焦磷酸测序技术检测SLCO1B1基因多态性方法的建立

目的:建立SLCO1B1A388G和T521C单核苷酸多态位点的焦磷酸测序方法,分析中国健康人群中分布频率。方法:制备300例健康人外周血gDNA,应用PyroMark ID焦磷酸测序仪进行多态位点分型分析。并通过重复性检验和毛细管电泳测序验证方法正确性。结果:建立了SL-CO1B1A388G和T521C多态性分析的焦磷酸测序新方法,经毛细管电泳测序验证和重复性验证,结果准确可靠。在300例标本中,388A、388G、521T、521C等位基因频率分别为28%、72%、89.5%和10.5%,符合Hardy-Weinberg平衡。结论:焦磷酸测序方法可准确、高通量、快速检测SLCO1B1A388G和T521C单核苷酸多态性,特别适宜大样本量的临床及科研批量检测需要。     

AS-PCR检测ABCG2 34G＞A多态性

目的：建立和优化检测ABCG2 34G＞A多态性的等位基因特异性PCR方法（allele-specific PCR,AS-PCR）,并对100例健康受试者进行分型检测。方法： 设计合成3＇-末端错配引物和包含内部错配位点的3＇-末端错配引物,进行AS-PCR扩增,比较两者的扩增特异性,应用AS-PCR检测100例健康受试者ABCG2 34位多态型,采用焦磷酸测序方法（pyrosequencing）进行抽样验证。结果： 含有第3位内部错配位点的3＇-末端错配引物扩增特异性明显优于含有第2位内部错配位点以及不含内部错配位点的3＇-末端错配引物。100例样本AS PCR分型结果与同批标本前期的焦磷酸测序结果一致。ABCG2 34AA,34GA和34GG型频率分别为7%、32%、61%。结论：本文所建立的AS-PCR方法在进行ABCG2 34位多态分型时,具有省时、快速和成本低等优点,经过在引物中引入内部错配位点等优化设计后,分型结果准确可靠,适合临床应用。     

焦磷酸测序技术检测LAMA5 rs944895基因多态性方法的建立

目的:建立LAMA5 rs944895基因多态性分析的焦磷酸测序方法,并分析该多态性在中国健康人群中的分布频率。方法:制备201例健康人外周血gDNA,应用PyroMark ID焦磷酸测序仪进行LAMA5 rs944895基因多态位点的焦磷酸测序,并经过重复性试验和毛细管电泳测序验证该方法的准确性。结果:建立了LAMA5rs944895基因多态性分析的焦磷酸测序新方法,检出率100%,重复性试验和毛细管电泳测序验证准确可靠。201例健康人中A等位基因频率为72.4%,G为27.6%;AA、AG、GG等位基因型频率分别为53.2%、38.3%和8.5%,符合Hardy-Weinberg平衡(P=0.55)。结论:LAMA5rs944895基因多态性分析的焦磷酸测序新方法具有快速、准确和高通量的优点,适合于在科研和临床应用中推广。     

焦磷酸测序技术检测UGT1A3和UGT2B7在中国汉族人群中的基因多态性

目的建立焦磷酸测序技术(pyrosequencing)研究二相代谢酶UGT1A3和UGT2B7基因多态性在中国汉族人群中的分布。方法应用带生物素标记扩增引物并经PCR扩增和Beads分离,制备UGT1A3和UGT2B7焦磷酸测序单倍摸板。在PYroMarkID焦磷酸测序上进行焦磷酸测序,检测233血样的DNA标本的17个SNP位点,以确定血样DNA标本的的基因型。结果 233例血样的DNA标本中,UGT1A3等位基因有9种表型,分别为UGT1A3*1*1、UGT1A3*1*2、UGT1A3*1*3、UGT1A3*1*4、UGT1A3*1*5、UGT1A3*2*3、UGT1A3*2*4、UGT1A3*3*3和UGT1A3*3*5。UGT2B7-1和UGT2B7-2各有3种基因型,分别为G/G型、G/T型、T/T和C/C型、C/T型、T/T型。结论我国汉族人群中UGT1A3和UGT2B7基因突变较高。     

