微流控芯片电泳-多重聚合酶链反应法同时测定多个单碱基多态性位点

以微流控芯片电泳为检测平台,建立了多重PCR扩增法同时测定多个单碱基多态性(SNP)位点的方法。先通过PCR扩增得一段含所有待测SNP位点的长片段;用限制性内切酶消化成短片段,再将酶切反应产物与脱氧核糖核酸适配器(DNAadapter)相连;以连接产物为模板,分成两管,分别用n条等位基因特异性引物和一条通用引物进行n重PCR扩增;最后用微流控芯片电泳法分离PCR扩增产物,根据两管扩增产物的芯片电泳图谱中扩增片段的大小判断SNP的类型。以细胞色素P4502D6(CYP2D6)基因中的5个SNP位点(100C>T、1661G>C、1758G>T、2470T>C和2850C>T)为检测对象,考察了各等位基因特异性引物之间的相互影响和扩增反应的特异性,采用微流控芯片电泳法成功测定了20名健康中国人的CYP2D6基因中5个SNP位点的基因多态性,与聚合酶链反应-限制性片段长度多态性法(PCR-RFLP)测定结果完全一致。     

基于微流控芯片的荧光定量PCR法快速检测乙肝病毒核酸

提出了一种基于微流控荧光定量聚合酶链式反应(Polymerase Chain Reaction,PCR)的血液病毒快速检测新技术。采用3D打印技术制作了一种集气动阀和"树型"结构为一体的微流控芯片;运用Comsol软件对芯片导热性能进行了仿真;根据血站血液核酸检测工作中乙型肝炎病毒(HBV)、丙型肝炎病毒(HCV)、人类免缺陷病毒(HIV)三种病毒的筛查流程,结合高温控性能的微流控荧光定量PCR分析系统,在所设计微流控芯片上开展了血液样本中HBV的检测研究。实验结果表明,该芯片具有良好的温度均匀性和导热性,芯片上可实现血液样本中HBV的快速检测,其Ct值在37左右呈弱阳性。该技术与目前血液筛查使用的大型核酸检测系统相比,具有操作过程简单、所占空间小、检测效率高且试剂消耗量少的优点,进一步优化实验条件可实现多病毒核酸的并行检测。     

基于磁性颗粒微阵列与双色荧光杂交的单核苷酸多态性分型方法研究

基于磁性颗粒微阵列与双色荧光杂交,建立了单核苷酸多态性(Single nucleoitide polymorphism,SNP)分型方法。将利用不对称扩增得到的含有待检测位点生物素标记的单链PCR产物固定在链亲和素修饰的金磁纳米颗粒(Gold magnetic nanoparticles,GMNPs)表面;将ssDNA-GMNPs混合物点样在底部固定有磁铁的载玻片上构建磁性颗粒微阵列,然后在基因框中与双色荧光探针杂交;杂交完全后,充分洗涤,通过扫描获得分型结果。通过优化不对称PCR的扩增条件,直接扩增出产量较高的单链DNA作为靶序列用于分型。利用本方法对24个样本MTHFR基因的C677T位点多态性进行了检测。实验证明,本方法步骤简单,易实现自动化操作、非常适用于分子诊断与法医鉴定。     

一种基于磁性纳米粒子PCR的高通量SNP分型方法

利用磁性纳米粒子PCR扩增(MNPs-PCR)和等位基因特异性双色荧光探针(Cy3, Cy5)杂交, 建立了一种单核苷酸多态性(SNP)分型的新方法. 应用该方法对9个样本MTHFR基因的C677T多态进行检测, 野生和突变型样本正错配信号比大于9.0, 杂合型正错配信号比接近1.0, 分型结果经测序验证. 此方法无须产物纯化、浓缩, 扫描分型结果快速、直观, 是一种操作简单、快速、高通量、高灵敏度的分型方法.     

