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Genome-wide association studies of lifetime and frequency of cannabis use in 131,895 individuals

Abstract

Cannabis is one of the most widely used drugs globally. We performed genome-wide association studies (GWASs) of lifetime (N = 131,895) and frequency (N = 73,374) of cannabis use. For lifetime cannabis use, we identified two loci, one near CADM2 (rs35827242, p = 4.63E-12) and another near GRM3 (rs12673181, p = 6.90E-09). For frequency of cannabis use, we identified one locus near CADM2 (rs4856591, p = 8.10E-09; r2 = 0.76 with rs35827242). Lifetime and frequency of cannabis use were heritable (12.88 vs. 6.63%) and genetically correlated with previous GWASs of lifetime use and cannabis use disorder (CUD), as well as other substance use and cognitive traits. Polygenic scores (PGSs) for lifetime and frequency of cannabis use predicted cannabis use phenotypes in All of Us participants. A phenome-wide association study using a PGS for lifetime cannabis use to interrogate a hospital cohort replicated prior associations with substance use and mood disorders, and uncovered novel associations with celiac and infectious diseases. This work demonstrates the utility of pre-addiction phenotypes in cannabis use genomic discovery.

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Fig. 1: GWASs of lifetime and frequency of cannabis use.
Fig. 2: SNP-based heritability and genetic correlation analysis comparisons across cannabis-related traits.
Fig. 3: Comparison of genetic correlations across anthropometric (light gray), health (medium gray), and psychiatric (dark gray) traits between lifetime cannabis use (lanes 1 and 2) and frequency of cannabis use (lanes 3 and 4).
Fig. 4: Percent proportion of lifetime, daily, and problematic cannabis use variance attributable to lifetime cannabis use PGS, frequency of cannabis use PGS, or both (joint-PGS) in European and African AoU cohorts.
Fig. 5: Forest plot of FDR-significant phenome associations with unconditioned (UC) lifetime cannabis use PGS, or with adjustment for cannabis use disorder (CUD), tobacco use disorder (TUD), or both (CUD-TUD).

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Data availability

We provide 23andMe summary statistics for the top 10,000 independent SNPs. 23andMe GWAS summary statistics will be made available through 23andMe to qualified researchers under an agreement with 23andMe that protects the privacy of the 23andMe participants. Please visit https://research.23andme.com/collaborate/#dataset-access/ for more information and to apply to access the data. We will share the Jupyter notebooks used for PGS analysis in AoU with registered All of Us researchers upon request.