Pyrosequencing检测CYP2C9^＊3基因多态性方法的建立及其可靠性研究

目的：建立基于焦磷酸测序技术（Pymsequencing）的高通量的CYP2C9^＊3突变检测方法。方法：应用带有生物素标记的扩增引物,经PCR扩增及Beads分离,制备该突变位点焦磷酸测序单链模板,并在PyroMark ID焦磷酸测序仪上进行焦磷酸测序,以经典ABI测序法测序结果作为标准对照,观察批量分析的可靠性并批量检测220例人DNA标本。结果：建立了基于焦磷酸测序技术的CYP2C9^＊3突变位点检测平台,实现了DNA标本的高通量检测。能一次获得96份DNA的CYP2C9^＊3突变位点检测结果。经重复性检测和标准的ABI测序可靠性检测,CYP2C9^＊3突变位点的突变检出率及重复率均达100％。结论：本方法可准确、高通量、快速检测CYP2C9^＊3突变,特别适宜该SNP位点批量检测需要。     

大肠癌中EGFR基因单核苷酸多态性及EGFR表达的分析

目的 探讨表皮生长因子受体(epidermal growth factor receptor,EGFR)基因外显子13G64A单核苷酸多态性及EGFR蛋白表达与大肠癌的相关性.方法 应用PCR - RFLP法结合DNA测序法对72例大肠癌患者外周血DNA中EGFR基因的外显子13G64A单核苷酸多态性位点的等位基因进行...     

焦磷酸测序技术检测k-ras基因突变方法的建立

目的:建立k-ras基因突变的焦磷酸测序方法,并分析该基因在结直肠癌中的突变率.方法:制备10份卫生部临床检验中心2013年全国k-ras基因突变检测室间质评模板DNA,对焦磷酸测序技术检测k-ras基因突变方法进行验证;制备230例结直肠癌标本gDNA,应用PyroMark Q24焦磷酸测序仪进行k-ras基因的焦磷酸测序.结果:建立了k-ras基因突变的焦磷酸测序新方法,检测正确率100％;230例结直肠癌标本中共检出基因突变型33例,总突变率14.34％ (33/230),其中12号密码子上34G＞T的突变率为1.74％ (4/230),35G ＞A的突变率为5.22％ (12/230),35G＞T的突变率为3.04％ (7/230),37G＞A的突变率为0.43％ (1/230),13号密码子上38G＞A的突变率为3.91％ (9/230).结论:k-ras基因突变的焦磷酸测序新方法具有快速、准确和高通量的优点,适合于在科研和临床基因扩增检验中推广.     

1例基因多态性与瑞舒伐他汀疗效个体差异的病例分析

目的 探讨一患者服用瑞舒伐他汀后短期降脂疗效减弱的可能原因。方法 焦磷酸测序技术检测患者ATP结合转运蛋白超家族成员2 （ABCG2）及有机阴离子转运体1B1（SLCO1B1）基因多态性。结果 患者为ABCG2 c.421 CA杂合子,SLCO1B1 c.388GG纯合子,SLCO1B1 c.521TT纯合子。结论 SLCO1B1 c.388G突变有可能与瑞舒伐他汀短期降脂疗效减弱有关。     

影响他汀类药物降脂治疗的相关基因的多态性及其与高脂血症的关系

目的观察他汀类药物降脂治疗相关的基因多态性位点CYP3A4*1G、CYP3A 5*3、MDRl C3435T、SLC21A6 A388G、SLC21A6 T521C、CYP7Al A-204C及ABCG8 T400K在河南地区的分布及其与高脂血症的关系。方法采用聚合酶链反应-限制性片断长度多态性(PCR-RFLP)和等位基因特异性-聚合酶链式反应(AS-PCR)技术对400名高脂血症病人和320名正常对照者进行基因分型。结果等位基因SLC21A6 A388G、SLC21A6 T521C、CYP3A4*1G、CYP3A5*3、MDR1 C3435T、CYP7A1 A-204C及ABCG8 400K的分布频率在高脂血症病人中分别为72.1%、16.2%、27.9%、73.7%、39.9%、34.7%和12.8%,在正常对照组中分别为71.5%、16.1%、27.4%、74.5%、39.4%、33.3%和7.4%;ABCG8 400K等位基因携带者患高脂血症的风险显著增加(OR=1.870,CI:1.259-2.777,P=0.002)。结论CYP3A5*3、MDR1 C3435T、SLC21A6 A388G、SLC21A6 T521C和ABCG8 T400K基因多态性分布可能存在地区或种族差异,ABCG8 400K等位基因是高脂血症的高风险因素。     

