单细胞PCR用于HLA分型的研究

目的 探讨单细胞PCR用于妊娠前HLA诊断分型.方法 分别采用碱、蛋白酶和冻融裂解法制备单细胞DNA模板,然后采用多重PCR分别扩增HLA-A,HLA-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.结果 酶裂解法可有效制备单细胞DNA模板,单细胞DNA扩增成功率95%,所设计引物可有效扩增HLA-A、B和DrB1序列,全部操作可在6 h内完成.结论 本研究建立的巢式多重PCR技术对单细胞HLA分型具有较高的扩增效率,操作时间短,可望应用于临床妊娠前诊断.     

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.     

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。     

PCR—SBT法HLA基因分型模棱两可结果的判读及解决对策

目的研究PCR—SBT法HLA基因分型结果判读中出现的模棱两可问题并提出解决策略。方法对306名随机抽取的组织配型患者的DNA采用PCR-序列特异性引物（Sequence Specific Primer,SSP）低分辨方法检测,同时采用PCR—SBT法进行HLA—A,B,DRB1高分辨基因分型。PCR—SBT法模棱两可结果用PCR—SSP高分辨方法复核确认。结果所有306例检测标本的高低分辨血清学抗原一致,经PCR—SBT基因测序方法检测有111份模棱两可结果,占36．3％（111／306）。其中HLA—A座位有30对等位基因存在模棱两可结果,占所有检测标本等位基因总数的3．3％;HLA—B座位有66对,占7．2％;HLA—DRB1座位有36对,占3．9％。所有模棱两可标本经PCR—SSP HLA基因高分辨分型试剂PCR—SSP等方法复核确认。结论针对PCR—SBT法进行HLA—A,B,DRB1高分辨基因分型模棱两可结果所建立的解决策略,对于提高HLA数据分型的速度和分型准确性有重要意义。     

SYBR Green Ⅰ聚合酶链反应检测人白细胞抗原-DRB1*12

目的 建立一种人白细胞抗原(HLA)基因分型方法。方法 用序列特异性引物和荧光染料SYBR GreenⅠ聚合酶链式反应(PCR)方法，对1份已知HLA—DRB1*12的标本和12份未知型别的临床标本进行HLA—DRB1*12位点检测和分型。结果 12份标本的扩增产物经熔解曲线分析，有3份标本为DRB1*12，产物用离心柱纯化后，直接进行DNA测序，结果证实为DRB1*12阳性。结论 SYBR Green Ⅰ PCR操作简便，结果准确，可成为一种HLA基因分型的新方法。     

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。     

多重PCR直接鉴定临床标本中的耐甲氧西林葡萄球菌

目的：应用多重PCR直接鉴定临床标本中的耐甲氧西林葡萄球菌（MRS），利于迅速的诊断和治疗。方法：采用QiaAmpDNABlood MiniKit，从血培养瓶、尿液、穿刺液的肉汤增菌液、脓汁、痰、阴道及子宫颈分泌物直接迅速提取制备模板DNA：通过多重PCR技术扩增标本的meca基因和葡萄球菌16SrRNA基因。结果：287例葡萄球菌感染的临床标本中，金黄色葡萄球菌的meca基因阳性率为54．4％（55／101），凝固酶阴性葡萄球菌meca基因阳性率为58．6％（109／186）。从模板DNA制备到多重PCR产物的检测不到4h。结论：建立的基于DNA分离和多重PCR检测MRS的技术具有敏感、快速、特异的特点，是一种可靠的实验诊断手段。     

PCR扩增产物磁珠纯化法应用于HLA测序分型的研究

目的 探讨PCR扩增产物磁珠纯化法应用于HLA测序分型的可能性.方法 采用本实验室建立的HLA-C基因测序分型方法 中的PCR扩增、测序反应和测序纯化等步骤,对96份标本特异性扩增HLA-C基因外显子1～4目的 序列片段约为2 000 bp,扩增产物分别采用OMEGA公司(瑞士)磁珠纯化法及USB公司(美国)的外切酶I...     

