端粒酶逆转录酶启动子热点突变的ARMS-LNA-qPCR检测方法建立

目的建立一种定量检测端粒酶逆转录酶(TERT)启动子区-124bp(C/T)和-146bp(C/T)位点突变率的实时荧光定量PCR方法。方法以常规PCR扩增含有TERT热点突变位点的纯化产物作为检测标本,采用等位基因扩增阻滞原理(ARMS)的引物,并结合锁核酸(LNA)探针作为野生等位基因抑制子,建立实时荧光定量PCR的TERT启动子热点突变率检测方法(ARMS-LNA-qPCR)。在30例表观健康人确定检测下限。结果所建方法的突变率标准曲线为:-124bp(C/T)突变率%=10(0.262×ΔCt+4.325)(P<0.001,R2=0.999),-146bp(C/T)突变率%=10(0.261×△Ct+3.895)(P<0.001,R2=0.999)。在表观健康人中所确定的-124bp和-146bp检测下限分别是0.07%和0.05%。结论所建ARMS-LNA-qPCR的TERT热点突变检测方法具有定量检测突变率并适合临床常规开展的优势。采用普通PCR纯化产物作为检测标本,使得所建方法具有检测各种类型标本的普适性。     

基于PCR-金磁纳米微粒层析技术检测乙醛脱氢酶2基因多态性方法的建立及应用

目的基于"PCR-金磁纳米微粒层析法"建立用于口腔拭子样本类型的乙醛脱氢酶2(ALDH2)Glu504Lys基因分型检测技术。方法以口腔拭子为样本类型,利用ARMS-PCR技术,针对ALDH2 Glu504Lys基因设计特异性引物,在实验室PCR常规反应条件上以金磁纳米层析试纸条为检测平台对各项条件进行优化,以确定最优PCR-金磁微粒ALDH2Glu504Lys口腔拭子反应体系和PCR反应程序。收集60例口腔拭子样本,利用金磁纳米层析检测技术进行检测,并用测序结果进行验证。结果检测的60例口腔拭子样本中杂合突变型16例,野生型42例,纯合突变型2例,金磁微粒层析法检测基因分型结果与测序结果符合率100%。结论建立了基于金磁纳米微粒ALDH2 Glu504Lys口腔拭子基因检测技术,该方法具有快速、简便和准确的特点,迎合了当下POCT的发展趋势,值得临床推广和应用。     

EGFR外显子19、21突变等位基因特异性PCR检测方法的建立

目的 建立一种人表皮生成因子受体(EGFR)外显子19、21突变等位基因特异性聚合酶链反应(PCR)检测方法.方法 根据EGFR外显子19、21野生型和突变型设计特异性引物,提取健康人和非小细胞肺癌患者血中有核细胞的基因组DNA作为模板,采用等位基因特异性聚合酶链式反应扩增EGFR外显子19、21突变基因.结果 特异性引物可以扩增EGFR外显子19缺失突变的2种类型和外显子21的错义突变.结论 等位基因特异性PCR法可以用于检测人EGFR外显子19、21突变.     

自动尿液细胞DNA定量分析对泌尿系统炎症与膀胱癌的鉴别诊断价值

目的:评估尿液细胞DNA定量分析在泌尿系统肿瘤诊断中的应用价值。方法:采集92例泌尿系统炎症和39例疑似膀胱癌患者的尿液分别进行DNA定量测定、常规细胞学检验和尿液液基细胞学检查,以病理诊断为金标准,评估3种方法对泌尿系统炎症与膀胱癌的鉴别诊断价值,分析尿液细胞DNA定量与肿瘤分型的关联。结果:尿液DNA倍体分析对膀胱癌诊断的敏感性和特异性分别为88.89%和97.09%,诊断符合率为94.66%。传统尿液细胞学检验的敏感性和特异性分别为51.85%和100%,准确性为90.07%。尿液液基细胞学检查对膀胱癌诊断的敏感性和特异性分别为81.48%和99.04%,诊断符合率为95.41%。尿液DNA倍体分析结果5C细胞的个数与尿路上皮癌分型存在关联,高级别尿路上皮癌组异倍体(5C)细胞数量较低级别组显著增高。结论:尿液DNA定量分析能够较好地鉴别泌尿系统炎症与膀胱癌,较传统细胞学检验有更好的提示作用。     

