全血改进线性指数聚合酶链式反应用于焦磷酸测序检测基因多态性

焦磷酸测序是目前基因多态性检测的主要方法之一,但是其前期的样本制备工作较为繁琐,限制了其在临床检测中的应用。为了简化焦磷酸测序的流程,本研究根据不对称PCR原理,改进了线性指数聚合酶链式反应(LATE-PCR)的引物设计方法,增加过量引物的长度和浓度,并结合全血直接扩增技术,建立了基于普通r Taq聚合酶和高p H缓冲液(Hp H Buffer)的全血改进LATE-PCR(Improved LATE-PCR,im LATE-PCR)方法。考察了方法的最优扩增体系、血液抗凝剂对其影响以及全血模板量。采用单管、一步法直接扩增出单链测序模板,成功地对24例临床血样的乙醇脱氢酶基因多态性进行了检测,检测结果可用于指导临床个体化用药。24例样本的基因型分别为ADH1B位点AA纯合6例、AG杂合14例、GG纯合4例;ADH1C位点GG纯合20例、AG杂合4例、AA纯合0例。     

荧光偏振技术分析全血XPD基因单核苷酸多态性的研究

将荧光偏振与非对称基因扩增技术联用,建立了可用于检测全血XPD基因单核苷酸多态性的新方法。用不等量(1∶5)的XPD基因上、下游引物对含单核苷酸多态性位点的目的片段进行非对称扩增,再用两种单核苷酸多态性序列特异的荧光标记探针对扩增产物进行检测。由于扩增得到的单链片段能够与各自不同的荧光标记探针特异结合,使荧光标记分子的分子量增加,偏振值(FP)增高。通过检测增高的FP值,可确定目的片段单核苷酸多态性。采用本方法对98例全血的XPD基因第751位密码子进行了单核苷酸多态性分析,并与传统的荧光偏振检测方法进行了比较,取得满意结果。     

指数线性聚合酶链式反应法制备焦磷酸测序反应的单链模板

建立了一种简单的焦磷酸测序用单链模板制备方法,以包含SNP6位点一段78bp序列为对象,采用非热启动Taq酶进行指数线性PCR扩增,通过加入甘油、BSA等PCR增强剂增加反应的效率和特异性,设计反应液A和B处理PCR产物中干扰焦测序的限制性引物、未完全反应的产物、焦磷酸和dNTPs等杂质, 处理后1～2 μL PCR产物就可直接用于焦测序检测.测定了BRCA1基因中5个乳腺癌相关的SNP位点,获得的图谱无非特异性信号,测得序列与参考序列一致,能够进行SNP分析,表明本方法可以制备高质量焦测序单链模板,且使焦测序的成本显著降低,操作更为简便,减少了操作过程中样本间的交叉污染,有利于焦测序样品预处理的自动化.     

人类白细胞抗原基因HLA-B*58∶01基因型的快速低成本鉴别方法

采用焦磷酸测序技术和改进的全血基因组提取方法,建立了位于6号染色体的银屑病易感基因1候选基因1(Psoriasis susceptibility 1 candidate 1,PSORS1C1)rs9263726位点的焦磷酸测序方法,检出限达到0.4 ng/μL基因组DNA,20例标本的焦磷酸法和Sanger法测序结果完全一致.利用本方法对683例标本的rs9263726位点进行测序,得到中国人群该位点野生型(GG型)分布频率为87.6％,突变的GA型分布频率为11.7％、AA型分布频率为0.7％.通过对随机选取的46例标本rs9263726位点与人类白细胞抗原基因HLA-B* 58∶01基因型的连锁关系进行分析,结果表明,该位点预测HLA-B* 58∶01基因型的灵敏度为100％、特异性为91.3％.本方法可用于HLA-B* 58∶01基因型的检测.     

