全基因组SNPs和CNVs与精神分裂症的关联分析研究

精神分裂症（SP）是典型的复杂性多基因遗传疾病,随着人类基因组测序计划的完成和基因组单倍体图谱计划的实施,应用人类基因组中数以百万计的单核苷酸多态性（SNPs）和拷贝数变异（CNVs）遗传标记对精神分裂症进行全基因组关联分析,为进一步了解控制人类SP发生的遗传特征提供了重要的线索。本文就全基因组SNPs和CNVs与精神分裂症的关联分析研究做一综述。     

藏族人群原发性高血压易感基因全基因组关联分析

目的通过全基因组关联分析(GWAS)发现并鉴定与藏族高血压关联的遗传变异。方法结合高通量芯片分析和高效DNA混合池策略的SNP-Ma P方法,对藏族原发性高血压(EH)患者与藏族正常对照进行了全基因扫描。筛选出有显著差异的位点后,用直接测序和PCR-RFLP的方法,进行群体验证,鉴定出各个基因型和相应等位基因的频率。结果在全基因组的遗传标记中,5个标签位点的等位基因频率在患者组与对照组之间存在显著差异(P9.2×10-8)。用直接测序和PCR-RFLP的方法进行群体验证,发现rs17136827和rs1866525两个位点的基因型和等位基因频率分布在两组间均无差异;rs9865108、rs12541835和rs4547758的基因型频率和等位基因频率在两组间的差异显著,携带C等位基因个体具有较高的EH发病风险。结论证实affymetrix Human SNP芯片和高效混合池策略结合的SNP-Ma P能够有效地大范围分析人类EH易感基因。rs9865108、rs12541835和rs4547758与藏族EH易感相关。     

DNA混合池技术全基因组关联研究筛查主动脉夹层易感基因的研究

目的筛选主动脉夹层发病机制相关的遗传易感基因。方法选取主动脉夹层患者为病例组（150例）,按照性别、年龄、是否吸烟、合并高血压、糖尿病情况与病例组匹配的原则入选排除主动脉夹层、重大心血管疾病及肿瘤的志愿者为对照组（250例）,均从外周血提取基因组DNA,采用DNA混合池技术为基础的Illumina Human660W—Quad芯片扫描,筛选主动脉夹层发病相关的遗传易感基因。结果对照组女性数量明显多于病例组（P〈0．01）;在年龄、吸烟、高血压、糖尿病人数方面差异均无统计学意义（P〉0．05）。根据芯片扫描结果,挑选silhouettewidth计算值大于0．7,最小等位基因频率（MAF）大于0．05,且SNPs位于已知名称基因上的前5个SNPs位点。结果发现,遗传变异位点SNP rs2970873（位于PPARGClA基因）、SNP rs12678080（位于SGCZ基因）、SNP rs489526（位于UNCl3C基因）、SNP rs6928665（位于TRAM2基因）和SNP rs17837003（位于ACCNl基因上）可能与主动脉夹层的发病机制有关。结论SNPsrs2970873、rs12678080、rs489526、rs6928665和rsl7837003可能与主动脉夹层发病机制相关。     

慢性乙型肝炎易感基因的全基因组关联研究进展

慢性乙型肝炎(chronic hepatitis B,CHB)是一种由遗传、病毒与环境因素共同导致的复杂疾病,具有高度的遗传异质性。自2009年首个CHB全基因组关联研究(genome-wide association studies,GWAS)报道以来,许多GWAS相继开展。文章首先对目前发表的CHB易感基因的GWAS结果进行汇总,发现染色体6p21.32区域中CHB易感位点最多。然而目前GWAS主要基于常见变异-常见疾病原则设计,只涉及了频率≥5%的单核苷酸多态性(single nucleotide polymorphism,SNP),没有涵盖人类基因组中重要的低频变异。同时GWAS鉴定到的最显著关联的SNP大多位于内含子、基因间区等非编码区域内,导致功能学研究无法开展。乙型肝炎病毒(hepatitis B virus,HBV)功能性受体钠离子-牛磺胆酸共转运蛋白的发现,加快了HBV感染的机制研究。同时第二代测序技术的发展为CHB易感基因的发现提供了契机。因此今后的研究应将GWAS的发现与功能学研究相结合,以逐步揭示HBV感染的遗传机制。     

