引物标记与掺入标记在HBV基因多态性芯片检测中应用的研究

目的 研究引物标记与掺入标记在乙型肝炎病毒（HBV）基因多态性芯片检测中的应用。方法 用掺入标记或引物标记荧光分子Cy5，扩增HBV P区、前C／C区，制备含荧光分子Cy5的目的片段后，分别与HBV基因多态性芯片杂交、扫描并分析结果。结果 掺入标记法信号强度略高于引物标记法，但非特异信号强度也高，两法检测42份乙型肝炎患者血清，结果完全一致，重复性均较好，批内CV15％－20％，引物标记法用于检测HBV基因多态性灵敏度达10^4 copies/ml。结论 引物标记法信号强度虽略低于掺入标记法，但检测灵敏度、特异性仍满足临床要求。     

寡核苷酸微阵列技术用于检测幽门螺杆菌克拉霉素耐药相关23S rRNA基因多态性

目的 幽门螺杆菌（Hp）克拉霉素耐药与23S rRNA基因A2142G、A2143G和C2182T点突变相关。本研究旨在探索建立一种快速、简便的检测方法，获取Hp克拉霉素耐药相关23S rRNA基因多态性的流行病学资料，为临床合理用药提供依据。方法收集胃黏膜标本，用于病理检查、提取DNA。根据核苷酸位点设计相应探针，探针3′端以氨基修饰，氨基与探针序列之间以间隔臂相连，将探针用芯片点样仪点至玻片上。下游引物5′末端用Cy3荧光标记，进行不对称PCR扩增。其产物与芯片杂交，杂交后洗涤、扫描芯片，观察信号强度。非荧光标记引物扩增PCR产物克隆至T载体，测序验证芯片结果。结果（1）寡核苷酸微阵列技术与测序检测Hb 23S rRNA基因多态性结果完全一致。（2）经病理和PCR证实为场阳性的54例标本，杂交结果显示A2142位点均为野生型（54/54）；A2143G突变率为11．11％（6/54），尚未发现A2143C和A2143T的突变；C2182T突变率为12．96％（7／54），尚未发现C2182A和C2182G的突变，其余均为野生型。结论（1）利用寡核苷酸微阵列技术检测坳克拉霉素耐药的23S rRNA基因多态性，快速、简便而准确，可以高通量并直接检测胃黏膜而不需进行细菌培养，为根除Hp选择用药提供科学依据，推动个体化治疗方案的实施。（2）本研究没有发现场23SrRNA基因2142点突变，A2143G和C2182T突变率分别为11．11％和12．96％。     

DNA芯片检测乙型肝炎病毒基因多态性

目的　建立DNA芯片检测乙型肝炎病毒 (hepatitisBvirus,HBV)基因多态性的研究方法并对实验条件进行优化。方法　设计多条寡核苷酸探针 ,在硅烷化芯片的特定位置上 ,用点样仪将探针固定 ,并与PCR扩增的HBV基因相应区段杂交 ,杂交结果影印至硝酸纤维素膜 ,经BCIP NBT避光显色 ,用放大镜观察杂交信号呈暗紫色圆点 ,根据特定位置上杂交信号的有无和与之相应的探针序列来判定基因突变的类型。结果　通过 1次杂交反应可检测HBV前C C区 (nt 1896 1814 )、BCP区 (nt1762 1764)和P区 (nt 52 8 552 )等多个位点的变异 ,与测序分析结果完全一致 ,具有较好的检测灵敏度和重复性。结论　DNA芯片检测HBV基因常见突变位点多态性 ,操作简便易行 ,技术要求不高 ,具有临床推广应用价值 ,而且可以方便地通过向寡核苷酸探针阵列中添加相应探针 ,扩大基因芯片的检测应用范围 ,为临床检测提供了新的方法     

