HLA—Cw基因测序分型的研究

目的建立HLA-Cw位点测序分型技术,以用于无关供/受者HLA-Cw基因配型等基础应用研究。方法对HLA-Cw位点的第2和第3外显子,设计、合成一对PCR引物和4条测序引物,探索最佳的PCR反应体系和扩增条件,采用PCR引物扩增HLA-Cw基因的第2、第3外显子和第2内含子,扩增产物经纯化后作为测序模板,进行4个测序反应,产物经酒精/EDTA/NaAc法纯化,用ABIPrismTM3100测序仪电泳检测,相关的分析软件分析HLA基因型。检测分型结果的可靠性采用基因型已知的U-CLA国际HLA室间质控的DNA样本进行验证。结果检测6例UCLA国际HLA室间质控的DNA样本,HLA-Cw等位基因型与UCLA公布的结果完全一致。结论本文的HLA-Cw基因测序分型方法准确、可靠,具有广泛的应用前景。     

HLA-Cw基因测序分型的研究

目的 建立HLA-Cw位点测序分型技术,以用于无关供/受者HLA-Cw基因配型等基础应用研究.方法 对HLA-Cw位点的第2和第3外显子,设计、合成一对PCR引物和4条测序引物,探索最佳的PCR反应体系和扩增条件,采用PCR引物扩增HLA-Cw基因的第2、第3外显子和第2内含子,扩增产物经纯化后作为测序模板,进行4个测序反应,产物经酒精/EDTA/NaAc法纯化,用ABI PrismTM3100测序仪电泳检测,相关的分析软件分析HLA基因型.检测分型结果的可靠性采用基因型已知的U-CLA国际HLA室间质控的DNA样本进行验证.结果 检测6例UCLA国际HLA室间质控的DNA样本,HLA-Cw等位基因型与UCLA公布的结果完全一致.结论 本文的HLA-Cw基因测序分型方法准确、可靠,具有广泛的应用前景.     

单细胞PCR用于HLA配型的研究

目的研究用筑巢式多重PCR技术对单细胞进行HLA配型，分析影响单细胞PCR扩增的因素。方法首先分别采用不同的细胞裂解方法制备单细胞DNA模板，然后采用多重PCR分别扩增HLA—A，B基因的第2、3外显子和第2内含子区域，HLA—DRB1基因的第2外显子区域，最后根据大量DNA的常规HLA分型结果对单细胞第1轮扩增产物进行第2轮筑巢式序列特异性引物PCR（PCR-SSP）分型。结果酶解法制备单细胞DNA模板效率最高，第1轮扩增成功率为93．3％，而碱裂法和冻融法分别为83．3％和73．3％；采用酶解法制备单细胞DNA模板进行第2轮PCR—SSP分型验证，20份标本扩增成功率为95％，有3份标本只扩增出一条染色体，等位基因脱扣发生率为15％，全部操作可在6h内完成。结论筑巢式多重PCR技术对单细胞HLA分型具有较高的扩增效率，操作时间短，可望应用于妊娠前诊断。     

IGF-1R、PRKCZ基因启动子区甲基化检测方法的探讨

目的 探讨人和小鼠的IG-1R 、PRKCZ基因启动子区DNA甲基化检测的方法.方法 用亚硫酸氢钠处理人外周血白细胞基因组DNA及小鼠骨骼肌组织中DNA标本,以修饰后的DNA为模板,对人和小鼠两个不同基因分别设计合适的引物对启动子区进行Touch-Down PCR扩增,PCR产物进行克隆测序.结果 在利用合适的引物对修饰后DNA模板进行扩增时均能扩增出目的 片段,克隆测序结果显示IGF-1R、PRKCZ基因启动子区甲基化的胞嘧啶碱基C不变,而非甲基化的胞嘧啶碱基C转变为胸腺嘧啶碱基T.结论 成功的建立了人和小鼠IGF-1R、PRKCZ基因启动子区甲基化的检测方法,为进一步探讨这两种基因启动子区甲基化与相关疾病的关系奠定基础.     