多重等位基因PCR检测线粒体12S rRNA基因突变

目的 探讨多重等位基因PCR法同时检测氨基糖甙类药物性耳聋相关的线粒体12S rRNA基因A1555G和C1494T突变的临床应用价值.方法 以3种基因型(野生型、A1555G突变型和C1494T突变型)的质粒标准品为模板,分别设计针对线粒体1555和1494位点野生型和突变型的特异性引物.用多重等位基因PCR技术同时检测A1555G和C1494T突变,并初步用于138例非综合征型耳聋患者的临床基因突变检测分析,最后通过DNA测序法评估其准确性.结果 采用多重等位基因特异性PCR同时检测138例非综合征型耳聋患者中A1555G和C1494T突变的检出率为7.97%(11/138),其中,A1555G突变型10例,C1494T突变型1例;DNA测序分析检测突变型检出率为7.97%(11/138).2种方法具有极好的一致性(Kappa=1.000,P＜0.01).结论 多重等位基因PCR是一种简便、准确、有效的A1555G和C1494T突变检测方法,可用于鉴定氨基糖甙类药物性耳聋相关的线粒体12S rRNA基因突变,从而有效预防氨基糖甙类药物性耳聋的发生.

Abstract：

Objective To investigate the clinical application of multiplex allele-specific PCR assays for simultaneous detection of the mitochondrial 12S rRNA A1555G and C1494T mutations associated with aminoglycoside-induced hearing impairment.Methods Three standard plasmids of different genotypes (wild-type, A1555G mutant and C1494T mutant) were constructed for templates and allele-specific primers aiming directly at wild-type and mutant of mitochondrial DNA nt1555 and nt1494 were designed for developing a multiplex allele-specific PCR technique to detect the A1555G and C1494T mutations.Then the method was applied to clinical screening of 138 non-syndromic hearing loss subjects and confirmed by DNA sequencing.Results Multiplex allele-specific PCR was successfully applied to the detection of A1555G and C1494T mutations in a cohort of 138 Han Chinese genetically unrelated hearing-loss subjects.Finally, 11(7.97%) unrelated affected subjects harbored the A1555G and C1494T mutations in the 12S rRNA gene(10 cases for A1555G and 1 cases for C1494T), which was well consistent with results of DNA sequencing [7.97%(11/138), Kappa=1.000, P＜0.01].Conclusion This study indicates that the multiplex allele-specific PCR assay is useful, convenient and reliable in the detection of the A1555G and C1494T mutations, which could identify the subjects at risk and effectively prevent of aminoglycoside-induced hearing loss.     

循环肿瘤细胞的磁分离法建立及在肺癌EGFR-TKI治疗中的应用

目的探索磁分离循环肿瘤细胞(circulating tumor cells,CTCs)联合竞争性等位基因特异性Taq ManPCR(Cast PCR)检测表皮生长因子受体(EGFR)基因突变的可行性。方法收集12例晚期非小细胞肺癌(non-small cell lung cancer,NSCLC)患者血液样本各7.5 m L,两步法磁分离CTCs,免疫荧光染色检测上皮细胞黏附分子(Ep CAM)和细胞角蛋白(Cytokeratin)后,流式细胞术检测CTCs数量及纯度;Cast PCR检测CTCs及循环DNA中EGFR基因del EGFR19、T790M和L858R突变;用EGFR基因突变检测试剂盒(ADx-ARMS法)检测癌组织的上述位点突变。结果高表达与不表达Ep CAM的CTCs分别在6例和12例NSCLC患者中被检测出;del EGFR19、T790M和L858R突变例数分别在2例、8例和5例NSCLC患者的CTCs中被检测出,其总检出率为83.3%(10/12);2例患者的循环DNA中检出L858R突变;ADx-ARMS法检测12例NSCLC患者癌组织中上述3种突变分别是2例、5例和3例,总检出率为75.0%(9/12)。CTCs与癌组织的突变具有一致性(Kappa=0.75,P=0.007),循环DNA与癌组织的突变一致性无统计意义(Kappa=0.06,P=0.546)。结论磁分离CTCs联合Cast PCR能有效检测EGFR基因突变,值得在NSCLC患者的EGFR酪氨酸激酶抑制剂(EGFR-TKI)治疗中推广应用。     