毛细管电泳-激光诱导荧光法检测HSP70-2基因多态性研究

建立了HSP70-2基因多态性的毛细管电泳-激光诱导荧光(CE-LIF)检测方法。采用试剂盒法提取人血清标本中全基因组DNA作为模板,选择特异引物进行PCR扩增反应,产物用Pst I限制性内切酶酶切;酶切产物用高灵敏度的SYBR Gold荧光染料标记后,用毛细管电泳-激光诱导荧光法检测。在优化的毛细管电泳-激光诱导荧光条件下,酶切产物在25 min内即可完成检测。GeneRular 100bp DNA ladder在同一天内连续测定6次,迁移时间和峰面积的RSD分别为1.8%~2.9%和2.8%~7.9%;连续6日测定迁移时间与峰面积的RSD分别为2.1%~4.3%和3.5%~9.3%。本研究共检测200份样品,其中G/G分型3份,A/G分型25份,A/A分型172份,检测结果与凝胶电泳结果一致。CE-LIF检测方法具有电泳时间短、试样消耗少、绿色环保等优点,能用于HSP70-2基因多态性的检测。     

基于克隆测序技术的人类白细胞抗原基因高分辨率分型方法的建立

运用优化的扩增和克隆测序技术,建立了人类白细胞抗原( HLA-B)基因的高分辨率分型方法。针对HLA-B基因保守区序列设计引物进行等位基因扩增,基于质粒不相容原理将杂合型等位基因有效克隆入质粒DNA中,经细菌培养后进行Sanger测序,根据测序结果经ClustalX2软件分析和IMTG/HLA数据库的BLAST比对即可完成HLA-B基因的高分辨率分型。利用建立的方法对7例临床样本进行了HLA-B基因分型,并且与第三方直接碱基序列分析基因分型技术( PCR-SBT)进行比对,结果完全一致。本方法无需专业分型软件,准确度高,成本低;采用通用引物进行等位基因的扩增和测序,无需传统方法中繁琐的引物设计和过程优化,实现了HLA-B基因的高分辨率分型。     

用于高度降解mRNA样本的非反转录基因表达量测定方法

许多生物样本(如石蜡包埋组织样本)中的mRNA易断裂为小片段,利用传统方法检测较困难。为了测定高度降解的mRNA,本研究针对待测mRNA短片段设计一对探针,当探针与待测模板杂交后,通过连接反应将两条探针5’与3’端相连,连接产物作为PCR扩增模板进行实时荧光定量检测,从而对待测mRNA进行定量测定。以人ACTB基因为待测靶标,通过测定不同浓度的待测靶标及与待测靶标序列不同的RNA片段,分别考察方法的灵敏度与特异性,并检测肺癌石蜡切片样本中ACTB基因的表达量,与传统的反转录定量PCR检测结果进行了对比。本方法的检出限为150 fmol/L,定量线性范围为150 fmol/L～300 pmol/L,并且具有良好的特异性。在对石蜡包埋组织样本中的基因表达量检测时,本方法扩增检测CT值比反转录实时定量PCR小,表明本方法更适合对高度降解的mRNA样本进行定量测定。     

实时荧光聚合酶链式反应偶联高特异性核酸侵入反应检测单核苷酸多态性

建立了实时荧光聚合酶链式反应( PCR)偶联高特性核酸侵入反应检测单核苷酸多态性( SNP)的方法。优化了体系中flap核酸内切酶1(FEN1酶)和野生型检测探针等用量,确定了最佳反应条件,即FEN1酶用量为1.5 U,野生型检测探针用量为0.125μmol/L,0.5μmol/L Invader突变型检测探针,各0.25μmol/L通用野生型( VIC)和突变型( FAM)荧光共振转移发卡探针,显著降低了野生型样本和突变型样本背景信号,避免了背景信号对检测结果分型的干扰。采用本方法对编码乙醛脱氢酶2( ALDH2)基因ALDH2*2位点21例样本、细胞色素P4502C19基因CYP2C19*2和CYP2C19*3位点各19例样本进行分型检测,结果表明, AL-DH2*2位点GG纯合10例,GA杂合8例,AA纯合3例;CYP2C19*2位点GG纯合9例,GA杂合8例,AA纯合2例;CYP2C19*3位点GG纯合18例,GA杂合1例。使用焦磷酸测序进行验证,两种方法检测结果一致。本方法特异性好、操作简便、耗时短、成本低,可实现对SNP单管闭管无污染的分型检测。     

