SIRT1基因多态性与广西永福地区人群长寿的关联性

目的 探讨SIRT1基因多态性与广西永福地区人群长寿的关联性.方法 采用长寿对照设计,选取广西壮族自治区永福县共500人为研究对象,包括长寿组223人、平均年龄(93.17±3.08)岁,对照组277人、平均年龄(46.92±17.12)岁.应用聚合酶链反应-高分辨熔解曲线技术结合测序验证法检测SIRT1基因上的rs3758391,rs3740051,rs2273773,rs4746720和rs10997870位点的单核苷酸多态性(single nucleotide polymorphisms,SNP)的分布情况,比较长寿组与对照组人群的等位基因、基因型频率的分布特征,分析SIRT1基因多态性与长寿的关联性.结果 长寿组rs4746720位点CT基因型频率高于CC和TT基因型频率,差异具有统计学意义(P=0.000,OR=2.098,95％CI:1.412-4.117),其等位基因频率在两组间分布的差异无统计学意义.rs3758391 、rs3740051 、rs2273773位点的基因型频率和等位基因频率在长寿组和对照组间分布的差异均无统计学意义.结论 SIRT1基因rs4746720单核苷酸多态性与广西永福地区长寿人群相关联.     

119例汉族人血浆MASP2水平及其基因多态性分析

本研究旨在了解本地区汉族人血浆甘露糖结合凝集素相关丝氨酸蛋白酶2(MASP2)水平及其基因多态性。收集并分离119例来我院参加体检的汉族人血浆,用ELISA法检测血清MASP2含量,并用序列分析法分析MASP2基因外显子3和外显子4的基因多态性。结果显示,汉族人总体血浆MASP2范围0.0~1759.9ng/ml,中位数226.5ng/ml,儿童和成人血浆MASP2中位数分别为627.4ng/ml和109.3ng/ml,儿童血浆MASP2水平显著高于成人(Z=-7.794,P=0.000)。序列分析显示MASP2基因外显子4区rs2273343多态性位点变异频率为0.033,外显子1区+11位点~外显子3区+681位点和外显子4区+1710位点~+1814位点间无多态性和新突变发现。本组儿童血浆MASP2水平高于成人,MASP2基因单核甘酸多态性位点罕见变异,仅外显子4的rs2273343位点存在变异。     

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。     

人类MOG1基因检测及其与青壮年猝死综合征的相关性研究

目的寻找MOG1基因的变异位点,探讨其与青壮年猝死综合征的关系。方法提取青壮年猝死综合征病例组及健康对照组的基因组DNA,采用聚合酶链式反应（PCR）方法扩增MOG1基因编码区外显子、外显子-内含子交界区以及3′侧翼区序列,直接行DNA测序以明确遗传变异类型,并进行统计学分析。结果在病例组中共检测到3个变异位点,其中2个为新发现的突变,分别为c.285G〉C（p.L95L）和c.＊4C〉T,另1个为单核苷酸多态性位点c.437＋16C〉T。在病例组和对照组中c.437＋16C〉T位点基因型分布（P=0.071）和等位基因频率（P=0.819）存在一定程度差异,但差异均无统计学意义。结论MOG1基因是否是中国人青壮年猝死综合征的易感基因还有待进一步研究。     

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.     

儿童孤独症患者γ-氨基丁酸(GABA)A类受体基因簇的罕见变异

目的:探讨儿童孤独症患者染色体15q12区域γ-氨基丁酸A类受体基因簇是否存在可能致病的罕见变异。方法:对96例符合DSM-IV孤独症诊断标准的中国汉族儿童孤独症患者γ-氨基丁酸A类受体基因簇进行靶向测序,采用Sanger测序法进行验证。进一步扩大样本筛查罕见变异,通过连续性校正χ2检验比较罕见变异的分布频率在384例儿童孤独症病例组和384例正常对照组的差异。结果:96例儿童孤独症患者靶向测序发现8个罕见变异,包括GABRG3基因的2个罕见错义突变[rs201602655(p. Val233Met)和rs201427468 (p. Pro365Ser)]和GABRB3基因非编码区的6个罕见突变。Sanger测序验证后进一步扩大样本,rs201602655杂合型变异在孤独症组出现的频率高于正常对照组(2. 1%vs. 0. 3%,P 0. 05)。功能预测提示rs201602655罕见变异为有害突变,可能导致GABRG3蛋白质的异常。结论:GABRG3基因在儿童孤独症存在影响氨基酸改变的罕见变异,是孤独症的易感基因可能参与孤独症的致病。     