免疫调节基因多态性与乳腺癌关联的研究进展

机体免疫系统的功能状态是影响乳腺癌发生和发展的一个重要因素，受复杂精确的调节网络所控制，该网络任何环节发生异常都会使正常免疫调节失去平衡，影响其功能的发挥。免疫调节基因决定了各种免疫调节因子的数量和质量，因此在免疫调节中发挥了关键作用。在基因组中，由核苷酸水平上的差异引起的DNA序列多态性称为单核苷酸多态性（SNP），它们构成了人类遗传变异的主要部分。乳腺癌相关的免疫调节基因的单核苷酸多态性及单体型研究成为近年来国外研究的热点之一，研究表明，免疫调节基因的多态性在调节乳腺癌患者的免疫功能方面起着重要作用，影响乳腺癌的治疗和预后。     

基因组多态性、单核苷酸多态性和“国际人类基因组单倍型图谱计划”

随着人类基因组测序计划的完成 ,人们进一步利用基因组测序的研究成果 ,深入地了解生命的基因现象 其中人类疾病基因组研究是一重要课题 ,并已取得了成果 复杂性疾病是多个微效基因作用累加 ,个体对疾病的易感性并在特定的环境因素下诱发发病 这些基因的SNPs及其特定组合是研究疾病基因组的重要内容 个体基因组差别称为基因组多态性 (genepolymorphism)在阐明人体对疾病、毒物的易感染与耐受性、疾病发生发展及临床表征的多样性 (Clinicalphenotypediversity)在个体对药物治疗的反应及预后上起着重要作用 所以对疾病基因多态性研究可…     

SNP检测技术进展与全基因组关联研究

单核苷酸多态性(Single nucleotide polymorphism, SNP)是第三代遗传标记,在基因定位、遗传疾病等研究中发挥着重要作用。随着SNP检测技术的发展,在大规模人群中研究全基因组的变异位点与复杂疾病的关系成为可能。文章系统地介绍了全基因组关联研究（Genome-wide association studies,GWA）中所采用的几种高通量SNP检测技术、原理、基因芯片及其商品信息,并对SNP技术在 GWA研究中涵待解决的问题进行了阐述。     

单核苷酸多态性检测技术进展与全基因组关联研究

单核苷酸多态性(Single nucleotide polymorphism,SNP)是第三代遗传标记,在基因定位、遗传疾病等研究中发挥着重要作用.随着SNP检测技术的发展,在大规模人群中研究全基因组的变异位点与复杂疾病的关系已经成为可能.文章系统地介绍了全基因组关联研究(whole genome association,GWA)中所采用的几种高通量的SNP检测技术、原理、基因芯片及其商品信息,并对SNP技术在GWA研究中亟待解决的问题进行了阐述.     

特应性皮炎全基因组关联研究进展北大核心CSCD

随着测序与分析技术的发展,近年来特应性皮炎(AD)的全基因组关联研究(GWAS)逐渐增加。本文系统地总结了AD的GWAS,发现自2009年以来共报道了11个AD的GWAS,以欧洲人群居多,仅见1个在中国汉族和1个在日本人群的报告。这些GWAS共发现36个染色体区域上76个SNPs与AD在全基因组水平上相关。相关基因主要与表皮皮肤屏障功能和免疫功能相关。这些发现为AD的精准分型和治疗带来新的视角。     