未修饰的纳米金结合等位特异性扩增来检测K-ras基因点突变

将等位基因特异性扩增的特异性与纳米金特殊的光学性质相结合, 发展了一种新的基因点突变检测方法. 以肿瘤中常见的K-ras癌基因第12位密码子作为点突变检测对象, 采用突变型引物对待测序列进行等位特异性扩增. 突变型样品扩增产物中大部分是双链DNA; 而野生型样品由于不能被顺利扩增, 产物中大部分是单链DNA. 以纳米金颗粒作为报告基团, 向两种不同基因型扩增产物中依次加入纳米金胶和盐溶液, 野生型基因扩增产物中的单链引物被吸附到纳米金颗粒表面, 使得纳米金在适宜浓度的盐溶液中不发生聚集; 突变型样品扩增产物中的双链DNA由于与纳米金颗粒间存在静电斥力而不能被吸附到纳米金颗粒表面, 纳米金在该浓度的盐溶液中发生聚集, 导致两种基因型的混合液在吸收光谱和颜色方面均存在显著差异, 从而实现了检测基因点突变的目的. 该检测方法直观、快速、简便, 实验成本低, 能够检测到pmol量级的样品, 为点突变检测提供了一种实用的新方法.     

聚合酶链反应用于高效的基因改造

本文报道利用近年来发展起来的基因体外扩增技术——聚合酶链反应(PCR)进行高效的基因定向改造的结果。在构建新的EcoRI基因表达质粒时,为了在EcoRⅠ基因SD序列前改变一个碱基引入SalⅠ切点以缺失其启动子,同时将Glul44改造成Lys,我们回收分离pER101的1.5kb SalⅠ/PatⅠ片段作为模板,合成各带一个错配的两个25聚DNA片段作为扩增引物,利用Taq DNA聚合酶进行PCR扩增,结果经过30个循环,从约0.05μg模板DNA得到约10μg的0.49kbDNA。根据理论计算,扩增产物中突变片段占99％以上。用SalⅠ/BglⅠ酶切克隆入pUCl9 SalⅡ/BamHI,任意取两个重组子进行序列分析结果表明都发生了预期的突变。扩增产物已被克隆入pER304,使得EcoRl(Lys-144)基因置于PL下游以实现其控制的高表达。     

Detection of C677T mutation in methylenetetrahydrofolate reductase gene by denaturing high performance liquid chromatography

In this paper, we described an assay for the detection of the C677T mutation in the methylenetetrahydrofolate reductase (MTHFR) gene using denaturing high-performance liquid chromatography (DHPLC). The conditions for DHPLC analysis were systematically investigated based on a general HPLC instrument (Prostar VARIAN). A 225 bp DNA fragment covering the 677 site of MTHFR gene was amplified by PCR technology using the purified DNA from whole blood or whole blood as template DNA. PCR products were directly injected without the need for purification. The C677T mutation could be clearly distinguished by DHPLC technology. Our data demonstrated that DHPLC was a powerful and alternative tool for detection of genetic variants and single-nucleotide polymorphisms to electrophoresis technology.     

Multiple genotyping based on multiplex PCR and microarray

The genetic variability has obtained more and more attention in the process of diagnosis and treatment of tumors.Herein,we have described a multiple genotyping method based on magnetic enrichmentmultiplex PCR (MEM-PCR) and microarray technology.Monodisperse magnetic beads were fabricated and modified with streptavidin.Four loci on two genes (M235T and A-6G loci on AGT gene,A1298C and C677T loci on MTHFR gene) were selected to study single nucleotide polymorphisms (SNP).Target sequences of these SNP loci were amplified using Cy3-labeled primers through multiplex PCR in one tube after the templates were enriched and purified by functional magnetic beads (MB).Four pairs of NH₂-labeled probes,corresponding to each locus,were fixed on CHO-modified glass slide by covalent binding.Hybridization between target sequences and probes was performed under suitable conditions.The spotting locations on microarray and the ratio of fluorescence intensity,produced by different loci,were used to distinguish the SNP genotypes.Finally,three of gastric cancer samples were collected and genotyping analysis for these four SNP loci was carried out successfully simultaneously by this method.     

