多基因SNP位点及多种危险因素与老年汉族冠心病的关联分析

目的:探索老年冠心病多基因遗传易感性基础及相关的危险因素。方法:采用病例-对照研究方法,共入选老年汉族冠心病患者246例,非冠心病患者185例,纳入性别、年龄、吸烟,饮酒,高血压史、糖尿病史、高脂血症史、同型半胱氨酸、氨基末端脑钠肽前体、超敏C反应蛋白、抗凝血酶III、胆固醇、甘油三酯、高密度脂蛋白、低密度脂蛋白共15种危险因素与冠心病的关联性进行logistic回归分析。同时使用美国Sequenom高通量基因多态性分型技术研究了10种基因11个单核苷酸基因多态性(SNP)位点与冠心病的关联性。结果:15种危险因素中,发现增龄、高血压、抗凝血酶III(ATIII)下降是冠心病主要的危险因素,P<0.05。11个SNPs中3个SNP,血小板糖蛋白GP1BA rs2243093(-5T/C),血管紧张素转化酶ACE rs4332(547C/T)与ATIII rs2227589(893C/T)与老年汉族患者冠心病相关联。rs2243093(-5T/C)突变基因型CC与TT+AT比较,P=0.029(OR=3.41,CI:1.19-9.75);rs4332(547C/T)杂合型TC与CC+TT相比,P=0.003(OR=0.56,CI:0.38-0.82);rs2227589(893C/T),CT+CT与野生基因型CC相比较,P=0.003(OR=1.79,CI:1.22-2.63)。结论:增龄、抗凝血酶III下降、高血压是影响老年冠心病的主要危险因素,血小板、抗凝血系统、肾素-血管紧张素系统三种机制参与了老年冠心病的发生与发展。     

双向等位基因特异性PCR与限制性片段长度多态性基因分型方法比较

目的:比较双向等位基因特异性PCR(Bi-PASA)法与聚合酶链式反应-限制性片段长度多态性(RFLP)法对EZH2基因单核苷酸多态性(SNPs)位点rs887569基因分型结果有无差异,并用Bi-PASA法对EZH2基因rs17171119位点基因分型后分析与结直肠癌(CRC)易感性的相关性。方法:提取96名CRC患者与100名体检健康者的外周血DNA,分别用Bi-PASA法与聚合PCR-RFLP法检测EZH2基因单核苷酸多态性(SNPs)位点rs887569基因型,对两种分型结果进行比较;使用Bi-PASA法对EZH2基因rs17171119位点进行基因分型后用病例-对照方法分析该SNPs在中国人群中的分布。结果:Bi-PASA与PCR-RFLP对EZH2基因rs887569位点基因分型的准确率分别为99.5%和100%;EZH2基因的rs17171119 SNPs位点多态性与结直肠癌易感性无显著相关性(P=0.938,OR=0.846,95%CI:0.586-1.221)。结论:Bi-PASA是一种简单有效检测SNPs的方法,分型结果较为可靠;rs17171119 SNPs位点多态性与结直肠癌易感性无关,但本结论还有待更大样本量基因分型的验证。     

中国汉人纤维蛋白原β链基因-148C/T,-455G/A多态性与冠心病关系的Meta分析

有关中国汉人纤维蛋白原β链基因多态性与冠心病关系的研究屡见报道,但不同的研究之间结果存在一定的差异.本研究根据相应的入选条件,通过文献检索收集中国汉人纤维蛋白原β链基因-148C/T,455G/A多态性与冠心病关系的病例-对照研究,剔除不符合要求的文献,对入选文献进行一致性检验并根据检验结果进行数据合并荟萃(Meta)分析,计算总OR值.共13篇文献符合要求纳入研究,其中7篇关于-148C/T多态性研究包括1488例冠心病患者和1234例对照人群,9篇关于-455G/A多态性的研究包括1023名患者和1081名对照者,入选研究无明显发表偏倚,入选研究的同质性检验显示各研究结果间存在明显的异质性,数据合并结果显示-148C/T多态性位点C/T T/T比C/C的OR值为1.31,95%CI为0.94~1.84(P=0.11),-455G/A多态性位点G/A A/A比G/G的OR值为1.75,95%CI为1.24~2.46(P=0.001).本研究的初步结果显示纤维蛋白原β链基因-455G/A多态性与中国汉人冠心病易感性相关,-455A等位基因可能是冠心病的遗传易感基因,-148C/T基因多态性与中国汉人冠心病易感性无明显关系.     