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。     

新疆哈萨克族人Furin基因变异与中心性肥胖的相关性研究

目的 研究哈萨克族人弗林蛋白基因(Furin)变异与中心性肥胖的相关性.方法 以哈萨克族自然人群横断面流行病学调查为基础选取478例肥胖者和378名正常个体进行病例-对照研究.从肥胖者中随机选择66例,对其Furin启动子、外显子区测序筛查其代表性变异；并采用TaqMan PCR技术对筛查出的Furin代表性变异在856名哈萨克族个体中进行分型,分析其与哈萨克族人肥胖的相关性.结果 在478例肥胖者中随机选择66例(男女各33例),共筛查出Furin的12个变异,其中rs6226、rs6227、rs2071410、rs4932178是代表性变异；这4个代表性变异均在大样本哈萨克族人中基因型分型成功(成功率≥99％);在总体、男性、女性哈萨克族自然人群中,rs6226、rs6227、rs2071410、rs4932178多态性位点的基因型、等位基因、单倍型频率在肥胖组及对照组分布差异无统计学意义(P＞0.05)；不同基因型携带者之间的腰围平均水平差异也无统计学意义(P＞0.05).结论 Furin变异与新疆哈萨克族中心性肥胖不相关,该变异可能不是哈萨克族人中心性肥胖的易感因素.     

中国山东地区先天性甲状腺功能减低症患者PAX8基因突变筛查研究

目的对中国山东地区先天性甲状腺功能减低症(简称甲低)患者PAX8第4外显子进行基因突变筛查,阐明中国山东地区甲低患者PAX8基因第4外显子突变特点。方法 453例标本来自山东甲状腺发育不全的先天性甲低患者,从外周血白细胞中提取全基因组DNA扩增PAX8第4外显子,对PCR产物进行直接测序分析。结果分析453例PAX8第4外显子测序结果未发现突变,但在1例患者第4内含子发现1个IVS4+83 T>C突变,在第4内含子区发现1个SNP位点(rs74370449,IVS4+101 G/A,变异频率为8.9%)。结论 PAX8基因第4外显子突变率在中国山东地区甲低患者中极低,PAX8第4内含子的突变可能与先天性甲低相关。     

Interleukin-18基因启动子区单核苷酸多态性与肝细胞癌遗传易感性关系的研究

目的探讨白细胞介素18(IL-18)基因启动子区-607C/A(rs1946518)和-137G/C(rs187238)单核苷酸多态性(SNP)与肝细胞癌(肝癌)遗传易感性的关系。方法应用序列特异性引物-聚合酶链反应(PCR-SSP)技术,检测228例肝癌患者和300例健康对照者IL-18基因启动子-607C/A(rs1946518)、-137G/C(rs187238)单核苷酸多态性位点基因型,分析肝癌患者和对照组基因型频率和等位基因频率分布。结果肝癌组SNP位点rs187238 G等位基因的频率明显高于对照组(OR=1.1891,95%CI=1.0106-1.5633,P=0.026)。携带rs187238 GG基因型的肝癌患者较多(OR=1.5168,95%CI=1.1490-1.8322,P=0.010)。分层分析发现,rs1946518位点上AA基因型与肝癌发病的关联在饮酒的肝癌患者中更加显著(P=0.024),而且rs187238位点上GC/CC基因型与肝癌发病的关联在出现肝癌复发的患者中更加显著(P=0.005)。结论 IL-18基因启动子区-137G/C(rs187238)GG基因型与肝癌遗传易感性有关联。而rs1946518位点AA基因型和rs187238位点GC/CC基因型分别与肝癌患者饮酒和肝癌复发有关联。     