Genotyping of two single nucleotide polymorphisms in 5,10-methylenetetrahydrofolate reductase by multiplex polymerase chain reaction and capillary electrophoresis

Two single nucleotide polymorphisms (SNPs) of 5,10-methylenetetrahydrofolate reductase (MTHFR) gene, A1298C and C677T, were widely considered to be related with various neoplasia disorders. We established a simple and effective capillary electrophoresis (CE) method for detection of two SNPs in MTHFR gene simultaneously. DNA samples were amplified by multiplex PCR with universal fluorescence-labeled primer and analyzed by single-strand conformation polymorphism (SSCP)-CE method. The CE method was performed using 1.5% hydroxyethyl cellulose in 1× TBE buffer containing 1 M urea. The PCR products after SSCP procedure were electrokinetically injected at −10 kV, 30 s. Separation voltage was −6 kV and the temperature was set at 20 °C. The optimal SSCP-CE method was applied to detect two polymorphisms in MTHFR gene of acute lymphoblastic leukemia (ALL) and attention-deficit/hyperactivity disorder (ADHD) patients. Genotyping results were evaluated in terms of relationships between outcomes for ADHD patients after ALL chemotherapy and ALL disease. The SSCP-CE method and multiplex PCR with universal fluorescence primer were used as the fast technique for screening two SNPs in MTHFR gene, A1298C and C677T. The genotyping data were coincident with DNA sequencing. This SSCP-CE method was found feasible for detecting mutation of MTHFR gene in populations.     

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.     

A Method for Detection of Point Mutation Combined by Mutagenically Separated PCR with High Performance Liquid Chromatography

A method for detecting a known point mutation has been developed by combining mutagenically separated polymerase chain reaction with high performance liquid chromatography. C677T mutation from methylenetetrahydrofolate reductase gene (MTHFR) was chosen as model samples to assess the feasibility of this method. The annealing temperature for MS-PCR and gradient conditions for HPLC were systematically optimized. Under the optimized conditions, three genotypes of wild type, homozygous mutant and heterozygote (C677C, T677T, C677T) were clearly distinguished, and the data are identical to those obtained from capillary electrophoresis (CE) and from denaturing HPLC (DHPLC). The relative standard deviation (RSD) of this method calculated on the basis of retention times is ± 0.13% (n=7). Our preliminary results demonstrate that MS-PCR combined with HPLC is a simple, effective and highly reproducible technique for known point mutation detection, and may have potential applications in large-scale clinical diagnosis.     

Characterization of solution-phase DNA hybridization by fluorescence correlation spectroscopy: Rapid genotyping of C677T from methylenetetrahydrofolate reductase gene

In this paper, fluorescence correlation spectroscopy (FCS) was applied to measure the hybridization fraction of the ssDNA probe with its perfectly matched 146 mer ssDNA and a base mismatched 146 mer ssDNA from human methylenetetrahydrofolate reductase (MTHFR) gene. The ssDNA fragments in this study were obtained by asymmetric PCR techniques. The measurements were performed on a laboratory-built FCS system based on the two components fitting procedure. The obtained results showed that FCS could discriminate the difference of thermal stability between perfectly matched and mismatched DNA duplex, and be used to characterize the genotype of C677T in MTHFR gene. Our data illustrated that FCS was a useful tool for rapid screening of single point genetic mutations/polymorphisms (SNP) combined with DNA hybridization.     

Genotyping of single nucleotide polymorphism in γ-glutamyl hydrolase gene by capillary electrophoresis

The γ-glutamyl hydrolase (GGH) gene plays an important role in methotrexate (MTX) metabolism, ensuring that MTX polyglutamates (MTX-(Glu)(n)) could be converted back into MTX. Accumulation of MTX-(Glu)(n) is a problem in MTX therapy. SNP 452 C>T has been reported to associate with lower catalytic activity and higher accumulation of long-chain MTX-(Glu)(n) in patients treated with higher doses of MTX treatment. We propose and establish a simple and effective CE method for detecting SNP in GGH gene. The DNA samples after amplification were analyzed by SSCP-CE method. The CE conditions were generated by using 1× TBE buffer containing 1.5%?w/v hydroxypropyl methyl cellulose under reverse polarity at 25°C. This method was applied to detect genotyping of acute lymphoblastic leukemia patients receiving MTX treatment. The results were confirmed by DNA sequencing with good agreement. Concentrations of MTX-(Glu)(n) in whole blood were analyzed by on-line stacking CE method. MTX-(Glu)(n) levels and genotypes in GGH gene of acute lymphoblastic leukemia patients were evaluated. The SSCP-CE method was found to be feasible for SNP screening in the GGH gene.     

