浙江地区汉族人群caspase-8、-10基因四个单核苷酸多态性位点的单倍型研究

目的分析汉族人群caspase-8、-10基因的单核苷酸多态性（single nucleotide polymorphisins，SNPs）位点及其构成的单倍型，为研究caspase-8、-10基因与多基因复杂疾病的关联分析奠定基础。方法采用PCR、变性高效液相色谱技术和DNA测序技术检测caspase-10基因的第2．5外显子，caspase-8基因的第8-10外显子及其部分侧翼序列的多态性位点；分析配对位点的连锁不平衡关系，最大期望值法估算它们构成的单倍型。结果（1）caspase-10基因的第2、5外显子分别检出一个SNP位点A2823G和A12799G，其中A12799G是新发现的低信息度的SNP；caspase-8基因中检测到3个SNP位点A43466G、G51484A、G52951A，分别位于第8、9外显子和第9内含子；它们均未改变所编码蛋白的一级结构；（2）caspase-10基因中A2823G位点与caspase-8基因中3个位点间已达到连锁平衡，caspase-8基因中A43466G与G52951A、G51484A与G52951A也达到连锁平衡，连锁不平衡系数分别接近于0；只有A43466G与G51484A存在强的连锁不平衡，连锁不平衡系数接近于1；（3）caspase-10基因的A2823G位点与caspase-8基因的3个位点预计产生11种单倍型，其中A-2823／A-43466／G-51484／G-52951是主要单倍型，频率为0．381l，其次是A．2823／A-43466／G-51484／A-52951，频率为0．2536；这4个SNP位点联用，多态信息含量可达到0．7106。结论浙江地区汉族人群caspase-10、-8基因中的SNP位点至少处于3个不同的单倍型块；联合多个相邻的位点构成单倍型，可以弥补单个SNP信息度较低的不足。     

5''HOXD基因与单纯性马蹄内翻足的相关性分析

目的检测HOXD10、HOXD12、HOXD13基因内4个已知单核苷酸多态（single nueleotide polymorphisins,SNP）rs2593778、rs847154、rs847151、rs13392701在单纯性马蹄内翻足核心家系中的分布情况，分析各个SNP位点及所构成单倍型与单纯性马蹄内翻足的相关性。方法应用限制性片段长度多态性技术结合测序，分析84个单纯性马蹄内翻足核心家系4个SNP位点基因型；应用ETDT软件统计分析各SNP位点基因型与单纯性马蹄内翻足的相关性；应用TRANSMIT软件构建单倍型并统计分析单倍型频率是否存在差异。结果位于HOXD12基因5’侧翼序列的SNP位点rs847154和位于HOXD13第1外显子的SNP位点rs13392701在单纯性马蹄内翻核心家系中存在传递不平衡（P〈0．05）；位于HOXD12基因第1外显子的SNP位点rs847151未检测到多态；位于HOXD10第1外显子的SNP位点rs2593778经ETDT分析无统计学意义。结论HOXD12基因5’侧翼序列的SNP位点rs847154和位于HOXD13第1外显子的SNP位点rs13392701与单纯性先天性马蹄内翻足有明显的相关性，提示HOXD12、HOXD13可能是单纯性马蹄内翻足重要的易感基因。     

GLI3基因与单纯性马蹄内翻足的关联分析及其突变筛查

目的对GLU基因与单纯性马蹄内翻足进行关联分析和突变筛查，探讨GLU基因与单纯性马蹄内翻足的相关性。方法应用限制性片段长度多态性分析技术，分析84个单纯性马蹄内翻足核心家系中GLI3基因内两个单核苷酸多态（single nucleotide polymorphisms, SNP）位点的基因型，并应用ETDT软伯统计分析各SNP位点基因型与单纯性马蹄内翻足的关联；应用变性梯度凝胶电泳技术对103例单纯性马蹄内翻足患者GLI3基因的第9至12外显子进行突变筛查。结果经ETDT分析，位于GLI3基因第4外显子的cSNP rs846266差异无统计学意义（χ^2=3．3582，P〉0．05）；第14外显子的cSNP rs929387差异有统计学意义（χ^2=7．2466，P〈0．05），在单纯性马蹄内翻足核心家系中存在传递不平衡；发现1例患者及其母亲的第9外显子有108（G→A）的同义点突变。结论GLI3基因与单纯性马蹄内翻足相关，其第9至12外显子可能并非该病的突变热点。     