人染色体8p11(CHRNB3-CHRNA6)区域基因多态性与中国汉族人群肺癌易感性的相关性

为探讨人染色体8p11(CHRNB3-CHRNA6)区域基因多态性与中国汉族人群肺癌遗传易感性之间的关系,文章采用病例-对照研究,对784例肺癌患者和782例性别、年龄、籍贯频数与之相匹配的健康对照中该区域6个标签SNP位点进行基因分型,并统计分析其基因型频率分布与肺癌易感性的关系,以及吸烟在其中的影响。结果发现rs16891561位点TT基因型在60岁以上人群(校正OR=0.42,95%CI=0.20-0.88;P=0.022)、女性人群(校正OR=0.34,95%CI=0.13-0.87;P=0.025)、非吸烟人群中(校正OR=0.32,95%CI=0.13-0.79;P=0.013)对肺癌发生具有保护效应;rs4236926位点TT基因型在60岁以上人群(校正OR=0.48,95%CI=0.23-0.99;P=0.048)、非吸烟人群(校正OR=0.32,95%CI=0.13-0.80;P=0.014)中对肺癌发生具有保护效应,这两种保护效应主要是与腺癌相关。对这两个位点进行累积效应分析发现,含有3~4个变异等位基因型的非吸烟者罹患肺癌的风险显著降低(校正OR=0.29,95%CI=0.11-0.71;P=0.007),并且,含有3~4个变异等位基因型的个体累计吸烟量("包-年"平均数=13.2)与其他个体相比显著降低。由此可见人染色体8p11(CHRNB3-CHRNA6)区域基因多态性与中国汉族人群肺癌易感性和吸烟行为相关。     

易感基因多态性与支气管哮喘的相关性研究

目的:探讨白介素-4(Interleukin-4,IL-4)基因589位点、白介素-4受体(interleukin-4 receptor,IL-4R)基因576位点多态性与内蒙古地区汉族支气管哮喘患者是否存在遗传易感性,是否与血清总IgE浓度相关.方法:采用聚合酶链式反应-限制性片段长度多态性(PCR-RFLP)方法检测内蒙古地区62例支气管哮喘患者和30例汉族正常人群IL-4基因的589位点、IL-4R基因的576位点多态性,进行基因型和基因频率分析,同时采用Elisa法检测患者血清总IgE浓度.结果:哮喘组IL-4基因启动子区-589(C/T)位点多态性分布频率与对照组比较,两组间基因型频率分析(X2=3.437,P=0.179),无显著性统计学差异(P＞0.05);两组基因频率分析(X2=9.405,P=0.002),有显著性差异(P＜0.05).哮喘组IL-4R基因启动子区-576(Q/R)位点多态性分布频率与对照组比较,两组间基因型频率分析(X2=0.815,P=0.665),无显著性统计学差异(P＞0.05),两组基因频率分析(X2=0.245,P=0.621),无显著性差异(P＞0.05).哮喘组血清总IgE浓度高于对照组,有显著性差异(t=6.367,P=0.00,P＜0.05).结论:内蒙古地区汉族人群哮喘组中,IL-4基因启动子区-589(C/T)位点多态性与支气管哮喘的发病无显著性差异;IL-4R基因-576(Q/R)位点多态性与支气管哮喘的发病无显著性差异;患者组血清总IgE显著高于对照组,但是与IL-4基因启动子区-589(C/T)位点多态性和IL-4R基因-576(Q/R)位点多态性没有相关性.     

