单核苷酸多态性与连锁不平衡研究进展

单核苷酸多态性(single nucleotide polymorphism,SNP)是人类基因组中最广泛的多态性现象,也是造成个体差异的最主要的遗传原因,发现和研究SNP的工作在目前人类基因组研究中倍受关注。连锁不平衡是不同遗传标记问存在着的非随机组合现象,SNP作为极具优势的遗传标记为深入研究连锁不平衡、以及利用连锁不平衡进行群体遗传学的参数估计、基因精细定位、关联分析等提供了良好的先决条件。最近,在SNP研究及连锁不平衡的度量和连锁不平衡性质的研究方面取得的一系列进展为遗传学在将来发展奠定了基础。     

人类基因组中的连锁不平衡方式

连锁不平衡(linkagedisequilibrium,LD)伴随突变的多态性出现,由于位点间重组,LD程度逐渐下降。对于一个特定群体而言影响LD的因素很多,一系列人口历史因素起着重要的作用。LD程度的度量,目前常用的两种配对检验方法为D′和r2。在染色体的部分区域存在一系列重组热点分割的单倍型块。目前LD主要应用于关联研究中以定位复杂的疾病基因。     

小家鼠群体基因组连锁不平衡研究

模式动物小鼠是复杂性状相关疾病遗传研究的重要资源.连锁不平衡(linkage disequilib-rium,LD)是群体基因组遗传的重要信息.如果群体LD程度高,相关连锁区段大,有助于用少量遗传位标来对目标基因进行初步定位;反之,如果群体LD程度低,相关连锁区段小,则利用高密度的遗传位标可以对目标基因进行精细定位.本文介绍了实验小鼠群体和野生小鼠群体相关的LD、与LD相关的部分遗传参数以及利用LD进行相关基因定位研究.并提示实验小鼠和野生小鼠各具优势,都是复杂性状基因定位的重要遗传资源.     

6号染色体微卫星标记与精神分裂症的连锁不平衡研究

目的 探索6号染色体的有关微卫星标记与精神分裂症的关系。方法 对115个精神分裂症同胞及核心家系，按照不同的诊断分类，以分布于6号染色体的28个微卫星标记，进行连锁不平衡研究，并分别按照阳性和阴性症状量表及发病年龄分成不同的亚组，在不同的亚组中进行连锁不平衡分析。以XDT和MAPMAKER／SIBS软件系统完成所有连锁不平衡关系具有显著性意义，P值均小于0.005。在以各项PANSS量表和不同发病年龄所分亚组的分析中表明，只有D6S1960位点与精神分裂症的连锁不平衡关系值始终具有显著性意义（P＜0.05）。结论 6号染色体短臂D6S1960附近可能存在精神分裂症的易感基因。     

中国北方汉族人群中载脂蛋白M基因多态性分布特征及连锁不平衡分析

目的研究中国北方汉族人群中载脂蛋白M基因（apolipoprotein M,APOM）多态性分布特征及其连锁不平衡关系。方法采用PCR扩增基因组DNA直接测序法结合PCR-限制性片段长度多态方法对330名中国北方汉族健康人群的APOM基因单核苷酸多态性（single nucleotide polymorphism,SNP）进行分析。结果中国北方汉族人APOM基因存在1号内含子rs805264位点、5号内含子rs707922位点及rs707921位点3个多态位点,不同种族及地区APOM基因SNP差异有统计学意义。APOM基因rs805264位点、rs707922位点及rs707921位点SNP在中国北方汉族人群中呈现明显的连锁不平衡,主要有G-G-C、A-T-A两种单体型。结论APOM基因SNP在中国北方汉族人群中存在显著连锁不平衡。     

TNF-α基因启动子区多态性与SARS发生关系的连锁不平衡研究

目的：研究TNF-α启动子区基因多态性连锁不平衡与严重急性呼吸道综合征（Sever acute respiratory syndrome,SARS）发生关系。方法：采用病例对照研究设计,检测75例SARS康复人员和95例健康人员的TNF-α基因启动子区多态性,分析TNF-α基因启动子区多态性位点的连锁作用与SARS-Cov易感性关系;在SARS康复病人中采用病例-病例对照研究设计,研究TNF-α基因多态性位点的连锁作用与SARS临床症状的关系。采用PCR-SBT（PCR Sequencing Based     