SCN7A 基因单核苷酸多态性与原发性与原发性高血压的相关研究

目的　检测中国人电压调控钠通道 7型α亚单位基因 (sodium channel,voltage- gated,type ,alpha polypeptide,SCN7A)调控区和编码区的单核苷酸多态性 (single nucleotide polymorphisms,SNPs) ,并探讨其与上海汉族人群原发性高血压的关系。　方法　采用直接测序法检测基因启动子、编码区和部分内含子的序列 ,以确定中国人群中 SCN7A基因 SNPs的位置及类型。采用聚合酶链反应 -限制性片段长度多态性及直接测序法 ,对上海汉族 96例原发性高血压患者和 96名正常血压对照者进行 SNP检测和关联研究。对所发现的 P<0 .0 5的 SNP位点 ,进一步扩大样本 (病例、对照组各 2 88例 )加以验证。结果　在 13132 bp的测序长度中 ,共发现 32个 SNP,包括启动子区 7个 ,编码区 10个 (其中改变氨基酸编码的 6个 ) ,3′非编码区 1个 ,内含子区 14个 ,其中 30个为新发现的 SNP。关联研究结果显示 SNP0 2 1在病例和对照组中的分布差异存在显著性 (P <0 .0 1) ,该 SNP多态可改变氨基酸的编码序列。　结论SCN7A基因变异可能与上海汉族人群原发性高血压相关。     

5′HOXD基因与单纯性马蹄内翻足的相关性分析

目的检测HOXD10、HOXD12、HOXD13基因内4个已知单核苷酸多态(single nucleotide poly-morphisms,SNP)rs2593778、rs847154、rs847151、rs13392701在单纯性马蹄内翻足核心家系中的分布情况,分析各个SNP位点及所构成单倍型与单纯性马蹄内翻足的相关性。方法应用限制性片段长度多态性技术结合测序,分析84个单纯性马蹄内翻足核心家系4个SNP位点基因型;应用ETDT软件统计分析各SNP位点基因型与单纯性马蹄内翻足的相关性;应用TRANSMIT软件构建单倍型并统计分析单倍型频率是否存在差异。结果位于HOXD12基因5′侧翼序列的SNP位点rs847154和位于HOXD13第1外显子的SNP位点rs13392701在单纯性马蹄内翻核心家系中存在传递不平衡(P<0.05);位于HOXD12基因第1外显子的SNP位点rs847151未检测到多态;位于HOXD10第1外显子的SNP位点rs2593778经ETDT分析无统计学意义。结论HOXD12基因5′侧翼序列的SNP位点rs847154和位于HOXD13第1外显子的SNP位点rs13392701与单纯性先天性马蹄内翻足有明显的相关性,提示HOXD12、HOXD13可能是单纯性马蹄内翻足重要的易感基因。     

人BLCAP基因单核苷酸多态性与宫颈癌的相关性

人膀胱癌相关蛋白 (BLCAP)基因是本研究室从细胞原癌、抑癌基因分类芯片中筛选并克隆的宫颈癌候选抑癌基因。为检测该基因调控区的单核苷酸多态性 (SNP)及其不同基因型与宫颈癌的相关性 ,采用病例 对照研究方法及动态等位基因杂交 (DASH)技术 ,对 30例原发性宫颈癌患者和 6 0例正常人BLCAP基因调控区的 2个SNP位点进行了检测。结果显示 :位于BLCAP基因下游调控区的SNPrs3795 14 7位点存在AA、AC和CC 3种基因型 ,且与宫颈癌发病存在显著相关性 (P <0 0 1)。SNPrs3795 14 7处在BLCAP基因下游调控区域 ,其多态类型可能在某种程度上影响BLCAP基因的表达调控 ,从而进一步支持了 :BLCAP基因与宫颈癌的发生、发展可能存在密切关系。     

