高通量SNP基因分型技术研究进展

在后基因组时代,单核苷酸多态性研究已迅速成为了生物医学许多领域的焦点。发展可靠、敏感、经济、稳定、高通量的SNP基因分型技术已迫在眉睫。本文主要着重于高通量SNP基因分型技术的原理、利弊以及这些技术在这个领域过去几年中的进展。     

单核苷酸多态性基因分型技术原理与进展

在基因组规模了解遗传变异与生物功能之间的关系可望为生物学带来全新的深入认识。本从等位基因分型机理、反应形式和检测方法等三个方面讨论SNP分型方法的现状,并简要介绍了目前应用的一些分型方法。     

应用FP-TDI技术进行高通量单核苷酸多态分型

FP-TDI (fluorescence polarization template-directed dye-terminator incorporation）是一种操作简单、实验投入少、适于高通量反应的单核苷酸多态等位基因分型技术.使用两种评价分型图像质量的数值指标,可以有效地对分型结果进行评价,使该技术得到了改进.在此基础上优化了实验条件,并应用该技术,对人类基因组3号染色体上随机选取的337个单核苷酸多态性位点进行了高通量分型,反应的一次成功率达到59.94%.     

海洋生物单核苷酸多态性基因分型技术的研究进展

单核苷酸多态性(single nucleotide polymorphism,SNP)是一类广泛分布于基因组中由单个碱基差异引起的DNA序列变异,SNP标记是第三代分子标记的代表。随着大规模测序技术的快速发展,大量的候选SNP位点被发现,候选SNP位点的发掘需要合适的分型技术。从等位基因分型机制、反应方式和检测等位基因方法等方面介绍当前海洋生物SNP分型技术的研究进展,以期为不同试验目的的研究选择合适的SNP分型技术提供参考。     

高通量飞行时间质谱基因分型方法的研究

为了考察飞行时间质谱基因分型方法 (MALDI-TOF) 的位点分型成功率和分型结果质量的关系,分析了 96 个 SNPs 位点的近 10 000 个基因分型数据 (用 MALDI-TOF “4 重”实验方法检测 ). 结果显示,位点分型成功率和分型结果的质量显著正相关 . 分型成功率低于 82% 的 SNP 位点,其高质量结果占的比例开始逐渐降低 . 提示 82% 的分型成功率可以作为衡量分型结果质量的数据点 . 为了进一步提高通量并降低成本,在 MALDI-TOF “ 4 重”实验方法的基础上,发展了两种“准 8 重”实验方法 . 用新的实验方法检测了 95 个样本的 32 个 SNPs 位点 . 结果显示“混合准 8 重”实验方法与“ 4 重”实验方法相比无显著差异,而“复点准 8 重”的结果差于“ 4 重”分型方法 .     

利用动态等位基因特异性杂交技术进行单核苷酸多态高通量分型

动态等位基因特异性杂交(dynamic allele-specific hybridization, DASH)是新发展起来的一种单核苷酸多态(single nucleotide polymorphisms, SNP)等位基因分型技术,具有快速、经济、准确、高通量、重复性好等优点.利用DASH技术,对96份正常人外周血DNA样品成功地进行了两个SNP位点的基因分型,并摸索实验条件,对该技术进行了优化.     

血痕Chelex 100抽提DNA用于人类TNF-α基因启动子区SNP分型

建立快速、简便的血样本采集及DNA抽提方法,可用于大规模的分子流行病学调查及群体遗传学研究。采用无菌纱布为载体取血,Chelex100快速抽提DNA,用TaqMan MGB探针对人类TNF-α基因启动子区-857（C／T）位点进行SNP分型。344份血样均得到明确的分型结果,获得的荧光信号强,本底低。深圳地区汉族群体-857位点基因型频率分别为：cc为0.78,ct为0.21,tt为0.01。血痕Chelex100抽提DNA为大规模血样本的采集,DNA的抽提提供了有效的手段。     

SNPs分子标记技术在昆虫学研究中的应用

单核苷酸多态性(single nucleotide polymorphisms,SNPs)主要是指在染色体基因组水平上由于单个核苷酸的变异而引起的DNA序列多态性,包括单碱基的转换或颠换引起的点突变,其中最少出现1种等位基因频率不小于1%,常以双等位基因的形式出现,稳定而可靠。在目前的昆虫基因组研究中,SNPs标记的研究主要集中在果蝇、蚊媒、家蚕等一些模式生物。本文对SNPs标记在昆虫的种类鉴定、遗传图谱构建、种群遗传学、抗药性分子机理等方面进行了综述,最后展望了SNPs在种群遗传、标记辅助选择和生物进化等研究领域中的应用前景。     