应用寡核苷酸芯片并行检测CYP1A1和 GSTM1基因多态性

利用寡核苷酸芯片检测方法分析CYP1A1单核苷酸多态性 (SNP)和GSTM1缺失与否 ,实验结果证明了寡核苷酸芯片技术可并行、准确、高效地检测基因的单核苷酸多态性和其他类型的基因多态型 ,可为疾病遗传易感性及单体型的研究提供强有力的研究工具。采用该寡核苷酸芯片 ,检测了 84份正常人的血液DNA样本 ,其中GSTM1基因缺失率达到 4 7 6 % ,接近报道数值。统计分析发现 ,CYP1A1m1 m2的 3种基因型组合TT AG、TT GG和TC GG的发生频率都为 0 ,而根据实验得到的m1和m2各自基因型数据计算 ,它们的发生频率应是11 4 %、2 6 %和 3 1% ,所以推测在所检测的样本中没有T(m1位点 )和G(m2位点 )的连锁组合 ,即m1和m2位点的组合只有 3种单体型 :T A、C A和C G ,其发生频率分别是 6 9 6 %、7 7%和 2 2 6 %。     

多巴胺D4受体基因启动子区多念性位点与注意缺陷多动障碍的关联研究

目的:探讨多巴胺D4受体基因启动子区-1240L/S,-616C/G和-521C/T三个多态性与注意缺陷多动障碍(Attention deficit hyperactivity disorder,ADHD)的关系.方法:取无亲缘关系的ADHD患者及对照组各166名,采用等位基因特异性扩增技术(allele specific amplification,ASA)及聚合酶链式反应琼脂糖凝胶电泳技术,检测ADHD患者和对照组基因型和等住基因的频率分布.结果:DRD4基因-521C/T的基因型及等位基因频率分布在ADHD组与正常对照组存在显著性差异(p＜0.05),ADHD组的T等位基因的频率显著高于正常对照组(x2=9.827,p=0.002,OR=1.639,95%CI=1.202-2.234).DRD4基因启动子区2个功能多态性位点-616C/G及-1240L/S的基因型及等位基因频率在正常组与ADHD组的分布无显著性差异(p＞0.05).结论:-521C/T位点与ADHD的易感性存在关联,且-521C/T等位基因是决定ADHD个体易感性的重要因素,含有T等位基因的个体罹患注意缺陷多动障碍的相对风险增高.     

IL-10基因多态性与子宫内膜异位症易感性的相关性研究

目的:探究白细胞介素-10(IL-10)基因多态性与子宫内膜异位症(EMs)易感性的相关性。方法:选取87例经病理组织学证实为EMs患者,对照组为100例健康女性,应用聚合酶链反应-限制性片段长度多态性(PCR-RFLP)分析方法,对两组妇女IL-10-1082、-819和-592位点的基因行多态性分析。结果:与对照组相比,EMs组-1082G/A位点等位基因及基因频率无差异(P0.05),-819 T/C和-592A/C位点等位基因或基因型频率较高(P0.05);与Ⅰ-Ⅱ期EMs患者相比,Ⅲ-Ⅳ期EMs患者-819T/C和-592A/C位点等位基因或基因型频率显著较高(P0.01)。结论:IL-10基因在-819T/C以及-592A/C位点的多态性与EMs的易感性有显著相关性。     