散发性肾癌中VHL基因的两个单核苷酸多态位点分析和杂合性缺失检测

目的检测79例散发性肾癌中抑癌基因VHL内部的两个单核苷酶多态(single nucleotide polymorphism，SNP)位点并分析杂合性缺失(loss of heterozygosity，LOH)发生情况，探讨VHL基因LOH与肾癌临床病理特征的关系。方法从肿瘤和正常肾组织中提取DNA，应用聚合酶链反应-限制性片段长度多态性方法检测VHL基因5′端SNP位点rs779805和3′端SNP位点rs1642742的基因型。在两个位点的杂合子中进行LOH检测，并分析VHL基因LOH与临床病理特征的关系。结果我们计算了两个位点的基因型、基因频率、杂合度、多态信息含量等遗传学参数。综合两个位点发现杂合子29例．其中12例(41．4％)存在LOH。VHL基因LOH与肾癌发生年龄、性别、临床分期、病理分级无显著相关性。结论在散发性肾癌中，VHL基因LOH是肿瘤发生的重要机理，其发生率达41．4％，VHL基因LOH与肾癌分期、分级无关。     

湖北汉族人群Tim-3基因启动子及编码区的分子突变

目的：检测湖北汉族人群Tim-3基因启动子区和编码区的单核苷酸多态性，寻找Tim-3基因的遗传标记。方法：采用分段扩增直接测序的方法检测60名湖北汉族人Tim-3基因的启动子区、全部的外显子区及部分内含子区，将测序结果与NCBI及HapMap计划库中其他人种的数据进行对比，确定湖北汉族人群Tim-3基因突变的位置、类型和频率。结果：在Tim-3基因启动子区和外显子区共发现9个SNPs，包含5个已报道的SNPs和4个新发现的突变位点。湖北汉族人群中检出的4个SNPsrs4704853、rs10515746、rs4704846、rs9313439与Ft本人分布相似（P〉0．05），与欧洲人及非洲人的分布则有统计学意义（P〈0．01）。结论：湖北汉族人群Tim-3基因的SNPs分布有别于其他人种，可为在汉族人群中研究Tim-3基因与疾病关联提供依据。     

广东汉族人群TLR2基因的多态性研究

目的:人类Toll样受体2(TLR2)是先天免疫系统中一个重要的病原微生物识别受体。本研究将建立广东汉族人群TLR2基因座位的功能性多态性图谱,为下一步疾病相关性研究打下基础。方法:收集200例健康、无亲缘关系的中国广东汉族人外周血液,随机抽取其中24例样品,对TLR2基因的启动子区、3个外显子以及它们周围的部分内含子序列进行聚合酶链式反应(PCR)扩增和直接测序,找出多态性位点,对剩余176例样品分别用序列特异性引物聚合酶链反应(PCR-SSP)及PCR技术对发现的单核苷酸多态性(SNPs)和插入/缺失(INDEL)多态性位点进行基因分型,分型结果进行Hardy-W e inberg平衡分析、中性进化分析以及连锁不平衡分析。结果:发现5个SNPs位点,其中2个位于启动子区的SNPs是首次发现,位于编码区的3个SNPs位点均为同义突变,频率最高的SNP是rs3804099,其次要等位基因频率为26.3%;在第1外显子区发现1个长度为22bp的INDEL多态位点(-196到-174),其缺失等位基因所占的频率为31.8%。所有多态性位点均符合Hardy-W e inberg平衡。中性检验显示广东汉族人群TLR2基因符合中性进化假说。连锁不平衡分析显示位于调控区的-18945 C/T和-18883 C/G 2位点之间完全连锁,而位于编码区的rs3804099和rs3804100两位点之间紧密连锁。结论:本研究首次建立了汉族正常人群TLR2基因座位的功能性多态性图谱,并研究了其分布频率,发现了一些种族特异性的多态性位点,为今后开展汉族人基因多态性与疾病相关性研究以及人群进化研究提供了重要资料。     

中国北方人群NBN基因外显子SNPs分布及其与乳腺癌的关系

目的探讨NBN基因与中国北方人群乳腺癌的相关性。方法对188例正常人及205例乳腺癌患者NBN基因的16个外显子进行直接测序。结果在中国北方人群乳腺癌样本中未发现NBN基因突变。对基因频率大于5%的NBN基因SNPs进行分析,发现rs709816(D399D,AG)的AG基因型较AA基因型发生乳腺癌的风险增加2.34倍,有显著的统计学差异,提示该SNP与乳腺癌的发生相关。结论 NBN基因第10外显子内SNP rs709816(AG)可能与中国北方人群乳腺癌发生相关。     