集成核酸提取的实时荧光PCR微全分析系统

集成核酸提取的实时荧光PCR微全分析系统将核酸提取、PCR扩增与实时荧光检测进行整合,在同一块微流控芯片上实现了核酸分析过程的全自动和全封闭,具有试剂用量少、分析速度快、操作简便等优点。本研究采用微机械加工技术制作集成核酸提取微流控芯片的阳极模,使用组合模具法和注塑法制作具有3D通道的PDMS基片,与玻璃基底通过等离子体键合封装成集成核酸提取芯片。构建了由微流体速度可调节(0~10 mL/min)的驱动控制装置、温控精度可达0.1℃的TEC温控平台、CCD检测功能模块等组成的微全分析系统。以人类血液裂解液为样品,采用硅胶膜进行芯片上核酸提取。系统根据设置好的时序自动执行,以2 mL/min的流体驱动速度完成20μL裂解液上样、清洗;以1 mL/min的流体驱动速度完成DNA洗脱,抽取PCR试剂与之混合注入到反应腔。提取的基因组DNA以链上内参基因GAPDH为检测对象,并以传统手工提取为对照,在该系统平台上进行PCR扩增和熔解曲线分析实验。片上PCR扩增结果显示,扩增曲线明显,Ct值分别为25.3和26.9。扩增产物进行熔解曲线分析得到的熔解温度一致,均为89.9℃。结果表明,此系统能够自动化、全封闭的在微流控芯片上完成核酸提取、PCR扩增与实时定量分析。     

液滴微流控系统在数字聚合酶链式反应中的应用研究进展

数字聚合酶链式反应( PCR)技术近年来发展迅速。与以实时荧光定量PCR为代表的传统PCR技术相比,数字PCR技术显著提高了定量分析的精确度和灵敏度。数字PCR的快速发展与近年来微流控技术在数字PCR技术中的广泛应用有着密切的联系。早期的研究和商业化产品使用的是大规模集成流路微流控芯片,加工过程复杂且价格高昂。近年来,液滴微流控芯片被应用到数字PCR技术中,它可以在短时间内产生102~107个微液滴,每一个微液滴都是最多只含有一个目的基因片段的PCR反应器。 PCR扩增后,通过对单个微液滴的观察计数,就可以获得绝对定量的分析数据。本文综述了不同种类的液滴微流控系统在数字PCR技术中的应用,以及液滴数字PCR微流控芯片在生物、医药、环境等领域的应用。     

微流控芯片荧光检测系统的研究进展北大核心CSCD

微流控芯片又称芯片实验室,具有检测高效、消耗试剂少、高通量、微型化和集成化等特点,许多检测方式(如光学检测、电化学检测)已经集成于微流控芯片上,而荧光检测是微流控芯片检测技术的常见手段之一。为此,在介绍了荧光检测技术的基本原理和光路结构的基础上,从激发光源、光传辅助手段和检测器等方面综述了微流控芯片荧光检测系统的研究进展,并对其发展进行了展望(引用文献55篇)。     

微流控芯片-激光诱导荧光快速检测4种食源性致病菌

建立了食品中4种常见食源性致病菌的微流控芯片快速检测方法。根据副溶血弧菌的Vpara(16S-23S rDNA IGS)基因、沙门菌的invA基因、大肠杆菌O157:H7的rfbO157基因和志贺菌的ipaH基因序列设计了4对特异性引物,对上述致病菌进行四重PCR扩增,采用微流控芯片-激光诱导荧光检测食品中4种常见致病菌的多重PCR扩增产物。优化了多重PCR扩增和微流控芯片电泳分离的实验条件。当芯片电泳的筛分介质HPMC-50浓度为2.2%、溴乙锭(EB)含量为3.75μmol/L、电场强度为120 V/cm时,pUC Mix DNAMarker-8和待测致病菌的多重PCR扩增产物可以实现基线分离,600 s内即可完成上述4种致病菌的同时检测,迁移时间的日内相对标准偏差为0.74%~2.09%。本方法能够检出1×102cfu/mL的副溶血弧菌、沙门菌、大肠杆菌O157:H7和志贺菌。方法特异性高,所设计的引物在10种非目的菌株体系中均未见扩增的片段。将本法应用于食品中上述致病菌的测定,获得了满意的结果,为常见食源性致病菌的快速检测提供了一种新的可靠分析手段,对保障食品安全具有重要的现实意义。     

