Rare, low frequency and common coding variants in CHRNA5 and their contribution to nicotine dependence in European and African Americans
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The common nonsynonymous variant rs16969968 in the α5 nicotinic receptor subunit gene (CHRNA5) is the strongest genetic risk factor for nicotine dependence in European Americans and contributes to risk in African Americans. To comprehensively examine whether other CHRNA5 coding variation influences nicotine dependence risk, we performed targeted sequencing on 1582 nicotine-dependent cases (Fagerström Test for Nicotine Dependence score⩾4) and 1238 non-dependent controls, with independent replication of common and low frequency variants using 12 studies with exome chip data. Nicotine dependence was examined using logistic regression with individual common variants (minor allele frequency (MAF)⩾0.05), aggregate low frequency variants (0.05>MAF⩾0.005) and aggregate rare variants (MAF<0.005). Meta-analysis of primary results was performed with replication studies containing 12 174 heavy and 11 290 light smokers. Next-generation sequencing with 180 × coverage identified 24 nonsynonymous variants and 2 frameshift deletions in CHRNA5, including 9 novel variants in the 2820 subjects. Meta-analysis confirmed the risk effect of the only common variant (rs16969968, European ancestry: odds ratio (OR)=1.3, P=3.5 × 10(-11); African ancestry: OR=1.3, P=0.01) and demonstrated that three low frequency variants contributed an independent risk (aggregate term, European ancestry: OR=1.3, P=0.005; African ancestry: OR=1.4, P=0.0006). The remaining 22 rare coding variants were associated with increased risk of nicotine dependence in the European American primary sample (OR=12.9, P=0.01) and in the same risk direction in African Americans (OR=1.5, P=0.37). Our results indicate that common, low frequency and rare CHRNA5 coding variants are independently associated with nicotine dependence risk. These newly identified variants likely influence the risk for smoking-related diseases such as lung cancer.
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GWAS implicated α4 and α5 nicotinic receptor subunits in vulnerability to nicotine dependence and a SNP regulating trafficking and gating of AMPA-selective glutamate receptors (CNIH3) in opioid dependence.
“For example, genome-wide association studies have implicated two acetylcholine receptors, the α4 nicotinic receptor subunit157 and α5 nicotinic receptor subunit,158 in the vulnerability to nicotine dependence and a single-nucleotide polymorphism associated with regulating the trafficking and gating properties of AMPA-selective glutamate receptors (CNIH3) in opioid dependence.159”
From Neurobiology of addiction: a neurocircuitry analysis (2016) · cites this paper as [158]
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Goel, T., Raine, J., Kibat, C., Collado, J. W., Banerjee, T. D., & Mathuru, A. S. (2025) · SSRN Electronic Journal · doi:10.2139/ssrn.5374566
- Authors
- Olfson, E., Saccone, N. L., Johnson, E. O., Chen, L.-S., Culverhouse, R., Doheny, K., Foltz, S. M., Fox, L., Gogarten, S. M., Hartz, S., Hetrick, K., Laurie, C. C., Marosy, B., Amin, N., Arnett, D., Barr, R. G., Bartz, T. M., Bertelsen, S., Borecki, I. B., Brown, M. R., Chasman, D. I., van Duijn, C. M., Feitosa, M. F., Fox, E. R., Franceschini, N., Franco, O. H., Grove, M. L., Guo, X., Hofman, A., Kardia, S. L. R., Morrison, A. C., Musani, S. K., Psaty, B. M., Rao, D. C., Reiner, A. P., Rice, K., Ridker, P. M., Rose, L. M., Schick, U. M., Schwander, K., Uitterlinden, A. G., Vojinovic, D., Wang, J.-C., Ware, E. B., Wilson, G., Yao, J., Zhao, W., Breslau, N., Hatsukami, D., Stitzel, J. A., Rice, J., Goate, A., & Bierut, L. J.
- Affiliations
- Washington University in St. Louis (US)
- RTI International (US)
- Johns Hopkins University (US)
- University of Washington (US)
- Erasmus MC (NL)
- University of Alabama at Birmingham (US)
- Columbia University Irving Medical Center (US)
- Icahn School of Medicine at Mount Sinai (US)
- The University of Texas Health Science Center at Houston (US)
- Brigham and Women's Hospital (US)
- University of Mississippi Medical Center (US)
- University of North Carolina at Chapel Hill (US)
- Harbor–UCLA Medical Center (US)
- University of Michigan (US)
- Kaiser Permanente Washington Health Research Institute (US)
- Fred Hutch Cancer Center (US)
- Jackson State University (US)
- Michigan State University (US)
- University of Minnesota (US)
- University of Colorado Boulder (US)
- Corresponding author
- Bierut, L J
- ORCID
- Olfson, E
- Saccone, N L
- Johnson, E O
- Culverhouse, R
- Doheny, K
- Foltz, S M
- Fox, L
- Gogarten, S M
- Hartz, S
- Hetrick, K
- Laurie, C C
- Amin, N
- Arnett, D
- Barr, R G
- Bartz, T M
- Bertelsen, S
- Borecki, I B
- Chasman, D I
- Feitosa, M F