Genetic polymorphisms and haplotype structures of HSPA5 gene in the Han population of Southern China

The heat shock 70 kDa protein 5 ( HSPA5 ) gene is known to be involved in stress-associated diseases. In this study, the promoter, exons, 3' untranslated region (3'UTR), and subtotal introns of the HSPA5 gene were sequenced in a sub-population of 161 healthy Han Chinese. Nine single-nucleotide polymorphisms (SNPs) including a new one (-86bp T > A from the estimated translation start site) were found and 15 haplotypes (frequencies > 1%) were inferred. Polymorphisms rs391957 and rs11355458 were completely linked in our population (r ² = 1.00). Using this information, fellow scientists may be able to decrease the number of SNPs to be genotyped in future disease case-control studies.     

The Clinical Genome and Ancestry Report: An interactive web application for prioritizing clinically implicated variants from genome sequencing data with ancestry composition

Genome sequencing is positioned as a routine clinical work‐up for diverse clinical conditions. A commonly used approach to highlight candidate variants with potential clinical implication is to search over locus‐ and gene‐centric knowledge databases. Most web‐based applications allow a federated query across diverse databases for a single variant; however, sifting through a large number of genomic variants with combination of filtering criteria is a substantial challenge. Here we describe the Clinical Genome and Ancestry Report (CGAR), an interactive web application developed to follow clinical interpretation workflows by organizing variants into seven categories: (1) reported disease‐associated variants, (2) rare‐ and high‐impact variants in putative disease‐associated genes, (3) secondary findings that the American College of Medical Genetics and Genomics recommends reporting back to patients, (4) actionable pharmacogenomic variants, (5) focused reports for candidate genes, (6) de novo variant candidates for trio analysis, and (7) germline and somatic variants implicated in cancer risk, diagnosis, treatment and prognosis. For each variant, a comprehensive list of external links to variant‐centric and phenotype databases are provided. Furthermore, genotype‐derived ancestral composition is used to highlight allele frequencies from a matched population since some disease‐associated variants show a wide variation between populations. CGAR is an open‐source software and is available at https://tom.tch.harvard.edu/apps/cgar/ .     

Genetic associations with C‐reactive protein level and white blood cell count in the KARE study

C‐reactive protein (CRP) and white blood cell (WBC) have been utilized as critical markers contributing to acute and chronic inflammation. Genome‐wide associations were examined to identify nucleotide sequence variants associated with the two markers using 8842 individuals in the Korean Association REsource (KARE) study. A total of six and three nucleotide variants turned out to be associated with CRP and WBC (P < 1.42 × 10^?7), and they were mutually exclusive. The only common variant associated with CRP was rs2393791 within hepatocyte nuclear factor 1 alpha (HNF1A) gene [minor allele frequency (MAF) = 0.478]. The only common variant associated with WBC [MAF = 0.468] was rs8078723, an intergenic single nucleotide polymorphism located between proteasome 26S subunits non‐ATPase 3 (PSMD3) and colony‐stimulating factor 3 (CSF3) in chromosome 17. The 2 variants were also associated with other inflammation‐related phenotypes (P < 0.05), and each phenotype was associated with the variant rs2393791 or with the variant rs8078723. We suggested that HNF1A gene was associated with CRP, and the region including PSMD3 and CSF3 genes was associated with WBC. The two inflammatory markers appeared to have distinct genetic components. Not only the functions of these two markers but also the functions of the corresponding genetic components might be largely complementary in determining inflammation process.     