PCR引物浓度对寡核苷酸液相杂交的影响

目的考察PCR引物浓度配比对液相微珠杂交效率的影响,寻求具有较强杂交信号和较好稳定性的PCR引物浓度配比。方法建立HLA-DRB1等位基因的相关数据库,选择在HLA-DRB1位点的第二外显子上设计探针,并且选择其保守序列作为阳性对照探针(DPC2),DPC2探针中间位点T突变成A作为阴性对照探针(DNC)。分别针对标本C2-008、C2-024、C2-025的等位基因序列设计出6条约21bp的寡核苷酸探针,各探针5’端用氨基(NH2)修饰。通过引物浓度梯度配比(1:100、1:50、1:20、1:8、1:4、1:2、1:1),对型别已知的细胞株DNA进行PCR扩增并得到目的片段(1:100配比除外),在相同条件下将PCR产物与寡核苷酸探针进行液相杂交检测。结果浓度配比为1:1的对称式扩增产物杂交结果不理想,而浓度配比分别为1:20、1:8、1:4、1:2的不对称扩增均得到了待检单链、双链DNA混合物,其中1:4浓度配比具有最好的扩增效率和稳定性。根据阳性信号与阳性标本是否相符表明:引物浓度配比为1:100的不对称PCR和1:1的对称PCR检测效果差,易出现假阴性;1:2、1:4、1:8、1:20配比检测效果较好,比较稳定。结论PCR引物浓度配比影响液相微珠杂交效率,不对称PCR产物有利于提高杂交效率,为快速成功配制PCR试剂奠定了基础,有利于寡核苷酸液相芯片的应用。     

PCR结合寡核苷酸探针杂交检测临床常见真菌的实验研究

目的 建立PCR结合生物标记的寡核甘酸探针斑点杂交技术,鉴定临床常见的真菌。方法 首先用真菌通用引物扩增白念球菌、热带念球菌、假热带念球菌、近平滑念球菌、光滑念球菌、解脂念球菌、克鲁斯念球菌、季也蒙念球菌、黄曲 霉、烟曲霉的核糖体大亚单位基因的保守区序列,然后用生物素标记的种特异性寡核苷酸探针与扩增产物杂交,并将此方法用于临床标本和临床分离菌株的检测。结果 通用引物可以扩增上述11种临床常见真菌的DNA,扩增片段长度在260bp左右。9种特异性探针分别与11种真菌标准菌株的PCR扩增产物杂交,结果表明每种探针都具有高度特异性。斑点杂交法和Southerm杂交法检测敏感性相同,为100fg;琼脂糖凝胶电泳法检测敏感性为1pg。通过69例临床标本和31例临床分析菌株的检测,PCR－杂交法的结果和真菌培养法的结果基本一致。结论 PCR结合生物素标记的寡核苷酸探针杂交技术可将9种临床常见真菌鉴定到种,方法快速、敏感、特异。     

EMB基因330密码子分子DNA探针设计及荧光检测

目的 针对结核杆菌耐乙胺丁醇embB330密码子位点设计分子DNA探针,尝试运用荧光分光光度计直接观测液相中分子DNA探针与embB330密码子扩增产物杂交后的荧光信号,从而检出该位点突变.方法 运用软件Beacon designer设计embB基因包含330密码子的分子DNA探针,应用荧光分光光度计检测embB306密码子扩增片段与探针杂交后荧光信号,比较扩增产物测序结果.结果 通过荧光分光光度计观测到结核标准株及embB330密码子突变株PCR产物与探针杂交后荧光信号存在显著差异;33株耐乙胺丁醇组与10株H37RV标准株对照组荧光信号强度比较,耐乙胺丁醇组embB330密码子突变检出率为3%,测序法突变检出率为3%.结论 分子DNA探针技术可以有效检测embB330密码子单碱基靶点突变;应用荧光分光光度计直接观测液相荧光杂交信号简单、灵敏.     

TORCH与优生：Ⅲ用聚合酶链反应结合地高辛分子杂交产前诊断弓形虫感染

根据本实验室筛选出的弓形虫(ZS2株)特异DNA克隆片段的部分顺序分析的数据，设计并合成特异的寡核苷酸引物对，建立多聚酶链反应(PCR)诊断弓形虫感染的方法。不同来源弓形虫株和阳性标本DNA的PCR产物经电泳检测，均出现特异的扩增片段。以地高辛标记的该PCR产物中弓形虫特异顺序的寡核苷酸为探针，对扩增产物进行斑点杂交分析，该探针能与阳性病例的扩增产物杂交，而不与阴性病例的扩增产物杂交。用PCR结合地高辛分子杂交方法对不良生育史孕妇进行产前诊断，34例外周血白细胞DNA检测，2例阳性，分别为出生水肿胎儿和死胎；76例羊水细胞DNA检测，3例阳性，其中2例出生为无脑儿；30例绒毛DNA检测，4例阳性，均为难免流产。PCR产物结合地高辛分子杂交方法可测出少至10fg（10^-1g)的弓形虫DNA，本方法更加特异敏感。     