巢式甲基化特异性聚合酶链反应在p16基因启动子过甲基化检测中的应用

目的　介绍巢式甲基化特异性聚合酶链反应 (nMSP)法 ,探讨了最佳PCR扩增条件 ,并用该法分析新鲜癌组织、石蜡包埋组织及肿瘤患者血清中p16基因启动子的甲基化状态。方法　将基因组DNA变性成为单链 ,用亚硫酸氢盐修饰单链DNA ,将所有未甲基化的胞嘧啶被转变为尿嘧啶 ,而甲基化的胞嘧啶则不变。设计针对甲基化和非甲基化等位基因特异引物 ,进行巢式聚合酶链反应扩增 ,最后经凝胶电泳检测目的片段。结果　在 3种类型的标本中都检测出了p16基因启动子甲基化。用甲基化特异性聚合酶链反应法 (MSP)和nMSP法分别检测 34例非小细胞肺癌 (NSCLC)患者血清 ,p16基因启动子甲基化阳性率分别为 5 3% (18/34)和 74 % (2 5 /34) ,nMSP法具有更高的灵敏度。结论　筑巢式甲基化特异性聚合酶链反应是一种灵敏度高、特异性强的甲基化检测方法 ,可广泛应用于不同类型标本基因启动子甲基化分析。     

用高保真DNA聚合酶介导的PCR检测β地中海贫血热点突变

目的用高保真DNA聚合酶介导的PCR检测β地中海贫血基因热点突变。方法选取已知中国人群β珠蛋白基因CD41-42、IVS-2nt654、TATAbox-28、CD17、CD71-72及CD26热点突变位点为检测靶点,分别设计3'末端与野生型基因位点或突变型基因位点完全配对的引物,并用硫化磷酸修饰,进行高保真DNA聚合酶介导的引物延伸反应。用多重PCR反应体系检测临床已知分别含CD26和TATAbox-28突变热点患者的DNA标本。结果对野生模板而言,仅有野生型等位基因相关引物有产物产生,而突变型等位基因位点特异性引物无产物产生。反之,使用突变模板,仅突变型等位基因位点相关引物有产物产生,而野生型等位基因位点特异性引物无产物产生。高保真DNA聚合酶介导的多重引物延伸反应筛查含有CD26或TATAbox-28突变的患者DNA标本时显示,突变引物混合物只有相应突变位点的产物产生,而野生引物混合物则有除突变位点以外的其他5个位点的产物产生。结论建立了基于高保真DNA聚合酶的筛查β地中海贫血基因热点突变的PCR技术。     

脊肌萎缩症家系运动神经元生存基因微小突变的鉴定

目的 建立一套运动神经元生存(SMN)基因微小突变检测体系,以评价其用于脊肌萎缩症(SMA)家系的价值.方法 采用RNA水平和基因组DNA水平双途径检测策略,用PCR-限制性片段长度多态性(RFLP)、位点特异性PCR、多重连接依赖性探针扩增(MLPA)和T克隆测序技术对2个SMA家系共7个成员行SMN基因微小突变分析.结果 用MLPA和T克隆测序技术检测家系A的SMA患者有1个拷贝的SMN1基因,其第228位密码子上存在1个无义突变L228X,该突变来源于患者父亲；家系B的SMA患者父亲有2个SMN1基因,其中1个SMN1基因存在移码突变22_23 insA.其余家系成员均为有1个SMN1基因拷贝的SMA携带者.结论 建立的SMN微小突变检测体系成功鉴定了2个SMN微小突变,为SMA家系的遗传咨询提供了可靠依据.     