Appropriate data cleaning methods for genome-wide association study

Genome-wide association studies (GWAS) using a large number of single nucleotide polymorphisms (SNPs) have successfully been applied to identify genetic variants of common diseases. However, genotyping using the new array technologies is often associated with spurious results that could unfavorably affect analyses of GWAS. Consequently, data cleaning is of paramount importance in excluding spurious genotyping results. In this study, we investigated the criteria required for the appropriate cleaning of 389 unrelated healthy Japanese samples analyzed using the GeneChip Human Mapping 500K Array Set for GWAS. The samples were randomly subdivided into two groups, and the allele frequencies in the groups were compared for individual SNPs as a quasi-case-control study. Then, observed results were filtered by four parameters (SNP call rate, confidence score obtained using the Bayesian Robust Linear Model with Mahalanobis genotype-calling algorithm, Hardy–Weinberg equilibrium, and minor allele frequency) and assessed for deviation from the null hypothesis. We found that appropriate data cleaning could be achieved using these four parameters. Our findings offer an avenue for obtaining appropriate data from GWAS. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A genome-wide association study of aging

Human longevity and healthy aging show moderate heritability (20%-50%). We conducted a meta-analysis of genome-wide association studies from 9 studies from the Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium for 2 outcomes: (1) all-cause mortality, and (2) survival free of major disease or death. No single nucleotide polymorphism (SNP) was a genome-wide significant predictor of either outcome (p < 5 × 10⁻⁸). We found 14 independent SNPs that predicted risk of death, and 8 SNPs that predicted event-free survival (p < 10⁻⁵). These SNPs are in or near genes that are highly expressed in the brain (HECW2, HIP1, BIN2, GRIA1), genes involved in neural development and function (KCNQ4, LMO4, GRIA1, NETO1) and autophagy (ATG4C), and genes that are associated with risk of various diseases including cancer and Alzheimer's disease. In addition to considerable overlap between the traits, pathway and network analysis corroborated these findings. These findings indicate that variation in genes involved in neurological processes may be an important factor in regulating aging free of major disease and achieving longevity.     

Novel insights into autoimmune liver diseases provided by genome-wide association studies

Autoimmune hepatitis (AIH), primary biliary cirrhosis (PBC) and primary sclerosing cholangitis (PSC) are complex disorders, resulting from the interaction of genetic and environmental factors. For many years, investigators have attempted to delineate the genetic architecture of these conditions, aiming to elucidate disease pathogenesis and identify molecular targets for pharmacotherapy. Early genetic studies consisted of HLA association studies and non-HLA candidate gene association studies, designed to identify association with selected HLA or non-HLA loci. HLA association studies identified HLA risk loci that are now well-established. Non-HLA candidate gene studies were less fruitful because they were mostly underpowered to detect modest effects and were frequently designed to investigate one or two functional polymorphisms, meaning that gene coverage was poor. Furthermore, weak associations detected in one small cohort were often never validated. If replication studies were undertaken, the results were often conflicting. More recently, a series of genome-wide association studies (GWAS) and related study designs have evaluated the impact of common genetic variants (frequency >5% in the general population) across the entire genome. These studies have identified several non-HLA risk loci for autoimmune liver disease. The majority of risk loci detected are similar to those of non-hepatic immune-mediated diseases, suggesting that outcomes from GWAS and related genetic studies reflect broad phenotypic themes rather than traditional clinical conditions. The specific genetic basis of these PBC and PSC associated inflammatory themes as determined by GWAS is described and discussed in the context of interacting genetic and non-genetic (including environmental) factors.     