一种快速定量检测p16基因甲基化方法的建立

目的建立一种基于错配杂交-化学发光检测的p16基因启动子区过甲基化的定量分析方法。方法用亚硫酸氢钠修饰基因组DNA,所有未甲基化的胞嘧啶都被转变为尿嘧啶,而甲基化的胞嘧啶则不发生变化。设计合成一对不含CpG位点的引物同时扩增甲基化或非甲基化目的DNA片段,用两根分别与甲基化及非甲基化CpG位点互补的寡核苷酸探针与扩增产物进行杂交,化学发光检测,通过两根探针的杂交信号强度之比确定样品DNA中甲基化的p16基因的比例。结果检测结果与肿瘤细胞DNA样品中甲基化的p16基因的量成正比,而且与其表达水平呈逆相关。结论与现有方法相比,本法是一种检测快速、操作简便的p16基因甲基化的定量检测方法。     

检测组织激肽释放酶基因寡核苷酸多态性方法的建立

目的：检测组织激肽释放酶启动子区寡核苷酸多态性，为开展基因诊断高血压研究奠定基础。方法：人外周静脉抗凝血提取基因组DNA，PCR扩增目标启动子片段，ASO(allele-specific oligonucleotide)斑点杂交检测基因型，并与测序法比较了解启动于等位基因多态性。结果：有4例杂交结果阳性，与测序结果吻合。结论：应用ASO斑点杂交技术检测该寡核苷酸多态性与测序法比较具有简便，快速，价廉，特异性高等优点，适于大规模人群筛查，是一种值得推广的研究方法。     

利用寡核苷酸芯片检测乙型肝炎病毒基因突变

目的　利用寡核苷酸芯片平行分析乙肝病毒表面抗原区S、前核心抗原pre C区、X区、聚合酶P区 12个已知的突变位点。方法　针对S、pre C、X、P区的 12个突变位点 ,设计位于乙肝病毒反义链的 2 4条寡核苷酸探针和两对PCR引物 ,探针长度为 14～ 18bp ,其 5′端连有氨基己烷和T15间隔子 ,合成后经点样仪点到醛基化玻片上。两对PCR引物分别用于扩增S与P区内的 5个突变位点和X、前C区内的 7个突变位点 ,其中上游引物含有荧光标记。不对称PCR扩增所得到的荧光标记的单链DNA与寡核苷酸阵列杂交、清洗后经扫描分析实验结果。结果　在对 12个乙肝阳性样品前核心抗原C和X区的突变检测中 ,存在 176 2A→T ,176 4G→A联合突变的有 2例、1896G→A突变的 3例、同时存在 176 2A→T、176 4G→A联合突变和 1896G→A突变的 1例、未存在任何突变的样品 6例。在 12个乙肝阳性样品的表面抗原S的突变检测中 ,未发现有突变出现。部分样品的随机测序结果与寡核苷酸阵列杂交结果一致。结论　寡核苷酸芯片适于快速、平行、大量检测突变     

Single nucleotide variation detection by ligation of universal probes on a 3D poyacrylamide gel DNA microarray

We attempted to simultaneously analyze single nucleotide variations (SNVs) in a number of samples by integrating the high fidelity of ligation of universal probes with the robustness of three‐dimensional (3D) polyacrylamide gel DNA microarray. By performing a ligation reaction between the 5′ phosphate terminus of the sequencing primer and the 3′ hydroxyl terminus of the labeled probe, we accurately identified a single nucleotide polymorphism (SNP) in the polymerase chain reaction (PCR) products of 33 genomic DNA samples and two point mutations in the PCR‐amplified 83 mitochondrial DNA (mtDNA) samples immobilized in gel. Fluorescent imaging allowed genotyping with a high call rate (100%). The average fluorescence intensity obtained by ligation of universal probes was about 85% of that acquired by dual‐color fluorescence hybridization, and the detection specificities of these two methods were similar. Because the fluorescently labeled probes can be used to detect all SNVs, ligation of universal probes was thought to be more cost effective. Our study demonstrated that this method can detect SNVs in an economic, authentic, and high‐throughput format on the 3D microarray platform. Hum Mutat 30:1–9, 2009. © 2009 Wiley‐Liss, Inc.     

通用型病毒检测芯片在三种人类致病病毒属检测中的应用

目的 研究制备对人类有致病作用的38个属的病毒寡核苷酸（oligo）基因芯片对三种人类致病病毒的检测能力。方法 应用生物信息学软件设计70-mer oligo探针，固定于玻片载体制备成基因芯片。以痘苗病毒天坛株、甲肝病毒、乙肝病毒作为检测样本，提取病毒核酸，经随机引物扩增、荧光标记，用于芯片杂交，清洗和干燥后对芯片进行扫描和数据分析。结果 芯片上oligo探针能与相应病毒的PCR扩增样品杂交，呈现阳性荧光信号。结论 建立的病毒寡核苷酸基因芯片能够检出和区分三种检测病毒，为进行未知病毒的基因芯片筛查方法的建立奠定了基础。     

Recent developments in signal amplification methods for in situ hybridization.