Ⅰ型干扰素受体启动子多态性与慢性乙型肝炎易感性的相关性研究

目的 研究Ⅰ型干扰素受体启动子(IFNAR1)的基因多态性在不同个体间的差异,以及它们与慢性乙型肝炎病毒(HBV)感染之间的相关性。方法 对320例慢性乙型肝炎患者、148例自发康复者、148例健康对照和114例正常高加索人的IFNAR1进行基因分型,分析基因的多态性与慢性HBV感染的易感性之间的相关性;构建IFNAR1启动子-荧光素酶报告基因载体,比较不同IFNAR1启动子变异体的转录活性。结果 在-568,-408,-77和-3位点发现基因多态性,其中-568和-77位点,以及-408和-3位点之间存在等位基因连锁。相关性分析结果表明,-568G、-408C和单体型-568G/-408C/-3C/-77(M)与病毒清除有关,-568C、-408T和单体型-568C/-408T/-3T/-77(L)与HBV感染的慢性化有关。启动子-荧光素酶报告基因载体的检测显示,-408和(或)-3位点的多态性可影响调节IFNAR1启动子的转录水平,而-568位点的多态性总体上对转录活性无明显的影响。-77(9)在高加索人中明显多见,携带这一基因型启动子的转录活性明显高于其他基因型启动子的转录活性。结论 IFNAR1的基因多态性与慢性HBV感染的易感性有相关性。     

亚甲基四氢叶酸还原酶基因C677T、G1793A 单核苷酸多态性 与散发性乳腺癌易感性的关系

目的:研究亚甲基四氢叶酸还原酶(MTHFR)基因C677T、G1793A位点单核苷酸多态性与散发性乳腺癌易感性关系。方法:采用聚合酶链反应-限制性片段长度多态性(PCR-RFLP)方法,对200例乳腺癌患者及200例正常对照者MTHFR基因C677T、G1793A位点单核苷酸多态性进行分析,logistic回归分析不同基因型与乳腺癌风险的关系。结果:乳腺癌组MTHFR 677TT基因型频率为25.00%显著高于正常对照组的10.50%(X2=14.401,P=0.001),CT基因型频率为44.50%低于正常对照组的54.50%,CC基因型频率在乳腺癌组和正常对照组中无差别;MTHFR 1793GA基因型频率为18.50%显著高于正常对照者的8.50%(X2=8.563,P=0.003)。乳腺癌患者MTHFR 677T和1793A等位基因频率分别为47.25%、9.25%,显著高于对照组中的37.75%、4.25%。MTHFR 677TT基因型携带者罹患乳腺癌的风险是677CC基因型携带者的2.732倍(95%CI=1.418～5.051,P=0.001),MTHFR1793GA基因型携带者罹患乳腺癌的风险是1793GG基因型携带者的2.444倍(95%CI=1.325～4.505,P=0.003)。另外,乳腺癌组中MTHFR C677T基因多态性与肿瘤大小相关(x2=7.431,P=0.024,MTHFR G1793A基因多态性与淋巴结转移情况(x2=8.939,P=0.011)、癌组织学分级(x2=9.983,P=0.007)相关。结论:MTHFR C677T、G1793A基因多态性与散发性乳腺癌的易感性相关。     

Allelic imbalance analysis by high-density single-nucleotide polymorphic allele (SNP) array with whole genome amplified DNA

Besides their use in mRNA expression profiling, oligonucleotide microarrays have also been applied to single-nucleotide polymorphism (SNP) and loss of heterozygosity (LOH) or allelic imbalance studies. In this report, we evaluate the reliability of using whole genome amplified DNA for analysis with an oligonucleotide microarray containing 11 560 SNPs to detect allelic imbalance and chromosomal copy number abnormalities. Whole genome SNP analyses were performed with DNA extracted from osteosarcoma tissues and patient-matched blood. SNP calls were then generated by Affymetrix® GeneChip® DNA Analysis Software. In two osteosarcoma cases, using unamplified DNA, we identified 793 and 1070 SNP loci with allelic imbalance, respectively. In a parallel experiment with amplified DNA, 78% and 83% of these SNP loci with allelic imbalance was detected. The average false-positive rate is 13.8%. Furthermore, using the Affymetrix® GeneChip® Chromosome Copy Number Tool to analyze the SNP array data, we were able to detect identical chromosomal regions with gain or loss in both amplified and unamplified DNA at cytoband resolution.     

