran Program: a mega-biobank to study genetic influences on health and disease. J. Clin. Epidemiol. 70, 214ā223 (2016).
Delaneau, O., Zagury, J.-F., Robinson, M. R., Marchini, J. L. & Dermitzakis, E. T. Accurate, scalable and integrative haplotype estimation. Nat. Commun. 10, 5436 (2019).
Das, S. et al. Next-generation genotype imputation service and methods. Nat. Genet. 48, 1284ā1287 (2016).
Auton, A. et al. A global reference for human genetic variation. Nature 526, 68ā74 (2015).
Fang, H. et al. Harmonizing genetic ancestry and self-identified race/ethnicity in genome-wide association studies. Am. J. Hum. Genet. 105, 763ā772 (2019).
Chang, C. C. et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience 4, 7 (2015).
Willer, C. J., Li, Y. & Abecasis, G. R. METAL: fast and efficient meta-analysis of genomewide association scans. Bioinformatics 26, 2190ā2191 (2010).
Yang, J., Lee, S. H., Goddard, M. E. & Visscher, P. M. GCTA: a tool for genome-wide complex trait analysis. Am. J. Hum. Genet. 88, 76ā82 (2011).
Altshuler, D. M. et al. Integrating common and rare genetic variation in diverse human populations. Nature 467, 52ā58 (2010).
Finucane, H. K. et al. Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types. Nat. Genet. 50, 621ā629 (2018).
Bernstein, B. E. et al. The NIH Roadmap Epigenomics Mapping Consortium. Nat. Biotechnol. 28, 1045ā1048 (2010).
Watanabe, K., Taskesen, E., van Bochoven, A. & Posthuma, D. Functional mapping and annotation of genetic associations with FUMA. Nat. Commun. 8, 1826 (2017).
de Leeuw, C. A., Mooij, J. M., Heskes, T. & Posthuma, D. MAGMA: generalized gene-set analysis of GWAS data. PLoS Comput. Biol. 11, e1004219 (2015).
Bakshi, A. et al. Fast set-based association analysis using summary data from GWAS identifies novel gene loci for human complex traits. Sci. Rep. 6, 32894 (2016).
Barbeira, A. N. et al. Exploiting the GTEx resources to decipher the mechanisms at GWAS loci. Genome Biol. 22, 49 (2021).
Zhu, Z. et al. Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets. Nat. Genet. 48, 481ā487 (2016).
Aguet, F. et al. Genetic effects on gene expression across human tissues. Nature 550, 204ā213 (2017).
Fromer, M. et al. Gene expression elucidates functional impact of polygenic risk for schizophrenia. Nat. Neurosci. 19, 1442ā1453 (2016).
Ng, B. et al. An xQTL map integrates the genetic architecture of the human brainās transcriptome and epigenome. Nat. Neurosci. 20, 1418ā1426 (2017).
Freshour, S. L. et al. Integration of the DrugāGene Interaction Database (DGIdb 4.0) with open crowdsource efforts. Nucleic Acids Res. 49, D1144āD1151 (2021).
Brown, B. C., Asian Genetic Epidemiology Network Type 2 Diabetes Consortium, Ye, C. J., Price, A. L. & Zaitlen, N. Transethnic genetic-correlation estimates from summary statistics. Am. J. Hum. Genet. 99, 76ā88 (2016).
Ge, T., Chen, C.-Y., Ni, Y., Feng, Y.-C. A. & Smoller, J. W. Polygenic prediction via Bayesian regression and continuous shrinkage priors. Nat. Commun. 10, 1776 (2019).
Dennis, J. K. et al. Clinical laboratory test-wide association scan of polygenic scores identifies biomarkers of complex disease. Genome Med. 13, 6 (2021).
Grotzinger, A. D. et al. Genomic structural equation modelling provides insights into the multivariate genetic architecture of complex traits. Nat. Hum. Behav. 3, 513ā525 (2019).
Zhou, H. et al. Genome-wide meta-analysis of problematic alcohol use in 435,563 individuals yields insights into biology and relationships with other traits. Nat. Neurosci. 23, 809ā818 (2020).
Johnson, E. C. et al. A large-scale genome-wide association study meta-analysis of cannabis use disorder. Lancet Psychiatry 7, 1032ā1045 (2020).
Schizophrenia Working Group of the Psychiatric Genomics Consortium Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421ā427 (2014).
Mullins, N. et al. Genome-wide association study of more than 40,000 bipolar disorder cases provides new insights into the underlying biology. Nat. Genet. 53, 817ā829 (2021).