RET基因调控区遗传变异与先天性巨结肠患病风险研究

目的先天性巨结肠（HSCR）是一种复杂的先天性疾病,RET是其主要的易感性基因。本研究对RET非编码区单核甘酸多态性（SNP）-5G〉A（rs10900296）,-1A〉C（rs10900297）和intron1 C〉T（rs2435357）进行分型分析,评估RET基因调控区SNPs及单倍型与先天性巨结肠之间的相关性。方法选取115名病例组病人和139名对照组正常人群,应用聚合酶链反应（PCR）技术和直接测序的方法进行基因分型。回归模型中使用OR值和95%置信区间（CI）作为基因型危险性的评价指标。结果 -5G〉A,-1A〉C,intron1C〉T各基因型频率在病例和对照人群的分布具有显著差异。-5 AA（OR=6.26,95%CI=3.62-10.83）,-1 CC（OR=7.54,95%CI=2.06-27.66）和intron1 TT（OR=19.22,95% CI=7.54-48.99）基因型均能显著增加HSCR发病的风险。单倍型A-C-T（OR=6.28,95% CI=3.77-10.46）和双体型A-C-T/A-C-T（OR=13.62,95% CI=3.48-53.30）分析同样表明与HSCR发病风险存在较强的相关性,并呈现出一定的累积效应。结论 RET基因调控区的基因多态性可能与HSCR的发病易感性有关,支持RET通路的常见变异在HSCR的发展过程中起着重要的作用的假设。     

The power of genome-wide association studies of complex disease genes: statistical limitations of indirect approaches using SNP markers

Genome-wide association studies using a dense map of single nucleotide polymorphism (SNP) markers seem to enable us to detect a number of complex disease genes. In such indirect association studies, whether susceptibility genes can be detected is dependent not only on the degree of linkage disequilibrium between the disease variant and the SNP marker but also on the difference in their allele frequencies. These factors, as well as penetrance of the disease variant, influence the statistical power of such approaches. However, the power of indirect association studies is not well understood. We calculated the number of individuals necessary for the detection of the disease variant in both direct and indirect association studies with a case-control design. The result shows that a remarkable reduction in the statistical power of indirect studies, compared with that of direct ones, is unavoidable in the genome-wide screening of complex disease genes. If there is a large difference in allele frequency between the disease variant and the marker, the disease variant cannot be detected. Because the frequency of the disease variant is unknown, SNP markers with various allele frequencies, or a large number of SNP markers, must be used in indirect association studies. However, if the number of SNP markers is increased, the obtained P value may not reach the significance level due to the Bonferroni adjustment. Thus, to test a possible association between functional variants and a complex disease directly, we should identify such SNPs in as many genes as possible for use in genome-wide association studies. Reveived: March 27, 2001 / Accepted: April 21, 2001     

Pharmacogenomics in Alzheimer's disease: a genome-wide association study of response to cholinesterase inhibitors

We conducted a genome-wide association study in a cohort of 176 Italian Alzheimer's disease (AD) patients with extreme phenotype of response to cholinesterase inhibitors. Patients were classified into responders in case of positive, stable, or ≤1 worsening of mini-mental state examination score and into nonresponders if >3 points worsening during a median follow-up of 0.85 years of treatment. Forty-eight single-nucleotide polymorphisms were selected for replication in 198 additional AD-treated patients. By using the dichotomous response trait and a quantitative trait approach (change of mini-mental state examination), a nominal replication and evidence of association when combining data were achieved for 2 single-nucleotide polymorphisms associated with response to treatment: rs6720975_A (p_combined = 2.9 × 10⁻⁵, beta regression coefficient: 1.61) and rs17798800_A (p_combined = 6.8 × 10⁻⁶, odds ratio = 0.38, 95% confidence interval = 0.25–0.58). Rs6720975 maps in the intronic region of PRKCE, a protein kinase involved in several cellular functions, whereas rs17798800 is intergenic and, according to expression quantitative trait locus (eQTL) analysis, it acts as a cis-regulator of NBEA, an A kinase–anchoring protein playing a substantial role in the maturation of the nervous system. Despite its limitations, this project paves the way for the application of personalized medicine in AD patients and for collaborative efforts in this field.     

A genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations

Sporadic amyotrophic lateral sclerosis (sALS) is a severe neurodegenerative disease that causes progressive motor neuron death. Although the etiology of sALS remains unknown, genetic variants are thought to predispose individuals to the disease. Several recent genome-wide association studies have identified a number of loci that increase sALS susceptibility, but these only explain a small proportion of the disease. To extend the current genetic evidence and to identify novel candidates of sALS, we performed a pooling genome-wide association study by 859,311 autosomal single-nucleotide polymorphisms of IlluminaHumanOmniZhongHua-8 combining pathway analysis in 250 typical sALS cases precluding age, clinical course, and phenotype interference and 250 control subjects from Chinese Han populations (CHP). The results revealed that 8 novel loci of 1p34.3, 3p21.1, 3p22.2, 10p15.2, 22q12.1, 3q13.11, 11q25, 12q24.33, and 5 previously reported loci of CNTN4 (kgp11325216), ATXN1 (kgp8327591), C9orf72 (kgp6016770), ITPR2 (kgp3041552), and SOD1 (kgp10760302) were associated with sALS from CHP. Furthermore, the pathway analysis based on the Gene Set Analysis Toolkit V2 showed that 10 top pathways were strongly associated with sALS from CHP, and among them, the 7 most potentially candidate pathways were phosphatidylinositol signaling system, Wnt signaling pathway, axon guidance, MAPK signaling pathway, neurotrophin signaling pathway, arachidonic acid metabolism, and T-cell receptor signaling pathway, a total of 39 significantly associate genes in 7 candidate pathways was suggested to involve in the pathogenesis of sALS from CHP. In conclusion, our results revealed several new loci and pathways related to sALS from CHP and extend the association evidence for partial loci, genes, and pathways, which were previously identified in other populations. Thus, our data provided new clues for exploring the pathogenesis of sALS.     

A genome-wide association study of Cloninger's temperament scales: Implications for the evolutionary genetics of personality

Variation in personality traits is 30-60% attributed to genetic influences. Attempts to unravel these genetic influences at the molecular level have, so far, been inconclusive. We performed the first genome-wide association study of Cloninger's temperament scales in a sample of 5117 individuals, in order to identify common genetic variants underlying variation in personality. Participants’ scores on Harm Avoidance, Novelty Seeking, Reward Dependence, and Persistence were tested for association with 1,252,387 genetic markers. We also performed gene-based association tests and biological pathway analyses. No genetic variants that significantly contribute to personality variation were identified, while our sample provides over 90% power to detect variants that explain only 1% of the trait variance. This indicates that individual common genetic variants of this size or greater do not contribute to personality trait variation, which has important implications regarding the genetic architecture of personality and the evolutionary mechanisms by which heritable variation is maintained.     

基于家系的Tim-3基因多态性与儿童变应性哮喘的关联研究

目的 以家系资料为基础,利用遗传不平衡原理探讨染色体5q33.2区Tim-3基因启动子两个多态性位点rs10053538和rs10515746与中国湖北地区汉族儿童变应性哮喘的关系.方法 应用限制性片段长度多态性技术结合测序方法,分析了118个儿童变应性哮喘核心家系Tim-3基因rs10053538和rs10515746的基因型;采用基于家系的关联分析方法,包括单体型相对风险分析(HRR)和传递不平衡检验(TDT),分析基因分型数据;应用Transmit软件构建单体型并进行单体型关联分析.结果 118个核心家庭HRR分析显示Tim-3基因启动子区两个多态性位点rs10053538和rs10515746不使病人具有更高的发病风险(X2=2.430,P>0.05;x2=1.368,P>0.05).118个满足经典TDT分析的核心家庭中,杂合子父母传递给患病子代的等位基因频率不比预期值高(x2=2.042,P>O.05;x2=0.750,P>O.05).Transmit双位点单体型分析也未见父母传递给子女各个单体型的观察值和期望值有明显差异(P>O.05).结论 中国湖北地区汉族人群中,Tim-3基因启动子区两个多态性位点rs10053538和rs10515746与儿童变应性哮喘不具有相关性.