人类遗传学的又一突破:亨廷顿氏病致病基因位点的识别及克隆

人类遗传学的又一突破：亨廷顿氏病致病基因位点的识别及克隆缪为民,柴建华（复旦大学遗传学研究所,上海２００４３３）通过定位克隆（Ｐｏｓｉｔｉｏｎａｌｃｌｏｎｉｎｇ）的方法可以对那些生化病理机制不明的遗传性疾病进行致病基因的研究［１］。自八十年代初以来,这一反向遗传学的策略已取得了辉煌的成果,迄今已有数十个致病基因陆续被发现。     

人类的致病基因

在人类基因组计划取得重大进展的背景下,有1000多种致病基因被克隆鉴定出来并加以分类。定位克隆,定位候选克隆及新兴的SNP标记均被用于搜索新的致病基因。对肿瘤,神经系统和视觉系统等致病遗传基因的研究已获初步成果。     

植物抗病遗传育种中的QTL定位和克隆(综述)

对植物抗病遗传育种中QTL定位与克隆研究进行综述。主要阐述了数量抗性的遗传学基础、作物抗病性QTL的定位作图、QTL作图的可靠性及应对措施、QTLs候选基因的证实和定位克隆等,并对植物抗病遗传育种未来的研究方向予以讨论。     

候选基因策略在植物遗传学中的应用

随着遗传学研究技术的快速发展和后基因组学时代的来临,候选基因的概念和研究方法越来越多地被人们所应用,成 为功能克隆、图位克隆、表型克隆、插入突变等方法之外的又一重要基因克隆策略。候选基因策略的基本原理和主要步骤,以 及其在植物遗传学中具有重要的应用实例。     

人类基因组研究新进展

人类基因组研究新进展柴建华（复旦大学遗传学研究所人类基因组实验室上海２００４３３）人类基因组研究在全世界范围内展开已经是第八个年头了。研究任务分为两个：一是染色体ＤＮＡ的大片段克隆、排序和核耷酸顺序分析;另一个是全部基因的顺序识别及功能研究,包括突变...     

复杂疾病基因定位策略与肿瘤易感基因鉴定

对于不存在某单一基因位点经典的孟德尔显性或隐性遗传模式的疾病,称为复杂疾病,肿瘤是最常见的类型之一 . 目前,以连锁和相关分析为基础的功能克隆、功能候选克隆、定位克隆、定位候选克隆、系统生物学等复杂疾病易感基因定位策略逐渐发展起来 . 其中,系统生物学策略由于整合了从 DNA 到蛋白质的各个层面的信息,对复杂疾病基因调控网络做出了良好诠释,使其成为最有潜力的方法之一 . 目前,虽然已有近 100 种肿瘤 / 遗传性癌综合症的易感基因被鉴定出来,但未来的复杂疾病易感基因定位工作仍充满了挑战 .     

基于二元网络异步重启随机游走算法预测肺癌风险致病基因

肺癌致病基因的发现及预测有助于认识肺癌的发生机理、诊断与防治,是人类基因组研究的重要目标。应用现有二元网络重启随机游走算法预测致病基因时,一般先在疾病表型网络、蛋白质作用网络及疾病-蛋白质二分图网络内随机游走一步,然后进行网络间跳转,这种策略不仅搜索效率较低,还可能遗漏蛋白质(或疾病)网络中的局部拓扑信息。鉴于此,作者提出一种二元网络异步重启游走(asynchronously random walk with restart,ARWRH)算法,构建疾病表型-蛋白质异构网络,深层次挖掘潜在肺癌风险致病基因。ARWRH算法首先在疾病表型网络、蛋白质作用网络及疾病表型-蛋白质二分图网络内随机游走不同步数,然后进行网络间跳转,迭代形成稳态概率向量,从而获得候选致病基因。仿真实验表明,ARWRH算法可有效预测肺癌潜在风险致病基因,多数预测结果获得了文献证据支持。     

ＥＳＴ在克隆新基因中的应用

随着基因定位（连锁图谱、物理图谱、转录图谱）和ＤＮＡ测序及生物信息技术的迅猛发展,ＥＳＴ已成为人类寻找新的未知基因以及克隆不同时空差异表达基因和疾病相关基因的重要标志物。随着ＥＳＴ数据库的进一步完善,网上克隆和定位候选克隆策略将成为克隆新基因的主要方法,并在虚拟的网上空间将模型生物基因组的研究成果成功地应用于人类基因组的研究中。     