Howard, D. M. et al. Genome-wide meta-analysis of depression identifies 102 independent variants and highlights the importance of the prefrontal brain regions. Nat. Neurosci. 22, 343ā352 (2019).
Grove, J. et al. Identification of common genetic risk variants for autism spectrum disorder. Nat. Genet. 51, 431ā444 (2019).
Demontis, D. et al. Discovery of the first genome-wide significant risk loci for attention deficit/hyperactivity disorder. Nat. Genet. 51, 63ā75 (2019).
Yu, D. et al. Interrogating the genetic determinants of Touretteās syndrome and other tic disorders through genome-wide association studies. Am. J. Psychiatry 176, 217ā227 (2019).
International Obsessive Compulsive Disorder Foundation Genetics Collaborative (IOCDF-GC) and OCD Collaborative Genetics Association Studies (OCGAS). Revealing the complex genetic architecture of obsessive-compulsive disorder using meta-analysis. Mol. Psychiatry 23, 1181ā1188 (2018).
Acknowledgements
This work was supported by Merit Review Awards from the US Department of Veterans Affairs Biomedical Laboratory Research and Development Service (no. I01 BX003341 (to A.C.J. and H.R.K.)) and Clinical Science Research and Development Service (no. I01 CX001734 (to K.M.K.)); the VISN 4 Mental Illness Research, Education and Clinical Center (to H.R.K.); NIAAA grant K01 AA028292 (to R.L.K.); and NIDA grant DA046345 (to H.R.K.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The views expressed in this article are those of the authors and do not necessarily represent the position or policy of the Department of Veterans Affairs or the US Government.
Author information
Authors and Affiliations
Consortia
Contributions
R.L.K., H.X. and H.R.K. conceived analyses. R.L.K. and H.R.K. wrote the first draft and prepared all drafts for submission; R.L.K. accomplished primary analyses; H.X., S.T., M.N. and H.Z. conducted additional analyses; R.L.K., L.K.D., S.S.-R. and J.G. supervised additional analyses; R.V.-S., E.E.H., C.T.R., M.N., L.K.D. and S.S.-R. provided critical support regarding phenotypes and data in individual datasets; and K.M.K., A.C.J. and H.R.K. provided resource support. All authors reviewed the manuscript and approved it for submission.
Corresponding author
Ethics declarations
Competing interests
H.R.K. is a member of advisory boards for Dicerna Pharmaceuticals, Sophrosyne Pharmaceuticals and Enthion Pharmaceuticals; a consultant to Sobrera Pharmaceuticals; the recipient of research funding and medication supplies for an investigator-initiated study from Alkermes, and a member of the American Society of Clinical Psychopharmacologyās Alcohol Clinical Trials Initiative, which was supported in the last three years by Alkermes, Dicerna, Ethypharm, Lundbeck, Mitsubishi and Otsuka. J.G. and H.R.K. are holders of US patent no. 10,900,082 titled: āGenotype-guided dosing of opioid agonists,ā issued 26 January 2021. The other authors declare no competing interests.
Peer review
Peer review information
Nature Neuroscience thanks Ditte Demontis and Andrew McIntosh for their contribution to the peer review of this work.
Additional information
Publisherās note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary information
Supplementary Information
Supplementary Material and Figs. 1ā9
Rights and permissions
About this article
Cite this article
Kember, R.L., Vickers-Smith, R., Xu, H. et al. Cross-ancestry meta-analysis of opioid use disorder uncovers novel loci with predominant effects in brain regions associated with addiction. Nat Neurosci 25, 1279ā1287 (2022). https://doi.org/10.1038/s41593-022-01160-z
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41593-022-01160-z
This article is cited by
-
Medical and genetic correlates of long-term buprenorphine treatment in the electronic health records
Translational Psychiatry (2024)
-
Shared genetics of ADHD, cannabis use disorder and cannabis use and prediction of cannabis use disorder in ADHD
Nature Mental Health (2024)
-
Pleiotropy and genetically inferred causality linking multisite chronic pain to substance use disorders
Molecular Psychiatry (2024)
-
Gene Ć environment effects and mediation involving adverse childhood events, mood and anxiety disorders, and substance dependence
Nature Human Behaviour (2024)
-
Application of polygenic scores to a deeply phenotyped sample enriched for substance use disorders reveals extensive pleiotropy with psychiatric and somatic traits
Neuropsychopharmacology (2024)