聚合酶链反应检测SEN病毒的方法学探讨

目的探讨聚合酶链反应(PCR)扩增SEN病毒(SENV)核酸的优化条件。方法将标本分别以Acupure DNA／RNA提取法(方法1)、SDS-蛋白酶K方法(方法2)及裂解液提取’兀V核酸法(方法3)抽提SENV DNA模板，并用3组针对SENV DNA不同区的引物进行扩增，比较不同模板提取方法、不同扩增引物及不同体积标本对SENV DNA检出率的影响。结果在191份血清中，方法1、方法2和方法3提取核酸后可分别检测出15份、9份和7份。采用方法1提取SENV DNA的基础上，采用2组套式引物分别扩增出15份和11份，一次PCR引物仅检出2份SENV DNA阳性标本；应用引物2扩增至少需要50μl血清。结论不同引物扩增方法和不同模板提取方法可能是影响SENV DNA检出率重要因素。     

乙型肝炎病毒基因的巢式聚合酶链反应-限制性片段长度多态性分型及初步应用

目的 用改进的乙型肝炎病毒(HBV)巢式聚合酶链反应—限制性片段长度多态性(PCR—RFLP)的基因分型方法初探广州地区HBV基因型分布状态。方法 设计巢式PCR扩增前S基因，经限制性内切酶AvaⅡ和DpnⅡ酶切鉴别HBV A—G基因型；并对140份乙型肝炎患者血清进行基因分型，其中随机挑选3份进行克隆测序，并对20份患者血清进行巢式PCR—RFLP重复分型试验，以验证此分型技术的稳定性和特异性。同时采用PCR和巢式PCR对92份乙型肝炎病毒e抗原(HBeAg)阴性血清进行HBV DNA阳性率检测比较。结果 基因分型与测序结果一致；基因分型重复试验符合率100％；92份HBeAg阴性血清经PCR和巢式PCR扩增HBV DNA的阳性率分别为20．7％和68．5％。140份乙型肝炎患者血清中HBV基因型以C型(94份)和B型(42份)为主，偶见A型(4份)。结论 巢式PCR—RFLP HBV基因分型方法具有良好的敏感性、特异性、稳定性，且操作简便，适用于临床和流行病学调查研究。     

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 and typing of HSV-1, HSV-2, and VZV by a multiplex polymerase chain reaction

The development of a multiplex polymerase chain reaction method for the rapid and accurate detection and typing of HSV-1, HSV-2, and VZV from clinical specimens is described. A sensitive multiplex polymerase chain reaction was achieved by optimization of parameters such as the primers, magnesium, and dNTPs concentrations. False-negative results that sometimes arise due to inhibitors of DNA amplification or failure of DNA extraction procedure used may be avoided by assaying each specimen with alpha-tubulin primers. Multiplex PCR amplified viral sequences from all 55 specimens obtained from patients with clinical evidence of HSV or VZV infection indicated 100% sensitivity. From 55 patients who were investigated by multiplex PCR, HSV-1 was detected in 28, HSV-2 in 20, and VZV in 7 specimens. The reported results indicate that the present multiplex PCR assay has a potential application in clinical diagnosis when a rapid and accurate detection and typing of involved viruses HSV-1, HSV-2, or VZV is needed.     

Rapid DNA typing of HLA-B27 allele by real-time PCR using lightcycler technology

For clinical diagnostic routine we developed a fast DNA typing of HLA-B27 by PCR and real-time detection using LightCycler technology. The method combines the sensitivity and specificity of PCR with the swiftness of the LightCycler system. The amplification step was performed with a primer set coding for a region in the third exon common to B*2701 to B*2705. The PCR cycles were monitored continuously using the SYBR Green I dye. Beta-globin was used as an internal control. An analysis of 32 samples with one PCR run was completed within 40 minutes. After amplification a melting curve analysis permitted the accurate identification of the PCR amplicons. The mean melting temperatures (Tm) were 90.5 degrees C and 87.3 degrees C, which are characteristic for HLA-B27 and beta-globin, respectively. A comparison of 300 samples which were typed for HLA-B27 with a conventional sequence-specific polymerase chain reaction (SSP-PCR) and with the new method demonstrated a perfect correlation (specificity 100%). In summary, the method described is fast, reliable, cost-effective and well adapted for routine laboratory testing.     

Diagnostic Applications of Next Generation Sequencing in Immunogenetics and Molecular Oncology

Summary

With the introduction of the next generation sequencing (NGS) technologies, remarkable new diagnostic applications have been established in daily routine. Implementation of NGS is challenging in clinical diagnostics, but definite advantages and new diagnostic possibilities make the switch to the technology inevitable. In addition to the higher sequencing capacity, clonal sequencing of single molecules, multiplexing of samples, higher diagnostic sensitivity, workflow miniaturization, and cost benefits are some of the valuable features of the technology. After the recent advances, NGS emerged as a proven alternative for classical Sanger sequencing in the typing of human leukocyte antigens (HLA). By virtue of the clonal amplification of single DNA molecules ambiguous typing results can be avoided. Simultaneously, a higher sample throughput can be achieved by tagging of DNA molecules with multiplex identifiers and pooling of PCR products before sequencing. In our experience, up to 380 samples can be typed for HLA-A, -B, and -DRB1 in high-resolution during every sequencing run. In molecular oncology, NGS shows a markedly increased sensitivity in comparison to the conventional Sanger sequencing and is developing to the standard diagnostic tool in detection of somatic mutations in cancer cells with great impact on personalized treatment of patients.KeyWords: NGS, HLA, Molecular oncology     

