Genome-wide meta-analysis of problematic alcohol use in 435,563 individuals yields insights into biology and relationships with other traits

Hang Zhou; Julia M. Sealock; Sandra Sanchez-Roige; Toni Kim Clarke; Daniel F. Levey; Zhongshan Cheng; Boyang Li; Renato Polimanti; Rachel L. Kember; Rachel Vickers Smith; Johan H. Thygesen; Marsha Y. Morgan; Stephen R. Atkinson; Mark R. Thursz; Mette Nyegaard; Manuel Mattheisen; Anders D. Børglum; Emma C. Johnson; Amy C. Justice; Abraham A. Palmer; Andrew McQuillin; Lea K. Davis; Howard J. Edenberg; Arpana Agrawal; Henry R. Kranzler; Joel Gelernter

doi:10.1038/s41593-020-0643-5

Genome-wide meta-analysis of problematic alcohol use in 435,563 individuals yields insights into biology and relationships with other traits

Hang Zhou
, Julia M. Sealock
, Sandra Sanchez-Roige
, Toni Kim Clarke
, Daniel F. Levey
, Zhongshan Cheng
, Boyang Li
, Renato Polimanti
, Rachel L. Kember
, Rachel Vickers Smith
, Johan H. Thygesen
, Marsha Y. Morgan
, Stephen R. Atkinson
, Mark R. Thursz
, Mette Nyegaard
, Manuel Mattheisen
, Anders D. Børglum
, Emma C. Johnson
, Amy C. Justice
, Abraham A. Palmer

Andrew McQuillin, Lea K. Davis, Howard J. Edenberg, Arpana Agrawal, Henry R. Kranzler, Joel Gelernter

Research output: Contribution to journal › Article › peer-review

276 Scopus citations

Abstract

Problematic alcohol use (PAU) is a leading cause of death and disability worldwide. Although genome-wide association studies have identified PAU risk genes, the genetic architecture of this trait is not fully understood. We conducted a proxy-phenotype meta-analysis of PAU, combining alcohol use disorder and problematic drinking, in 435,563 European-ancestry individuals. We identified 29 independent risk variants, 19 of them novel. PAU was genetically correlated with 138 phenotypes, including substance use and psychiatric traits. Phenome-wide polygenic risk score analysis in an independent biobank sample (BioVU, n = 67,589) confirmed the genetic correlations between PAU and substance use and psychiatric disorders. Genetic heritability of PAU was enriched in brain and in conserved and regulatory genomic regions. Mendelian randomization suggested causal effects on liability to PAU of substance use, psychiatric status, risk-taking behavior and cognitive performance. In summary, this large PAU meta-analysis identified novel risk loci and revealed genetic relationships with numerous other traits.

Original language	English
Pages (from-to)	809-818
Number of pages	10
Journal	Nature Neuroscience
Volume	23
Issue number	7
DOIs	https://doi.org/10.1038/s41593-020-0643-5
State	Published - Jul 1 2020

Bibliographical note

Publisher Copyright:
© 2020, The Author(s), under exclusive licence to Springer Nature America, Inc.

Funding

This research used data from MVP, and was supported by funding from the Department of Veterans Affairs Office of Research and Development, Million Veteran Program Grant nos. I01BX003341 and I01CX001849; and the VA Cooperative Studies Program study, no. 575B. This publication does not represent the views of the Department of Veterans Affairs or the United States Government. A list of members and affiliations of MVP appears in the Supplementary Information. Supported also by NIH (NIAAA) no. P50 AA12870 (to J.G.), a NARSAD Young Investigator Grant from the Brain & Behavior Research Foundation (to H.Z.) and NIH grants nos. 5T32GM080178 (to J.M.S.) and K02DA32573 (to A.A.), and the National Institute for Healthcare Research (NIHR) Imperial Biomedical Research Centre (BRC; to S.R.A. and M.R.T.). This research also used summary data from the PGC Substance Use Disorders (SUD) working group. PGC–SUD is supported by funds from NIDA and NIMH to MH109532 and, previously, had analyst support from NIAAA to U01AA008401 (COGA). PGC–SUD gratefully acknowledges its contributing studies and the participants in those studies, without whom this effort would not be possible. This research also used individual-level/ summary data from UKB, a population-based sample of participants whose contributions we gratefully acknowledge; project ID 41910. We thank the iPSYCH-Broad Consortium for access to data on the iPSYCH cohort. The iPSYCH project is funded by the Lundbeck Foundation (nos. R102-A9118 and R155-2014-1724) and the universities and university hospitals of Aarhus and Copenhagen. Genotyping of iPSYCH samples was supported by grants from the Lundbeck Foundation and the Stanley Foundation, and The Danish National Biobank resource was supported by the Novo Nordisk Foundation. Data handling and analysis on the GenomeDK HPC facility was supported by NIMH (no. 1U01MH109514-01 to A.D.B.). High-performance computer capacity for handling and statistical analysis of iPSYCH data on the GenomeDK HPC facility was provided by the Centre for Integrative Sequencing, Aarhus University, Denmark (grant to A.D.B.). The UCL and STOPAH case samples were genotyped with funding from the NIHR BRC. UCL cases and controls were collected with UK Medical Research Council project grants nos. G9623693N, G0500791, G0701007 and G1000708, and with support from the NIHR. Genotyping of the UCL control sample was supported by grants from the Stanley Foundation. The UK Household Longitudinal Study (Understanding Society) is led by the Institute for Social and Economic Research at the University of Essex and funded by the Economic and Social Research Council. The survey was conducted by NatCen, and the genome-wide scan data were analyzed and deposited by the Wellcome Trust Sanger Institute. Information on how to access the data can be found on the Understanding Society website: https://www.understandingsociety.ac.uk/. A.M. is supported by the University College London Hospitals NHS Foundation Trust NIHR BRC.