基于致病基因网络模块性预测风险致病基因

相关疾病基因的发现和预测有助于认识疾病发生机理及该疾病的诊断与防治,是人类基因组研究的重要目标。临床表现重叠的疾病经常由同一功能模块中的一个或多个基因变异引起,且导致疾病表型相似的基因间经常发生直接或间接相互作用,也就是致病基因具有网络模块性。鉴于此,基于k近邻思想扩展异构网络游走RWRH算法中的初始游走概率向量,作者提出一种改进的异构网络随机游走KRWRH算法,在基因-表型异构网络中深层次挖掘潜在风险致病基因。KRWRH算法通过扩展种子集合构建起始概率向量,种子集合包含已知致病基因及其k近邻基因;然后在异构网络中随机游走,通过迭代形成稳态概率向量,从而获得候选致病基因。通过对孟德尔遗传在线数据库中的18种遗传疾病进行仿真验证,说明KRWRH算法可有效预测潜在风险致病基因。     

DNA纤维上的原位杂交技术

ＤＮＡ纤维上的荧光原位杂交（Ｆｉｂｅｒ－ＦＩＳＨ）技术是一种非重要的分子细胞遗传学技术。对于高分辨物理图的绘制、基因组和染色体结构的研究、致病基因的定位克隆等都有很大作用,本文介绍了该技术的基本操作和应用,以及与引物原位ＤＮＡ合成（ＰＲＩＮＳ）等技术相结合进行更精确基因定位的潜力。     

An integrative approach for the identification of quantitative trait loci

The genetic dissection of complex traits is one of the most difficult and most important challenges facing science today. We discuss here an integrative approach to quantitative trait loci (QTL) mapping in mice. This approach makes use of the wealth of genetic tools available in mice, as well as the recent advances in genome sequence data already available for a number of inbred mouse strains. We have developed mapping strategies that allow a stepwise narrowing of a QTL mapping interval, prioritizing candidate genes for further analysis with the potential of identifying the most probable candidate gene for the given trait. This approach integrates traditional mapping tools, fine mapping tools, sequence-based analysis, bioinformatics and gene expression.     

催乳素受体基因的研究进展

本文介绍催乳素受体的结构,催乳素受体基因的发育性表达及作用,催乳素受体基因的作用机理与分子调控,催乳素受体基因的定位以及其与繁殖性状的关系等。提示催乳素受体基因可作为繁殖性状的一个候选基因。 Abstract:This review introduced the structure of prolactin receptor,the developmental expression and function,action　mechanism and molecular regulation,mapping of prolactin receptor gene and its relationship with reproductive traits.These revealed that prolactin receptor gene could be used as a candidate gene for reproductive traits.     

Ovine alpha-amylase genes: isolation, linkage mapping and association analysis with milk traits

On the basis of comparisons between cattle and sheep genome mapping information the ovine alpha-amylase gene was examined as a possible genetic marker for milk traits in sheep. The objective of the present study was to isolate, map and determine whether this gene is a candidate gene for milk traits. DNA fragments (832 and 2360 bp) corresponding to two different AMY genes were isolated, and one SNP in intron 3 and one GTG deletion in exon 3 of the 2360 bp DNA fragment were found. The 2360 bp ovine AMY DNA fragment was located on chromosome 1 by linkage mapping using the International Mapping Flock. No association was found between estimated breeding values for milk yield, protein and fat contents and AMY genotypes in a daughter design comprising 13 Manchega families with an average of 29 daughters (12-62) per sire.     

Using bioinformatics and systems genetics to dissect HDL-cholesterol genetics in an MRL/MpJ x SM/J intercross

A higher incidence of coronary artery disease is associated with a lower level of HDL-cholesterol. We searched for genetic loci influencing HDL-cholesterol in F2 mice from a cross between MRL/MpJ and SM/J mice. Quantitative trait loci (QTL) mapping revealed one significant HDL QTL (Apoa2 locus), four suggestive QTL on chromosomes 10, 11, 13, and 18 and four additional QTL on chromosomes 1 proximal, 3, 4, and 7 after adjusting HDL for the strong Apoa2 locus. A novel nonsynonymous polymorphism supports Lipg as the QTL gene for the chromosome 18 QTL, and a difference in Abca1 expression in liver tissue supports it as the QTL gene for the chromosome 4 QTL. Using weighted gene co-expression network analysis, we identified a module that after adjustment for Apoa2, correlated with HDL, was genetically determined by a QTL on chromosome 11, and overlapped with the HDL QTL. A combination of bioinformatics tools and systems genetics helped identify several candidate genes for both the chromosome 11 HDL and module QTL based on differential expression between the parental strains, cis regulation of expression, and causality modeling. We conclude that integrating systems genetics to a more-traditional genetics approach improves the power of complex trait gene identification.     

Candidate genes for drought tolerance and improved productivity in rice (Oryza sativa L.)

