近交系小鼠数量性状基因的定位克隆策略

许多影响人类健康的重大疾病如高血压、哮喘和肥胖等都是复杂性状相关疾病.模式动物小鼠作为复杂性状研究的重要遗传资源,至今已有2900个数量性状基因座(QTL)在小鼠中被初步定位,然而国内对于小鼠复杂性状相天基因研究的报道并不多.本文埘近交系小鼠在复杂性状研究中的优势以及利用近交系小鼠进行QTL初步定位和精细定位的策略进行了综述,并重点介绍小鼠QTL克隆所面临的挑战,提出利用合作杂交计划和野生小鼠资源解决QTL基因研究费时费力且定位分辨率低等一系列瓶颈问题的新思路.     

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.     

野生小家鼠遗传多样性与复杂性状研究

模式动物小鼠已成为复杂性状相关疾病（complex trait）遗传研究的主要资源,过去20年中已有数千个调控各种复杂性状的数量性状座位（QTLs）在小鼠组被初步定位,但现有实验小鼠遗传多样性缺乏已成为复杂性状进一步研究的主要障碍。本文重点介绍野生小家鼠遗传多样性,及野生小家鼠遗传多样性应用于复杂性状研究的前景。     

SLE模型新西兰小鼠高IgG血症易感基因的定位

目的：定位自发性ＳＬＥ模型００（ＮＺＢｘＮＺＷ）Ｆ１小鼠高ＩｇＧ血症的遗传易感基因。方法：建立（ＮＺＢｘＮＺＷ）Ｆ１ｘＮＺＷ回交小鼠模型,采用覆盖小鼠１９条染色体的多态性微卫星遗传标记及数量性状位点（ＱＴＬ）分析进行基因定位。结果：高ＩｇＧ血症易感基因与小鼠第１条染色体末端９２．３ｃＭ处微卫星遗传标记ＤＩＭｉｔ３６肯定连锁（Ｌｏｄｓ值〉３）,该位点附近９２．０ｃｍ处存在Ｆｅｇｒ２ｂ基因,且回交小鼠     

中国野生小鼠1号染色体遗传结构研究

目的 对我国25个不同地区野生小鼠遗传多样性进行检测.方法 本研究利用1号染色体上20对微卫星标记,采用多重PCR技术对我国25个不同地区野生小鼠遗传多样性进行检测,统计了野生小鼠群体等位基因数、期望杂合度、等位基因范围、G-W统计量以及群体间的遗传距离.利用MEGA软件进行系统发生分析.结果 野生小鼠群体在20个STR位点上平均等位基因数为(15.4±3.5),而实验小鼠群体在20个STR位点上平均等位基因数为(5.3±1.0).而对于两个群体之间的平均期望杂合度来说,野生小鼠群体(0.886±0.04)明显高于实验小鼠群体(0.727±0.112)(t=-6.7025,P=1.04×10-6).在野生小鼠群体中20个STR位点的G-W统计量为(0.781±0.132),明显高于实验小鼠群体的G-W统计量(0.377±0.184)(t=-8.8744,P=1.76×10-8).结论 这些指标都说明野生小鼠具有更丰富的遗传多样性.根据不同野生小鼠群体与实验小鼠群体间的聚类分析,显示野生小鼠群体与实验小鼠群体明显聚为两个类别.

