Genome-wide association study across European and African American ancestries identifies a SNP in DNMT3B contributing to nicotine dependence

D. B. Hancock; Y. Guo; G. W. Reginsson; N. C. Gaddis; S. M. Lutz; R. Sherva; A. Loukola; C. C. Minica; C. A. Markunas; Y. Han; K. A. Young; D. F. Gudbjartsson; F. Gu; D. W. McNeil; B. Qaiser; C. Glasheen; S. Olson; M. T. Landi; P. A.F. Madden; L. A. Farrer; J. Vink; N. L. Saccone; M. C. Neale; H. R. Kranzler; J. McKay; R. J. Hung; C. I. Amos; M. L. Marazita; D. I. Boomsma; T. B. Baker; J. Gelernter; J. Kaprio; N. E. Caporaso; T. E. Thorgeirsson; J. E. Hokanson; L. J. Bierut; K. Stefansson; E. O. Johnson

doi:10.1038/mp.2017.193

Genome-wide association study across European and African American ancestries identifies a SNP in DNMT3B contributing to nicotine dependence

D. B. Hancock
, Y. Guo
, G. W. Reginsson
, N. C. Gaddis
, S. M. Lutz
, R. Sherva
, A. Loukola
, C. C. Minica
, C. A. Markunas
, Y. Han
, K. A. Young
, D. F. Gudbjartsson
, F. Gu
, D. W. McNeil
, B. Qaiser
, C. Glasheen
, S. Olson
, M. T. Landi
, P. A.F. Madden
, L. A. Farrer

J. Vink, N. L. Saccone, M. C. Neale, H. R. Kranzler, J. McKay, R. J. Hung, C. I. Amos, M. L. Marazita, D. I. Boomsma, T. B. Baker, J. Gelernter, J. Kaprio, N. E. Caporaso, T. E. Thorgeirsson, J. E. Hokanson, L. J. Bierut, K. Stefansson, E. O. Johnson

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

69 Scopus citations

Abstract

Cigarette smoking is a leading cause of preventable mortality worldwide. Nicotine dependence, which reduces the likelihood of quitting smoking, is a heritable trait with firmly established associations with sequence variants in nicotine acetylcholine receptor genes and at other loci. To search for additional loci, we conducted a genome-wide association study (GWAS) meta-analysis of nicotine dependence, totaling 38,602 smokers (28,677 Europeans/European Americans and 9925 African Americans) across 15 studies. In this largest-ever GWAS meta-analysis for nicotine dependence and the largest-ever cross-ancestry GWAS meta-analysis for any smoking phenotype, we reconfirmed the well-known CHRNA5-CHRNA3-CHRNB4 genes and further yielded a novel association in the DNA methyltransferase gene DNMT3B. The intronic DNMT3B rs910083-C allele (frequency=44–77%) was associated with increased risk of nicotine dependence at P=3.7 × 10⁻⁸ (odds ratio (OR)=1.06 and 95% confidence interval (CI)=1.04–1.07 for severe vs mild dependence). The association was independently confirmed in the UK Biobank (N=48,931) using heavy vs never smoking as a proxy phenotype (P=3.6 × 10⁻⁴, OR=1.05, and 95% CI=1.02–1.08). Rs910083-C is also associated with increased risk of squamous cell lung carcinoma in the International Lung Cancer Consortium (N=60,586, meta-analysis P=0.0095, OR=1.05, and 95% CI=1.01–1.09). Moreover, rs910083-C was implicated as a cis-methylation quantitative trait locus (QTL) variant associated with higher DNMT3B methylation in fetal brain (N=166, P=2.3 × 10⁻²⁶) and a cis-expression QTL variant associated with higher DNMT3B expression in adult cerebellum from the Genotype-Tissue Expression project (N=103, P=3.0 × 10⁻⁶) and the independent Brain eQTL Almanac (N=134, P=0.028). This novel DNMT3B cis-acting QTL variant highlights the importance of genetically influenced regulation in brain on the risks of nicotine dependence, heavy smoking and consequent lung cancer.