荧光杂交探针实时聚合酶链式反应快速检测甘露聚糖结合凝集素启动子区基因变异方法的建立

目的建立用荧光杂交探针实时聚合酶链式反应（Real-timePCR）检测人甘露聚糖结合凝集素（MBL）启动子区基因变异新型的基因分型法——Tm基因分型法。方法收集30例健康献血员外周抗凝全血,提取基因组DNA。通过LightCycler实时PCR仪描绘扩增的目标DNA片段的熔解曲线,根据熔解温度（Tm）峰值判定待测标本的基因变异类型。最后,用基因测序法检测PCR产物来验证Tm基因分型法的准确性。结果建立了新型的Tm基因分型法,且测定PCR产物的时间仅180min,检测结果与测序法完全吻合。结论Tm基因分型法检测人MBL启动子区基因变异快速、准确,重复性好,具有广泛的临床应用前景。     

PCR试验加样过程中无DNA原则控制污染的探讨

目的　探究在PCR操作过程中如何预防污染的一些基本操作方法。方法　首先制定了PCR操作过程中的无DNA原则 ,对实验室的划分 ,操作总原则 ,Eppendorf管开、关 ,有螺旋的离心管开、关 ,装有反应体系Eppendorf管的放置 ,标记反应管的操作 ,移液器的使用方法等进行规范化 ,最大限度地避免DNA污染反应体系。然后通过扩增新鲜扁桃体组织中珠蛋白基因及模拟手套被质粒污染的情况下扩增质粒基因 ,验证该无DNA操作过程对避免污染的有效性。结果　按本实验的规范方法进行操作 ,所有阴性对照均未出现假阳性。结论　采用这种无DNA原则进行PCR操作 ,是控制反应体系污染的一种有效方法。     

Hsa-miR-17基因启动子区PCR扩增及鉴定体系的构建

目的建立Has-miR-17编码基因启动子区的PCR扩增及鉴定体系。方法提取人源细胞系基因组DNA为实验样本,以Has-miR-17编码基因上游启动子区序列为目标序列,行序列特征分析并设计特异PCR扩增及测序引物,利用添加DMSO和使用5’加尾引物的体系优化策略建立Has-miR-17基因启动子区PCR扩增及鉴定体系并行性能评估。同时另以10例人源细胞系为样本初步验证该PCR及鉴定体系的应用效果。结果经电泳鉴定与测序分析确认在联合使用5'加尾PCR引物和5%DMSO的条件下Has-miR-17基因启动子区PCR扩增及鉴定体系已成功建立,其检测下限达10 ng/μl且特异度好、重复性佳。利用该体系成功实现对10例人源细胞株Has-miR-17基因启动子区的PCR扩增及鉴定。结论已成功建立Has-miR-17编码基因启动子区的PCR扩增及鉴定体系。     

一例供者携带的C* 03:100等位基因的测序分析

目的 检测与分析1例骨髓志愿捐献者携带的等位基因C* 03:100.方法 采用快速DNA提取试剂盒从全血样本中提取基因组DNA,经HLA-C基因商品化测序分型试剂盒扩增,纯化后的扩增产物作为模板由试剂盒配套的第2,3和4外显子正反向测序引物及自行研制的第5外显子正反向、第6外显子正向和第7外显子反向测序,经乙醇/醋酸钠/EDTA纯化的测序反应产物于ABI PrismTM 3730测序仪电泳检测.结果 将电泳后的数据导入Assign-SBT 3.5.1.45分析软件分析,分型结果为C*03:02:02,03:100.结论 临床移植配型HLA-C基因分型增加第5,6和7外显子区域的多态性检测可提高分型结果的准确性,对临床组织配型工作具有重要意义.     