Evaluation of TERT promoter mutations in urinary cell-free DNA and sediment DNA for detection of bladder cancer

BackgroundCell-free DNA (cfDNA) is proposed to be a valuable source of biomarkers in liquid biopsies for various diseases as it is supposed to partially originate from tumor cells. However, data about the diagnostic implications of cfDNA in urine for the detection of bladder cancer (BCa) is sparse.MethodsWe evaluated the usability of urinary cfDNA for diagnostic purposes compared to urine sediment DNA (sDNA) in 53 BCa patients and 36 control subjects by analyzing two abundant point-mutations (C228T/C250T) in the TERT promoter using Next-Generation Sequencing.ResultsMutations were detected in 77% of the urinary sDNA compared to 63% of the cfDNA samples. Moreover, the TERT mutation allele frequencies (MAF) were highly correlated in cfDNA and sDNA. In comparison, the accuracy of the TERT assay was higher in sDNA (84%) compared to cfDNA or voided urine cytology (both 77%). Interestingly, MAFs from leukocyte-rich urines were higher in cfDNA than in sDNA, indicating a diagnostic advantage of cfDNA in such urines.ConclusionsUrine-based mutation detection has the ability to augment and surpass voided urine cytology as the current gold-standard for the non-invasive detection and surveillance of BCa. The analysis of cell-free DNA provides no general diagnostic advantage compared to urine sediment DNA.     

中国北方人群获得性骨髓衰竭综合征患者端粒酶基因突变的研究

目的 研究中国北方人群骨髓衰竭综合征(BMF)患者端粒酶复合体基因突变发生的频率.方法 收集北方地区4家综合医院诊断明确的BMF患者90例(包括再生障碍性贫血、骨髓增生异常综合征、阵发性睡眠性血红蛋白尿症),正常对照45名.提取患者外周血DNA.PCR方法扩增TERC基因及TERT基因第一、二外显子,双脱氧核酸终止法测序.结果 90例BMF患者中发现2例TERC基因突变和2例TERT突变.TERC突变为n37 A→G和n 66G→C.TERT基因突变为n1870 G→T,造成氨基酸缺失E/*和n1780 G→T,造成氨基酸替换S/I.除TREC n37 A→G突变外,均为首次报道.其中1例TERT突变患者最终诊断为先天性角化不良(DKC),而非获得性BMF.90例患者最终确诊获得性BMF患者共89例,其中发现3例突变.中国北方BMF人群中端粒酶基因突变发生率为3.4%.结论 首次报道了我国BMF患者端粒酶基因的3种突变.中国北方人群中获得性BMF患者端粒酶复合体基因突变发生率为3.4%.端粒酶基因突变可引起端粒的缩短,可能是疾病发生的原因之一.     

家族性高胆固醇血症患者二例的LDLR基因复合杂合新突变分析

目的 探讨2例临床确诊的湖北籍FH患者的LDLR基因突变状况,为FH的基因诊断提供依据.方法 收集2例临床确诊的FH患者及其父母血脂检测指标等临床资料,通过PCR扩增LDLR基因的1～18个外显子和内含子区域,再将扩增产物进行正、反双向核苷酸序列分析,并与GenBank中LDLR基因的正常序列对比找出突变后,结合FH先证者的临床表型证实致病突变的类型.结果 氧化酶法测定1号、2号FH先证者血浆TC,分别为12.79、11.98 mmol/L;经核苷酸序列分析,其ApoB100基因涵盖的3 500～3 531区域均未见突变;LDLR基因均为复合杂合突变,1号FH先证者LDLR基因第4外显子的665位碱基G>T为杂合错义突变,且该突变为新的点突变,第9内含子的1 358+32位碱基C>T突变也为新的点突变,并均由其父母遗传.2号先证者第9外显子1 257位碱基C>A突变导致终止密码子提前出现,但其核苷酸改变与比利时报道的C>G不同,第13外显子检测到1 879位碱基G>A杂合错义突变,且分别来源于其父母.结论 2例FH先证者均存在LDLR基因复合杂合突变,1号FH先证者的第4外显子665位碱基G>T和第9内含子1 358+32位碱基C>T、2号FH先证者的第9外显子1 257位碱基C>A突变均为新突变,这可能是导致FH的分子机制.