Abstract：

Objective Recent studies have shown that the genetic diversity of wild mouse (Mus musculus )is far more extensive than the laboratory mice, and these diversities are useful for genetic studies of complex traits and can be important genetic resources. This sutdy is to detect the diversity of wild mice captured in 25 regions of China. Methods In this study, 20 STR loci of Chr1 were selected and analyzed, using multiplexed tandem PCR ( MT-PCR ) technology to detect the diversity of wild mice captured. The allele number, expected heterozygosity, allele range, G-W index of wild mice, and genetic distance between wild mouse populations were calculated by Alequin software. MEGA software is used for phylogenetic analysis. Results Wild mice had number of alleles of ( 15.4±3.5 ) for 20 STR loci,while the laboratory mcie had (5.3 ± 1.0 ) alleles. The wild had higher level of average expected heterozygosity (0. 886 ±0.04 ) for 20 STR loci than the laboratory derived hybrids (0. 727 ± 0. 112 ),(t= -6.7025, P=1.04 × 10-6). The G-W stat of 20 STRloci were (0.781 ± 0. 132) in wild population, significantly higher than those of laboratory mice whose G-W stat were (0.377± 0. 184 )(t= -8.8744, P=1.76×10-8). Conclusion Wild mouse (Mus musculus) has more extensive genetic diversity. According to the cluster analysis between wild mice and laboratory mice, they were clearly clustered into two categories.     

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。     

基因型错误对定位QTL的LD指数的效应

连锁不平衡(LD)在基因定位中起着关键作用,因而是现代遗传研究中的一个重要工具。但是,连锁不平衡背景的估计受多种因素的影响,其中之一就是基因型错误。已经有研究考察了基因型错误对四个常用LD 指数D, r, Q, 和d的影响。而基因型错误对于定位数量性状位点(QTL)的LD 指数的效应还没有得到研究。本文从分析的角度调查了基因型错误存在时LD 指数lx 的性质。结果表明,指数lx 因依赖于基因型错误率因而值变小了,当基因型错误率达到0.03, lx值的改变量(减小值)将超过50％,特别是在标记基因频率比较高的时候。基因型错误的影响也通过基于血管紧张肽转化酶(ACE)基因的10个SNPs单体型频率的模拟研究得到了证实。     

基因型错误对定位QTL的LD指数效应

连锁不平衡(LD)在基因定位中起着关键作用，因而是现代遗传研究中的一个重要工具。但是，连锁不平衡背景的估计受多种因素的影响，其中之一就是基因型错误。已经有研究考察了基因型错误对四个常用LD 指数D, r, Q, 和d的影响。而基因型错误对于定位数量性状位点(QTL)的LD 指数的效应还没有得到研究。本文从分析的角度调查了基因型错误存在时LD 指数lx 的性质。结果表明，指数lx 因依赖于基因型错误率因而值变小了，当基因型错误率达到0.03， lx值的改变量(减小值)将超过50％，特别是在标记基因频率比较高的时候。基因型错误的影响也通过基于血管紧张肽转化酶(ACE)基因的10个SNPs单体型频率的模拟研究得到了证实。     

用DNA标记建立人类染色体的连锁图

一种基于用限制酶直接检测DNA顺序多态性的较新的遗传标记系统使人们有可能建立起详细的人类遗传连锁图。由克隆化DNA片段所确定的新遗传座位代表着已知的特定基因或其功能未知的随机座位。除了用物理方法将这些新标记定位在特定染色体上的特定区段外,还可通过家系研究来估计它们的连锁距离和基因顺序。据估计,人类基因组的大小为33摩尔根;如果标记座位的间距为0.4摩尔根,新     

新西兰小鼠CD8+T细胞数量异常的易感基因定位

目的 :定位自发性SLE模型 (NZB×NZW)F1小鼠CD8 T细胞数量异常的遗传易感基因。方法 :建立 (NZB×NZW )F1×NZW回交小鼠模型 ,采用覆盖小鼠 1 9条常染色体的多态性微卫星遗传标记及数量性状位点分析进行基因定位。结果 :CD8 T细胞数量异常的易感基因与小鼠第 1条染色体尾端 92 3cM处的微卫星遗传标记D1Mit36肯定连锁 (Lods值 >3) ,且回交小鼠该遗传标记B W型组的外周血淋巴细胞中CD8 T细胞百分比明显低于W W型组 (P <0 0 0 1 )。结论 :(NZB×NZW )F1小鼠外周血CD8 T细胞数量异常的候选易感基因位于第 1条染色体尾端 92 3cM附近 ,来源于NZB小鼠。     