实时荧光PCR实验过程污染的监测与防范

正实时荧光PCR 技术是一种实时监测PCR扩增产物,通过CT值和标准曲线的关系对待测样品中的特定DNA序列进行定量分析的方法。其优点是扩增量大、特异性强、灵敏度高、精确定量,但易污染,一直是困扰各实验室的大问题,极微量的污染就可能造成假阳性反应,导致实验结果失败。为了保证实验过程稳定、结果可靠,验证整个操作流程中是否存在污染的可能,必须进行污染的监测。通过有效地监测,采取正确的应对措施,防止或消除污染。1 对照实验是监测PCR污染的重     

单细胞人白细胞抗原多基因位点检测的配型预选性研究及意义

目的　探索单细胞扩增前引物延伸法 (PEP)全基因组扩增 ,后续多重巢式聚合酶链反应 (MN PCR)同步扩增人类白细胞抗原 (HLA) A、B和DR基因位点检测技术 ,进行配型预选研究的价值。方法　采用PEP MN PCR方法测定单个淋巴细胞和单个胚胎细胞的HLA A、B和DR基因型。结果　PEP MN PCR对单个淋巴细胞的扩增率、扩增准确率、假阴性率和假阳性率分别为 91 7%、95 7%、3 0 %和 1 7% ,而单个胚胎细胞则分别为 97 7%、97 5 %、2 3%和 2 6 % ,两种细胞检测结果比较差异均无显著性意义 (P >0 0 5 )。结论　单细胞PEP MN PCR检测HLA多基因位点有较高的扩增效率和扩增准确率 ,具有应用于植入前胚胎遗传学分析 ,筛选HLA匹配胚胎 ,提供脐血造血干细胞移植治疗同胞疾病的应用价值。     

Detection of Epstein-Barr virus DNA by polymerase chain reaction in blood and tissue biopsies from patients with Sjogren''s syndrome

Polymerase chain reaction has been used to detect increased levels of EBV DNA in salivary gland (SG) biopsies and PBL from patients with Sjogren's syndrome (SS). These results suggest that EBV, which has a normal site of latency in a small number of SG epithelial cells, may be reactivated in SS patients and provide a target for immune attack. The great sensitivity of polymerase chain reaction (PCR) and the ability to analyze very small tissue biopsies (37) make this technique well suited for clinical diagnosis. Specific methods to prevent artefactual contamination of tissue biopsy DNA with viral DNA of other samples (i.e., lyophilization of samples before DNA extraction) and the use of an internal positive control (i.e., inclusion of primers for a single copy human gene) during PCR amplification are presented. Since EBV reactivation occurs with markedly increased frequency in patients with lymphoproliferative and immunodeficiency diseases, as well as transplant recipients receiving cyclosporin A (10), rapid methods of viral detection such as PCR may allow better monitoring of medications and early detection of EBV-related lymphomas that may arise in these patients.     

Comparative semi-automated analysis of (CAG) repeats in the Huntington disease gene: use of internal standards.

Huntington disease (HD) belongs to the group of neurodegenerative disorders characterized by unstable expanded trinucleotide repeats. In the case of HD, the expansion of a CAG repeat occurs in the IT15 gene. The detection of the expanded CAG repeats has usually involved the electrophoretic separation of polymerase chain reaction (PCR) amplification products using conventional agarose and acrylamide gel electrophoresis. We have undertaken the comparative analysis of sizing CAG repeats of the IT15 gene using radioactive and fluorescent PCR amplification, and the subsequent separation of these products by slab gel and capillary electrophoresis. The assays have been performed on both cloned and sequenced CAG repeats, as well as genomic DNA from HD patients with a wide range of repeat lengths. The mobility of the CAG repeat amplification products of the IT15 gene is greater using capillary electrophoresis compared to slab gel electrophoresis. The analysis of 40 DNA samples from HD patients indicates that the mobility difference increases with the length of the repeat. However, we have devised an allele ladder for sizing the CAG repeats. This ladder provides a mandatory internal calibration system for diagnostic purposes and enables the confident use of either capillary or slab gel electrophoresis for sizing HD alleles.     

