Haplotypes with Copy Number and Single Nucleotide Polymorphisms in CYP2A6 Locus Are Associated with Smoking Quantity in a Japanese Population

Natsuhiko Kumasaka, Masayuki Aoki, Yukinori Okada, Atsushi Takahashi, Kouichi Ozaki, Taisei Mushiroda, Tomomitsu Hirota, Mayumi Tamari, Toshihiro Tanaka, Yusuke Nakamura, Naoyuki Kamatani, Michiaki Kubo

Research output: Contribution to journalArticle

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Abstract

Smoking is a major public health problem, but the genetic factors associated with smoking behaviors are not fully elucidated. Here, we have conducted an integrated genome-wide association study to identify common copy number polymorphisms (CNPs) and single nucleotide polymorphisms (SNPs) associated with the number of cigarettes smoked per day (CPD) in Japanese smokers (N = 17,158). Our analysis identified a common CNP with a strong effect on CPD (rs8102683; P = 3.8 × 10-42) in the 19q13 region, encompassing the CYP2A6 locus. After adjustment for the associated CNP, we found an additional associated SNP (rs11878604; P = 9.7 × 10-30) located 30 kb downstream of the CYP2A6 gene. Imputation of the CYP2A6 locus revealed that haplotypes underlying the CNP and the SNP corresponded to classical, functional alleles of CYP2A6 gene that regulate nicotine metabolism and explained 2% of the phenotypic variance of CPD (ANOVA F-test P = 9.5 × 10-52). These haplotypes were also associated with smoking-related diseases, including lung cancer, chronic obstructive pulmonary disease and arteriosclerosis obliterans.

Original languageEnglish
Article numbere44507
JournalPloS one
Volume7
Issue number9
DOIs
Publication statusPublished - 25-09-2012

Fingerprint

DNA Copy Number Variations
Polymorphism
Haplotypes
single nucleotide polymorphism
Single Nucleotide Polymorphism
cigarettes
haplotypes
Nucleotides
Smoking
Tobacco Products
genetic polymorphism
loci
Population
Arteriosclerosis Obliterans
Pulmonary diseases
Genes
nicotine
Genome-Wide Association Study
lung neoplasms
Nicotine

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

Kumasaka, Natsuhiko ; Aoki, Masayuki ; Okada, Yukinori ; Takahashi, Atsushi ; Ozaki, Kouichi ; Mushiroda, Taisei ; Hirota, Tomomitsu ; Tamari, Mayumi ; Tanaka, Toshihiro ; Nakamura, Yusuke ; Kamatani, Naoyuki ; Kubo, Michiaki. / Haplotypes with Copy Number and Single Nucleotide Polymorphisms in CYP2A6 Locus Are Associated with Smoking Quantity in a Japanese Population. In: PloS one. 2012 ; Vol. 7, No. 9.
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Kumasaka, N, Aoki, M, Okada, Y, Takahashi, A, Ozaki, K, Mushiroda, T, Hirota, T, Tamari, M, Tanaka, T, Nakamura, Y, Kamatani, N & Kubo, M 2012, 'Haplotypes with Copy Number and Single Nucleotide Polymorphisms in CYP2A6 Locus Are Associated with Smoking Quantity in a Japanese Population', PloS one, vol. 7, no. 9, e44507. https://doi.org/10.1371/journal.pone.0044507

Haplotypes with Copy Number and Single Nucleotide Polymorphisms in CYP2A6 Locus Are Associated with Smoking Quantity in a Japanese Population. / Kumasaka, Natsuhiko; Aoki, Masayuki; Okada, Yukinori; Takahashi, Atsushi; Ozaki, Kouichi; Mushiroda, Taisei; Hirota, Tomomitsu; Tamari, Mayumi; Tanaka, Toshihiro; Nakamura, Yusuke; Kamatani, Naoyuki; Kubo, Michiaki.

In: PloS one, Vol. 7, No. 9, e44507, 25.09.2012.

Research output: Contribution to journalArticle

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T1 - Haplotypes with Copy Number and Single Nucleotide Polymorphisms in CYP2A6 Locus Are Associated with Smoking Quantity in a Japanese Population

AU - Kumasaka, Natsuhiko

AU - Aoki, Masayuki

AU - Okada, Yukinori

AU - Takahashi, Atsushi

AU - Ozaki, Kouichi

AU - Mushiroda, Taisei

AU - Hirota, Tomomitsu

AU - Tamari, Mayumi

AU - Tanaka, Toshihiro

AU - Nakamura, Yusuke

AU - Kamatani, Naoyuki

AU - Kubo, Michiaki

PY - 2012/9/25

Y1 - 2012/9/25

N2 - Smoking is a major public health problem, but the genetic factors associated with smoking behaviors are not fully elucidated. Here, we have conducted an integrated genome-wide association study to identify common copy number polymorphisms (CNPs) and single nucleotide polymorphisms (SNPs) associated with the number of cigarettes smoked per day (CPD) in Japanese smokers (N = 17,158). Our analysis identified a common CNP with a strong effect on CPD (rs8102683; P = 3.8 × 10-42) in the 19q13 region, encompassing the CYP2A6 locus. After adjustment for the associated CNP, we found an additional associated SNP (rs11878604; P = 9.7 × 10-30) located 30 kb downstream of the CYP2A6 gene. Imputation of the CYP2A6 locus revealed that haplotypes underlying the CNP and the SNP corresponded to classical, functional alleles of CYP2A6 gene that regulate nicotine metabolism and explained 2% of the phenotypic variance of CPD (ANOVA F-test P = 9.5 × 10-52). These haplotypes were also associated with smoking-related diseases, including lung cancer, chronic obstructive pulmonary disease and arteriosclerosis obliterans.

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