应用SNPstream技术检测MASP2基因的多态性

目的：应用一种高通量单核苷酸多态性（SNP）检测方法——SNPstream技术检测甘露聚糖结合凝集素相关丝氨酸蛋白酶-2（MASP2）基因的多态性。方法：收集北京汉族人群SARS病例96例和正常对照96例,用SNPstream技术检测样本的MASP2基因多态性,并用PCR产物直接测序技术对其中一个位点rs2273346进行分型,以验证SNPstream技术的准确性。结果：192例样本的MASP2基因rs2273346位点SNPstream技术分型结果与测序结果完全相符,2种方法的基因型分型结果具有很好的一致性。结论：SNPstream技术是高通量SNP检测的良好工具,准确性高,所需样本量低,在大规模人群SNP筛检中具有良好的发展前景。     

TNFa-308基因启动子多态性与新疆维吾尔族人乙型肝炎易感性的相关性研究

目的：研究TNF-α基因单核苷酸多态性（SNP）308G—A位点与新疆地区维吾尔族人乙型肝炎之间的关系。方法：以聚合酶链式反应－限制性内切酶长度多态性（PCR-RFLP）技术,对120例乙肝患者和120例正常对照者TNF—α基因SNP308多态性位点进行基因分型。结果：SNP308多态性位点G／G基因型和G／A基因型频率在病例组为77％和23％,正常对照组为88％和12％,2组基因型和等位基因频率分布差异有显著性（p〈0．05）。结论：TNF—α基因启动子308多态性位点与新疆维吾尔族人乙肝有明显相关性。     

贵州从江侗族威宁彝族、荔波瑶族谷胱甘肽S-转移酶M l、Tl 和Pl 的基因多态性研究

目的：研究贵州从江侗族、威宁彝族、荔波瑶族的GSTs基因多态性。方法：在隔离自然人群中,采用多重等住基因特异聚合酶链反应方法分析GSTM1和GSTT1基因多态性,同时采用PCR-RFLP的方法和TaqMan-MGB探针基因分型方法分析GSTP1（A1578G）基因多态性。结果：贵州从江侗族、成宁彝族、荔波瑶族的GSTM1和GSTT1纯合缺失基因型频率分别为59．6％～71．2％、39．4％～72.5％。其GSTP1（A1578G）基因型频率分别为：野生型（AA）为63.3％～75％、杂合子（AG）为23.2％～35．8％、纯合突变型（GG）为0～1.9％。等位基因频率：A为81．2％～86．6％,G为13．4％～18.8％。结论：贵州从江侗族、威宁彝族、荔波瑶族的GSTM1纯合缺失基因型频率在民族间差异无统计学意义,GSTP1（A1578G）基因型频率和等住基因频率在民族间差异无统计学意义,且其等位基因频率均符合Hardy-Weinberg平衡,但其GSTT1纯合缺失基因型频率在民族间差异有统计学意义（P〈0．05）。     

双色荧光杂交芯片在检测 P 1A 1M P I 基C 因多态性中的应用

目的：应用一种新的高通量SNP检测方法-双色荧光杂交芯片技术检测CYPIA1 MspI基因多态性。方法：收集江苏汉族人群原发性肺癌患者75例和相应对照77例,应用双色荧光杂交芯片技术检测了152例样本的CYPIAI基因MspI基因多态性,并应用PCR-RFLP技术验证双色荧光杂交芯片的特异性。结果：152例样本的CYPIAI基因双色荧光杂交芯片技术分型结果与PCR-RFLP结果完全相符,两种方法的基因型分型结果具有很好的一致性。结论：双色荧光杂交芯片技术是一个高通量SNP检测的良好工具,特异性高,在大规模人群SNP筛检中具有良好的发展前案。     

一种简易SNP检测方法的建立

目的：建立一种快速、简单的SNP（Single Nucleotide Polymorphisms）检测方法。方法：设计带生物素标记的扩增引物对检测用具有单碱基差异的野生型和突变型靶序列分别进行扩增,然后通过紫外交联的方式将相应检测靶序列的探针固定在硝酸纤维素膜上,借助Taq酶完成膜上单引物延伸,从而对探针捕获的靶序列进行延伸固定在膜上,最后使用生物素．亲和素酶联显色（ABs-ELISA）反应肉眼观察结果。结果：阳性和阴性对照探针显示正常。野生型探针和突变型探针能够分别特异性结合靶序列,并通过生物素和亲和索显色系统放大为一种肉眼可判断结果的检测形式。结论：建立了一种基于硝酸纤维素膜载体上进行核酸扩增的SNP检测方法。     