Metal ion CHElate-aSSisted LIGAtion (CHESS LIGA) for SNP detection on microarrays

We developed a metal ion chelate-assisted ligation for SNP detection by microarray. An oligonucleotide probe was separated into two 9-10-mers bearing iminodiacetic residues at the gap point. Duplex formation with the DNA target was possible only if nickel ions were added, but a nucleotide substitution opposite the gap point prevented duplex formation. Here we demonstrate the application of this approach for SNP detection (A1298C) within the 5,10-methylenetetrahydrofolate reductase gene on a microarray.     

Single-feature polymorphism discovery in the barley transcriptome

A probe-level model for analysis of GeneChip gene-expression data is presented which identified more than 10,000 single-feature polymorphisms (SFP) between two barley genotypes. The method has good sensitivity, as 67% of known single-nucleotide polymorphisms (SNP) were called as SFPs. This method is applicable to all oligonucleotide microarray data, accounts for SNP effects in gene-expression data and represents an efficient and versatile approach for highly parallel marker identification in large genomes.     

Estimation of relative allele frequencies of single-nucleotide polymorphisms in different populations by microarray hybridization of pooled DNA

Single-nucleotide polymorphisms (SNPs) are considered useful polymorphic markers for genetic studies of polygenic traits. A new practical approach to high-throughput genotyping of SNPs in a large number of individuals is needed in association study and other studies on relationships between genes and diseases. We have developed an accurate and high-throughput method for determining the allele frequencies by pooling the DNA samples and applying a DNA microarray hybridization analysis. In this method, the combination of the microarray, DNA pooling, probe pair hybridization, and fluorescent ratio analysis solves the dual problems of parallel multiple sample analysis, and parallel multiplex SNP genotyping for association study. Multiple DNA samples are immobilized on a slide and a single hybridization is performed with a pool of allele-specific oligonucleotide probes. The results of this study show that hybridization of microarray from pooled DNA samples can accurately obtain estimates of absolute allele frequencies in a sample pool. This method can also be used to identify differences in allele frequencies in distinct populations. It is amenable to automation and is suitable for immediate utilization for high-throughput genotyping of SNP.     

Development of a MLST-biased SNP microarray for Candida albicans

We have developed a single nucleotide polymorphism (SNP) detection microarray for the human pathogenic yeast, Candida albicans, consisting of synthetic oligonucleotides bound to microscope slides. The array consists of multiple replicates of 79 SNPs, derived from 19 discrete loci located on all eight chromosomes. These loci include seven genes consisting of 57 SNPs that comprise a multi-locus sequence typing (MLST) consensus scheme for the species. The remaining 22 SNPs are from 12 additional loci located at intervals on the remaining chromosomes. In order to include highly informative polymorphisms from the MLST set on the array we performed a linkage analysis of major genotypes between the two pairs of MLST-linked genes. In addition, we performed a matched-set analysis for each SNP located within individual MLST loci. This analysis resulted in the reduction of informatively redundant mutations in the array for a large percentage of strains. We believe that a SNP array will be helpful in extending our knowledge of the epidemiology and genetics of C. albicans as a supplement to MLST typing.     

寡核苷酸芯片技术用于检测过氧化物酶体活化物激活受体基因多态性

 通过寡核苷酸芯片技术检测PPARα基因Leu162Val、Val227Ala多态性和PPARγ Pro12Ala的基因多态性,建立一种快速、简便、准确的方法,为研究非酒精性脂肪性肝病的发病机制、临床诊断和治疗提供依据.收集人体外周血标本,提取DNA进行PCR扩增,设计相应的探针和引物,制备检测芯片,PCR产物与芯片杂交后,扫描芯片并分析结果.PCR产物进行测序验证.寡核苷酸芯片技术检测PPARα基因Leu162Val、Val227Ala多态性和PPARγ Pro12Ala基因多态性结果与测序结果一致.寡核苷酸芯片技术检测非酒精性脂肪性肝病(NAFLD)密切相关的PPAR基因多态性快速、准确,值得临床推广和应用.     