E-选择素基因多态性与新疆哈萨克族原发性高血压的相关性研究

目的探讨E-选择素（E-selectin）基因第2外显子＋G98T和第4外显子＋A561C位点单核苷酸多态性在新疆哈萨克族人群中的分布,并分析E-selectin基因多态性与原发性高血压的相关性。方法采用聚合酶链反应-限制性片段长度多态性（PCR-RFLP）的分析方法,检测了新疆哈萨克族人群无血缘关系的150例原发性高血压患者和150名对照者E-selectin基因＋G98T位点及＋A561C位点多态性,同时用生化分析仪检测相关生化指标。结果①新疆哈萨克族人群中E-selectin基因＋G98T多态性位点存在GG、GT二种基因型,其中以GG基因型发生频率最高（91．3％）,GT基因型频率次之（8．7％）;同时也存在AA、AC二种基因型,其中以AA基因型发生频率最高（88．0％）,AC基因型频率次之（12．0％）;②E-selectinAc基因型在高血压组和对照组间的分布差异存在显著性（X2=5．31,P〈0．025）。结论新疆哈萨克族人群中存在E-selectin＋G98T和＋A561C两位点单核苷酸多态性,其中A561C基因多态性与原发性高血压具有相关性,C等位基因可能是新疆哈萨克族原发性高血压发病的遗传易感基因。     

Genetic polymorphisms of cytochrome P450 2B6 gene in Han Chinese.

Cytochrome P450 (CYP2B6) is an important enzyme that metabolizes more than eight compounds and about 3.0% of therapeutic drugs. The genetic polymorphisms of CYP2B6 have earlier been studied in Caucasian, Japanese and Korean, but the data are lacking for Han Chinese. The aim of this study was to investigate the frequencies of allelic variants of CYP2B6 in healthy Han Chinese and compare with those in other ethnic groups reported in the literature. Polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) method was used to test the five common non-synonymous single nucleotide polymorphisms (SNPs) of CYP2B6 gene, namely, 64C>T, 516G>T, 777C>A, 785A>G and 1459C>T in unrelated healthy Han Chinese (n=193). The study demonstrated that the frequencies of 64C>T, 516G>T, 777C>A, 785A>G and 1459C>T SNPs in Han Chinese were 0.03, 0.21, 0, 0.28 and 0.003, respectively. The frequencies of all five SNPs tested in female were higher than those in male, but the statistical difference was insignificant (P>0.05). Compared to the data reported in the literature, the frequencies of common CYP2B6 allelic variants in Chinese are similar to those of other Asian populations including Japanese and Korean, but markedly different from those in Caucasians. These results indicate the presence of marked ethnic difference in CYP2B6 SNP frequencies between Chinese and Caucasian. Further studies are required to explore the impact of these SNPs of CYP2B6 gene on the clinical response (efficacy and toxicity) to drugs that are substrates for CYP2B6 in patients.     

Influence of genetic polymorphisms on intestinal expression and rifampicin-type induction of ABCC2 and on bioavailability of talinolol

OBJECTIVES: To evaluate whether ABCC2 gene polymorphisms are associated with expression and/or function of the efflux pump. METHODS: We investigated the allele frequency of ABCC2 -24C>T, -23G>A, c.1249G>A, c.1446C>G, c.1457C>T, c.2302C>T, c.2366C>T, c.3542G>T, c.3561G>A, c.3563T>A, c.3972C>T, c.4348G>A, and 4544G>A in 374 nonrelated German healthy volunteers and determined the impact on duodenal mRNA and protein content of ABCC2. For functional analysis, the disposition of intravenously (30 mg) and orally administered talinolol (100 mg) was measured among 31 individuals. Moreover, the effects of rifampicin-type induction (600 mg, 8 days) of duodenal ABCC2 were quantified in 22 participants with regard to genetic polymorphisms. RESULTS: The allele frequencies were 18.3% (-24T), 21.1% (1249A), 1.4% (1446G), 0.1% (3542T), 4.5% (3563A), 34.2% (3972T), and 4.4% (4544A); carriers of -23G>A, 1457C>T, 2302C>T, 2366C>T, 3561G>A, and 4348G>A were not identified. The -24T allele was in strong linkage with 3972T, and 3563A with 4544A, whereas 1249A was weakly linked with other variant alleles. None of the single nucleotide polymorphisms investigated influenced significantly intestinal ABCC2 mRNA and protein content. The variant ABCC2 1249G>A (V417I), however, was associated with lower oral bioavailability (P=0.001), and increased residual clearance of intravenous talinolol (P=0.021). Intestinal ABCC2 mRNA and protein expression were upregulated by rifampicin treatment, a genetic influence could be detected in only four cases heterozygote for 3563T>A or 4544G>A. CONCLUSION: The 1249G>A (V417I) polymorphism is obviously associated with higher activity of the intestinal transporter.     