Abstract：

Objective To determine LDLR gene mutation in 2 clinically diagnosed FH patients from Hubei province and provide basis for gene diagnosis of FH.Methods Clinical data of 2 FH patients and their parents were collected.The promoter region and exon 1 to exon 18 region of LDLR gene were amplified through PCR and the amplified products were analyzed by forward and reverse DNA sequencing.The mutations were identified after comparison with LDLR gene sequence in GenBank.The pathogenic gene mutations were confirmed according to both genotype and phenotype of FH probands.Results The levels of plasma TC of two probands were 12.79 and 11.98 mmol/L.respectively.No gene mutations were detected in region 3 500 to 3 531 of ApoB100. The mutations of LDLR gene were compound heterozygous mutations. The novel mutation 665G > T detected in the exon 4 of No. 1 proband's LDLR gene was heterozygous missense mutation. The novel mutation 1 358 +32C > T was detected in the exon 9 of No. 1 proband's LDLR gene.The mutations 665G > T ( paternal origin) and 1 358 + 32C > T ( maternal origin) were inherited from the parents. A novel mutation 1 257 C > A was detected in the exon 9 of No. 2 proband's LDLR gene, resulting the presence of a premature termination codon, which was different from 1 257 C > G reported in Belgium.Another heterozygous missense mutation 1 879 G > A was detected in exon 13. They were derived from paternal origin and maternal origin, respectively. Conclusions There are three novel gene mutations:665G >T, 1 358 +32C > T, 1 257C > A found in two probands with compound heterozygous mutations in LDLR respectively. They maybe play a potential role in FH pathogensis.     

Allele specific PCR with microfluorometry: application to the detection of del F508 mutation in cystic fibrosis.

BACKGROUND: A simple and practical screening method, allowing the mass detection of targeted DNA mutations, was developed by combined use of allele specific PCR (ASP) and subsequent fluorogenic intercalation to the amplicon. METHODS: Crude DNAs were extracted from dried blood spots (DBS) by a simple boil method. Highly specific polymerase chain reaction (PCR) amplification was achieved by adopting Taq DNA polymerase (Amersham Pharmacia) modified with TaqStart Antibody (Clontech). A fluorogenic DNA intercalator, SYBR Green I (Molecular Probes), was directly added to the PCR products and the resultant fluorescence was measured by a conventional fluorometric microplate reader, microfluorometry (MFL). RESULTS: The most common mutation in cystic fibrosis (CF), del F508, was successfully detected with clear differentiation as homozygotes (n=4) and heterozygotes (n=9) from control subjects (n=18). Fluorescence intensities, with mean+/-S.D. in arbitrary unit, were 895+/-249, 900+/-184 and 257+/-53, respectively. Those from control newborns (n=352) were 250+/-27 with the range of 188-475. CONCLUSIONS: The proposed ASP/MFL provides a simple, objective and economical detection of known mutations or single nucleotide polymorphisms (SNPs). The usefulness of this method was clearly shown in the detection of del F508 in CF.     

A locked nucleic acid clamp-mediated PCR assay for detection of a p53 codon 249 hotspot mutation in urine

Hepatocellular carcinoma (HCC) has a 5-year survival rate of <10% because it is difficult to diagnose early. Mutations in the TP53 gene are associated with approximately 50% of human cancers. A hotspot mutation, a G:C to T:A transversion at codon 249 (249T), may be a potential DNA marker for HCC screening because of its exclusive presence in HCC and its detection in the circulation of some patients with HCC. A locked nucleic acid clamp-mediated PCR assay, followed by melting curve analysis (using the SimpleProbe), was developed to detect the TP53 249T mutation. In this assay, the locked nucleic acid clamp suppressed 10(7) copies of wild-type templates and permitted detection of 249T-mutated template, with a sensitivity of 0.1% (1:1000) of the mutant/wild-type ratio, assessed by a reconstituted standard within 2 hours. With an amplicon size of 41 bp, it detects target DNA sequences in short fragmented DNA templates. The detected mutations were validated by DNA sequencing analysis. We then tested DNA isolated from urine samples of patients with HCC for p53 mutations and identified positive TP53 mutations in 9 of 17 samples. The possibility of using this novel TP53 249T assay to develop a urine or blood test for HCC screening is discussed.     