Evaluation of resequencing on number of tag SNPs of 13 atherosclerosis-related genes in Thai population

In the candidate gene approach, information about the distribution of single nucleotide polymorphisms (SNPs) is a crucial requirement for choosing efficient markers necessary for a case-control association study. To obtain such information, we discovered SNPs in 13 genes related to atherosclerosis by resequencing exon-flanking regions of 32 healthy Thai individuals. In total, 194 polymorphisms were identified, 184 of them SNPs, four insertions, and the rest deletions. Fifty-nine of the SNPs were characterized as novel polymorphisms, and these accounted for 30% of the identified SNPs. Comparing allele frequency distributions of the Thai population with other Asian populations shows similar patterns. In contrast, a low correlation pattern (r = 0.521) was found when comparing with either Caucasian or African populations. However, some rare alleles (rs11574541 and rs10874913) are found in the Thai population but not in other Asian populations. Most of the novel SNPs found were located outside the haplotype blocks generated by known SNPs in the Thai population. Only 5.77% of the novel SNPs lies in these defined haplotype blocks. The selection of haplotype-tagging SNPs shows that 8 of 13 genes benefited from the ethnic-specific genotype information. That is, when at least one novel SNP was present, the tagging SNPs chosen were altered. Functional prediction of 16 nonsynonymous SNPs (nsSNPs) by three different algorithm tools demonstrated that five nsSNPs possibly alter their corresponding protein functions. These results provide necessary information for conducting further genetic association studies involving the Thai population and demonstrate that resequencing of candidate genes provides more complete information for full genetic studies. Chintana Tocharoentanaphol and Somying Promso contributed equally to this work.     

浙江地区汉族人群caspase-3基因三个位点的单倍型研究

目的分析汉族人群caspase-3基因的单核苷酸多态性(singlenucleotidepolymorphisms,SNPs)位点及其构成的单倍型,为研究caspase-3基因对凋亡调节机制的个体差异提供线索。方法用变性高效液相色谱技术和DNA测序技术检测caspase-3基因的调控区、第2～7外显子及部分侧翼序列的多态性位点;分析位点间的连锁不平衡关系,估算它们构成的单倍型。结果共检出3个SNP位点(C829A、A17532C、C20541T),分别位于caspase-3基因的5′端调控区、第4内含子和3′调控区;3个位点间存在强连锁不平衡,其中位点A17532C与C20541T呈完全连锁不平衡;54.3%的C-829/A-17532/C-20541是汉族人群的主要单倍型。结论浙江地区汉族人群caspase-3基因上的3个SNP位点间存在强连锁不平衡,它们构成的主要单倍型不同于北美人群。     

Sequence variation, linkage disequilibrium and association with Crohn's disease on chromosome 5q31

Chromosome 5q31 contains a cluster of genes involved in immune response, including a 250 kb risk haplotype associated with Crohn's disease (CD) susceptibility. Recently, two functional variants in SLC22A4 and SLC22A5 (L503F and G-207C), encoding the cation transporters OCTN1 and OCTN2, were proposed as causal variants for CD, but with conflicting genetic evidence regarding their contribution. We investigated this locus by resequencing the coding regions of 10 genes in 24 CD cases and deriving a linkage disequilibrium (LD) map of the 27 single nucleotide polymorphisms (SNPs) detected. Ten SNPs representative of the LD groups observed, were tested for CD association. L503F in SLC22A4 was the only nonsynonymous SNP significantly associated with CD (P=0.003), but was not associated with disease in the absence of other markers of the 250 kb risk haplotype. Two other SNPs, rs11242115 in IRF1 and rs17166050 in RAD50, lying outside the 250 kb risk haplotype, also showed CD association (P=0.019 and P=0.0080, respectively). The RAD50 gene contains a locus control region regulating expression of the Th2 cytokine genes at this locus. Other as yet undiscovered SNPs in this region may therefore modulate gene expression and contribute to the risk of CD, and perhaps of other inflammatory phenotypes.     