Funders	Funder number
University College London Hospitals NHS Foundation Trust
Department of Veterans Affairs Office of Rehabilitation Research and Development
Young Investigator Grant
Economic and Social Research Council
NIHR Imperial Biomedical Research Centre
VA Boston Cooperative
National Institute for Health Research
Morgan Stanley Foundation Incorporated
National Institutes of Health (NIH)
University of London, King's College London, UK
National Alliance for Research on Schizophrenia and Depression
Million Veteran Program Science Meeting
Novo Nordisk Fonden
National Institute on Alcohol Abuse and Alcoholism	U10AA008401, P50AA012870
Brain and Behavior Research Foundation	K02DA32573, 5T32GM080178, 27835
UK Industrial Decarbonization Research and Innovation Centre	G1000708
Biomedical Laboratory Research and Development, VA Office of Research and Development	I01BX003341, 575B
National Institute of Mental Health	U01MH109514, U01MH109532
Lundbeckfonden	R155-2014-1724, R102-A9118
NIHR Maudsley Biomedical Research Centre	G0500791, G9623693N, G0701007
National Institute on Drug Abuse	K02DA032573
National Institute of General Medical Sciences DP2GM119177 Sophie Dumont National Institute of General Medical Sciences	T32GM080178
U.S. Department of Veterans Affairs	I01CX001849

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

ASJC Scopus subject areas

General Neuroscience

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10.1038/s41593-020-0643-5

Cite this

Zhou, H., Sealock, J. M., Sanchez-Roige, S., Clarke, T. K., Levey, D. F., Cheng, Z., Li, B., Polimanti, R., Kember, R. L., Smith, R. V., Thygesen, J. H., Morgan, M. Y., Atkinson, S. R., Thursz, M. R., Nyegaard, M., Mattheisen, M., Børglum, A. D., Johnson, E. C., Justice, A. C., ... Gelernter, J. (2020). Genome-wide meta-analysis of problematic alcohol use in 435,563 individuals yields insights into biology and relationships with other traits. Nature Neuroscience, 23(7), 809-818. https://doi.org/10.1038/s41593-020-0643-5

@article{54e751dea7c140c2bc024ea2dd590bab,

title = "Genome-wide meta-analysis of problematic alcohol use in 435,563 individuals yields insights into biology and relationships with other traits",

abstract = "Problematic alcohol use (PAU) is a leading cause of death and disability worldwide. Although genome-wide association studies have identified PAU risk genes, the genetic architecture of this trait is not fully understood. We conducted a proxy-phenotype meta-analysis of PAU, combining alcohol use disorder and problematic drinking, in 435,563 European-ancestry individuals. We identified 29 independent risk variants, 19 of them novel. PAU was genetically correlated with 138 phenotypes, including substance use and psychiatric traits. Phenome-wide polygenic risk score analysis in an independent biobank sample (BioVU, n = 67,589) confirmed the genetic correlations between PAU and substance use and psychiatric disorders. Genetic heritability of PAU was enriched in brain and in conserved and regulatory genomic regions. Mendelian randomization suggested causal effects on liability to PAU of substance use, psychiatric status, risk-taking behavior and cognitive performance. In summary, this large PAU meta-analysis identified novel risk loci and revealed genetic relationships with numerous other traits.",

author = "Hang Zhou and Sealock, \{Julia M.\} and Sandra Sanchez-Roige and Clarke, \{Toni Kim\} and Levey, \{Daniel F.\} and Zhongshan Cheng and Boyang Li and Renato Polimanti and Kember, \{Rachel L.\} and Smith, \{Rachel Vickers\} and Thygesen, \{Johan H.\} and Morgan, \{Marsha Y.\} and Atkinson, \{Stephen R.\} and Thursz, \{Mark R.\} and Mette Nyegaard and Manuel Mattheisen and B{\o}rglum, \{Anders D.\} and Johnson, \{Emma C.\} and Justice, \{Amy C.\} and Palmer, \{Abraham A.\} and Andrew McQuillin and Davis, \{Lea K.\} and Edenberg, \{Howard J.\} and Arpana Agrawal and Kranzler, \{Henry R.\} and Joel Gelernter",

note = "Publisher Copyright: {\textcopyright} 2020, The Author(s), under exclusive licence to Springer Nature America, Inc.",

year = "2020",

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doi = "10.1038/s41593-020-0643-5",