近交系小鼠双色荧光正相杂交芯片技术体系的建立和优化

目的探讨采用单核苷酸多态性（SNP）检测方法-双色荧光正相杂交芯片技术对近交系小鼠遗传质量监测及相关影响因素。方法运用基于芯片的双色荧光正相杂交检测SNP技术,进行芯片杂交动力学研究,考察信号值（Cy3,Cy5）和ratio值（Cy5/Cy3）与PCR产物点样浓度、PCR产物长度和荧光标记探针长度之间的关系,研究PCR产物点样浓度、PCR产物长度和荧光标记探针长度对SNP分型的影响。结果采用正反标记实验后,Ratio值随着PCR产物点样浓度的增加呈稳定趋势;PCR双链产物长度对信号值影响比较大,点样时其长度不宜太长,最好不超过450 bp;随荧光标记探针长度的增加,基因分型能力明显下降,长度为15 bp最佳,长度超过20 bp时,已基本没有区分能力。结论PCR产物点样浓度、PCR产物长度和荧光标记探针长度是双色荧光正相杂交SNP分型系统的重要影响因素,采取适当的PCR产物点样浓度、PCR产物长度和荧光标记探针长度,并采用正反标记实验,可以取得稳定、准确的基因分型效果。为进一步进行近交系小鼠遗传质量监测的研究奠定基础。     

一种用于CYP3A5基因分型的电化学传感器阵列设计

目的：设计一种用于检测CYP3A5基因分型的电化学传感器阵列及其不同基因型的判别方法。方法：设计的电化学基体由印刷电路板（PCB）组成,该电路板包含一组金电极。每个金电极表面修饰有包含单链捕获探针的自组装单分子膜。设计中使用二茂铁做为电活性指示剂,基因分型检测是通过两种不同电势的二茂铁衍生物分别标记等位基因特异性信号探针来实现。结果：该设计能构建一种快速准确、操作简便的DNA电化学传感器阵列检测系统。结论：本文设计为使用电化学方法检测基因分型提供了一种新方法和新技术。     

白血病患者骨髓中RASSFlA基因启动子甲基化状态及其临床意义

目的：通过检测各类型白血病骨髓中RASSFlA基因启动子区甲基化水平,探讨其对白血病分型的临床检测意义。方法：抽选93例不同类型白血病患者（观察组）予以甲基化特异性PCP（MSP）方法进行骨髓RASSFlA基因甲基化状态检测,研究不同类型白血病甲基化状态差异,同期抽选93例非白血病者为对照研究（对照组）。结果：观察组中有13例（13．98％）检测到RASSFlA基因甲基化,而对照组中RASSFlA基因甲基化率为0％,比较差异显著（P〈0．05）。不同类型白血病RASSFlA甲基化率比较：淋巴系显著高于髓系（P〈O．05）,急性与慢性白血病比较差异无显著性（P〉0．05）。结论：白血病骨髓中MSP法检测存在RASSFlA甲基化;而RASSFlA基因在淋巴系白血病中的甲基化概率明显增高,因此,对RASSFlA进行甲基化检测有可能作为白血病临床诊断分型的生物学指标之一。     

应用TaqMan探针荧光定量PCR技术鉴定Lepr~(db/+)小鼠子代基因型

目的建立一种高效的应用Taq Man探针荧光定量PCR技术对Lepr~(db/+)小鼠子代基因分型的方法。方法提取228例Lepr~(db/+)小鼠子代鼠尾DNA,针对Lepr基因的突变位点(rs1801133)设计1对PCR引物和2条Taq Man探针。设定条件进行实时荧光PCR扩增,用SDS软件对SNP位点进行分型。通过2月龄动物的肥胖表现型验证并进行Hardy-Weinberg平衡检验。结果用建立的Taq Man探针荧光定量PCR方法对228份样本进行检测,其中GG基因型64份,基因型频率为0.1929;GT基因型123份,基因型频率为0.5395;TT基因型41份基因型频率为0.2807。Taq Man探针荧光定量PCR方法分型结果与通过肥胖表现型分型结果比较,灵敏度为97.56%,特异度为99.47%。结论应用Taq Man探针荧光定量PCR技术可实现对Lepr~(db/+)小鼠子代基因位点的早期分型检测,方法简便,高效。     