一种基于磁性颗粒和通用连接子扩增技术的单核苷酸多态性分型方法

提出了一种应用磁性颗粒和通用连接子扩增技术(Linker-PCR)的多位点单核苷酸多态性(SNP)分型方法. 该方法首先通过酶切将样本基因组DNA打断, 然后将通用连接子通过T4 DNA连接酶与各个酶切片段连接, 利用生物素标记的通用引物将样本进行全基因组扩增. 扩增后, 将生物素标记的Linker-PCR扩增产物固定到亲合素修饰的磁性颗粒表面, 通过与双色荧光标记的等位基因特异性探针杂交, 对待测位点进行分型. 利用该方法, 我们对10个样本MTHFR基因上的2个SNP位点进行了分型, 分型结果准确、正错配信号比大于3. 由于利用Linker-PCR技术来实现对靶序列的全基因组扩增, 该方法非常适用于大量样本的多基因多位点的SNP分型研究.     

激光技术在聚合酶链式反应微流控芯片中的应用

评述了激光技术在聚合酶链式反应(polymerase chain reaction,PCR)微流控芯片领域中的应用进展,包括激光技术在PCR微流控芯片微加工、微流体物理参数测量、温度循环控制以及芯片上在线产物检测(包括荧光实时定量/终点和毛细管电泳检测)中的应用。最后,展望了激光技术在未来基于PCR的微全分析系统(micro-total analysis system,μTAS)中的新应用。     

An allelic ladder based upon reference alleles for mtDNA SNP analysis using the SNaPshot technique

The analysis of mitochondrial DNA (mtDNA) single-nucleotide polymorphisms (SNPs) using the SNaPshot technique (Applied Biosystems) is a fast and sensitive method for the reliable identification of disease-associated mtDNA SNPs, genetic ancestry mtDNA SNPs and forensically important mtDNA SNPs. The detection of many SNPs in one multiplex PCR and one subsequent multiplex minisequencing reaction is challenging for laboratories who want to establish this technique, due to the problem that there is no allelic ladder available for mtDNA SNP analysis via SNaPshot technique. Normally, the laboratory has to invent long-term testing and studies. The interpretation of false and correct alleles is up to some specialists knowing the expected and the estimated size of each allele SNP. We here present a protocol to assemble up to 84 alleles of 42 different mtDNA SNPs in an allelic ladder that is based upon reference alleles. We recommend using allelic ladders/reference alleles for SNP analysis to maintain high-quality analysis standards.     

Exploring of tri-allelic SNPs using pyrosequencing and the SNaPshot methods for forensic application

Tri-allelic single nucleotide polymorphisms (SNPs) are potential forensic markers for DNA analysis. Currently, only a limited number of tri-allelic SNP loci have been proved to be fit for forensic application. In this study, we aimed to develop an effective method to select and genotype tri-allelic SNPs based on both Pyrosequencing (PSQ) and the SNaPshot methods. 50 candidate SNPs were chosen from NCBI's dbSNP database and were analyzed by PSQ. The results revealed that 20 SNPs were tri-allelic and were located on 16 autosomal chromosomes. Then 20 SNP loci were combined in one multiplex polymerase chain reaction to develop a single base extension (SBE)-based SNP-typing assay. A total of 100 unrelated Chinese individuals were genotyped by this assay and allele frequencies were estimated. The total discrimination power was 0.999999999975 and the cumulative probability of exclusion was 0.9937. These data demonstrated that the strategy is a rapid and effective method for seeking and typing tri-allelic SNPs. In addition, the 20 tri-allelic SNP multiplex typing assay may be used to supplement paternity testing and human identification.     