Development of a quadriplex polymerase chain reaction for human cytomegalovirus detection

The development of a quadriplex PCR method with amplification of HCMV in a single‐step procedure using primers taken from four different regions of the viral genome is described. Different concentrations of dNTPs and MgCl₂ were assayed in order to optimize the constitution of the buffer for the multiplex PCR. The specificity of the PCR was tested with 100ng, 10ng, and 1ng of genomic MRC‐5 cell DNA infected with CMV in the presence of 10μg of uninfected MRC‐5 cell DNA. The sensitivity of the PCR was evaluated by the amplification of various amounts (100ng, 10ng, 1ng, and 0.1ng) of genomic MRC‐5 cell DNA infected with CMV. The specificity and sensitivity assays were performed for each pair of primers and for the combined four primer pairs in the multiplex PCR. CMV was consistently detected from 10ng of genomic MRC‐5 cell DNA with each primer pair. When all four sets of primers were combined in a single reaction tube, the sensitivity of the assay was equivalent to 10ng of genomic MRC‐5 cell DNA, whereas amplification from 1ng genomic MRC‐5 cell DNA produced only a subset of the amplimers. By amplifying four target‐sequences of HCMV simultaneously with minimum incubation time at each temperature, a quadriplex, highly sensitive PCR assay was performed. The use of four primer sets designed in different genomic regions of HCMV allowed the detection of variants and achieved maximal sensitivity and specificity which are essential for a diagnostic utilization. J. Clin. Lab. Anal. 13:99–105, 1999. © 1999 Wiley‐Liss, Inc.     

巢式聚合酶链式反应检测布鲁氏菌核酸DNA方法的建立

目的建立一种具有灵敏性高,特异性强的巢式聚合酶链式反应(PCR)方法检测血液标本中布鲁氏菌核酸DNA。方法使用细菌基因组提取试剂盒提取纯菌核酸DNA;使用血液等组织基因组核酸DNA提取试剂盒提取血液标本核酸DNA,对提取的核酸DNA先行常规PCR预扩增,以扩增的PCR产物为模板进行荧光定量PCR第二次扩增(即巢式PCR)。对纯菌提取的核酸DNA进行灵敏度和和特异性测试,构建巢式PCR的Ct值与核酸DNA拷贝数之关系曲线;检测临床血液标本核酸DNA,同时比较常规两种PCR方法检测结果。结果常规PCR检测的灵敏度为512个核酸DNA拷贝数;巢氏PCR检测有效范围为921.6 ng/μl^6.8 fg/μl,对应的Ct值为12.04~37.50,其指数关系为:y=(e-0.695x)×1012;R2=0.9986,巢式PCR扩增效率为2.28×109倍,检测限为2个布鲁氏核酸DNA拷贝数。巢式PCR的灵敏度为91.67%,特异度为93.10%,阳性预测值为91.67%,阴性预测值为93.10%。对一起羊养殖场采集的25份血液标本应用巢式PCR方法检测,结果阳性率为92.00%(23/25);27份健康人群血液标本没有检测出(无Ct值)。结论巢式PCR具有较好的灵敏性和特异性,特别适合于血液标本布鲁氏菌核酸DNA的检测。     

Application of optical trapping for cells grown on plates: optimization of PCR and fidelity of DNA sequencing of p53 gene from a single cell