Quantification of key red blood cell folates from subjects with defined MTHFR 677C>T genotypes using stable isotope dilution liquid chromatography/mass spectrometry

Red blood cell (RBC) folate levels are established at the time of erythropoiesis and therefore provide a surrogate biomarker for the average folate status of an individual over the preceding four months. Folates are present as folylpolyglutamates, highly polar molecules that cannot be secreted from the RBCs, and must be converted into their monoglutamate forms prior to analysis. This was accomplished using an individual's plasma pteroylpolyglutamate hydrolase by lysing the RBCs in whole blood at pH 5 in the presence of ascorbic acid. Quantitative conversion of formylated tetrahydrofolate derivatives into the stable 5,10-methenyltetrahydrofolate (5,10-MTHF) form was conducted at pH 1.5 in the presence of [(13)C(5)]-5-formyltetrahydrofolate. The resulting [(13)C(5)]-5,10-MTHF was then used as an internal standard for the formylated forms of tetrahydrofolate that had been converted into 5,10-MTHF as well any 5,10-MTHF that had been present in the original sample. A stable isotope dilution liquid chromatography-multiple reaction monitoring/mass spectrometry method was validated and then used for the accurate and precise quantification of RBC folic acid, 5-methyltetrahydrofolate (5-MTHF), tetrahydrofolate (THF), and 5,10-MTHF. The method was sensitive and robust and was used to assess the relationship between different methylenetetrahydrofolate reductase (MTHFR) 677C>T genotypes and RBC folate phenotypes. Four distinct RBC folate phenotypes could be identified. These were classified according to the relative amounts of individual RBC folates as type I (5-MTHF >95%; THF <5%; 5,10-MTHF <5%), type II (5-MTHF <95%; THF 5% to 20%; 5,10-MTHF <5%), type III (5-MTHF >55%; THF >20%; 5,10-MTHF >5%), and type IV (5-MTHF <55%; THF >20%; 5,10-MTHF >5%).     

The influence of MTHFR C677T polymorphism in chronic lymphocytic leukemia

Some factors have been associated with the etiology of chronic lymphocytic leukemia (CLL), among them the Methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism. The aim of this study was to evaluate the role of MTHFR C677T polymorphism in CLL. A case‐control study was conducted with 219 individuals from Brazilian central population. MTHFR C677T polymorphism was determined through PCR‐RFLP followed by PAGE. The T allele frequence was higher in patients diagnosed with CLL than healthy subjects. However, when stratified by gender, the TT genotype was exclusively found in men diagnosed with CLL (p < 0.05). Adjusted multiple logistic regression analysis demonstrated that age was significantly linked to CLL predisposition (odds ratio = 1.08; p < 0.001). Studies evaluating the influence of genetic factors may provide insights on susceptibility for CLL.     

Analysis of the variations in IL-28RA gene and their association with allergic rhinitis

IL-28RA is one of the important candidate genes for complex trait of genetic diseases, but there is no published information of the genetic variation in this gene. We scanned the seven exons and their boundary introns sequence of IL-28RA including the promoter regions to analyze genetic variation sites, and identified eighteen single nucleotide polymorphisms (SNPs) and two variation sites. We chose seven SNPs (g.-1193 A>C, g.-30 C>T, g.17654 C>T, g.27798 A>G, g.31265 C>T, g.31911 C>T and g.32349 G>A) of them for large sample size genotyping, and assessed the association of genotype and allele frequencies of these SNPs between allergic rhinitis patients and non-allergic rhinitis controls. We also compared the genotype frequencies between Korean controls and Han Chinese control or Korean Chinese control. We investigated the frequencies of haplotype constructed by these SNPs between allergic rhinitis patients and non-allergic rhinitis controls. Our results suggested that the g.32349 G>A polymorphism of IL-28RA might be associated with susceptibility to allergic rhinitis (P=0.032), but seems to have no relationship with serum total IgE levels. The haplotype frequencies by these SNPs also show significant association between controls and allergic rhinitis patients.