DMPK : Vol. 20 (2005) , No. 1 pp.24-33

Single Nucleotide Polymorphisms and Haplotypes of CYP1A2 in a Japanese Population

Akiko SOYAMA¹⁾, Yoshiro SAITO¹⁾²⁾, Nobumitsu HANIOKA¹⁾³⁾, Keiko MAEKAWA¹⁾²⁾, Kazuo KOMAMURA⁴⁾⁵⁾, Shiro KAMAKURA⁴⁾, Masafumi KITAKAZE⁴⁾, Hitonobu TOMOIKE⁴⁾, Kazuyuki UENO⁶⁾, Yu-ichi GOTO⁷⁾, Hideo KIMURA⁷⁾, Masaaki KATOH⁸⁾, Kenji SUGAI⁸⁾, Osamu SAITOH⁸⁾, Mitsuru KAWAI⁸⁾, Teiichi OHNUMA⁸⁾, Taisuke OHTSUKI⁸⁾, Chieko SUZUKI⁸⁾, Narihiro MINAMI⁷⁾⁸⁾, Naoyuki KAMATANI⁹⁾, Shogo OZAWA¹⁾¹⁰⁾ and Jun-ichi SAWADA¹⁾²⁾

1) Project Team for Pharmacogenetics, National Institute of Health Sciences
2) Division of Biochemistry and Immunochemistry, National Institute of Health Sciences
3) Faculty of Pharmaceutical Sciences, Okayama University
4) Division of Cardiology, Okayama University
5) Department of Cardiovascular Dynamics Research Institute, National Cardiovascular Center
6) Department of Pharmaceutical Sciences, Niigata University of Pharmacy and Applied Life Sciences
7) National Institute of Neuroscience, National Center of Neurology and Psychiatry
8) National Center Hospital for Mental, Nervous and Muscular Disorders, National Center of Neurology and Psychiatry
9) Division of Genomic Medicine, Department of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University
10) Division of Pharmacology, National Institute of Health Sciences

(Received: September 7, 2004)
(Accepted for publication: December 20, 2004)

Abstract:

In order to identify genetic polymorphisms and haplotype frequencies of CYP1A2 in a Japanese population, the enhancer and promoter regions, all the exons with their surrounding introns, and intron 1 were sequenced from genomic DNA from 250 Japanese subjects. Thirty-three polymorphisms were found, including 13 novel ones: 2 in the enhancer region, 5 in the exons, and 6 in the introns. The most common single nucleotide polymorphism (SNP) was -163C>A (CYP1A2^*1F allele) with a 0.628 frequency. In addition to six previously reported non-synonymous SNPs, three novel ones, 125C>G (P42R, CYP1A2^*15 allele, MPJ6_1A2032), 1130G>A (R377Q, ^*16 allele, MPJ6_1A2033), and 1367G>A (R456H, ^*8 allele, MPJ6_1A2019), were found with frequencies of 0.002, 0.002, and 0.004, respectively. No polymorphism was found in the known nuclear transcriptional factor-binding sites in the enhancer region. Based on linkage disequilibrium analysis, the CYP1A2 gene was analyzed as one haplotype block. Using the 33 detected polymorphisms, 14 haplotypes were unambiguously identified, and 17 haplotypes were inferred by aid of an expectation-maximization-based program. Among them, the second major haplotype CYP1A2^*1L is composed of -3860G>A (^*1C allele), -2467delT (^*1D allele), and -163C>A (^*1F allele). Network analysis suggested that relatively rare haplotypes were derived from three major haplotypes, ^*1A, ^*1M, and ^*1N in most cases. Our findings provide fundamental and useful information for genotyping CYP1A2 in the Japanese, and probably Asian populations.

Keywords:

CYP1A2, SNP, haplotype, Japanese