构建基于荧光多重cPCR的小鼠基因拷贝数检测方法

目的建立基于竞争性聚合酶链式反应(competitive polymerase chain reaction,cPCR)小鼠基因拷贝数变异(copy number variations,CNVs)的检测方法,用于检测野生小家鼠来源一号染色体替换系群体(population of specific chromosome 1 substitution strains,PCSSs)的CNVs。方法选取小鼠一号染色体上11个CNVs位点,及7、9和X染色体上各1个内对照位点,分别构建克隆质粒为竞争性粒模板,应用cPCR技术,建立荧光通用引物多重cPCR检测方法。结果多重cPCR方案适用于小鼠一号染色体上11个CNV位点的拷贝数检测,且能准确检测X染色体的拷贝数。结论实现小鼠快速、高通量的CNVs检测,可准确检测小鼠1号染色体中11个CNV位点的拷贝数变异。     

一种基于二代测序拷贝数变异检测的新方法

区域捕获测序是针对基因组特定区段如对MHC(Major histocompatibility complex)区域、外显子区域等测序的有效手段,但是由于捕获测序中探针设计不均匀而造成区域内测序深度变异很大,因此,与基于全基因组的测序数据相比,其拷贝数变异的检测难度更大.目前已经出现了捕获测序下拷贝数变异(copy number variations,CNV)的检测方法,但对CNV的检测准确性仍然很低,特别是对于低频率CNV来说效果极差.因此,本研究开发了一个新的拷贝数变异检测方法,其特点是:(1)以区域内划分的区间为单位检测区间内的CNV,而不是直接对每个个体检测CNV;(2)全面利用群体内所有个体信息,通过区间内read深度在群体的分布规律来检测CNV的分离规律,假设区间内只有1个CNV,那么区间内的read深度将服从三峰的混合正态分布.将该方法应用于21 327个银屑病个体区域捕获测序的CNV检测中,结果表明,XHMM,ExomeDepth和本方法跟金标准重叠的窗口总数与金标准总窗口数的百分比(即重叠率)分别是7％、18％和62％.与XHMM和ExomeDepth相比,新方法在区间内CNV检测覆盖度可以分别提高55个百分点和44个百分点.本研究完善拷贝数变异检测方法,为疾病的诊断治疗提供一定的理论依据.     

基因组拷贝数变异及其突变机理与人类疾病

拷贝数变异(Copy number variation,CNV)是由基因组发生重排而导致的,一般指长度为1 kb以上的基因组大片段的拷贝数增加或者减少,主要表现为亚显微水平的缺失和重复。CNV是基因组结构变异(Structural variation,SV)的重要组成部分。CNV位点的突变率远高于SNP(Single nucleotide polymorphism),是人类疾病的重要致病因素之一。目前,用来进行全基因组范围的CNV研究的方法有:基于芯片的比较基因组杂交技术(array-based comparative genomic hybridization,aCGH)、SNP分型芯片技术和新一代测序技术。CNV的形成机制有多种,并可分为DNA重组和DNA错误复制两大类。CNV可以导致呈孟德尔遗传的单基因病与罕见疾病,同时与复杂疾病也相关。其致病的可能机制有基因剂量效应、基因断裂、基因融合和位置效应等。对CNV的深入研究,可以使我们对人类基因组的构成、个体间的遗传差异、以及遗传致病因素有新的认识。     

基因拷贝数变异与人类疾病

拷贝数变异(copy number variation,CNV)是人类遗传多样性的一类重要形式。在前期的研究中,人们通过寡核苷酸分型、比较基因组杂交以及测序等技术手段,在人类基因组中鉴定出了大量拷贝数变异位点。这些变异可能是由于基因组重组或复制过程中的差错而产生。CNV在人群中的覆盖率远远高于寡核苷酸多态性(single nucleotide polymorphism,SNP),它们可以通过多种机制改变基因的表达水平,如基因剂量效应、基因断裂-融合效应,以及远距调控效应,进而引起多种人类复杂疾病。认识基因组中的拷贝数变异对于我们更好地认识基因与疾病的关系、遗传-环境因素的相互作用,以及基因组变异与物种进化的关系具有重要的意义。     

香猪ADAMTS-1基因克隆及遗传效应分析

为了研究繁殖候选基因ADAMTS-1对香猪繁殖性状的调控机理,本研究以高产、低产两个香猪群体为实验材料,克隆ADAMTS-1基因全长,分析其存在的多态性位点,并对第七外显子5 996位进行产仔数的遗传效应分析,同时检测两个香猪群体中该基因的拷贝数变异。结果表明,ADAMTS-1基因包含8个内含子和9个外显子区域。该基因第七外显子5 996位存在多态性,香猪品种中以B等位基因为主,基因型频率BBAB,未检测到纯合AA基因型的个体,而西方猪种中以AA或AB型为主。高产和低产两个香猪群体中的ADAMTS-1基因的拷贝数都是复制型为主,但存在拷贝数的差异,高产香猪群体中的拷贝数增加较多,多为3个或3个以上拷贝,而低产群体中多为双拷贝,低产群体中的拷贝数明显低于高产群体。结果提示,ADAMTS-1基因的拷贝数变异以及第7外显子5 996位的多态性可能是影响香猪繁殖力的重要因素之一。     