Original language	English
Pages (from-to)	1911-1919
Number of pages	9
Journal	Molecular Psychiatry
Volume	23
Issue number	9
DOIs	https://doi.org/10.1038/mp.2017.193
State	Published - Sep 1 2018

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10.1038/mp.2017.193

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Hancock, D. B., Guo, Y., Reginsson, G. W., Gaddis, N. C., Lutz, S. M., Sherva, R., Loukola, A., Minica, C. C., Markunas, C. A., Han, Y., Young, K. A., Gudbjartsson, D. F., Gu, F., McNeil, D. W., Qaiser, B., Glasheen, C., Olson, S., Landi, M. T., Madden, P. A. F., ... Johnson, E. O. (2018). Genome-wide association study across European and African American ancestries identifies a SNP in DNMT3B contributing to nicotine dependence. Molecular Psychiatry, 23(9), 1911-1919. https://doi.org/10.1038/mp.2017.193

@article{a139a7ca76bf45e3a4e5862e61b54290,

title = "Genome-wide association study across European and African American ancestries identifies a SNP in DNMT3B contributing to nicotine dependence",

abstract = "Cigarette smoking is a leading cause of preventable mortality worldwide. Nicotine dependence, which reduces the likelihood of quitting smoking, is a heritable trait with firmly established associations with sequence variants in nicotine acetylcholine receptor genes and at other loci. To search for additional loci, we conducted a genome-wide association study (GWAS) meta-analysis of nicotine dependence, totaling 38,602 smokers (28,677 Europeans/European Americans and 9925 African Americans) across 15 studies. In this largest-ever GWAS meta-analysis for nicotine dependence and the largest-ever cross-ancestry GWAS meta-analysis for any smoking phenotype, we reconfirmed the well-known CHRNA5-CHRNA3-CHRNB4 genes and further yielded a novel association in the DNA methyltransferase gene DNMT3B. The intronic DNMT3B rs910083-C allele (frequency=44–77\%) was associated with increased risk of nicotine dependence at P=3.7 × 10−8 (odds ratio (OR)=1.06 and 95\% confidence interval (CI)=1.04–1.07 for severe vs mild dependence). The association was independently confirmed in the UK Biobank (N=48,931) using heavy vs never smoking as a proxy phenotype (P=3.6 × 10−4, OR=1.05, and 95\% CI=1.02–1.08). Rs910083-C is also associated with increased risk of squamous cell lung carcinoma in the International Lung Cancer Consortium (N=60,586, meta-analysis P=0.0095, OR=1.05, and 95\% CI=1.01–1.09). Moreover, rs910083-C was implicated as a cis-methylation quantitative trait locus (QTL) variant associated with higher DNMT3B methylation in fetal brain (N=166, P=2.3 × 10−26) and a cis-expression QTL variant associated with higher DNMT3B expression in adult cerebellum from the Genotype-Tissue Expression project (N=103, P=3.0 × 10−6) and the independent Brain eQTL Almanac (N=134, P=0.028). This novel DNMT3B cis-acting QTL variant highlights the importance of genetically influenced regulation in brain on the risks of nicotine dependence, heavy smoking and consequent lung cancer.",

author = "Hancock, \{D. B.\} and Y. Guo and Reginsson, \{G. W.\} and Gaddis, \{N. C.\} and Lutz, \{S. M.\} and R. Sherva and A. Loukola and Minica, \{C. C.\} and Markunas, \{C. A.\} and Y. Han and Young, \{K. A.\} and Gudbjartsson, \{D. F.\} and F. Gu and McNeil, \{D. W.\} and B. Qaiser and C. Glasheen and S. Olson and Landi, \{M. T.\} and Madden, \{P. A.F.\} and Farrer, \{L. A.\} and J. Vink and Saccone, \{N. L.\} and Neale, \{M. C.\} and Kranzler, \{H. R.\} and J. McKay and Hung, \{R. J.\} and Amos, \{C. I.\} and Marazita, \{M. L.\} and Boomsma, \{D. I.\} and Baker, \{T. B.\} and J. Gelernter and J. Kaprio and Caporaso, \{N. E.\} and Thorgeirsson, \{T. E.\} and Hokanson, \{J. E.\} and Bierut, \{L. J.\} and K. Stefansson and Johnson, \{E. O.\}",