Association of polymorphisms in the melanocortin receptor type 2 (MC2R, ACTH receptor) gene with heroin addiction

The melanocortin receptor type 2 (MC2R or adrenocorticotropic hormone, ACTH receptor) gene (MC2R) encodes a protein involved in regulation of adrenal cortisol secretion, important in the physiological response to stressors. A variant of MC2R, -179A>G, results in reduction of promoter activity and less adrenal action. We hypothesize that altered stress responsivity plays a key role in the initiation of substance abuse. By direct resequencing of the promoter region and exons 1 and 2 of the MC2R gene in 272 subjects including Caucasians, Hispanics and African Americans with approximately equal numbers of former heroin addicts and normal volunteers, we identified five novel variants each with allele frequency <2%. Previously reported polymorphisms -184G>A (rs2186944), -179A>G, 833A>C (rs28926182), 952T>C (rs4797825), 1005C>T (rs4797824) and 1579T>C (rs4308014) were each in allelic frequency >/=2% in one or more ethnic groups. These polymorphisms were genotyped in 632 subjects (260 Caucasians, 168 Hispanics, 183 African Americans and 21 Asians) using TaqMan assays. Significant differences in genotype frequency among ethnic groups studied were found for each of the six variants analyzed. We found a significant association (p=0.0004, experiment-wise p=0.0072) of the allele -184A with a protective effect from heroin addiction in Hispanics. Also, in Hispanics only we found the haplotype GACT consisting of four variants (-184G>A, -179A>G, 833A>C and 1005C>T) to be significantly associated with heroin addiction (p=0.0014, experiment-wise p=0.0168), whereas another haplotype, AACT, consisting of the same variants, was associated with a protective effect from heroin addiction (p=0.0039, experiment-wise p=0.0468).     

Identification of genetic variants that influence circulating IGF1 levels: a targeted search strategy

An important class of genetic variants that affect disease susceptibility may lie within regulatory elements that influence gene expression. Regulatory sequences are difficult to identify and may be distant from the genes they regulate, but many lie within evolutionarily conserved regions (ECRs). We used comparative genomics to identify 12 ECRs up to 75 kb 5' to and within introns of IGF1. These were screened by high-resolution melting curve analysis, and 18 single-nucleotide polymorphisms (SNPs) were identified, including five novel variants. We analysed two large population-based series of healthy women to test the nine SNPs with minor allele frequency (MAF) >1% within ECRs. Three of the nine SNPs within ECRs (rs35455143, rs35765817 and rs3839984) were significantly associated with circulating IGF1 levels in a multivariate analysis (P 70 kb 5' of IGF1. Two (rs35455143 and rs35765817) are in strong LD with each other and appear to have opposite effects on circulating IGF1. Our results on a subset of other SNPs in or near IGF1 were consistent with previously reported associations with IGF1 levels, although only one (rs35767: P = 0.05) was statistically significant. We believe that this is the first systematic study of an association between a phenotype and SNPs within ECRs extending over a large region adjacent to a gene. Targeting ECRs appears to be a useful strategy for identifying a subset of potentially functional non-coding regulatory SNPs.     

Significant association of DRD2 enhancer variant rs12364283 with heroin addiction in a Pakistani population

The dopamine D2 receptor encoded by DRD2 has been implicated in multiple psychiatric disorders, mediated at least in part by two intronic variants affecting mRNA splicing, rs1076560 and rs2283265, and a less frequent enhancer variant, rs12364283, which increases DRD2 mRNA expression. This study tests whether these functionally validated variants confer susceptibility toward heroin addiction in a Pakistani population. A total of 540 heroin addicts and 467 healthy controls were genotyped, basic allele and genotype tests were performed. Neither rs1076560 nor rs2283265 significantly associated with heroin addiction. The enhancer rs12364283 occurs more frequently in heroin‐dependent cases than controls (MAF 13% vs. 7%, respectively), revealing significant association with heroin addiction (p = 3.0E‐06, OR 2.1). This study identifies rs12364283 of DRD2 as a potential risk factor for heroin addiction in the Pakistani study population. This enhancer variant had been shown to increase DRD2 mRNA expression, a possible factor in increased vulnerability to heroin addiction. Further studies are needed to validate this association of rs12364283.     