中国人群中精神分裂症与22号染色体的连锁不平衡研究

目的 探讨精神分裂症易感基因与22号染色体的分子遗传学联系,寻找、定位精神分裂症的易感基因。方法 在中国汉族人群中,选择了22号染色体上6个二核苷酸重复标记位点,应用荧光标记半自动基因分型技术,对126个精神分裂症同胞对核心家系进行基因分型和连锁不平衡检验（transmission/disequilibrium test,TDT)。结果 IL8Rβ位点TDT－χ^2值为25．30,P值为0．01,具有统计学意义,显示IL－2Rβ与精神分裂症的易感基因存在连锁不平衡;其他D22S944、D22S264、D22S303、D22S278、CYP2D6五个位点的P值均大于0．05,不存在连锁不平衡。结论 IL2Rβ基因或邻近区域可能存在精神分裂症的易感基因。     

定位人类复杂性状位点的连锁不平衡指数研究进展

随着遗传领域中快速增长的单核苷酸多态性(single nucleotide polymorphism,SNP)和详细的人类单体型数据的获得,群体水平上的连锁不平衡(linkage disequilibrium,LD)定位或关联研究被广泛用来精细定位人类复杂性状位点.一个简单的LD定位方法的关键是选取一个优良的指数来有效地度量性状基因与它紧密相连的遗传标记之间的连锁不平衡程度.本文就精细定位人类复杂性状位点的连锁不平衡指数作一综述.     

纤维蛋白原Bβ基因启动区单核苷酸多态性及连锁不平衡分析

目的　探讨纤维蛋白原 B(fibrinogen,FGB)基因启动区 - 14 8C/ T、- 4 5 5 G/ A、- 85 4 G/ A3个位点单核苷酸多态性 (single nucleotide polymorphism,SNP)在中国南方汉族人群的分布特征及连锁不平衡关系。方法　应用聚合酶链反应 -限制性片段长度多态性技术结合 DNA测序分析检测 377名中国南方汉族人 FGBβ基因型和等位基因的分布频率 ,群体数理遗传学方法分析 FGBβ 3个基因位点 SNP的遗传平衡吻合度和相互间连锁不平衡关系。结果　 3个 FGBβ SNP位点等位基因频率分布符合 Hardy-Weinberg平衡。检出了 FGBβ3个位点 SNP的共 9种基因型 ,- 14 8CC、CT、TT基因型频率分别为0 .5 97、0 .35 8和 0 .0 4 5 ;- 4 5 5 G/ A SNP各基因型频率与 - 14 8C/ T SNP相同 ;- 85 4 GG、GA、AA基因型频率分别为 0 .82 0、0 .178和 0 .0 0 2。各 SNP位点的少见型等位基因频率分别是 0 .2 2 4 (- 14 8T)、0 .2 2 4 (-4 5 5 A)、0 .0 92 (- 85 4 A) ;常见型等位基因频率分别为 0 .776 (- 14 8C)、0 .776 (- 4 5 5 G)、0 .90 8(- 85 4 G)。男女性别间各基因型和等位基因分布频率差异无显著性 (P>0 .0 5 )。经连锁不平衡检验 ,- 14 8C与 - 4 5 5 GSNP为完全一致型 ,- 85 4 G/ A与 - 14 8C/ T、- 4 5 5 G/ A为随机分布。结     

应用连锁不平衡检验法进行单纯性先天性心脏病易感基因 …

将人类单纯性先天性心脏病（ｃｏｎｇｅｎｉｔａｌｈｅａｒｔｄｅｆｅｃｔ，ＣＨＤ）易感基因初步定位，为进一步对其克隆奠定基础，方法在胚胎心脏发育调控相关基因－ＨＯＸ基因Ａ簇、Ｂ簇所在在的染色体区域７ｐ１４－１５、１７ｑ２１内选择３个微卫星ＤＮＡ标记Ｄ７Ｓ１８０８、Ｄ７Ｓ６７３、Ｄ１７Ｓ７９１，应用荧光标记聚合酶边反应技术扩增微卫星征 段，对３９个单纯性ＣＨＤ核心家系的１１２名成员进行基因型，并进行遗传     

Gene-based interaction analysis by incorporating external linkage disequilibrium information

Gene-gene interactions have an important role in complex human diseases. Detection of gene-gene interactions has long been a challenge due to their complexity. The standard method aiming at detecting SNP-SNP interactions may be inadequate as it does not model linkage disequilibrium (LD) among SNPs in each gene and may lose power due to a large number of comparisons. To improve power, we propose a principal component (PC)-based framework for gene-based interaction analysis. We analytically derive the optimal weight for both quantitative and binary traits based on pairwise LD information. We then use PCs to summarize the information in each gene and test for interactions between the PCs. We further extend this gene-based interaction analysis procedure to allow the use of imputation dosage scores obtained from a popular imputation software package, MACH, which incorporates multilocus LD information. To evaluate the performance of the gene-based interaction tests, we conducted extensive simulations under various settings. We demonstrate that gene-based interaction tests are more powerful than SNP-based tests when more than two variants interact with each other; moreover, tests that incorporate external LD information are generally more powerful than those that use genotyped markers only. We also apply the proposed gene-based interaction tests to a candidate gene study on high-density lipoprotein. As our method operates at the gene level, it can be applied to a genome-wide association setting and used as a screening tool to detect gene-gene interactions.     