note = "Publisher Copyright: {\textcopyright} 2018, Springer Nature Limited.",

year = "2018",

month = sep,

day = "1",

doi = "10.1038/mp.2017.193",

language = "English",

volume = "23",

pages = "1911--1919",

journal = "Molecular Psychiatry",

issn = "1359-4184",

number = "9",

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Hancock, DB, Guo, Y, Reginsson, GW, Gaddis, NC, Lutz, SM, Sherva, R, Loukola, A, Minica, CC, Markunas, CA, Han, Y, Young, KA, Gudbjartsson, DF, Gu, F, McNeil, DW, Qaiser, B, Glasheen, C, Olson, S, Landi, MT, Madden, PAF, Farrer, LA, Vink, J, Saccone, NL, Neale, MC, Kranzler, HR, McKay, J, Hung, RJ, Amos, CI, Marazita, ML, Boomsma, DI, Baker, TB, Gelernter, J, Kaprio, J, Caporaso, NE, Thorgeirsson, TE, Hokanson, JE, Bierut, LJ, Stefansson, K & Johnson, EO 2018, 'Genome-wide association study across European and African American ancestries identifies a SNP in DNMT3B contributing to nicotine dependence', Molecular Psychiatry, vol. 23, no. 9, pp. 1911-1919. https://doi.org/10.1038/mp.2017.193

TY - JOUR

T1 - Genome-wide association study across European and African American ancestries identifies a SNP in DNMT3B contributing to nicotine dependence

AU - Hancock, D. B.

AU - Guo, Y.

AU - Reginsson, G. W.

AU - Gaddis, N. C.

AU - Lutz, S. M.

AU - Sherva, R.

AU - Loukola, A.

AU - Minica, C. C.

AU - Markunas, C. A.

AU - Han, Y.

AU - Young, K. A.

AU - Gudbjartsson, D. F.

AU - Gu, F.

AU - McNeil, D. W.

AU - Qaiser, B.

AU - Glasheen, C.

AU - Olson, S.

AU - Landi, M. T.

AU - Madden, P. A.F.

AU - Farrer, L. A.

AU - Vink, J.

AU - Saccone, N. L.

AU - Neale, M. C.

AU - Kranzler, H. R.

AU - McKay, J.

AU - Hung, R. J.

AU - Amos, C. I.

AU - Marazita, M. L.

AU - Boomsma, D. I.

AU - Baker, T. B.

AU - Gelernter, J.

AU - Kaprio, J.

AU - Caporaso, N. E.

AU - Thorgeirsson, T. E.

AU - Hokanson, J. E.

AU - Bierut, L. J.

AU - Stefansson, K.

AU - Johnson, E. O.