In situ hybridization (ISH) allows for the histologic and cytologic localization of DNA and RNA targets. However, the application of ISH techniques can be limited by their inability to detect targets with low copies of DNA and RNA. During the last few years, several strategies have been developed to improve the sensitivity of ISH by amplification of either target nucleic acid sequences prior to ISH or signal detection after the hybridization is completed. Current approaches involving target amplification (in situ PCR, primed labeling, self-sustained sequence replication), signal amplification (tyramide signal amplification, branched DNA amplification), and probe amplification (padlock probes and rolling circle amplification) are reviewed with emphasis on their applications to bright field microscopy. More recent developments such as molecular beacons and in situ strand displacement amplification continue to increase the sensitivity of in situ hybridization methods. Application of some of these techniques has extended the utility of ISH in diagnostic pathology and in research because of the ability to detect targets with low copy numbers of DNA and RNA.     

Rapid detection of common viruses using multi-analyte suspension arrays

A method that uses specific oligonucleotide probes coupled to a specific array of fluorescent microspheres in multi-analyte suspension arrays was employed for the detection of common viruses, such as Herpes virus (HSV), Human papillomavirus (HPV) and Hepatitis B virus (HBV). Sixteen species-specific probes and 9 sets of specific primers were designed based on conserved sequences of these viruses in the GenBank database. Serial symmetric PCR, asymmetric PCR and multiple PCR assays were employed to evaluate the sensitivity, specificity and reproducibility of multi-analyte suspension arrays analyzed on a Luminex-100 analyzer instrument. The symmetric PCR amplification of four types of HSV, four types of HPV and HBV genotypes of B, C and D, combined with their corresponding species-specific probes and specificities were completely concordant with the results from a comparative sequence analyses. There was no significant difference in the median fluorescence intensity (MFI) value between symmetric PCR and asymmetric PCR when the viral DNA concentration was above 10⁴ copies/test. Both PCR products were negative in the multi-analyte suspension arrays with viral DNA concentrations less than 10³ copies/test. A multi-analyte suspension array is a flexible, high-throughput, relatively simple method for rapid identification of common viruses in the clinical laboratory.     

A strategy for detection of known and unknown SNP using a minimum number of oligonucleotides applicable in the clinical settings

Detection of unknown single nucleotide polymorphism (SNP) relies on large scale sequencing expeditions of genomic fragments or complex high-throughput chip technology. We describe a simplified strategy for fluorimetric detection of known and unknown SNP by proportional hybridization to oligonucleotide arrays based on optimization of the established principle of signal loss or gain that requires a drastically reduced number of matched or mismatched probes. The array consists of two sets of 18-mer oligonucleotide probes. One set includes overlapping oligos with 4-nucleotide tiling representing an arbitrarily selected "consensus" sequence (consensus-oligos), the other includes oligos specific for known SNP within the same genomic region (variant-oligos). Fluorescence-labeled DNA amplified from a homozygous source identical to the consensus represents the reference target and is co-hybridized with a differentially-labeled test sample. Lack of hybridization of the test sample to consensus- with simultaneous hybridization to variant-oligos designates a known allele. Lack of hybridization to consensus- and variant-oligos indicates a new allele. Detection of unknown variants in heterozygous samples depends upon fluorimetric analysis of signal intensity based on the principle that homozygous samples generate twice the amount of signal. This method can identify unknown SNP in heterozygous conditions with a sensitivity of 82% and specificity of 90%. This strategy should dramatically increase the efficiency of SNP detection throughout the human genome and will decrease the cost and complexity of applying genomic wide analysis in the context of clinical trials.     

Detection of Mycoplasma pneumoniae by polymerase chain reaction and nonradioactive hybridization in microtiter plates.