A SNaPshot assay for genotyping 44 individual identification single nucleotide polymorphisms

Single nucleotide polymorphisms (SNPs), which have relatively low mutation rates and can be genotyped after PCR with shorter amplicons compared with short tandem repeats (STRs), are being considered as potentially useful markers in forensic DNA analysis. Those SNPs with high heterozygosity and low Fst (F-statistics) in human populations are described as individual identification SNPs, which perform the same function as STRs used in forensic routine work. In the present study, we developed a multiplex typing method for analyzing 44 selected individual identification SNPs simultaneously by using multiplex PCR reaction in association with fluorescent labeled single base extension (SBE) technique. PCR primers were designed and the lengths of the amplicons ranged from 69 to 125?bp. The population genetics data of 79 unrelated Chinese individuals for the 44 SNP loci were investigated and a series of experiments were performed to validate the characteristic of the SNP multiplex typing assay, such as sensitivity, species specificity and the performance in paternity testing and analysis of highly degraded samples. The results showed that the 44-SNPs multiplex typing assay could be applied in forensic routine work and provide supplementary data when STRs analysis was partial or failed.     

Single nucleotide polymorphism analysis by allele-specific primer extension with real-time bioluminescence detection in a microfluidic device

A microfluidic approach for rapid bioluminescent real-time detection of single nucleotide polymorphism (SNP) is presented. The method is based on single-step primer extension using pyrosequencing chemistry to monitor nucleotide incorporations in real-time. The method takes advantage of the fact that the reaction kinetics differ between matched and mismatched primer-template configurations. We show here that monitoring the initial reaction in real time accurately scores SNPs by comparing the initial reaction kinetics between matched and mismatched configurations. Thus, no additional treatment is required to improve the sequence specificity of the extension, which has been the case for many allele-specific extension assays. The microfluidic approach was evaluated using four SNPs. Three of the SNPs included primer-template configurations that have been previously reported to be difficult to resolve by allele-specific primer extension. All SNPs investigated were successfully scored. Using the microfluidic device, the volume for the bioluminescent assay was reduced dramatically, thus offering a cost-effective and fast SNP analysis method.     

连接反应介导的等位基因特异性扩增-微流控芯片电泳法同时检测多个SNP位点

以CYP2D6基因中的6个SNP位点为测定对象, 开展多个SNP位点同时测定的方法学研究.     

Developing a new nonbinary SNP fluorescent multiplex detection system for forensic application in China

Nonbinary single‐nucleotide polymorphisms (SNPs) are potential forensic genetic markers because their discrimination power is greater than that of normal binary SNPs, and that they can detect highly degraded samples. We previously developed a nonbinary SNP multiplex typing assay. In this study, we selected additional 20 nonbinary SNPs from the NCBI SNP database and verified them through pyrosequencing. These 20 nonbinary SNPs were analyzed using the fluorescent‐labeled SNaPshot multiplex SNP typing method. The allele frequencies and genetic parameters of these 20 nonbinary SNPs were determined among 314 unrelated individuals from Han populations from China. The total power of discrimination was 0.9999999999994, and the cumulative probability of exclusion was 0.9986. Moreover, the result of the combination of this 20 nonbinary SNP assay with the 20 nonbinary SNP assay we previously developed demonstrated that the cumulative probability of exclusion of the 40 nonbinary SNPs was 0.999991 and that no significant linkage disequilibrium was observed in all 40 nonbinary SNPs. Thus, we concluded that this new system consisting of new 20 nonbinary SNPs could provide highly informative polymorphic data which would be further used in forensic application and would serve as a potentially valuable supplement to forensic DNA analysis.     