Pharmacogenetics of CYP1A2, novel polymorphisms and haplotypes in three distinct Asian populations

CYP1A2 play an important role in the metabolism of many carcinogens and clinically important drugs. CYP1A2 activity has been found to be influenced by the presence of polymorphic variants which were reported to display wide interethnic variation. This study investigates the frequency distribution and linkage disequilibrium patterns of CYP1A2 genetic polymorphisms, and characterize their haplotype structures in three healthy Asian populations in Singapore (Chinese, Malay, and Indian). The entire CYP1A2 gene was screened in 126 healthy subjects from all three ethnic groups (N=42 each). A total of 25 polymorphisms was identified, of which nine were novel. The polymorphisms, -2467delT and -163C>A were detected at high frequencies in all Asian ethnic groups. Significant interethnic differences were observed in the genotypic frequency distribution of IVS2-99G>A (P<0.01) and 1548C>T (P=0.05) across the three ethnic groups while -163C>A (P=0.02) was found to differ between Chinese and Malays. Haplotype analyses revealed four to six major haplotypes in each ethnic population which accounted for more than 60% of the cumulative haplotype frequencies. Future studies should be done to investigate the functional roles of these haplotypes.     

Genetic variations and haplotypes of CYP2C19 in a Japanese population

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.     

Breast cancer resistance protein (ABCG2) and drug disposition: intestinal expression, polymorphisms and sulfasalazine as an in vivo probe

Breast cancer resistance protein (BCRP) is an efflux transporter expressed in tissues that act as barriers to drug entry. Given that single nucleotide polymorphisms (SNPs) in the ABCG2 gene encoding BCRP are common, the possibility exists that these genetic variants may be a determinant of interindividual variability in drug response. The objective of this study is to confirm the human BCRP-mediated transport of sulfasalazine in vitro, evaluate interindividual variation in BCRP expression in human intestine and to determine the role of ABCG2 SNPs to drug disposition in healthy patients using sulfasalazine as a novel in vivo probe. To evaluate these objectives, pinch biopsies were obtained from 18 patients undergoing esophagogastro-duodenoscopy or colonoscopy for determination of BCRP expression in relation to genotype. Wild-type and variant BCRP were expressed in a heterologous expression system to evaluate the effect of SNPs on cell-surface trafficking. A total of 17 healthy individuals participated in a clinical investigation to determine the effect of BCRP SNPs on sulfasalazine pharmacokinetics. In vitro, the cell surface protein expression of the common BCRP 421 C>A variant was reduced in comparison with the wild-type control. Intestinal biopsy samples revealed that BCRP protein and mRNA expression did not significantly differ between patients with 34GG/421CC versus patients with 34GG/421CA genotypes. Remarkably, in subjects with 34GG/421CA genotype, sulfasalazine area under the concentration-time curve was 2.4-fold greater compared with 34GG/421CC subjects (P<0.05). This study links commonly occurring SNPs in BCRP with significantly increased oral sulfasalazine plasma exposure in humans. Accordingly, sulfasalazine may prove to have utility as in vivo probe for assessing the clinical impact of BCRP for the disposition and efficacy of drugs.     

Pharmacogenetics of response to simvastatin in Chinese patients with hyperlipidaemia

Objective To examine the relationship of single-nucleotide polymorphisms(SNPs)in candidate genes with the lipid responses to simvastatin.Methods Chinese patients were treated with simvastatin 40 mg daily for at least 6 weeks.20 SNPs in 11 genes were genotyped.Results 95 patients age(mean±SD)57.5±10.6 years completed the treatment.The Adiponectin 45T>G polymorphism was significantly related to absolute reductions in total cholesterol(TC)and LDL-cholesterol with a trend(P=0.053)for percentage reductions in TC(TT∶TG∶GG=-38.4%∶-35.6%∶-32.6%).Similar findings were seen with LDL-Receptor(LDLR)SNPs(2052T>C and 1866C>T)with absolute reductions in TC and LDL-cholesterol significantly associated.The Breast Cancer Resistance Protein(ABCG2)421C>A polymorphism was related(P<0.05)to HDL-cholesterol response(CC∶CA∶AA=+0.50%∶-5.73%∶-11.41%).Conclusions Adiponectin,LDLR and ABCG2 SNPs had some influence on the lipid responses to simvastatin.     