慢性髓细胞白血病急变期MICM分型回顾性分析

目的：探讨慢性髓细胞白血病急变期（CML-Be）患者的细胞形态学（M）、免疫学（I）、细胞遗传学（C）和分子生物学（M）的特征及应用价值。方法：对38例CML．BC患者的MICM分型进行回顾性分析。结果：以FAB分型为基础的形态学确诊率达94．7％;免疫分型结果为：38例CML-BC中CML-AML占71．0％,其中37．0％伴淋系表达;CML-ALL占23．7％,均为B细胞性,其中66．67％伴髓系表达;CML-MAL（混合性白血病）占5．3％,均为B系和髓系混合表达;CD34＋26例（68．4％）,cD7＋10例（26．3％）,均与CD34共表达。细胞遗传学结果显示：CML特征性Ph染色体检出率为94．3％（36／38）,附加异常染色体检出率为60．5％（23／38）,发生频率较高的类型是＋Ph、＋8和i（17q）;FISH检测BCR／ABL融合基因阳性率为100％,der（9）缺失占14．7％。RT—PCR检测20例患者BCR／ABL融合基因均为阳性,其中b2a2型（12／20）,b3a2型（8／20）,1例（1／20）,b2a2和b3a2双阳性（1／20）。结论：CML—BC是造血干细胞疾病,原始细胞分化阻滞在早期阶段,预后差。MICM分型对CML-BC的诊断、治疗和预后判断均有重要价值。     

Assessment of DHPLC usefulness in the genotyping of GSTP1 exon 5 SNP: comparison to the PCR-RFLP method

Single-nucleotide polymorphism (SNP) analysis can be performed by several methods such as PCR-RFLP, real time PCR and mass spectrometry. Denaturating High Pressure Liquid Chromatography (DHPLC) analysis allows the detection of DNA mutations in heteroduplex samples. GSTP1 exon 5 gene presents a single-nucleotide polymorphism (a to g) that results into an amino-acid substitution (Ile to Val). Ile and Val variants are identified respectively by a and b alleles. This polymorphism affects enzyme activity and is highly frequent within Caucasian populations and therefore widely studied in the context of SNP related to cancer susceptibility. Our goal was to evaluate DHPLC usefulness in detecting a well-known SNP in comparison to PCR-RFLP, in the field of molecular epidemiological studies. Fifty Caucasian people were genotyped by both methods. Heterozygous samples were identified easily at two temperatures using the DHPLC method. Discrimination between a/a and b/b homozygous genotypes was done by pooling every homozygous sample with a known a/a sample. Our genotyping using both methods resulted in the characterisation of 32 (64%) a/a homozygous, 18 (36%) a/b heterozygous and 5 (10%) b/b homozygous. All samples were also identically genotyped by the two methods. Our results show that DHPLC is a good alternative to classical PCR-RFLP method in genotyping SNPs. Advantages of this chromatographic method were no restriction site needed and a reduced technical time thanks to an automated injection. Moreover, unlike classical RFLP gel analysis, DHPLC chromatograms provided objective criteria for sample classification.     

Mutagenic primer design for mismatch PCR-RFLP SNP genotyping using a genetic algorithm

Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) is useful in small-scale basic research studies of complex genetic diseases that are associated with single nucleotide polymorphism (SNP). Designing a feasible primer pair is an important work before performing PCR-RFLP for SNP genotyping. However, in many cases, restriction enzymes to discriminate the target SNP resulting in the primer design is not applicable. A mutagenic primer is introduced to solve this problem. GA-based Mismatch PCR-RFLP Primers Design (GAMPD) provides a method that uses a genetic algorithm to search for optimal mutagenic primers and available restriction enzymes from REBASE. In order to improve the efficiency of the proposed method, a mutagenic matrix is employed to judge whether a hypothetical mutagenic primer can discriminate the target SNP by digestion with available restriction enzymes. The available restriction enzymes for the target SNP are mined by the updated core of SNP-RFLPing. GAMPD has been used to simulate the SNPs in the human SLC6A4 gene under different parameter settings and compared with SNP Cutter for mismatch PCR-RFLP primer design. The in silico simulation of the proposed GAMPD program showed that it designs mismatch PCR-RFLP primers. The GAMPD program is implemented in JAVA and is freely available at http://bio.kuas.edu.tw/gampd/.     