Amplification of human genomic DNA sequences with polymerase chain reaction using a single oligonucleotide primer

We present two examples of exponential nucleic acid amplification with the polymerase chain reaction (PCR) in the presence of only one amplification primer. Cloning and sequencing of the PCR products generated by amplification of human genomic DNA revealed that the amplified sequence contained only one primer and its complement, at the two ends of the PCR product. Although these experiments were performed with primers derived from the sequence of the prostate specific antigen (PSA) gene and the normal epithelial cell-specific 1 gene (NES1), the amplified sequences were novel and had no homology with either PSA or NES1 DNA. While both PSA and NES1 genes reside on chromosome 19q13.3-q13.4, the amplified sequences were found by mapping to reside on chromosome 5q12 and 5p15.1-p15.3, respectively. When we examined the mechanism of amplification by PCR using one primer in these two cases, we found that there was a high homology between the PSA primer or the NES1 primer and the two regions flanking the amplified sequence of chromosome 5q12 or 5p15. This indicated that the single PSA or NES1 primer could anneal on both strands of the DNA of that region, and mediate the exponential amplification. Since this phenomenon occurred to us twice with a limited number of different PCR reactions performed in our laboratory (< 20), we believe that it may represent a common artifact of PCR. Moreover, it appears that the palindromic primer binding sites can anneal to each other forming DNA cruciforms.     

Evaluation of loop-mediated isothermal amplification for detection of Toxoplasma gondii in water samples and comparative findings by polymerase chain reaction and immunofluorescence test (IFT)

The development and evaluation of a 1-step single-tube accelerated loop-mediated isothermal amplification (LAMP) assay for the rapid detection of Toxoplasma in water samples is described. The method has been evaluated based on the amplification of B1 and TgOWP Toxoplasma genes, and it demonstrated a sensitivity detection limit of 0.1 tachyzoites' DNA for both genes. LAMP detection was evaluated and compared with nested polymerase chain reaction (PCR) in 26 water sample pellets spiked with known numbers of Toxoplasma oocysts. After DNA extraction, the detection sensitivity in spiked pellets was 100% by LAMP and 53.8% by PCR. Subsequently, 52 natural water samples of different origin were directly investigated by 3 assays: LAMP, PCR, and immunofluorescence test (IFT). Twenty-five (48%) of 52 have been found positive for Toxoplasma DNA by LAMP, whereas nested PCR products were generated in 7 of 52 (13.5%) water samples. All 52 water samples were negative for Toxoplasma by IFT. These data clearly indicate LAMP as a rapid, specific, and sensitive tool for the detection of Toxoplasma contamination in water samples.     

Rapid differentiation of five common alpha-thalassemia genotypes by polymerase chain reaction

The alpha-thalassemias are common genetic disorders that arise from reduced synthesis of the alpha-globin chains. At present, large-scale carrier screening and clinically valuable antenatal detection programs have not been established for the congenital disorder alpha-thalassemia (alpha-thal). We have developed a simple nonradioactive polymerase chain reaction (PCR) approach that can detect and differentiate several common alpha-globin gene deletional alpha-thals regardless of the break points. When three primer sets were used--two gene-specific sets for the alpha1- and alpha2-globin genes and one set for the beta-actin gene (serving as an internal control)--PCR products from genomic DNA were simultaneously amplified and analyzed after coamplification and gel electrophoresis. The number of alpha-globin genes present in the subjects was determined by the intensity of alpha1 and alpha2 bands normalized with that of beta-actin when using densitometry. Our results demonstrate that five common genotypes of deletional alpha-thal are differentiated by the ratios of alpha1/beta-actin and alpha2/beta-actin. We also examined the feasibility of coupling this allele-specific amplification to a color-complementary assay. This easy and reproducible PCR assay is suitable for identifying alpha-thal carriers in screenings of large populations and improving genetic counseling.     

