title: Screening CYP3A single nucleotide polymorphisms in a Han Chinese population with a genotyping chip.
abstract: Human cytochrome P450 (CYP)3A is a major P450 enzyme found in the liver and gastrointestinal tract. It plays an important role in the metabolism of a wide variety of drugs, some endogenous steroids and harmful environmental contaminants. It has been shown that CYP3A alleles encoding enzymes with little or no activity are largely created by single nucleotide polymorphisms (SNPs) in the sequences of these genes. The most prevalent of these SNPs are often of low allelic frequency, and many are specific to certain ethnic groups. Therefore, an accurate determination of their frequency in any given ethnic population requires investigations involving large sample sizes. A genotyping chip with enzyme-colorimetric detection was developed and used for simultaneous analysis of 22 known CYP3A SNPs in 451 Han Chinese subjects. Following multiplex polymerase chain reaction and allele-specific primer extension labeling, an enzymatic colorimetry detection system was employed to visualize genotype patterns on a nylon membrane. With this robust system, accurate discrimination ratios were obtained, and approximately 9,922 genotypes were determined. We found that the major CYP3A SNPs in the Chinese subjects were CYP3A4*4 (allele frequency 2.4%), CYP3A4*5 (0.7%), CYP3A4*18A (2.7%) and CYP3A5*3C (70.2%). Most of the major CYP3A4 SNPs found in other ethnicities were not found in this study. Using these SNPs, 11 haplotypes were identified. Comparison between present and previous studies shows that CYP3A4*4 and CYP3A4*5 alleles were Chinese-specific. The genotyping chip developed in this study is an efficient, economic and accurate system for screening multiple SNPs in a large population. Application of such technology is expected to be less labor intensive and easier to adapt to specific searches when compared with other methodologies.
authors.affiliation: Institute of Basic Medical Sciences, National Cheng Kung University, College of Medicine, Tainan, Taiwan.
authors.forename: Chin-Hung
authors.initials: CH
authors.lastname: Liu
authors.forename: Konan
authors.initials: K
authors.lastname: Peck
authors.forename: Jin-Ding
authors.initials: JD
authors.lastname: Huang
authors.forename: Min-Shung
authors.initials: MS
authors.lastname: Lin
authors.forename: Chin-Hsiung
authors.initials: CH
authors.lastname: Wang
authors.forename: Wen-Pin
authors.initials: WP
authors.lastname: Hsu
authors.forename: Hong-Wen
authors.initials: HW
authors.lastname: Wang
authors.forename: Hui-Ling
authors.initials: HL
authors.lastname: Lee
authors.forename: Ming-Liang
authors.initials: ML
authors.lastname: Lai
mesh_terms: D000483:Alleles; D044466:Asian People / Q000208:ethnology* / Q000235:genetics*; D051544:Cytochrome P-450 CYP3A; D003577:Cytochrome P-450 Enzyme System / Q000097:blood / Q000235:genetics*; D005787:Gene Frequency; D005820:Genetic Testing; D006239:Haplotypes; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D011153:Population / Q000235:genetics
chemical_list: D003577:Cytochrome P-450 Enzyme System; C104464:CYP3A protein, human; C510164:CYP3A5 protein, human; D051544:Cytochrome P-450 CYP3A; C510163:CYP3A4 protein, human