Genetic architecture of regulatory variation in Arabidopsis thaliana

Studying the genetic regulation of expression variation is a key method to dissect complex phenotypic traits. To examine the genetic architecture of regulatory variation in Arabidopsis thaliana, we performed genome-wide association (GWA) mapping of gene expression in an F(1) hybrid diversity panel. At a genome-wide false discovery rate (FDR) of 0.2, an associated single nucleotide polymorphism (SNP) explains >38% of trait variation. In comparison with SNPs that are distant from the genes to which they were associated, locally associated SNPs are preferentially found in regions with extended linkage disequilibrium (LD) and have distinct population frequencies of the derived alleles (where Arabidopsis lyrata has the ancestral allele), suggesting that different selective forces are acting. Locally associated SNPs tend to have additive inheritance, whereas distantly associated SNPs are primarily dominant. In contrast to results from mapping of expression quantitative trait loci (eQTL) in linkage studies, we observe extensive allelic heterogeneity for local regulatory loci in our diversity panel. By association mapping of allele-specific expression (ASE), we detect a significant enrichment for cis-acting variation in local regulatory variation. In addition to gene expression variation, association mapping of splicing variation reveals both local and distant genetic regulation for intron and exon level traits. Finally, we identify candidate genes for 59 diverse phenotypic traits that were mapped to eQTL.     

The canine genome

The dog has emerged as a premier species for the study of morphology, behavior, and disease. The recent availability of a high-quality draft sequence lifts the dog system to a new threshold. We provide a primer to use the dog genome by first focusing on its evolutionary history. We overview the relationship of dogs to wild canids and discuss their origin and domestication. Dogs clearly originated from a substantial number of gray wolves and dog breeds define distinct genetic units that can be divided into at least four hierarchical groupings. We review evidence showing that dogs have high levels of linkage disequilibrium. Consequently, given that dog breeds express specific phenotypic traits and vary in behavior and the incidence of genetic disease, genomic-wide scans for linkage disequilibrium may allow the discovery of genes influencing breed-specific characteristics. Finally, we review studies that have utilized the dog to understand the genetic underpinning of several traits, and we summarize genomic resources that can be used to advance such studies. We suggest that given these resources and the unique characteristics of breeds, that the dog is a uniquely valuable resource for studying the genetic basis of complex traits.     

Robust Quantitative Trait Association Tests in the Parent-Offspring Triad Design: Conditional Likelihood-Based Approaches

Association studies, based on either population data or familial data, have been widely applied to mapping of genes underlying complex diseases. In family-based association studies, using case-parent triad families, the popularly used transmission/disequilibrium test (TDT) was proposed for avoidance of spurious association results caused by other confounders such as population stratification. Originally, the TDT was developed for analysis of binary disease data. Extending it to allow for quantitative trait analysis of complex diseases and for robust analysis of binary diseases against the uncertainty of mode of inheritance has been thoroughly discussed. Nevertheless, studies on robust analysis of quantitative traits for complex diseases received relatively less attention. In this paper, we use parent-offspring triad families to demonstrate the feasibility of establishment of the robust candidate-gene association tests for quantitative traits. We first introduce the score statistics from the conditional likelihoods based on parent-offspring triad data under various genetic models. By applying two existing robust procedures we then construct the robust association tests for analysis of quantitative traits. Simulations are conducted to evaluate empirical type I error rates and powers of the proposed robust tests. The results show that these robust association tests do exhibit robustness against the effect of misspecification of the underlying genetic model on testing powers.     