BACKGROUND: Optical trapping has traditionally been used to visually select and isolate nonadherent cells grown in suspension because cells grown in monolayers will rapidly reattach to surfaces if suspended in solution. We explored methods to slow cell reattachment that are also compatible with high-fidelity PCR. METHODS: Using HeLa cells grown on plates and suspended after trypsinization, we measured the efficiency of capture by retention and movement of the cell by the laser. Success for removing a captured cell by pipette was determined by PCR amplification of the 5S rRNA gene. After optimizing PCR amplification of a 2049-bp region of the p53 gene, we determined PCR fidelity by DNA sequencing. RESULTS: Addition of bovine serum albumin to suspended cells slowed reattachment from seconds to minutes and allowed efficient trapping. The success rate of removing a cell from the trap by pipette to a PCR tube was 91.5%. The 5S PCR assay also revealed that DNA and RNA that copurify with polymerases could give false-positive results. Sequence analysis of four clones derived from a single cell showed only three polymerase errors in 7200 bp of sequence read and revealed difficulties in reading the correct number in a run of 16 A:T. Comparison of the HeLa and wild-type human sequences revealed several previously unreported base differences and an (A:T)(n) length polymorphism in p53 introns. CONCLUSIONS: These results represent the first use of optical trapping on adherent cells and demonstrate the high accuracy of DNA sequencing that can be achieved from a single cell.     

多重PCR在幽门螺杆菌检测及分型中的应用

应用多重ＰＣＲ同时扩增１６ＳｒＲＮＡ和ｃａｇＡ基因来检测幽门螺杆菌感染及其分型。ＰＣＲ产物经ＤＮＡ序列测定证实为转异性扩增，敏感度为１０＾２ＣＦＵ／ｍｌ。４８株Ｈｐ菌株中，Ｉ型菌株（ｃａｇＡ＋）２６株（５４．２％）；５５０份胃粘液标本，Ｈｐ阳性（１６ＳｒＲＮＡ基因＋）２１６份（４７．５％），其中Ｉ型Ｈｐ１３９份（５３．３％）。     

Multiplex polymerase chain reaction: a practical approach

Considerable time and effort can be saved by simultaneously amplifying multiple sequences in a single reaction, a process referred to as multiplex polymerase chain reaction (PCR). Multiplex PCR requires that primers lead to amplification of unique regions of DNA, both in individual pairs and in combinations of many primers, under a single set of reaction conditions. In addition, methods must be available for the analysis of each individual amplification product from the mixture of all the products. Multiplex PCR is becoming a rapid and convenient screening assay in both the clinical and the research laboratory. The development of an efficient multiplex PCR usually requires strategic planning and multiple attempts to optimize reaction conditions. For a successful multiplex PCR assay, the relative concentration of the primers, concentration of the PCR buffer, balance between the magnesium chloride and deoxynucleotide concentrations, cycling temperatures, and amount of template DNA and Taq DNA polymerase are important. An optimal combination of annealing temperature and buffer concentration is essential in multiplex PCR to obtain highly specific amplification products. Magnesium chloride concentration needs only to be proportional to the amount of dNTP, while adjusting primer concentration for each target sequence is also essential. The list of various factors that can influence the reaction is by no means complete. Optimization of the parameters discussed in the present review should provide a practical approach toward resolving the common problems encountered in multiplex PCR (such as spurious amplification products, uneven or no amplification of some target sequences, and difficulties in reproducing some results). Thorough evaluation and validation of new multiplex PCR procedures is essential. The sensitivity and specificity must be thoroughly evaluated using standardized purified nucleic acids. Where available, full use should be made of external and internal quality controls, which must be rigorously applied. As the number of microbial agents detectable by PCR increases, it will become highly desirable for practical purposes to achieve simultaneous detection of multiple agents that cause similar or identical clinical syndromes and/or share similar epidemiological features.     

HLA-B40交叉反应组血清学与高分辨度DNA分型的比较研究

目的 比较研究中国汉族人群ＨＬＡＢ４０ 交叉反应组血清学分型与高分辨度ＤＮＡ 分型结果。方法研究样本１９９ 份,包括血清学分型Ｂ４０ 组阳性样本１７７ 份、可疑阳性１２ 份和阴性对照１０ 份。同时对血清学分型和高分辨度顺序特异引物聚合酶链反应（ＰＣＲＳＳＰ） ＤＮＡ 分型进行比较。结果 ＤＮＡ分型成功率９９ ．５ ％ ,总耗时５ 小时,特异性和敏感性好,可准确分辨出Ｂ４０ 组１０ 个等位基因。血清学分型成功率９９ ．４ ％ ,总耗时２ 小时,总误差２０ 个,误差率１１ ．２ ％ 。检出中国汉族人群Ｂ４０ 组各等位基因所占比例：Ｂ６０ 为６７ ．４ ％ 、Ｂ６１ 为２０ ．８ ％ 、Ｂ４８０１ 为９ ．６ ％ 、Ｂ４００５ 为２ ．２ ％ 。结论 高分辨度ＰＣＲＳＳＰ 方法用于ＨＬＡＢ４０ 组分型比血清学分型更加精确,适合于临床应用。