Influence of DNA target melting behavior on real-time PCR quantification

BACKGROUND: Quantitative real-time PCR is increasingly used to quantify copy numbers of nucleic acids for clinical applications. We observed that the measurements of allele imbalances of the tumor suppressor gene p16 and the oncogene ErbB-2 yielded results with variable precision under certain experimental conditions. METHODS: We used the LightCycler(TM) real-time PCR system to quantify different genomic target sequences using hybridization probes or SYBR Green for detection. RESULTS: With two primer/template systems (p16 and ErbB-2), we observed sinusoidal scattering of the threshold cycle values depending on the capillary position in the thermostated reaction chamber. This scattering depended on the denaturation temperature only when complete genomic DNA was used as template and did not occur when PCR product or restricted or boiled genomic DNA was used or the denaturation temperature in the first cycles was increased (and other targets, such as p53, HBB, IGF-1, GAPDH, and PBGD, did not show this behavior). CONCLUSIONS: Before a primer system is used for precise quantitative real-time PCR, the dependence of the quantification results on the positions of reaction tubes in the thermocycler should be tested. Our data indicate that amplification efficiencies, especially in the first cycles, depend not only on the priming efficiencies of the primers and the melting temperature of the amplicon, but also on the melting behavior of the amplicon's genomic vicinity. Complete denaturation of genomic DNA is necessary to maximize precision of quantitative PCR. Higher denaturation temperatures in the initial cycles or boiling of DNA before the PCR can improve the accuracy of quantification in some cases.     

Overcoming bacterial DNA contamination in real-time PCR and RT-PCR reactions for LacZ detection in cell therapy monitoring

Since the introduction of the polymerase chain reaction the presence of contaminating bacterial DNA in the Taq polymerase preparations has hampered the use of this technique in microbiology. Lately, this inconvenience has equally impeded gene quantification in the field of cell or gene therapy, where bacterial genes such as LacZ are often used as tags to detect vectors or cells after their injection in the recipient organism. Several means to overcome the DNA contamination of Taq Polymerase have been reported with variable degrees of decontamination efficiency and alteration of the PCR reaction. Here we propose two protocols to efficiently quantify DNA or RNA from the LacZ gene by real-time PCR using either decontamination by low concentrations of DNAse I prior to PCR amplification or a highly purified Taq Polymerase which is devoid of detectable contamination.     

巢式聚合酶链式反应检测脑脊液标本中病原体的方法评价

目的探讨巢式聚合酶链式反应(PCR)检测脑脊液标本中病原体的可行性,为疾病的快速临床诊断提供参考。方法源自细菌16S rRNA基因序列设计的巢式PCR技术方法,包括2对引物,2次PCR扩增,第1对引物首次PCR扩增脑脊液标本提取的核酸DNA,第2对引物再次PCR扩增,其DNA模板为第1轮PCR扩增产物。将第2轮PCR扩增产物进行测序,对序列进行比对分析,从而确定感染的病原体。使用DNA微量分光光度测定布鲁氏菌纯菌核酸DNA,将DNA进行倍比稀释,用于巢式PCR敏感性测试。结果巢式PCR能够检测的最低限约为1个核酸DNA拷贝数。应用巢式PCR检测40份临床患者的脑脊液标本,扩增结果表明有37份标本获得约1 460 bp的预期扩增条带(不同细菌扩增片段有差异),测序比对结果显示,检出脑膜炎奈瑟菌7份、产碱假单胞菌1份、草假单胞菌22份、嗜麦芽窄食单胞菌2份、肺炎链球菌1份、未知细菌性病原体4份、未检出3份。结论巢式PCR能够快速检测与鉴定脑脊液标本中的细菌性病原体。     

Real-time polymerase chain reaction in transfusion medicine: applications for detection of bacterial contamination in blood products