- Franceschini, N
- Franco, O H
- Grove, M L
- Guo, X
- Morrison, A C
- Psaty, B M
- Rao, D C
- Reiner, A P
- Rice, K
- Ridker, P M
- Rose, L M
- Schwander, K
- Uitterlinden, A G
- Ware, E B
- Wilson, G
- Yao, J
- Zhao, W
- Hatsukami, D
- Stitzel, J A
- Rice, J
- Goate, A
- Bierut, L J
- Venue
- Molecular Psychiatry
- Published
- 2015-08-04
- Volume
- 21
- Issue
- 5
- Pages
- 601-607
- ISSN
- 1359-4184 (ISSN-L)
- 1476-5578
- PMC
- PMC4740321
- OpenAlex
- W1066198400
- Cited by
- 43
- References
- 38
- Citations by year
- 2026: 1 · 2025: 3 · 2024: 3 · 2023: 3 · 2022: 3 · 2021: 1 · 2020: 4 · 2019: 2 · 2018: 9 · 2017: 5 · 2016: 8 · 2015: 1
- FWCI
- 5.65
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Molecular Psychiatry (publishedVersion)
- PubMed (publishedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (publishedVersion)
- PubMed Central (acceptedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion)
- RePub (Erasmus University Rotterdam) (submittedVersion, other-oa)
- RePub (Erasmus University Rotterdam) (submittedVersion)
- Funders
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (047.017.043)
- Nestec
- National Institutes of Health (n01hc95164-17-0-1, n01hc085082-026, n01hc085081-021, n01hc085079-024, 1r01hl120393-01a1, n01hc085083-027, n01hc95165-34-0-1, n01hc085080-026, n01hc95161-24-0-1, n01hc095169-003, UL1TR000124, HHSN268201100004C, n01hc95166-21-0-1, n01hc085086-022, n01hc95162-31-0-1, n01hc95168-27-0-1, n01hc95160-18-0-1, n01hc095167-000, HHSN268201100001C, HHSN268201100002C, 5u01hl054472-10, n01hc95163-22-0-1, 1rc2hl103010-01, n01hc55222-0-0-0, n02hl64278-6-0-0, 5r01hl043851-10, UL1TR000448, n01hc95159-40-0-1, TL1TR000449, UL1TR000040, HHSN268201100003C)
- National Institute on Alcohol Abuse and Alcoholism (F30AA023685, U10AA008401)
- National Institute on Aging (HHSN-271-2011-00004C,, R01AG055406, R01AG023629)
- National Heart, Lung, and Blood Institute (R01HL071917, HHSN268201 100012C, R01HL080467, HHSN268201300050C, HHSN268201100007I, R01HL071205, U10HL054497, N01 HC085086, HHSN268201100007C, HL-54509, HHSN268201300046C, HL 54497, N01-HC095169, R21HL123677, HL-054481, HHSN2682 01100008C, N01-HC-095165, HH-SN-268201100006C, R01HL071252, HL-54471, HHSN268201100011C, HL 54496, HL 54472, U10HL054464, HHSN2682011-00005I, HL54495, R01HL085251, HL-54515, U01-HL054472, N01 HC085079, N01 HC095163, HHSN2682011-00001I, R01‐HL043851, R01-HL120393, N01 HC085083, HHSN2682011-00002I, R01HL071259, HL-54473, HL-054457, HHSN2682011-00009I, R01 HL-59367, U10HL054509, U01HL054495, U01HL054497, N01 HC085080, R01HL087652, HHSN268201100005C, R01HL103612, R01HL068986, HHSN 268200800007C, R01HL071251, N02 HL064278, HL054464, HHSN268201300048C, HHSN268201100005G, R01HL087660, HHSN268201100010C, U10HL054473, U01HL054496, U10HL054471, RC2HL-103010, R01HL118305, N01-HC-095159, U01HL54473, N01 HC095168, N01-HC-095162, U01HL054471, R01HL119443, HHSN2682011‐00004I, N01-HC-095161, HHSN268201100011I, HHSN268201300049C, HL 103010, HL071917, HL118305, R01HL071051, R01HL071250, UC2HL103010, R01HL087641, HHSN268201200036C, R01HL059367, HHSN268201100046C, R01-HL55673, U10HL054457, U10HL054495, HHSN26820 1100009C, N01 HC095167, N01HC085082, HL119443, R01HL105756, U01HL080295, HL080467, N01-HC-095160, N01 HC055222, N01 HC095166, U01HL054457, N01 HC095164, U01HL054509, HHSN2682011-00008I, HHSN2682011-00003I, U10HL054481, N01 HC085081, HHSN268201300047C, R01HL071258, U01HL054473, U01HL054464, U10HL054515, R01HL117078, U10HL054472, R01HL055673, RC2HL102419, U01HL054481, R01HL077612, R01HL086694, U10HL054496, HL-87660)
- National Institute on Drug Abuse (K08DA032680, K08DA030398, R01DA026911, R01DA038076, R01DA025888)
- National Cancer Institute (P01CA089392, U19CA148127, CA 047988, UM1CA182913, P01 CA89392, R01CA047988, U19CA148172)
- National Institute of General Medical Sciences (T32 GM-07200, T32GM007200)
- National Institute of Diabetes and Digestive and Kidney Diseases (DK063491, R01DK089256, P30DK063491)
- National Institute of Neurological Disorders and Stroke (R01NS041558, NS041558)
- National Center for Research Resources (UL1RR025005)
- National Center for Advancing Translational Sciences
- Topics
- Health Sciences › Medicine › Physiology › Smoking Behavior and Cessation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nicotinic Acetylcholine Receptors Study
- Keywords
- CHRNA5, nicotine dependence, nicotinic acetylcholine receptors, rs16969968, non-synonymous mutations, low-frequency variants, rare variants, African Americans, European Americans, genetic risk factors, smoking, lung cancer risk, frameshift deletion
- MeSH terms
- Adult, Black or African American, Female, Humans, Male, Middle Aged, Nerve Tissue Proteins, Receptors, Nicotinic, Tobacco Use Disorder, Genetic Variation, Genetic Predisposition to Disease, White People
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