Investigation of linkage and association/linkage disequilibrium of HLA A‐, DQA1‐, DQB1‐, and DRB1‐alleles in 69 sib‐pair‐ and 89 trio‐families with schizophrenia

The hypothesis that HLA antigens confer susceptibility to schizophrenic disorders has been tested by studying linkage and association in a family sample with 69 sib‐pair families. Suggestive evidence for linkage was obtained by nonparametric multipoint LOD score analysis with a maximum around DQB CAR (P = 0.0004), a microsatellite marker that is in linkage disequilibrium with the HLA antigen DQB1. Spurious evidence for negative association as calculated by the transmission disequilibrium test was found for HLA‐ DRB1*11 (chi‐square = 11.72, corrected P value = 0.03) and for the haplotype DQB1*301—DQA1*501—DRB1*11 (chi‐square = 11.3, corrected P value = 0.043). No evidence of association with these alleles was obtained in a sample of 89 trios with schizophrenic offspring and parents. Our results are not in favor of a direct involvement of the HLA system in development of schizophrenia, but are compatible with the possible existence of a susceptibility gene in the MHC region at chromosome 6p 21.31. © 2002 Wiley‐Liss, Inc.     

甲叉四氢叶酸还原酶C677T与精神分裂症的连锁不平衡研究

目的 通过对甲叉四氢叶酸还原酶（methylenetetrahydrofolate reductase,MTHFR)C677T错义突变与精神分裂症的连锁不平衡研究，探讨该突变与精神分裂症的关系。方法 对115个精神分裂症同胞及核心家系中，用XDT和MAPMAKER／SIBS软件系统进行MTHFRC677T与精神分裂症的连锁不平衡分析。按照不同的诊断范围将家系分类，分别在全体家系及发病年龄小于25岁的家系中进行连锁不平衡分析。结果 在4种不同的诊断分类下，对全体家系进行连锁不平衡分析未发现阳性结果。对发病年龄小于25岁的患者家系进行分析时发现，在4种不同的诊断灵感上均具有显著性意义，P值分别小于0．05及0．01。结论 MTHFR C677T错义突变可能为影响精神分裂症易感性的基因之一，尤其是在发病年龄较早的患病群体中。     

Detecting linkage disequilibrium in the presence of locus heterogeneity

Locus heterogeneity is a common phenomenon in complex diseases and is one of the most important factors that affect the power of either linkage or linkage disequilibrium (LD) analysis. In linkage analysis, the heterogeneity LOD score (HLOD) rather than LOD itself is often used. However, the existing methods for detecting linkage disequilibrium, such as the TDT and many of its variants, do not take into account locus heterogeneity. We propose two novel likelihood-based methods, an LD-Het likelihood and an LD-multinomial likelihood, to test linkage disequilibrium (LD) that explicitly incorporate locus heterogeneity in the analysis. The LD-Het is applicable to general nuclear family data but requires a working penetrance model. The LD-multinomial is only applicable to affected sib-pair data but does not require specification of a trait model. For affected sib-pair data, both methods have similar power to detect LD under the recessive model, but the LD-multinomial model has greater power when the underlying model is dominant or additive.     

On the validity of the likelihood ratio test and consistency of resulting parameter estimates in joint linkage and linkage disequilibrium analysis under improperly specified parametric models

It has been shown that parametric analysis of linkage disequilibrium conditional on linkage using an overly deterministic model can be optimal for family-based association analysis. However, if one applies this strategy carelessly, there is a risk of false inference. We analyse properties of such likelihood ratio tests when the assumed disease mode of inheritance is inaccurate. Under some conditions, problems result if one is not careful to consider what null hypothesis is being tested. We show that: (a) tests for which the null hypothesis assumes the absence of both linkage and association are independent of the true mode of inheritance; (b) likelihood ratio tests assuming either linkage or association under the null hypothesis may depend on the true mode of inheritance, leading to inconsistent parameter estimates, in particular under extremely deterministic models; (c) this problem cannot be eliminated by increasing sample size or adding population controls--as sample size increases, the chance of false positive inference goes to 100%; (d) this issue can lead to systematic false positive inference of association in regions of linkage. This is important because highly deterministic models are often used intentionally in model-based analyses because they can have more power than the true model, and are implicit in many model-free analysis methods.