Effect of secondary structure on single nucleotide polymorphism detection with a porous microarray matrix; implications for probe selection

Oligonucleotide arrays capable of detecting single nucleotide polymorphisms (SNPs) from amplified nucleic acid have many applications. The expected SNP is usually placed approximately in the center of the probe to ensure the maximum shift in Tm between complementary and SNP sequences. Unfortunately, different short probes (< 30 bases) selected using widely accepted criteria do not perform consistently in this type of assay. Here we present a systematic study on the effect of secondary structure on the ability of oligonucleotide probes to detect an SNP, using real-time array monitoring of a porous microarray substrate that incorporates a novel intra-array mixing system. These results demonstrate that, although positioning of an SNP in the middle of the probe is highly destabilizing, the effect of stable secondary structure on the signal obtained is so dramatic that such probes may be very insensitive. Therefore, if the SNP flanking sequence contains significant secondary structure, then more sensitive probes with good specificity may be obtained by positioning the mutation towards one end of the probe.     

Associations Between Milk Performance Traits in Holstein Cows and 16 Candidate SNPs Identified by Arrayed Primer Extension (APEX) Microarray

An oligonucleotide microarray—which allows for parallel genotyping of many SNPs in genes involved in cow milk protein biosynthesis—was used to identify which of the 16 candidate SNPs are associated with milk performance traits in Holstein cows. Four hundred cows were genotyped by the developed and validated microarray. Significant associations were found between four single SNPs, namely DGAT1 (acyloCoA:diacylglycerol acyltransferase), LTF (lactoferrin), CSN3 (kappa-casein), and GHR (growth hormone receptor) and with fat and protein yield and percentage. Many significant associations between combined genotypes (two SNPs) and milk performance traits were found. The associations between the combined genotypes DGAT1/LTF and DGAT1/LEPTIN analyzed traits are presented as examples.

The microarray based on APEX (Arrayed Primer Extension) is a fast and reliable method for multiple SNP analysis of potential application in marker-assisted selection. After further development, the chip may prospectively be used for dairy cattle paternity analysis and evolutionary studies.     

High-throughput polymorphism screening and genotyping with high-density oligonucleotide arrays

A highly reliable and efficient technology has been developed for high-throughput DNA polymorphism screening and large-scale genotyping. Photolithographic synthesis has been used to generate miniaturized, high-density oligonucleotide arrays. Dedicated instrumentation and software have been developed for array hybridization, fluorescent detection, and data acquisition and analysis. Specific oligonucleotide probe arrays have been designed to rapidly screen human STSs, known genes and full-length cDNAs. This has led to the identification of several thousand biallelic single-nucleotide polymorphisms (SNPs). Meanwhile, a rapid and robust method has been developed for genotyping these SNPs using oligonucleotide arrays. Each allele of an SNP marker is represented on the array by a set of perfect match and mismatch probes. Prototype genotyping chips have been produced to detect 400, 600 and 3000 of these SNPs. Based on the preliminary results, using oligonucleotide arrays to genotype several thousand polymorphic loci simultaneously appears feasible.     

Unrecognized sequence homologies may confound genome-wide association studies

Genome-wide association studies (GWAS) have become a preferred method to identify new genetic susceptibility loci. This technique aims to understanding the molecular etiology of common diseases, but in many cases, it has led to the identification of loci with no obvious biological relevance. Herein, we show that previously unrecognized sequence homologies have caused single-nucleotide polymorphism (SNP) microarrays to incorrectly associate a phenotype to a given locus when in fact the linkage is to another distant locus. Using genetic differences between male and female subjects as a model to study the effect of one specific genomic region on the whole SNP microarray, we provide strong evidence that the use of standard methods for GWAS can be misleading. We suggest a new systematic quality control step in the biological interpretation of previous and future GWAS.