Effect of genotyping error in model-free linkage analysis using microsatellite or single-nucleotide polymorphism marker maps

Errors while genotyping are inevitable and can reduce the power to detect linkage. However, does genotyping error have the same impact on linkage results for single-nucleotide polymorphism (SNP) and microsatellite (MS) marker maps? To evaluate this question we detected genotyping errors that are consistent with Mendelian inheritance using large changes in multipoint identity-by-descent sharing in neighboring markers. Only a small fraction of Mendelian consistent errors were detectable (e.g., 18% of MS and 2.4% of SNP genotyping errors). More SNP genotyping errors are Mendelian consistent compared to MS genotyping errors, so genotyping error may have a greater impact on linkage results using SNP marker maps. We also evaluated the effect of genotyping error on the power and type I error rate using simulated nuclear families with missing parents under 0, 0.14, and 2.8% genotyping error rates. In the presence of genotyping error, we found that the power to detect a true linkage signal was greater for SNP (75%) than MS (67%) marker maps, although there were also slightly more false-positive signals using SNP marker maps (5 compared with 3 for MS). Finally, we evaluated the usefulness of accounting for genotyping error in the SNP data using a likelihood-based approach, which restores some of the power that is lost when genotyping error is introduced.     

Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina GoldenGate assay

Single nucleotide polymorphisms (SNPs) are indispensable in such applications as association mapping and construction of high-density genetic maps. These applications usually require genotyping of thousands of SNPs in a large number of individuals. Although a number of SNP genotyping assays are available, most of them are designed for SNP genotyping in diploid individuals. Here, we demonstrate that the Illumina GoldenGate assay could be used for SNP genotyping of homozygous tetraploid and hexaploid wheat lines. Genotyping reactions could be carried out directly on genomic DNA without the necessity of preliminary PCR amplification. A total of 53 tetraploid and 38 hexaploid homozygous wheat lines were genotyped at 96 SNP loci. The genotyping error rate estimated after removal of low-quality data was 0 and 1% for tetraploid and hexaploid wheat, respectively. Developed SNP genotyping assays were shown to be useful for genotyping wheat cultivars. This study demonstrated that the GoldenGate assay is a very efficient tool for high-throughput genotyping of polyploid wheat, opening new possibilities for the analysis of genetic variation in wheat and dissection of genetic basis of complex traits using association mapping approach. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

An alternative method for genotyping of the <Emphasis Type="Italic">ACE</Emphasis> I/D polymorphism

The mistyping of the angiotensin I-converting enzyme insertion/deletion (ACE I/D) has been well documented, and new methods have been suggested here to improve the genotyping efficiency. Buccal cell samples were collected from 157 young Caucasians, and genotyped using previously known and newly developed PCR amplification genotyping techniques, as well as PCR-RFLP tests for three single nucleotide polymorphisms (rs4327, rs4341 and rs4343). Inconsistent genotyping results were found when using only the PCR amplification genotyping techniques across repeated attempts (8% to 45%), however, individual SNP genotyping was highly consistent (100%). Two SNPs (rs4341 and rs4343) were in complete LD and SNP rs4327 was in high LD with the ACE I/D. The ACE I/D was in HW equilibrium in the portion of the population with consistent genotyping results, whereas the three SNPs were not in HW equilibrium. The mistyping of ACE I/D by only PCR amplification can be improved using alternative methods.     

Genotyping of single nucleotide polymorphisms in cytokine genes using real-time PCR allelic discrimination technology

Single nucleotide polymorphisms (SNPs), particularly those within regulatory regions of genes that code for cytokines often impact expression levels and can be disease modifiers. Investigating associations between cytokine genotype and disease outcome provides valuable insight into disease etiology and potential therapeutic intervention. Traditionally, genotyping for cytokine SNPs has been conducted using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), a low throughput technique not amenable for use in large-scale cytokine SNP association studies. Recently, Taqman real-time PCR chemistry has been adapted for use in allelic discrimination assays. The present study validated the accuracy and utility of real-time PCR technology for a number of commonly studied cytokine polymorphisms known to influence chronic inflammatory diseases. We show that this technique is amenable to high-throughput genotyping and overcomes many of the problematic features associated with PCR-RFLP including post-PCR manipulation, non-standardized assay conditions, manual allelic identification and false allelic identification due to incomplete enzyme digestion. The real-time PCR assays are highly accurate with an error rate in the present study of <1% and concordance rate with PCR-RFLP genotyping of 99.4%. The public databases of cytokine polymorphisms and validated genotyping assays highlighted in the present study will greatly benefit this important field of research.     