Implication of common and disease specific variants in CLU, CR1, and PICALM

Two recent genome-wide association studies (GWAS) for late onset Alzheimer's disease (LOAD) revealed 3 new genes: clusterin (CLU), phosphatidylinositol binding clathrin assembly protein (PICALM), and complement receptor 1 (CR1). In order to evaluate association with these genome-wide association study-identified genes and to isolate the variants contributing to the pathogenesis of LOAD, we genotyped the top single nucleotide polymorphisms (SNPs), rs11136000 (CLU), rs3818361 (CR1), and rs3851179 (PICALM), and sequenced the entire coding regions of these genes in our cohort of 342 LOAD patients and 277 control subjects. We confirmed the association of rs3851179 (PICALM) (p = 7.4 × 10(-3)) with the disease status. Through sequencing we identified 18 variants in CLU, 3 of which were found exclusively in patients; 8 variants (out of 65) in CR1 gene were only found in patients and the 16 variants identified in PICALM gene were present in both patients and controls. In silico analysis of the variants in PICALM did not predict any damaging effect on the protein. The haplotype analysis of the variants in each gene predicted a common haplotype when the 3 single nucleotide polymorphisms rs11136000 (CLU), rs3818361 (CR1), and rs3851179 (PICALM), respectively, were included. For each gene the haplotype structure and size differed between patients and controls. In conclusion, we confirmed association of CLU, CR1, and PICALM genes with the disease status in our cohort through identification of a number of disease-specific variants among patients through the sequencing of the coding region of these genes.     

Integrated effect of EGFR and PAR-1 signaling crosstalk on airway hyperresponsiveness

Among previous genetic studies for asthma, inconsistent findings were often reported. We used a new approach to examine an integrated effect of haplotype blocks, newly termed 'haplotype cluster' over two different types of receptors which share common intracellular pathways on airway hyperresponsiveness (AHR). We recruited 165 young atopic adults without respiratory symptoms and measured airway responsiveness to methacholine and classified them into two groups, those with AHR (PC20?<8.0?mg/ml) and without AHR. In addition, we identified haplotype blocks or cluster tagging single nucleotide polymorphisms (SNPs) through two genes, epidermal growth factor receptor (EGFR) and protease activated receptor (PAR)-1, in all subjects, and compared the frequencies of haplotype block or cluster between subject groups. Significant differences in the frequencies were observed in the haplotype blocks within the EGFR gene (rs4947972, rs12718945 and rs2072454; rs4947972, rs12718945 and rs2227983; and rs4947972, rs12718945 and rs2293347) and the PAR-1 gene (rs37243 and rs253072). An integrated effect was also observed in one haplotype cluster consisting of both regions of the EGFR gene (rs2293347) and the PAR-1 gene (rs253072) (P=0.0426). Our results suggest the possibility that the integrated effect of functionally-related EGFR and PAR-1 genes (haplotype cluster) is associated with susceptibility to AHR.     

The CHRNA5/CHRNA3/CHRNB4 Nicotinic Receptor Regulome: Genomic Architecture,Regulatory Variants,and Clinical Associations

Functionally related genes often cluster into a genome region under coordinated regulation, forming a local regulome. To understand regulation of the CHRNA5/CHRNA3/CHRNB4 nicotinic receptor gene cluster, we integrate large‐scale RNA expression data (brain and peripheral) from GTEx (Genotype Tissue Expression), clinical associations (GRASP), and linkage disequilibrium data (1000 Genomes) to find candidate SNPs representing independent regulatory variants. CHRNA3, CHRNA5, CHRNB4 mRNAs, and a well‐expressed CHRNA5 antisense RNA (RP11‐650L12.2) are co‐expressed in many human tissues, suggesting common regulatory elements. The CHRNA5 enhancer haplotype tagged by rs880395 not only increases CHRNA5 mRNA expression in all tissues, but also enhances RP11‐650L12.2 and CHRNA3 expression, suggesting DNA looping to multiple promoters. However, in nucleus accumbens and putamen, but not other brain regions, CHRNA3 expression associates uniquely with a haplotype tagged by rs1948 (located in the CHRNB4 3′UTR). Haplotype/diplotype analysis of rs880395 and rs1948 plus rs16969968 (a nonsynonymous CHRNA5 risk variant) in GWAS (COGEND, UW‐TTURC, SAGE) yields a nicotine dependence risk profile only partially captured by rs16969968 alone. An example of local gene clusters, this nicotinic regulome is controlled by complex genetic variation, with broad implications for interpreting GWAS.