Thirty novel genetic variations in the SLC29A1 gene encoding human equilibrative nucleoside transporter 1 (hENT1)

Thirty-nine genetic variations, including thirty novel ones, were found in the human SLC29A1 gene, which encodes equilibrative nucleoside transporter 1, from 256 Japanese cancer patients administered gemcitabine. The found novel variations included -8,166G>A, -81,10A>G, -7,947G>A, -7,789T>C, -5,595G>A, -3,803_-3,783delTCGGGGAGGTGGCAGTGGGCG, -3,548G>C, -3,414G>A, -1355T>C, -34C>G, IVS1+141G>A, IVS1+260C>T, IVS1-82C>T, 177C>G, IVS3-6C>T, 564C>T, IVS8+44T>C, IVS8+90T>C, IVS8+97T>C, IVS8+131C>T, IVS8+169G>A, 933T>C, 954C>T, IVS11-52G>C, IVS11-46G>A, 1,288G>A, 1,641C>G, 1,703_1,704delGT, 1812C>T, and 1861C>T. The frequencies were 0.051 for IVS8+169G>A, 0.012 for -7,947G>A, 0.006 for IVS1+141G>A and 1,703_1,704delGT, 0.004 for -8,166G>A, -8,110A>G, -3,548G>C, -1,355T>C, -34C>G, IVS8+44T>C, and 1,812C>T, and 0.002 for the other 19 variations. Among them, 177C>G and 1,288G>A resulted in amino acid substitutions Asp59Glu and Ala430Thr, respectively. Using the detected polymorphisms, linkage disequilibrium analysis was performed, and 28 haplotypes were identified or inferred. Our findings would provide fundamental and useful information for genotyping SLC29A1 in the Japanese and probably other Asian populations.     

Genetic polymorphism of bile acid CoA: amino acid N-acyltransferase in Japanese individuals

In the present study, we identified three novel single nucleotide polymorphisms (SNPs), 147C>T in exon 2 (silent), 602G>C in exon 3 (Arg201Pro), and 1134C>T in exon 4 (silent), in the gene of bile acid CoA: amino acid N-acyltransferase (BAAT) by resequencing the entire coding region and the exon-intron junctions of 100 Japanese individuals. The allelic frequencies were 0.005 for 147C>T, 0.095 for 602G>C, and 0.015 for 1134C>T. The two known SNPs, 59G>A (Arg20Gln, rs1572983) and UTR1513G>A (rs2229594), were detected at a frequency of 0.500 and 0.425, respectively. In the haplotype analysis for the 59G>A and 602G>C polymorphisms, the allelic frequency of 59G-602G, 59G-602C, 59A-602G and 59A-602C was 0.405, 0.095, 0.500 and 0.000, respectively. On the other hand, the allelic frequency of the nonsynonymous SNP 602G>C was 0.194 in a Caucasian population.     

MDR1 genetic polymorphisms and comparison of MDR1 haplotype profiles in Korean and Vietnamese populations

Two representative genetic variants of the MDR1 gene, 3435C>T and 2677G>T/A, show wide interethnic differences in its genetic polymorphism. In this study, the authors evaluated the genetic polymorphisms of MDR1 and directly compared MDR1 haplotype profiles of the Korean and Vietnamese populations. The 3435C>T and 2677G>T/A variations were analyzed in 632 Koreans and 142 Vietnamese using pyrosequencing. The allelic frequencies of 3435C>T did not significantly differ between the Korean (39.3%) and Vietnamese (36.6%) groups. However, the frequencies of mutant alleles at 2677 locus (T or A allele) showed a significant difference between Koreans (56.2%) and Vietnamese (41.9%), as the frequency of 2677A allele in the Korean subjects (17.1%) was much higher than that of the Vietnamese subjects (6.3%). Linkage analysis revealed that 2677A allele is closely linked to 3435C allele. The frequency of 2677A-3435C haplotype in Koreans was 15.4%, which was significantly higher than that found in Vietnamese subjects (6.3%). In conclusion, the frequencies of MDR1 variants and haplotype profiles showed significant differences between the Korean and Vietnamese populations, especially with respect to the 2677G>T/A variants. Because the 2677A allele was recently found to be functional in vivo and was detected at a high frequency in Koreans, the genotyping of this variant is necessary for pharmacogenetic studies of MDR1 in this population. In addition, by virtue of strong linkage disequilibrium, 2677A-3435C haplotype may help improve the predictability of MDR1 genetic polymorphism for MDR1 functional changes.