SNiPORK - a microarray of SNPs in candidate genes potentially associated with pork yield and quality - development and validation in commercial breeds

SNiPORK is an oligonucleotide microarray based on the arrayed primer extension (APEX) technique, allowing genotyping of single nucleotide polymorphisms (SNPs) in genes of interest for pork yield and quality traits. APEX consists of a sequencing reaction primed by an oligonucleotide anchored with its 5' end to a glass slide and terminating one nucleotide before the polymorphic site. Extension with one fluorescently labeled dideoxynucleotide complementary to the template reveals the polymorphism. Ninety SNPs were selected from those associated directly or potentially with pork traits. Of the 90 SNPs, 5 did not produce a positive signal. For 85 SNPs, 100% repeatiblity was proved by double genotyping of 13 randomly chosen boars. In addition, the accuracy of genotyping was verified in 2 sib-families by a Mendelian inheritance of 49-50 homozygous genotypes from sire to sons. Three genotype discrepancies were found (97% accuracy rate). All inaccurities were confirmed by an alternative method (sequencing and PCR-RFLP assays). Moreover, the exclusion power of the chip was evalueted by an SNP inheritance analysis of unrelated boars within each sib-family. In the validation step, 88 boars (13 Pietrain, 31 Landrace, 16 Large White, 8 Duroc, 7 Hampshire x Pietrain crosses, and 13 other hybrid lines) were screened to validate SNPs. Among the 85 selected SNPs, 12 were found to be monoallelic, the rest showing at least two genotypes for the entire population under study. The primary application of the SNiPORK chip is the simultaneous genotyping of dozens of SNPs to study gene interaction and consequently better understand the genetic background of pork yield and quality. The chip may prospectively be used for evolutionary studies, evaluation of genetic distances between wild and domestic pig breeds, traceability tests, as well as the starting point for developing a platform for identification and paternity analysis.     

基于PCR-LDR平台的近交系小鼠遗传质量快速检测方法

目的建立基于PCR-LDR平台的近交系小鼠SNP快速分型方法,用于检测实验小鼠的遗传质量与品系纯度。方法利用可移植性极高的PCR-LDR技术,以常见近交系小鼠为研究对象,选取了21条染色体上的45个SNP位点,分别设计引物和探针,经过筛选和验证,建立了多重PCR-LDR(polymerase chain reaction and ligase detection reaction,PCR-LDR)分型方案。结果四组多重PCR-LDR可实现45个SNP位点的基因分型,其中43个、44个与45个SNP在样本中的检出率分别为100%、90.9%与36.4%。所有样本经分型确定为纯合体,并得到了常见近交系小鼠SNP位点信息。结论实现了常见近交系小鼠快速、高通量的基因分型,可用于遗传质量检测和品系鉴定。     

Detection of mutations by fill-in ligation reaction with enzyme-linked immunosorbent assay for rapid medical diagnosis

Several approaches for parallel genotyping have been developed with increasingly available information on DNA variation. However, these methods require either complex laboratory procedures or expensive instrumentation. None of these procedures is readily performed in local clinical laboratories. In this study, we developed a flexible genotyping method involving fill-in ligation reaction with enzyme-linked immunosorbent assay successfully applied to detect important single-nucleotide polymorphisms (SNPs) for EGFR c.2573T?>?G (L858R), EGFR c.2582T?>?A (L861Q), and EGFR c.2155G?>?T (G719C). This assay exhibited excellent specificity, with a sensitivity as low as 0.5%. Eight out of 62 clinical samples were identified as heterozygotes for the SNP site of L858R, whereas only two samples were identified as heterozygotes by direct sequencing. The developed method enabled accurate identification of SNP in a simple and cost-effective manner adapted to routine analysis.