猪PID1基因CDS区的克隆及其mRNA表达与肌内脂肪沉积关系

为了探索PID1(Phosphotyrosine interaction domain containing1)基因的表达与脂肪沉积的关系,文章利用兼并引物进行RT-PCR从猪脂肪和肌肉组织中克隆PID1基因CDS(Coding region)区全序列,并采用荧光定量PCR方法对大白猪、鲁莱黑猪、莱芜猪3个猪品种的肝脏、脂肪和肌肉组织PID1基因mRNA表达进行了相对定量分析。结果表明:经克隆、测序,得到了猪PID1基因654bp全编码区序列,通过Blast比对,与人、大鼠、牛有93.88%、66.94%、88.07%的同源性。PID1基因在同一个品种猪中mRNA表达水平总体表现为:肝脏脂肪肌肉。在不同品种3种组织中PID1基因mRNA表达水平总体表现为:莱芜猪鲁莱黑猪大白猪,其中肝脏中差异显著(P0.05),但是在脂肪和肌肉组织中莱芜猪与鲁莱黑猪差异不显著(P0.05)。对于高肌内脂肪(LWH)、中等肌内脂肪(LWI)和低肌内脂肪(LWL)沉积的3组莱芜猪,PID1基因在肝脏组织中的表达水平是LWH显著高于LWL(P0.05),在肌肉组织中则是LWH显著高于LWI和LWL(P0.05)。PID1基因在莱芜猪品种内3个组织中mRNA表达量与IMF含量相关均不显著,而在品种间3个组织中mRNA表达量与IMF含量呈显著正相关(P0.05)。结果提示:PID1的表达可能与脂肪沉积性状存在一定的关系。     

人乳铁蛋白 (hLF) 转基因山羊的遗传背景分析

以随机整合方式获得的转基因动物外源基因的拷贝数、整合位点及染色体核型等遗传背景并不清楚,可能会存在外源基因的沉默整合、无效整合、毒性整合以及其表达水平不可预测等问题。文中选取了6只原代(F0)及其相对应的子一代(F1)的人乳铁蛋白(hLF)转基因山羊作为研究对象,分别颈静脉采血、提取DNA,通过染色体核型分析、实时荧光定量PCR(qPCR)、ELISA和Westernblotting等检测技术,研究其外源基因的遗传背景与表达水平。结果显示,6只F0代转基因山羊的染色体没有明显的形态变异、数量改变等异常情况。相对拷贝数高低不同(2–16),且能够稳定地遗传给下一代,F0和F1代hLF基因拷贝数一致。F1代转基因山羊表达hLF水平最高可达1.12 g/L(L3-1,拷贝数8)。结果表明,整合的外源基因能够稳定地遗传下一代,也没有对转基因山羊个体的生长发育造成障碍,而且拷贝数高低与hLF表达水平无明显的相关性,这为转基因山羊及其他转基因动物的新品种培育奠定了基础,解析了遗传背景。     

基因组拷贝数变异研究进展

基因组结构变异分为两个层次:显微水平(microscopic)和亚显微水平(submicroscopic)。显微水平的基因组结构变异主要是指显微镜下可见的染色体畸变,包括整倍体或非整倍体、缺失、插入、倒位、易位、脆性位点等结构变异。亚显微水平的基因组结构变异是指DNA片段长度在1Kb-3Mb的基因组结构变异,包括缺失、插入、重复、重排、倒位、DNA拷贝数目变化(copy numbervariation,CNV),这些统称为CNV或者CNP(copy number polymorphisms,CNP)。对CNV的研究能够帮助研究者建立遗传检测假说,进而发现疾病易感基因,同时加深对表型变异的理解,为今后研究人类生物功能、进化、疾病奠定基础。本文主要从CNV的研究历史、分子机制、研究方法、研究意义等四个方面进行综述.。     

基因拷贝数变异-导致精神分裂症和自闭症的潜在风险

<正>基因重排可以导致基因拷贝数变异(CNV),即1 kb以上的基因组大片段的拷贝数增加或减少。对于小部分精神分裂症或自闭症患者而言,由等位基因CNV所造成的认知障碍或成为致病的主要因素。近日,冰岛人类遗传学研究与分析公司deCODE Genetics的科学家对一组冰岛的CNV携带者展开了相关研究。他们发现CNV携带者存在类似精神分裂症患者的大脑认知异常现象,且具有患精神分裂症或自闭症的风险。认知测试的结果显示,CNV携带者的IQ与正常人无明显区别,但CNV     