Large‐scale functional LIPA variant characterization to improve birth prevalence estimates of lysosomal acid lipase deficiency

Lysosomal acid lipase (LAL) deficiency is an autosomal recessive disorder caused by LIPA gene mutations that disrupt LAL activity. We performed in vitro functional testing of 149 LIPA variants to increase the understanding of the variant effects on LAL deficiency and to improve disease prevalence estimates. Chosen variants had been reported in literature or population databases. Functional testing was done by plasmid transient transfection and LAL activity assessment. We assembled a set of 165 published LAL deficient patient genotypes to evaluate this assay's effectiveness to recapitulate genotype/phenotype relationships. Rapidly progressive LAL deficient patients showed negligible enzymatic activity (<1%), whereas patients with childhood/adult LAL deficiency typically have 1–7% average activity. We benchmarked six in silico variant effect prediction algorithms with these functional data. PolyPhen‐2 was shown to have a superior area under the receiver operating curve performance. We used functional data along with Genome Aggregation Database (gnomAD) allele frequencies to estimate LAL deficiency birth prevalence, yielding a range of 3.45–5.97 cases per million births in European‐ancestry populations. The low estimate only considers functionally assayed variants in gnomAD. The high estimate computes allele frequencies for variants absent in gnomAD, and uses in silico scores for unassayed variants. Prevalence estimates are lower than previously published, underscoring LAL deficiency's rarity.     

Mutation intolerant genes and targets of FMRP are enriched for nonsynonymous alleles in schizophrenia

Risk of schizophrenia is conferred by alleles occurring across the full spectrum of frequencies from common SNPs of weak effect through to ultra rare alleles, some of which may be moderately to highly penetrant. Previous studies have suggested that some of the risk of schizophrenia is attributable to uncommon alleles represented on Illumina exome arrays. Here, we present the largest study of exomic variation in schizophrenia to date, using samples from the United Kingdom and Sweden (10,011 schizophrenia cases and 13,791 controls). Single variants, genes, and gene sets were analyzed for association with schizophrenia. No single variant or gene reached genome‐wide significance. Among candidate gene sets, we found significant enrichment for rare alleles (minor allele frequency [MAF] < 0.001) in genes intolerant of loss‐of‐function (LoF) variation and in genes whose messenger RNAs bind to fragile X mental retardation protein (FMRP). We further delineate the genetic architecture of schizophrenia by excluding a role for uncommon exomic variants (0.01 ≤ MAF ≥ 0.001) that confer a relatively large effect (odds ratio [OR] > 4). We also show risk alleles within this frequency range exist, but confer smaller effects and should be identified by larger studies.     

Noncoding RET variants explain the strong association with Hirschsprung disease in patients without rare coding sequence variant

The pathogenesis of Hirschsprung disease is complex. Although the RET proto-oncogene is the most frequently affected gene in Hirschsprung disease, rare coding sequence variants explain only a small part of Hirschsprung disease cases. We aimed to assess the genetic background of Hirschsprung disease using a genome-wide association analysis combined with sequencing all RET exons in samples from 105 Hirschsprung disease cases (30 familial and 75 sporadic) and 386 controls.As expected, variants in or near RET showed the strongest overall association with Hirschsprung disease and the most statistically significant association was observed when using a recessive genetic model (rs2435357, NC_000010.10:g.43582056T?>?C; genotype TT, OR?=?17.31, P?=?1.462?×?10^?21). Previously published associations in variants in SEMA (rs11766001, NC_000007.13:g.84145202A?>?C; allele C, OR?=?2.268, P?=?0.009533) and NRG1 (rs4541858, NC_000008.10:g.32410309A?>?G; allele G, OR?=?1.567, P?=?0.015; rs7835688, NC_000008.10:g.32411499G?>?C; allele C, OR?=?1.567, P?=?0.015) were also replicated in the genome-wide association analysis. Sequencing revealed a total of 12 exonic RET rare variants. Of these, eight amino acid changing rare variants and two frameshift variants caused or possibly caused Hirschsprung disease.Only a minority of the Hirschsprung disease cases (9/30 familial; 7/75 sporadic) carried one of the rare variants. Excluding the rare variant carriers from the genome-wide association analysis did not appreciably change the association of rs2435357 with Hirschsprung disease. We estimate that approximately two thirds of the sporadic cases may be statistically attributed to the recessive action of the common non-coding RET variants. Thus, even though most cases do not carry rare RET variants, combinations of rare variants and the common non-coding RET variant cause the majority of the cases in our population.