Candidate genes are sequenced genes of known biological action involved in the development or physiology of a trait. Twenty-one putative candidate genes were designed after an exhaustive search in the public databases along with an elaborate literature survey for candidate gene products and/or regulatory sequences associated with enhanced drought resistance. The downloaded sequences were then used to design primers considering the flanking sequences as well. Polymerase chain reaction (PCR) performed on 10 diverse cultivars that involvedJaponica, Indica and local accessions, revealed 12 polymorphic candidate genes. Seven polymorphic candidate genes were then utilized to genotype 148 individuals of CT9993 × IR62266 doubled haploid (DH) mapping population. The segregation data were tested for deviation from the expected Mendelian ratio (1:1) using a Chi-square test (<1%). Based on this, four candidate genes were assessed to be significant and the remaining three, as non-significant. All the significant candidate genes were biased towards CT9993, the female parent in the DH mapping population. Single-marker analysis strongly associated (<1%) them to different traits under both well-watered and low-moisture stress conditions. Two candidate genes,EXP15 andEXP13, were found to be associated with root number and silicon content in the stem respectively, under both well-watered and low-moisture stress conditions     

家养动物复杂性状基因定位的统计分析和实验设计

复杂性状基因定位的研究是人类、动植物研究中的1个热点领域。在畜禽的研究中,其目的是定位与生产性状、繁殖性状和疾病相关的基因。在人类中,复杂性状基因定位的研究具有极大的挑战性。尽管基因定位的结果积累得很快,但能得以确认的结果却很少。关于畜禽基因定位的研究结果同样也增长很快,目前在鸡、猪、奶牛等物种中几个大尺度的基因定位工作也正在开展中。虽然在不远的将来能够得到新的、可确信的结果,但是如何精确地理解这些复杂性状的基因仍然需要一定的时间。近来,复杂性状基因定位的方法已被用于通过基因表达的数据研究转录调节因子的定位工作中,这是基因定位研究中1个新的领域。基因定位的统计分析和实验设计是基因定位研究中的关键性步骤,研究的目的在于讨论畜禽复杂性状基因定位的统计分析和实验设计的研究进展及今后的发展。     

Integration of expression profiles and genetic mapping data to identify candidate genes in intracranial aneurysm.

Intracranial aneurysm (IA) is a complex genetic disease for which, to date, 10 loci have been identified by linkage. Identification of the risk-conferring genes in the loci has proven difficult, since the regions often contain several hundreds of genes. An approach to prioritize positional candidate genes for further studies is to use gene expression data from diseased and nondiseased tissue. Genes that are not expressed, either in diseased or nondiseased tissue, are ranked as unlikely to contribute to the disease. We demonstrate an approach for integrating expression and genetic mapping data to identify likely pathways involved in the pathogenesis of a disease. We used expression profiles for IAs and nonaneurysmal intracranial arteries (IVs) together with the 10 reported linkage intervals for IA. Expressed genes were analyzed for membership in Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathways. The 10 IA loci harbor 1,858 candidate genes, of which 1,561 (84%) were represented on the microarrays. We identified 810 positional candidate genes for IA that were expressed in IVs or IAs. Pathway information was available for 294 of these genes and involved 32 KEGG biological function pathways represented on at least 2 loci. A likelihood-based score was calculated to rank pathways for involvement in the pathogenesis of IA. Adherens junction, MAPK, and Notch signaling pathways ranked high. Integration of gene expression profiles with genetic mapping data for IA provides an approach to identify candidate genes that are more likely to function in the pathology of IA.     

水稻米香基因的遗传分析与精细定位

香味是水稻重要的品质性状之一,由100多种挥发性化合物组成,其中2-乙酰基-1-吡咯啉（2AP）是稻米香气中最主要的成分,且由一对隐性基因（fgr）控制,fgr基因位于水稻第八号染色体上。本研究根据初定位结果,利用籼粳稻基因组序列在RG1／RG28区域内发展高密度的分子标记,结合大分离群体来定位水稻的米香基因。结果显示,fgr基因位于第八条染色体的WJ-7和WJ-8分子标记之间约408kb的区间内。这一结果将对于水稻米香基因的克隆与分离提供了重要依据。     

基于节点-模块置信度及局部模块度双重约束挖掘前列腺癌候选疾病模块

前列腺癌病因及发病机理研究有助于前列腺癌预防和治疗.目前,前列腺癌生化试验研究方法成本高、耗时,而基于网络计算方法容易受基因表达谱数据不完整、噪声高及实验样本数量少等约束.为此,本文提出一种基于节点-模块置信度及局部模块度的双重约束算法(命名为NMCOM),挖掘前列腺癌候选疾病模块.NMCOM算法不依赖基因表达谱数据,采用候选基因与致病表型之间一致性得分,候选基因与致病基因之间语义相似性得分融合排序策略,选取起始节点,并基于节点-模块置信度及局部模块度双重约束挖掘前列腺癌候选疾病模块.通过对挖掘出的模块进行富集分析,最终得到18个有显著意义的候选疾病基因模块.与单一打分排序方法及随机游走重开始方法相比,NMCOM融合排序策略的平均排名比小、AUC值大,且挖掘出结果明显优于其他模块挖掘算法,模块生物学意义显著.NMCOM算法不仅能准确有效地挖掘前列腺癌候选疾病模块,且可扩展挖掘其他疾病候选模块.