In order to improve the diagnosis of a Mycoplasma pneumoniae infection, we developed a polymerase chain reaction (PCR)-based assay. The gene encoding elongation factor Tu (tuf) was selected as the target sequence. Oligonucleotides derived from variable stretches of the tuf gene were able to prime the amplification of a 950-bp fragment exclusively when M. pneumoniae DNA was used as the template. The sensitivity of the assay was increased 10-fold when the amplification products were hybridized with an internal M. pneumoniae-specific oligonucleotide. The use of three to four genome copies for PCR was sufficient for obtaining a hybridization signal. In addition, we substituted radioactive filter hybridization with a microtiter plate assay. Via a biotin moiety of one PCR primer, the amplification products were immobilized on streptavidin-coated microtiter plates. Subsequent hybridization with a digoxigenin-labeled oligonucleotide resulted in the same sensitivity and specificity as those obtained by filter hybridization. Clinical application of the assay was performed on 102 throat swab specimens from patients with respiratory tract infections. Of 21 culture-positive samples, 19 were confirmed to be positive in the PCR-based assay (sensitivity, 90%). Furthermore, 14 of 19 seropositive but culture-negative samples gave a positive hybridization signal. Of 62 culture-negative and seronegative specimens, 60 gave a negative result in our assay (specificity, 97%). Of the 33 samples that were positive in our PCR-based assay, 5 samples initially gave false-negative results because of the presence of inhibitory substances in those specimens. Inhibition of Taq polymerase in these five cases was prevented by an additional step of phenol extraction and subsequent ethanol precipitation.     

激光捕获显微切割联合基因芯片在肿瘤差异表达基因研究中的应用

 目的 为激光捕获显微切割（LCM）联合基因芯片在肿瘤差异表达基因研究中应用摸索可行的技术方法。方法 采用 LCM 技术分别自原发性膀胱移行癌患者手术切除的癌组织和癌旁正常组织冻存标本获取细胞，提取 RNA，用 Agilent 2100 Bioanalyzer 芯片分析系统进行 RNA 完整度（RIN）检测。取总 RNA 100 ng 进行线性扩增和荧光标记，获得 aRNA 探针。取等量的癌组织探针与癌旁正常组织探针，与 Agilent 人全基因组寡核苷酸基因表达谱芯片杂交。通过自身比较实验分析芯片的假阳性基因数，计算假阳性率（FPR）。通过数据分析寻找癌组织与癌旁正常组织差异表达基因。 结果 LCM 所获微量 RNA 的 RIN 都在 8.0 以上，表明LCM 后 RNA 完整度较高。100 ng RNA 经过线性扩增与荧光标记，获 aRNA 产量约 16 µg，片段大小 0.5 ~ 2.5 kb。芯片自身比较实验结果良好，FPR < 1%，验证了实验系统的可靠性。相对于癌旁正常组织，癌组织发生表达上调的基因有 286 条，下调的基因 112 条。 结论 以 LCM 技术获得的细胞提取 RNA 用于制备基因芯片探针，获得了可信的芯片杂交结果，为肿瘤基因差异表达研究提供了可行的技术方法。     

PCR multiplex sur le LightCycler utilisant des sondes d'hydrolyse et d'hybridation : application à la quantification du provirus VIH-1

Quantification of HIV provirus DNA by aid of PCR multiplex using LIGHT Cycler. The quantitation of HIV provirus DNA in peripheral blood mononuclear cells (PBMCs) may be useful to gain insight into the natural history of infection and the continued efficacy of antiretroviral therapy. A quantitative PCR with the Light Cycler strategy has been developed to evaluate HIV DNA in PBMCs together with the amplification of cellular gene (β-globin) used as an internal control. Fluorescent hydrolysis probe and hybridization probes were used to detect HIV DNA and the β-globin sequence, respectively, in the same run. Co-amplification with β-globin did not interfere with HIV-1 quantification and the sensitivity of HIV detection was 5 copies. This assay was compared with an HIV DNA competitive PCR and the correlation between the two methods was good (Δ log = 0.19). The possibility to use simultaneously fluorescent hydrolysis and hybridization probes enlarges the analytic ability of real time PCR LightCycler technology.     

Simultaneous analysis of foodborne pathogenic bacteria by an oligonucleotide microarray assay

A rapid and accurate method for simultaneous identification of foodborne infectious pathogens was developed based on oligonucleotide microarray technology. The proposed identification method is based on PCR amplification of the target region of the groEL genes with degenerate primers, followed by the PCR products hybridization with oligonucleotide probes specific for species. The groEL gene amplification products of seventeen species of pathogenic bacteria were hybridized to the oligonucleotide array. Hybridization results were analyzed with digoxigenin-linked enzyme reaction. Results indicated that fifteen species of pathogenic bacteria showed high sensitivity and specificity for the oligonucleotide array, while two other species gave cross-reaction with the E. coli. Our results suggested that microarray analysis of foodborne infectious pathogens might be very useful for simultaneous identification of bacterial pathogens. The oligonucleotide array can also be applied to samples collected in clinical settings of foodborne infections. The superiority of oligonucleotide array over other tests lies on its rapidity, accuracy and efficiency in the diagnosis, treatment and control of foodborne infections.