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Zhou, H, Sealock, JM, Sanchez-Roige, S, Clarke, TK, Levey, DF, Cheng, Z, Li, B, Polimanti, R, Kember, RL, Smith, RV, Thygesen, JH, Morgan, MY, Atkinson, SR, Thursz, MR, Nyegaard, M, Mattheisen, M, Børglum, AD, Johnson, EC, Justice, AC, Palmer, AA, McQuillin, A, Davis, LK, Edenberg, HJ, Agrawal, A, Kranzler, HR & Gelernter, J 2020, 'Genome-wide meta-analysis of problematic alcohol use in 435,563 individuals yields insights into biology and relationships with other traits', Nature Neuroscience, vol. 23, no. 7, pp. 809-818. https://doi.org/10.1038/s41593-020-0643-5

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T1 - Genome-wide meta-analysis of problematic alcohol use in 435,563 individuals yields insights into biology and relationships with other traits

AU - Zhou, Hang

AU - Sealock, Julia M.

AU - Sanchez-Roige, Sandra

AU - Clarke, Toni Kim

AU - Levey, Daniel F.

AU - Cheng, Zhongshan

AU - Li, Boyang

AU - Polimanti, Renato

AU - Kember, Rachel L.

AU - Smith, Rachel Vickers

AU - Thygesen, Johan H.

AU - Morgan, Marsha Y.

AU - Atkinson, Stephen R.

AU - Thursz, Mark R.

AU - Nyegaard, Mette

AU - Mattheisen, Manuel

AU - Børglum, Anders D.

AU - Johnson, Emma C.

AU - Justice, Amy C.

AU - Palmer, Abraham A.

AU - McQuillin, Andrew

AU - Davis, Lea K.

AU - Edenberg, Howard J.

AU - Agrawal, Arpana

AU - Kranzler, Henry R.

AU - Gelernter, Joel

PY - 2020/7/1

Y1 - 2020/7/1

N2 - Problematic alcohol use (PAU) is a leading cause of death and disability worldwide. Although genome-wide association studies have identified PAU risk genes, the genetic architecture of this trait is not fully understood. We conducted a proxy-phenotype meta-analysis of PAU, combining alcohol use disorder and problematic drinking, in 435,563 European-ancestry individuals. We identified 29 independent risk variants, 19 of them novel. PAU was genetically correlated with 138 phenotypes, including substance use and psychiatric traits. Phenome-wide polygenic risk score analysis in an independent biobank sample (BioVU, n = 67,589) confirmed the genetic correlations between PAU and substance use and psychiatric disorders. Genetic heritability of PAU was enriched in brain and in conserved and regulatory genomic regions. Mendelian randomization suggested causal effects on liability to PAU of substance use, psychiatric status, risk-taking behavior and cognitive performance. In summary, this large PAU meta-analysis identified novel risk loci and revealed genetic relationships with numerous other traits.

AB - Problematic alcohol use (PAU) is a leading cause of death and disability worldwide. Although genome-wide association studies have identified PAU risk genes, the genetic architecture of this trait is not fully understood. We conducted a proxy-phenotype meta-analysis of PAU, combining alcohol use disorder and problematic drinking, in 435,563 European-ancestry individuals. We identified 29 independent risk variants, 19 of them novel. PAU was genetically correlated with 138 phenotypes, including substance use and psychiatric traits. Phenome-wide polygenic risk score analysis in an independent biobank sample (BioVU, n = 67,589) confirmed the genetic correlations between PAU and substance use and psychiatric disorders. Genetic heritability of PAU was enriched in brain and in conserved and regulatory genomic regions. Mendelian randomization suggested causal effects on liability to PAU of substance use, psychiatric status, risk-taking behavior and cognitive performance. In summary, this large PAU meta-analysis identified novel risk loci and revealed genetic relationships with numerous other traits.

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ER -

Genome-wide meta-analysis of problematic alcohol use in 435,563 individuals yields insights into biology and relationships with other traits

Abstract

Bibliographical note

Funding

UN SDGs

ASJC Scopus subject areas

Access to Document

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