PY - 2018/9/1

Y1 - 2018/9/1

N2 - Cigarette smoking is a leading cause of preventable mortality worldwide. Nicotine dependence, which reduces the likelihood of quitting smoking, is a heritable trait with firmly established associations with sequence variants in nicotine acetylcholine receptor genes and at other loci. To search for additional loci, we conducted a genome-wide association study (GWAS) meta-analysis of nicotine dependence, totaling 38,602 smokers (28,677 Europeans/European Americans and 9925 African Americans) across 15 studies. In this largest-ever GWAS meta-analysis for nicotine dependence and the largest-ever cross-ancestry GWAS meta-analysis for any smoking phenotype, we reconfirmed the well-known CHRNA5-CHRNA3-CHRNB4 genes and further yielded a novel association in the DNA methyltransferase gene DNMT3B. The intronic DNMT3B rs910083-C allele (frequency=44–77%) was associated with increased risk of nicotine dependence at P=3.7 × 10−8 (odds ratio (OR)=1.06 and 95% confidence interval (CI)=1.04–1.07 for severe vs mild dependence). The association was independently confirmed in the UK Biobank (N=48,931) using heavy vs never smoking as a proxy phenotype (P=3.6 × 10−4, OR=1.05, and 95% CI=1.02–1.08). Rs910083-C is also associated with increased risk of squamous cell lung carcinoma in the International Lung Cancer Consortium (N=60,586, meta-analysis P=0.0095, OR=1.05, and 95% CI=1.01–1.09). Moreover, rs910083-C was implicated as a cis-methylation quantitative trait locus (QTL) variant associated with higher DNMT3B methylation in fetal brain (N=166, P=2.3 × 10−26) and a cis-expression QTL variant associated with higher DNMT3B expression in adult cerebellum from the Genotype-Tissue Expression project (N=103, P=3.0 × 10−6) and the independent Brain eQTL Almanac (N=134, P=0.028). This novel DNMT3B cis-acting QTL variant highlights the importance of genetically influenced regulation in brain on the risks of nicotine dependence, heavy smoking and consequent lung cancer.

AB - Cigarette smoking is a leading cause of preventable mortality worldwide. Nicotine dependence, which reduces the likelihood of quitting smoking, is a heritable trait with firmly established associations with sequence variants in nicotine acetylcholine receptor genes and at other loci. To search for additional loci, we conducted a genome-wide association study (GWAS) meta-analysis of nicotine dependence, totaling 38,602 smokers (28,677 Europeans/European Americans and 9925 African Americans) across 15 studies. In this largest-ever GWAS meta-analysis for nicotine dependence and the largest-ever cross-ancestry GWAS meta-analysis for any smoking phenotype, we reconfirmed the well-known CHRNA5-CHRNA3-CHRNB4 genes and further yielded a novel association in the DNA methyltransferase gene DNMT3B. The intronic DNMT3B rs910083-C allele (frequency=44–77%) was associated with increased risk of nicotine dependence at P=3.7 × 10−8 (odds ratio (OR)=1.06 and 95% confidence interval (CI)=1.04–1.07 for severe vs mild dependence). The association was independently confirmed in the UK Biobank (N=48,931) using heavy vs never smoking as a proxy phenotype (P=3.6 × 10−4, OR=1.05, and 95% CI=1.02–1.08). Rs910083-C is also associated with increased risk of squamous cell lung carcinoma in the International Lung Cancer Consortium (N=60,586, meta-analysis P=0.0095, OR=1.05, and 95% CI=1.01–1.09). Moreover, rs910083-C was implicated as a cis-methylation quantitative trait locus (QTL) variant associated with higher DNMT3B methylation in fetal brain (N=166, P=2.3 × 10−26) and a cis-expression QTL variant associated with higher DNMT3B expression in adult cerebellum from the Genotype-Tissue Expression project (N=103, P=3.0 × 10−6) and the independent Brain eQTL Almanac (N=134, P=0.028). This novel DNMT3B cis-acting QTL variant highlights the importance of genetically influenced regulation in brain on the risks of nicotine dependence, heavy smoking and consequent lung cancer.

UR - https://www.scopus.com/pages/publications/85038380855

U2 - 10.1038/mp.2017.193

DO - 10.1038/mp.2017.193

M3 - Article

C2 - 28972577

AN - SCOPUS:85038380855

SN - 1359-4184

VL - 23

SP - 1911

EP - 1919

JO - Molecular Psychiatry

JF - Molecular Psychiatry

IS - 9

ER -

Genome-wide association study across European and African American ancestries identifies a SNP in DNMT3B contributing to nicotine dependence

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