Improved adapter-ligation-mediated allele-specific amplification for multiplex genotyping by using software

Adapter-ligation-mediated allele-specific amplification (ALM-ASA) is a potential method for multiplex SNPs typing at an ultra low cost. Here, we describe a kind of software, which designs allele-specific primers for ALM-ASA assay on multiplex SNPs. DNA sequences containing SNPs of interest are submitted into the software which contains various endonucleases for options. Based on the SNP sequence information and the selected endonucleases, the software is capable of automatically generating sets of information needed to perform genotyping experiments. Each set contains a suitable endonuclease, qualified allele-specific primers with orientations and melting temperatures, sizes of allele-specific amplicons, and gel electropherograms simulated according to the sizes of the allele-specific amplicons and the mobility of DNA fragments in 2% agarose gel. Seven SNPs in the arylamines N-acetyltransferase 2 (NAT2) gene, five SNPs in the BRCA1 gene, five SNPs in the COMT gene, six SNPs in the CYP2E1 gene, five SNPs in the MPO gene, and six SNPs in the NRG1 gene were selected for evaluating the software. Without extra optimization, seven SNPs in the NAT2 gene were successfully genotyped for genomic DNA samples from 127 individuals by using the first set of allele-specific primers yielded by the software. Although several steps are used in the ALM-ASA assay, the whole genotyping process can be completed within 3 h by optimizing each step. Profiting from the software, the ALM-ASA assay is easy-to-perform, labor-saving, and accurate.     

Improving the analysis of Y‐SNP haplogroups by a single highly informative 16 SNP multiplex PCR‐minisequencing assay

The SNP haplogroups of the Y‐chromosome are nonrandomly distributed among human populations. They are used for tracing the phylogeographical history of paternal lineages of male individuals and can be a useful tool for approaching the patrilineal bio‐geographic ancestry of unknown forensic evidences. With the aim of facilitating the inference of the principal informative worldwide Y‐SNP haplogroups, we have selected the minimum possible number of key Y‐SNPs to be amplified in a sensitive single multiplex PCR and detected by minisequencing. This assay, that includes 16 Y‐SNPs, was tested for male human specificity, sensitivity, and reproducibility. Its effectiveness was assessed in a set of degraded DNA samples and in a panel of male individuals from different worldwide populations. All these tests demonstrated the convenience of this assay for assigning the major Y haplogroups to forensic evidences by one single PCR‐minisequencing reaction.     

Development of a novel forensic STR multiplex for ancestry analysis and extended identity testing

There is growing interest in developing additional DNA typing techniques to provide better investigative leads in forensic analysis. These include inference of genetic ancestry and prediction of common physical characteristics of DNA donors. To date, forensic ancestry analysis has centered on population‐divergent SNPs but these binary loci cannot reliably detect DNA mixtures, common in forensic samples. Furthermore, STR genotypes, forming the principal DNA profiling system, are not routinely combined with forensic SNPs to strengthen frequency data available for ancestry inference. We report development of a 12‐STR multiplex composed of ancestry informative marker STRs (AIM‐STRs) selected from 434 tetranucleotide repeat loci. We adapted our online Bayesian classifier for AIM‐SNPs: Snipper, to handle multiallele STR data using frequency‐based training sets. We assessed the ability of the 12‐plex AIM‐STRs to differentiate CEPH Human Genome Diversity Panel populations, plus their informativeness combined with established forensic STRs and AIM‐SNPs. We found combining STRs and SNPs improves the success rate of ancestry assignments while providing a reliable mixture detection system lacking from SNP analysis alone. As the 12 STRs generally show a broad range of alleles in all populations, they provide highly informative supplementary STRs for extended relationship testing and identification of missing persons with incomplete reference pedigrees. Lastly, mixed marker approaches (combining STRs with binary loci) for simple ancestry inference tests beyond forensic analysis bring advantages and we discuss the genotyping options available.