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Acknowledgements

HHAT is funded by a Canadian Institute of Health Research (CIHR) Postdoctoral Fellowship (#491556). JYK is funded by a CIHR Canada Research Chair in Translational Neuropsychopharmacology. PF, the 23andMe Research Team, and SLE are employed by 23andMe, Inc. AAP is supported by NIDA (P50DA037844 and P30DA060810). SSR is funded through the National Institute on Drug Abuse (NIDA DP1DA054394) and the Tobacco-Related Disease Research Program (T32IR5226). We would like to thank the research participants and employees of 23andMe for making this work possible. Participants provided informed consent and volunteered to participate in the research online, under a protocol approved by the external AAHRPP-accredited Institutional Review Board (IRB), Ethical & Independent (E&I) Review Services. As of 2022, E&I Review Services is part of Salus IRB (https://www.versiticlinicaltrials.org/salusirb). The following members of the 23andMe Research Team contributed to this study: Stella Aslibekyan, Adam Auton, Elizabeth Babalola, Robert K. Bell, Jessica Bielenberg, Katarzyna Bryc, Emily Bullis, Daniella Coker, Gabriel Cuellar Partida, Devika Dhamija, Sayantan Das, Teresa Filshtein, Kipper Fletez-Brant, Will Freyman, Karl Heilbron, Pooja M. Gandhi, Karl Heilbron, Barry Hicks, David A. Hinds, Ethan M. Jewett, Yunxuan Jiang, Katelyn Kukar, Keng-Han Lin, Maya Lowe, Jey C. McCreight, Matthew H. McIntyre, Steven J. Micheletti, Meghan E. Moreno, Joanna L. Mountain, Priyanka Nandakumar, Elizabeth S. Noblin, Jared O’Connell, Aaron A. Petrakovitz, G. David Poznik, Morgan Schumacher, Anjali J. Shastri, Janie F. Shelton, Jingchunzi Shi, Suyash Shringarpure, Vinh Tran, Joyce Y. Tung, Xin Wang, Wei Wang, Catherine H. Weldon, Peter Wilton, Alejandro Hernandez, Corinna Wong, Christophe Toukam Tchakouté. We would also like to thank The Externalizing Consortium for sharing the GWAS summary statistics of externalizing. The Externalizing Consortium: Principal Investigators: Danielle M. Dick, Philipp Koellinger, K. Paige Harden, Abraham A. Palmer. Lead Analysts: Richard Karlsson Linnér, Travis T. Mallard, Peter B. Barr, Sandra Sanchez-Roige. Significant Contributors: Irwin D. Waldman. The Externalizing Consortium has been supported by the National Institute on Alcohol Abuse and Alcoholism (R01AA015416 -administrative supplement), and the National Institute on Drug Abuse (R01DA050721). Additional funding for investigator effort has been provided by K02AA018755, U10AA008401, P50AA022537, as well as a European Research Council Consolidator Grant (647648 EdGe to Koellinger). The content is solely the responsibility of the authors and does not necessarily represent the official views of the above funding bodies. The Externalizing Consortium would like to thank the following groups for making the research possible: 23andMe, Add Health, Vanderbilt University Medical Center’s BioVU, Collaborative Study on the Genetics of Alcoholism (COGA), the Psychiatric Genomics Consortium’s Substance Use Disorders working group, UK10K Consortium, UK Biobank, and Philadelphia Neurodevelopmental Cohort. We gratefully acknowledge All of Us participants for their contributions, without whom this research would not have been possible. We also thank the National Institutes of Health’s All of Us Research Program for making available the participant data examined in this study. The All of Us Research Program is supported by the National Institutes of Health, Office of the Director: Regional Medical Centers: 1 OT2 OD026549; 1 OT2 OD026554; 1 OT2 OD026557; 1 OT2 OD026556; 1 OT2 OD026550; 1 OT2 OD 026552; 1 OT2 OD026553; 1 OT2 OD026548; 1 OT2 OD026551; 1 OT2 OD026555; IAA #: AOD 16037; Federally Qualified Health Centers: HHSN 263201600085U; Data and Research Center: 5 U2C OD023196; Biobank: 1 U24 OD023121; The Participant Center: U24 OD023176; Participant Technology Systems Center: 1 U24 OD023163; Communications and Engagement: 3 OT2 OD023205; 3 OT2 OD023206; and Community Partners: 1 OT2 OD025277; 3 OT2 OD025315; 1 OT2 OD025337; 1 OT2 OD025276.

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SSR and AAP conceived the idea. PF and SLE contributed formal analyses and curation of 23andMe data. HHAT contributed to formal analyses, investigation, and data visualization. contributed to formal data analysis and data visualization. JJM, MVJ, RBC, and SP contributed to formal analyses. HHAT and SSR wrote the manuscript. HHAT, PF, JJM, MVJ, RBC, SP, SLE, JYK, LKD, ECJ, AAP and SSR reviewed and edited the manuscript.

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Correspondence to Sandra Sanchez-Roige.

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PF, the 23andMe Research Team, and SLE were employed by 23andMe, Inc. PF and SLE hold stock or stock options in 23andMe, Inc. The remaining authors have nothing to disclose.

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All methods were performed in accordance with the relevant guidelines and regulations. Participants provided informed consent and volunteered to participate in research online under a protocol approved by the external AAHRPP-accredited Institutional Review Board (IRB), Ethical & Independent (E&I) Review Services.

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Thorpe, H.H.A., Fontanillas, P., Meredith, J.J. et al. Genome-wide association studies of lifetime and frequency of cannabis use in 131,895 individuals. Mol Psychiatry (2025). https://doi.org/10.1038/s41380-025-03219-2

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