Fine mapping of the IBD1 locus did not identify Crohn disease-associated NOD2 variants: implications for complex disease genetics

Crohn disease (CD) is a chronic relapsing inflammatory condition of the gastrointestinal tract. Recently, polymorphisms in NOD2 (CARD15), a gene mapping to the chromosome 16 IBD1 susceptibility locus, have been associated with susceptibility to CD. One group identified the gene by using classic positional cloning methods. Here, we report linkage and fine mapping analyses using 27 microsatellite markers encompassing the IBD1 susceptibility locus in 131 CD affected sibling pairs, and a simplex family cohort. No evidence for linkage was observed, and microsatellite markers close to NOD2 did not show association. However, significant association was confirmed in 294 CD trios for the NOD2 variants Arg702Trp and Leu1007fsinsC. Our fine mapping study of the IBD1 locus did not enable us to identify NOD2 as a CD gene, despite the presence of association with disease-causing alleles. This study illustrates the difficulties facing microsatellite linkage and linkage disequilibrium mapping methods for identifying disease genes in complex traits.     

The allelic architecture of human disease genes: common disease-common variant...or not?

Linkage disequilibrium (LD) plays a central role in current and proposed methods for mapping complex disease genes. LD-based methods work best when there is a single susceptibility allele at any given disease locus, and generally perform very poorly if there is substantial allelic heterogeneity. The extent of allelic heterogeneity at typical complex disease loci is not yet known, but predictions about allelic heterogeneity have important implications for the design of future mapping studies, including the proposed genome-wide association studies. In this article, we review the available data and models relating to the number and frequencies of susceptibility alleles at complex disease loci-the 'allelic architecture' of human disease genes. We also show that the predicted frequency spectrum of disease variants at a gene depends crucially on the method of ascertainment, for example from prior linkage scans or from surveys of functional candidate loci.     

Admixture Mapping Using Interval Transmission/Disequilibrium Tests

Family‐based studies of genetic association and linkage play a key role in mapping susceptibility genes of complex human diseases. Recent admixture between genetically differentiated populations can result in high levels of linkage disequilibrium even at far apart loci. This has been capitalized upon to reduce the burden of genotyping in a genomewide association scan. Here the authors describe an alternative approach for admixture mapping. The genome is divided into several non‐overlapping intervals and the information of the markers in the same interval is integrated—the ‘interval transmission/disequilibrium test’ (ITDT). This method requires information in the form of the marker allele frequencies in the founding populations. However, computer simulations show that the performances of ITDT are hardly affected by imprecise allele‐frequency information. Simulations also show that an interval‐by‐interval scan using ITDT perform much better than a conventional marker‐by‐marker scan using TDT, even under conditions where the admixture process occurred over many generations and the individuals in the admixed populations show considerable variation in admixture proportion. Hence the ITDT is a promising new genomewide scan method.     

Role of HLA class II genes in susceptibility and resistance to multiple sclerosis: studies using HLA transgenic mice

Multiple sclerosis (MS), an inflammatory and demyelinating autoimmune disease of CNS has both, a genetic and an environmental predisposition. Among all the genetic factors associated with MS susceptibility, HLA class II haplotypes such as DR2/DQ6, DR3/DQ2, and DR4/DQ8 show the strongest association. Although a direct role of HLA-DR alleles in MS have been confirmed, it has been difficult to understand the contribution of HLA-DQ alleles in disease pathogenesis, due to strong linkage disequilibrium. Population studies have indicated that DQ alleles may play a modulatory role in the progression of MS. To better understand the mechanism by which HLA-DR and -DQ genes contribute to susceptibility and resistance to MS, we utilized single and double transgenic mice expressing HLA class II gene(s) lacking endogenous mouse class II genes. HLA class II transgenic mice have helped us in identifying immunodominant epitopes of PLP in context of various HLA-DR and -DQ molecules. We have shown that HLA-DR3 transgenic mice were susceptible to PLP_91–110 induced experimental autoimmune encephalomyelitis (EAE), while DQ6 (DQB1*0601) and DQ8 (DQB1*0302) transgenic mice were resistant. Surprisingly DQ6/DR3 double transgenic mice were resistant while DQ8/DR3 mice showed higher disease incidence and severity than DR3 mice. The protective effect of DQ6 in DQ6/DR3 mice was mediated by IFNγ, while the disease exacerbating effect of DQ8 molecule was mediated by IL-17. Further, we have observed that myelin-specific antibodies play an important role in PLP_91–110 induced EAE in HLA-DR3DQ8 transgenic mice. Based on these observations, we hypothesize that epistatic interaction between HLA-DR and -DQ genes play an important role in predisposition to MS and our HLA transgenic mouse model provides a novel tool to study the effect of linkage disequilibrium in MS.     