Multiplex tetra-primer amplification refractory mutation system PCR to detect 6 common germline mutations of the MUTYH gene associated with polyposis and colorectal cancer

BACKGROUND: We describe a simple tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR) for detecting MUTYH mutations, which are associated with colorectal adenomas and colorectal cancer. METHODS: We designed specific T-ARMS-PCR assays for 6 mutations (Y165C, G382D, 1395_7delGGA, Y90X, 1103delC, and R231H) selected on the basis of the frequency of their occurrence. We also designed a set of 3 multiplex T-ARMS PCR assays, each for detection of 2 mutations. We tested DNA samples from patients with attenuated or classic adenomatous polyposis coli and no detectable APC germline mutations. RESULTS: All mutations were easily detected with both the specific and multiplex T-ARMS-PCR assays. Results were confirmed by DNA HPLC analysis in all 54 patients, and each mutation was confirmed by direct DNA sequencing. CONCLUSIONS: T-ARMS-PCR does not require any special equipment, and it provides rapid, reproducible, and cost-effective detection of common MUTYH mutations. Multiplex T-ARMS-PCR allows the detection of 6 common MUTYH mutations with use of as few as 3 single tube PCR reactions. It could be useful to carry out large population-based epidemiologic studies.     

Renewable standard reference material for the detection of TP53 mutations.

BACKGROUND: Numerous DNA-based tests are currently in use or under development for the detection of mutations associated with disease. Most of the current methods use PCR amplification technologies and detection after separation or chromatography of the products. We have developed a panel of standard reference materials consisting of 12 plasmid clones containing a 2.0 kb region of the TP53 gene, including exons 5-9. Eleven of these clones contain a single mutation within the mutational hot spots of the TP53 gene, the twelfth is wild-type in this region of the gene. The mutations are amino acid (aa) 128: C to T; aa 175: G to A; aa 237: T to C; aa 245: G to A; aa 248: C to T; aa 248: G to A; aa 249: G to T; aa 273: C to T; aa 273: G to A; aa 282: C to T; and aa 328: T to C. These standard reference materials (SRMs), created by site-directed mutagenesis of wild-type TP53 from a human cell line, include the specific mutations most commonly found to be associated with cancer. Their use will improve disease detection by serving as validation materials to monitor errors in measurement methods, including PCR amplification, amplicon separation, and data analysis from different technology platforms. METHODS AND RESULTS: The single point mutations of the panel were validated by capillary electrophoresis single-strand conformational polymorphism analysis, denaturing gradient gel electrophoresis, and denaturing high-performance liquid chromatography, as well as full sequence analysis of both DNA strands of the cloned material. For both heteroduplex analysis methods, the presence of the mutations was resolved for each SRM. CONCLUSION: The generation of a standard TP53 reference panel and demonstration that the panel can successfully validate mutation detection across different mutation scanning technology platforms. Hence, this panel functions as an SRM to normalize results obtained from different laboratories using different techniques.     

Allele dropout in PCR-based diagnosis of Wilson disease: mechanisms and solutions

BACKGROUND: We investigated the mechanisms leading to allele dropout-the nonamplification of 1 of the alleles-in PCR-based diagnosis of Wilson disease (WD). METHODS: We extracted genomic DNA from blood samples from 6 WD patients (P1-P6) with allele dropouts detected in a previous study of WD in a Hong Kong Chinese population. We amplified the ATP7B gene by PCR and performed direct DNA sequencing of all exons of the ATP7B gene. To support the proposed mechanism of allele dropout, we used proofreading DNA polymerase, primer design avoiding single-nucleotide polymorphism sites, and duplex PCR. RESULTS: Patients P1-P4 were all apparently homozygous for a known disease-causing mutation, c.2975C > T (p.P992L) in exon 13. Patient P5 was apparently homozygous for a novel mutation, c.2524G > A, and patient P6 was apparently homozygous for another known mutation, c.522_523insA (p.K175K-fs). In all cases, we determined that the patients were actually heterozygous for these mutations. CONCLUSION: Our results confirm that allele dropout is the mechanism causing apparent homozygosity of heterozygous mutations in these WD patients.