Genetic Variations and Haplotypes of CYP2C19 in a Japanese Population

Abstract

Forty-eight single nucleotide variations, including 27 novel ones, were found in the 5'- regulatory region, all of the exons and their surrounding introns of CYP2C19 in 253 Japanese subjects (134 diabetic patients and 119 healthy volunteers). Identified novel variations were as follows: -2772G>A, 2767_-2760delGGTGAACA, -2720T>C, -2547delG, -2545G>T, -2545_-2544 delGC, and -2040C>T in the enhancer region; -778C>T, -777G>A, -529G>C, -189C>A, and -185A>G in the promoter region; 151A>G (S51G), 481G>C (A161P), 986G>A (R329H), 1078G>A (D360N), and 1119C>T (D373D) in the exons, and IVS1+128T>A, IVS3+163G>A, IVS4+271A>G, IVS5-49A>G, IVS6-210C>T, IVS6-196T>A, IVS6-32T>A, IVS7+84G>A, IVS7-174C>T, and IVS8+64C>T in the introns. Since we found no significant differences in the variation frequencies between healthy volunteers and diabetic patients, the data for all subjects were treated as one group in further analysis. The allele frequencies were 0.265 for IVS6-196T>A, 0.045 for -2772G>A and -2720T>C, 0.024 for -2040C>T, 0.014 for IVS7-174C>T, 0.010 for -529G>C, 0.006 for IVS1+128T>A and 481G>C (A161P), 0.004 for -2767_-2760delGGTGAACA and IVS6-210C>T, and 0.002 for the other 17 variations. In addition, the two known nonsynonymous single nucleotide polymorphisms, 681G>A (splicing defect, (*)2 allele) and 636G>A (W212X; (*)3 allele) were detected at 0.267 and 0.128 frequencies, respectively. No variation was detected in the known binding sites for constitutive androstane receptor and glucocorticoid receptor. Linkage disequilibrium analysis showed several close linkages of variations throughout the gene. By using the variations, thirty-one haplotypes of CYP2C19 and their frequencies were estimated. Our results would provide fundamental and useful information for genotyping CYP2C19 in the Japanese and probably other Asian populations.

Cytochrome 2C19 Polymorphism and Response to Adjunctive Cilostazol Versus High Maintenance-Dose Clopidogrel in Patients Undergoing Percutaneous Coronary Intervention

“…Genetic distributions of the CYP2C19 polymorphisms were similar to the published East Asian frequencies, 26 and did not significantly deviate from Hardy-Weinberg equilibrium (CYP2C19*2: Pϭ0.33 and CYP2C19*3: Pϭ0.80, respectively). As expected, [27][28][29] carriage of the CYP2C19 mutant allele (*2 or *3) was relatively high, 67.2% of total (nϭ90) (see the Appendix in the online-only Data Supplemental Table 1): 63 carriers with 1 mutant allele (47.0%: nϭ31 in the high-MD group and nϭ32 in the triple group) and 27 carriers with 2 mutant alleles (20.2%: nϭ12 in the high-MD group and nϭ15 in the triple group), and 44 wild-type homozygotes (wt/wt) (32.8%: nϭ22 in the high-MD group and nϭ22 in the triple group). There were no differences in preprocedural platelet measures between carriers of the CYP2C19*2 versus *3 variant allele (see the Appendix in the online-only Data Supplemental Tables 2 and 3).…”

“…26 Genomic DNA was extracted from leukocytes of whole-blood specimens with an extraction kit (QIAamp DNA Blood Mini Kit, Qiagen, Hilden, Germany). Because the allelic frequencies of the CYP2C19*4 to *6 are extremely rare in East Asians, 27,28 genotyping for CYP2C19*2 (rs4244285, c.681GϾA) and CYP2C19*3 (rs4986893, c.636GϾA) were conducted using single base primer extension assay using SNaPshot assay kit (Applied Biosystems, Foster City, Calif). 29 Briefly, the genomic DNA region containing 1 of the 2 single nucleotide polymorphism (SNP) was amplified with polymerase chain reaction (PCR) separately.…”

Pre-Procedural Platelet Reactivity After Clopidogrel Loading in Korean Patients Undergoing Scheduled Percutaneous Coronary Intervention

“…Because the allelic frequencies of CYP2C19 4 to 6 are extremely rare in East Asians (less than 0.4%) 20,21) , two CYP2C19 mutant alleles, CYP2C19 2 (rs4244285, c. 681G A, p. P227P) and 3 (rs4986893, c. 636G A, p. W212X), were investigated using the ABI SNaPshot reaction and the ABI 3100 automated genetic analyzer (Applied Biosystems, Foster City, CA, USA). PCR was carried out in a total volume of 10 L which contained 30 ng genomic DNA, 0.2 mol/L of each primer (with primer sequences available on request), 0.25 mmol/L of each dATP, dNTP, dTTP, and dGTP (Invitrogen, SanDiego, CA, USA), 0.5 units of Taq DNA polymerase, and 1.0 L of 10 X buffer contain-ing 25 mmol/L MgCl2 (Qiagen, Hilden, Germany).…”

The high prevalence of the poor and ultrarapid metabolite alleles of CYP2D6, CYP2C9, CYP2C19, CYP3A4, and CYP3A5 in Taiwanese population

“…Nevertheless, we could not determine whether or not these two inactive alleles are on the same chromosome or on a different one. The participants who were heterozygous with both CYP2C19*2 and *3 loci should be defined as PM according to the haplotype analysis in the Japanese population because CYP2C19*2 and *3 were suggested to exist exclusively on the same chromosome in this previous report (Fukushima-Uesaka et al 2005). In general, the PM, IM (intermediate metabolizer), EM and UM phenotypic categories correspond to two inactive alleles, one inactive allele, two normal active alleles, and two over-active alleles respectively.…”