Bacterial contamination of blood components, particularly of platelet concentrates (PCs), represents the greatest infectious risk in blood transfusion. Although the incidence of platelet bacterial contamination is approximately 1 per 2,000 U, the urgent need for a method for the routine screening of PCs to improve safety for patients had not been considered for a long time. Besides the culturing systems, which will remain the criterion standard, rapid methods for sterility screening will play a more important role in transfusion medicine in the future. In particular, nucleic acid amplification techniques (NATs) are powerful potential tools for bacterial screening assays. The combination of excellent sensitivity and specificity, reduced contamination risk, ease of performance, and speed has made real-time polymerase chain reaction (PCR) technology an appealing alternative to conventional culture-based testing methods. When using real-time PCR for the detection of bacterial contamination, several points have to be considered. The main focus is the choice of the target gene; the assay format; the nucleic acid extraction method, depending on the sample type; and the evaluation of an ideal sampling strategy. However, several factors such as the availability of bacterial-derived nucleic acid amplification reagents, the impracticability, and the cost have limited the use of NATs until now. Attempts to reduce the presence of contaminating nucleic acids from reagents in real-time PCR have been described, but none of these approaches have proven to be very effective or to lower the sensitivity of the assay. Recently, a number of broad-range NAT assays targeting the 16S ribosomal DNA or 23S ribosomal RNA for the detection of bacteria based on real-time technology have been reported. This review will give a short survey of current approaches to and the limitations of the application of real-time PCR for bacterial detection in blood components, with emphasis on the bacterial contamination of PCs.     

Comparison of quantitative competitive polymerase chain reaction-enzyme-linked immunosorbent assay with LightCycler-based polymerase chain reaction for measuring cytomegalovirus DNA in patients after hematopoietic stem cell transplantation

Development of highly sensitive quantitative assays for cytomegalovirus (CMV) DNA detection is crucial for identification of immunodeficient patients at high risk of CMV disease. We designed 2 internally controlled competitive quantitative assays, enzyme-linked immunosorbent assay (ELISA)-based and real-time polymerase chain reaction (PCR) tests, using amplification of the same segment of the CMV genome. The aim of this study was to compare sensitivity, specificity, and laboratory performance characteristics of these assays. In both assays, a 159-bp segment of UL83 gene was amplified. External and internal controls were constructed by cloning the amplification product and heterogenous DNA segment flanked by target sequences for CMV-derived primers into bacterial plasmids, respectively. Real-time PCR was performed on LightCycler (Roche Diagnostics, Mannheim, Germany), and amplicons were detected using fluorescence resonance energy transfer probes. Alternatively, PCR products were labeled by digoxigenin, hybridized to immobilized probes, and detected by ELISA. The assays were tested on genomic DNA isolated from laboratory strains of CMV, QCMD control panel, and CMV DNA-positive peripheral blood DNA samples from hematopoietic stem cell transplant recipients, previously characterized by pp65 antigenemia and qualitative nested PCR. Real-time and ELISA-based PCR assays showed a linear course of 1-10(8) and 10-10(5) copies of CMV DNA per reaction, respectively. When compared with ELISA-based PCR, real-time PCR showed superiority in inter- and intra-assay reproducibility. Both assays were highly specific in detecting CMV DNA. No difference in amplification efficiency of internal or external standards and wild-type CMV DNA was found. The assays exhibited 83% concordance in CMV DNA detection from clinical samples, all discrepant samples having low CMV DNA copy numbers. There was a good correlation between viral DNA loads measured by the 2 assays. Statistically significant correlation was observed between the numbers of CMV DNA copies and pp65-positive leukocytes in the samples tested. Both variants of competitive PCR are adequately sensitive to be used for CMV DNA quantitation in clinical samples. LightCycler PCR, having superior performance characteristics and being less time-consuming, seems to be more suitable for routine diagnosis.