人类基因组单核苷酸多态性的研究进展

随着分子遗传学的进展 ,疾病遗传学研究从简单的单基因疾病转向复杂的多基因疾病 (如骨质疏松症、糖尿病、心血管疾病、精神性紊乱、各种肿瘤等 )与药物基因组学的研究。与前者相比 ,多基因性状或遗传病的形成 ,受许多对微效加性基因作用。这些不同基因构成的遗传背景中 ,可能有易感性主基因 (ｍａｊｏｒｇｅｎｅ)起着重要作用。它们同时还受环境因素的制约 ,彼此间相互作用错综复杂 ,所以任一基因的多态性对疾病发生仅起微弱的作用。鉴于此 ,需要在人类基因组中找到一种数目多、分布广泛且相对稳定的遗传标记。单核苷酸多态性 (ｓｉｎｇｌ…     

应用RAPD技术分析奥利亚罗非鱼和尼罗罗非鱼的基因多态性

以随机扩增多态DNA技术(RAPD）分析了奥利亚罗非鱼和尼罗罗非鱼两个养殖群体的群体内及群体间遗传关系,并探讨了该技术在种群鉴定中的应用。RAPD引物筛选结果表明,所测试的20个随机引物中(Table 1),除一个引物未扩增出任何片段外,其余19个引物均扩增出1～11个大小不等的片段,长度大部分在500—3000bp之间,共扩增出220个片段,平均每个引物产生55个片段。两群体间共有片段70条,大部分引物的扩增产物具有种间多态性,种群间相似系数为0.727。以筛选的引物对两种群不同个体(Fig．1,Table 2)及种群混合样品(Fig.2,Table 3)进行RAPD分析。结果表明,不同引物在扩增图谱上表现很大差异：奥利亚罗非鱼不同个体间表现为一致的扩增图谱,种内相似系数达1000,显示了其种群内遗传变异的缺乏;尼罗罗非鱼种内相似系数为0．827,个体间存在不同程度的多态性;两个种群间的相似系数分别为0．767和0.742,表明种间有较高的同源性,遗传距离为0．235,略低于国外的报道．此外,两个养殖群体间的扩增图谱比较也暗示了遗传渐渗现象的存在。实验表明,RAPD标记可以作为一种可靠的遗传标记,用于不同鱼类种群的鉴定,RAPD分析方法是一种快速,简便且行之有鼓的鉴定鱼类种群的方法。     

Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays

We present a genotyping method for simultaneously scoring 116,204 SNPs using oligonucleotide arrays. At call rates >99%, reproducibility is >99.97% and accuracy, as measured by inheritance in trios and concordance with the HapMap Project, is >99.7%. Average intermarker distance is 23.6 kb, and 92% of the genome is within 100 kb of a SNP marker. Average heterozygosity is 0.30, with 105,511 SNPs having minor allele frequencies >5%.     

Multiplex Genotyping of Cytokine Gene SNPs Using Fluorescence Bead Array

Single nucleotide polymorphisms (SNPs) of genes that affect cytokine production and function are known to influence the susceptibility and progression of immune-related conditions such as infection, autoimmune diseases, transplantation, and cancer. We established a multiplex genotyping method to analyze the SNPs of cytokine genes by combining the multiplex PCR and bead array platform. Thirteen cytokine gene regions, including 20 SNPs, were amplified, and allele-specific primer extension was performed in a single tube. High-quality allele-specific primers were selected for signals greater than 1000 median fluorescence intensity (MFI) for positive alleles, and less than 500 MFI for negative alleles. To select and improve the extension primers, modifications for the reverse direction, length or refractory were performed. 24 primers in the forward or reverse direction step and 12 primers in length or refractory modifications were selected and showed high concordance with results by nucleotide sequencing. Among the 13 candidate cytokine genes, the SNPs of 12 cytokine genes, including IL-1α, IL-1R, IL-1RA, IL-1β, IL-2, IL-4, IL-4Rα, IL-6, IL-10, IL-12, TGF-β1, and TNF-α, were successfully defined with the selected allele-specific primers in healthy Korean subjects. Our genotyping system provides a fast and accurate detection for SNPs of multiple cytokine genes to investigate their association with immune-related diseases and transplantation outcomes.     

A Simple CELI Endonuclease-Based Protocol for Genotyping both SNPs and InDels

Modern genetic analyses rely on efficient genotyping of single-nucleotide polymorphisms (SNP) or insertion/deletion length polymorphisms (InDel) in genomes. Methods available to genotype these polymorphisms include sequencing, cleaved amplified polymorphic sequence, high-resolution DNA melting, and microarray analyses, which are all rather tedious or expensive to set up for daily use. Here, we report a simplified label-free CELI endonuclease (CELI)-based protocol that enables us to detect both SNPs and InDels for fragment lengths between 500 and 6 kb. PCR-amplified target DNA fragments were annealed, cleaved by CELI, and analyzed either cost-effectively by agarose gel electrophoresis or automatically by capillary electrophoresis. The optimal amplification sizes, potential blind ends, and the maximum pooling capacities were examined for both electrophoresis protocols. We believe that the CELI-based genotyping protocol can be used in the detection of mutations, marker-assisted breeding, map-based cloning, and genome-wide association studies.     