Linkage Disequilibrium and Haplotype Architecture for two ABC Transporter Genes (ABCC1 and ABCG2) in Chinese Population: Implications for Pharmacogenomic Association Studies

Information about linkage disequilibrium (LD) patterns and haplotype structures for candidate genes is instructive for the design and analysis of genetic association studies for complex diseases and drug response. ABCC1 and ABCG2 are genes coding for two multidrug resistance (MDR) associated transporters; they are also related to some pathophysiological traits. To pinpoint the LD profiles of these MDR genes in Chinese, we systemically screened 27 unrelated individuals for single nucleotide polymorphisms (SNPs) in the coding and regulatory regions of these genes, and thereby characterized their haplotype structures. Despite marked variations in haplotype diversity, LD pattern and intragenic recombination intensity between the two genes, both loci could be partitioned into several LD blocks, in which a modest number of haplotypes accounted for a high fraction of the sampled chromosomes. We concluded that each locus has its own genomic LD profile, but that they still share a common segmental LD architecture with low haplotype diversity. Our data will benefit genetic association studies of complex traits and drug response possibly related to these genes.     

Information capture using SNPs from HapMap and whole-genome chips differs in a sample of inflammatory and cardiovascular gene-centric regions from genome-wide estimates

Large-scale genetic association studies are now widely conducted using SNPs selected from the International HapMap Project or provided on commercial "whole genome" chips. As only a subset of human genetic variation has been identified, it is unknown what proportion of the total genetic variation can be captured in this way, although recent genome-wide estimates of SNP capture rates have been encouraging. We estimated the expected gene-centric information capture for whole-genome chips using sequence data from 306 inflammatory/cardiovascular genes and found SNP capture rates notably lower than previous genome-wide estimates. Further investigation indicates that a major explanation for these lower capture rates is the aggregation of particular sequence features that influence both linkage disequilibrium and the amenability of SNPs for genotyping within the broad class of inflammatory/ cardiovascular genes. This suggests that the power of genetic association studies in some complex traits will depend not only upon established factors, such as allele frequency and penetrance, but may also be influenced by the distribution of sequence features in the class of genes expected to underlie the disease of interest.     

Selected Methodological Issues in Meiotic Mapping of Obesity Genes in Humans: Issues of Power and Efficiency

This paper focuses on methods for mapping novel obesity genes in humans via meiotic mapping techniques. By novel we mean genes that are as yet unidentified as playing a role in obesity. We begin by presenting a discussion of why we believe it is important to seek out novel obesity genes and, in particular, novel genes of small effect. In light of the arguably Herculean task of finding genes of small effect with conventional gene mapping methods, we discuss alternative methods and procedures that may enhance our ability to map novel obesity genes of small effect. Many of these methods have been discussed previously in the literature and are summarized here. These include reconceptualizing power in the context of genomewide scans, multivariate linkage approaches, the use of phenotypically extreme subjects, and the use of large sibships. These are discussed in the context of linkage studies. Association studies and disequilibrium mapping are also discussed, and again, issues involving the use of extreme phenotypes and multiple testing are included. We also provide a brief discussion of DNA pooling and transmission disequilibrium tests for quantitative traits. Finally, we advocate data pooling techniques (e.g., meta-analysis) to enhance the power and efficiency of the entire field of the genetics of obesity.