Genotyping single nucleotide polymorphisms (SNPs) across species in Old World Monkeys

The development of DNA markers is becoming increasingly useful in the field of primatology for studies on paternity, population history, and biomedical research. In this study, we determine the efficacy of using cross-species amplification to identify single nucleotide polymorphisms (SNPs) in closely related species. The DNA of 93 individuals representing seven Old World Monkey species was analyzed to identify SNPs using cross-species amplification and genotyping. The loci genotyped were 653 SNPs identified and validated in rhesus macaques. Of the 653 loci analyzed, 27% were estimated to be polymorphic in the samples studied. SNPs identified at the same locus among different species (coincident SNPs) were found in six of the seven species studied with longtail macaques exhibiting the highest number of coincident SNPs (84). The distribution of coincident SNPs among species is not biased based on proximity to genes in the samples studied. In addition, the frequency of coincident SNPs is not consistent with expectations based on their phylogenetic relationships. This study demonstrates that cross-species amplification and genotyping using the Illumina Golden Gate Array is a useful method to identify a large number of SNPs in closely related species, although issues with ascertainment bias may limit the type of studies where this method can be applied.     

三色荧光技术在SNP检测中的应用

利用三色荧光标记的A、C、T双脱氧核苷酸单碱基延伸的方法结合编码寡核苷酸芯片技术检测单核苷酸多态性 (SNP)的基因型。以beta地中海贫血样本基因 (HBB基因 )突变作为模型的研究结果显示该方法能同时对多位点的SNP进行检测。     

炭疽芽孢杆菌分子分型研究进展

随着分子生物学的发展,分子分型技术被广泛应用于鉴别炭疽芽孢杆菌菌株间的遗传相关性和流行病学特征。我们就近年来常用的炭疽芽孢杆菌分子分型方法的优缺点和研究进展进行综述。     

后GWAS时代结直肠癌致病SNP功能机制的研究进展

结直肠癌(colorectal cancer, CRC)是受遗传与环境因素共同影响的复杂疾病,其中遗传因素发挥重要作用。至今,全基因组关联研究(genome-wide association studies, GWAS)已经发现了大量与结直肠癌风险相关的遗传变异。随之而来的后GWAS时代,越来越多的研究侧重于利用多组学数据和功能实验对潜在的致病位点进行解析。分析表明绝大多数风险单核苷酸多态性(single nucleotide polymorphism,SNP)位于非编码区,可能通过影响转录因子结合、表观遗传修饰、染色质可及性、基因组高级结构等,调控靶基因表达。本文对后GWAS时代结直肠癌致病位点的机制研究进行综述,阐述了后GWAS对于理解结直肠癌分子机制的重要意义,并探讨了结直肠癌GWAS的应用和前景,为实现GWAS成果转化提供参考。     

丙型肝炎病毒基因分型研究进展及临床意义

丙型肝炎是经血或血制品传播的急慢性肝炎类疾病,可转化为肝硬化或肝癌.其致病因子丙型肝炎病毒是一种高异质性RNA病毒,可根据其基因变程度的不同分为多个基因型与亚型,其基因分型与地理分布,病情进展及干扰素的治疗效果有关,近年来发展出了多种检测基因分型的方法.本文就近年来丙型肝炎基因分型的各种检测方法作一比较并综述了基因分型的临床意义,为临床对各种检测方法的选择提供一定的依据.     

Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology

Background

The dissection of complex traits of economic importance to the pig industry requires the availability of a significant number of genetic markers, such as single nucleotide polymorphisms (SNPs). This study was conducted to discover several hundreds of thousands of porcine SNPs using next generation sequencing technologies and use these SNPs, as well as others from different public sources, to design a high-density SNP genotyping assay.

Methodology/Principal Findings

A total of 19 reduced representation libraries derived from four swine breeds (Duroc, Landrace, Large White, Pietrain) and a Wild Boar population and three restriction enzymes (AluI, HaeIII and MspI) were sequenced using Illumina''s Genome Analyzer (GA). The SNP discovery effort resulted in the de novo identification of over 372K SNPs. More than 549K SNPs were used to design the Illumina Porcine 60K+SNP iSelect Beadchip, now commercially available as the PorcineSNP60. A total of 64,232 SNPs were included on the Beadchip. Results from genotyping the 158 individuals used for sequencing showed a high overall SNP call rate (97.5%). Of the 62,621 loci that could be reliably scored, 58,994 were polymorphic yielding a SNP conversion success rate of 94%. The average minor allele frequency (MAF) for all scorable SNPs was 0.274.

Conclusions/Significance

Overall, the results of this study indicate the utility of using next generation sequencing technologies to identify large numbers of reliable SNPs. In addition, the validation of the PorcineSNP60 Beadchip demonstrated that the assay is an excellent tool that will likely be used in a variety of future studies in pigs.