单基因遗传病的种类判断和概率计算

单基因遗传病(简称单基因病)是指受1对等位基因控制的遗传病,它可以分为5类:Y染色体遗传病,X 染色体上的显性遗传病,X染色体上的隐性遗传病,常染色体上的显性遗传病,常染色体上的隐性遗传病。这5类单基因病的判断及其相关概率的计算是遗传和变异这一章的重点,亦是难点所在。现总结一些规律供参考。     

Identification of Copy Number Variations in Xiang and Kele Pigs

Xiang and Kele pigs are two well-known local Chinese pig breeds that possess rich genetic resources and have enormous economic and scientific value. We performed a comprehensive genomic analysis of the copy number variations (CNVs) in these breeds. CNVs are one of the most important forms of genomic variation and have profound effects on phenotypic variation. In this study, PorcineSNP60 genotyping data from 98 Xiang pigs and 22 Kele pigs were used to identify CNVs. In total, 172 candidate CNV regions (CNVRs) were identified, ranging from 3.19 kb to 8175.26 kb and covering 80.41 Mb of the pig genome. Approximately 56.40% (97/172) of the CNVRs overlapped with those identified in seven previous studies, and 43.60% (75/172) of the identified CNVRs were novel. Of the identified CNVRs, 82 (47 gain, 33 loss, and two gain-loss events that covered 4.58 Mb of the pig genome) were found only in a Xiang population with a large litter size. In contrast, 13 CNVRs (8 gain and 5 loss events) were unique to a Xiang population with small litter sizes, and 30 CNVRs (14 loss and 16 gain events) were unique to Kele pigs. The CNVRs span approximately 660 annotated Sus scrofa genes that are significantly enriched for specific biological functions, such as sensory perception, cognition, reproduction, ATP biosynthetic processes, and neurological processes. Many CNVR-associated genes, particularly the genes involved in reproductive traits, differed between the Xiang populations with large and small litter sizes, and these genes warrant further investigation due to their importance in determining the reproductive performance of Xiang pigs. Our results provide meaningful information about genomic variation, which may be useful in future assessments of the associations between CNVs and important phenotypes in Xiang and Kele pigs to ultimately help protect these rare breeds.     

Copy number variants in Italian Large White pigs detected using high‐density single nucleotide polymorphisms and their association with back fat thickness

The aim of this study was to identify copy number variants (CNVs) in Italian Large White pigs and test them for association with back fat thickness (BFT). Within a population of 12 000 performance‐tested pigs, two groups of animals with extreme and divergent BFT estimated breeding values (EBVs; 147 with negative and 150 with positive EBVs) were genotyped with the Illumina Porcine SNP60 BeadChip. CNVs were detected with penncnv software. We identified a total of 4146 CNV events in 170 copy number variation regions (CNVRs) located on 15 porcine autosomes. Validation of detected CNVRs was carried out (i) by comparing CNVRs already detected by other studies and (ii) by semiquantitative fluorescent multiplex (SQFM) PCR of a few CNVRs. Most of CNVRs detected in Italian Large White pigs (71.2%) were already reported in other pig breeds/populations, and 82.1% of the CNV events detected by penncnv were confirmed by SQFM PCR. For each CNVR, we compared the occurrence of CNV events between the pigs of the high and low BFT EBV tails. Sixteen regions showed significance at P < 0.10, and seven were significant at P < 0.05 but were not significant after Bonferroni correction (Fisher's exact test). These results indicated that CNVs could explain a limited fraction of the genetic variability of fat deposition in Italian Large White pigs. However, it was interesting to note that one of these CNVRs encompassed the ZPLD1 gene. In humans, a rare CNV event including this gene is associated with obesity. Studies identifying CNVs in pigs could assist in elucidating the genetic mechanisms underlying human obesity.     

Analysis of Genome-Wide Copy Number Variations in Chinese Indigenous and Western Pig Breeds by 60 K SNP Genotyping Arrays

Copy number variations (CNVs) represent a substantial source of structural variants in mammals and contribute to both normal phenotypic variability and disease susceptibility. Although low-resolution CNV maps are produced in many domestic animals, and several reports have been published about the CNVs of porcine genome, the differences between Chinese and western pigs still remain to be elucidated. In this study, we used Porcine SNP60 BeadChip and PennCNV algorithm to perform a genome-wide CNV detection in 302 individuals from six Chinese indigenous breeds (Tongcheng, Laiwu, Luchuan, Bama, Wuzhishan and Ningxiang pigs), three western breeds (Yorkshire, Landrace and Duroc) and one hybrid (Tongcheng×Duroc). A total of 348 CNV Regions (CNVRs) across genome were identified, covering 150.49 Mb of the pig genome or 6.14% of the autosomal genome sequence. In these CNVRs, 213 CNVRs were found to exist only in the six Chinese indigenous breeds, and 60 CNVRs only in the three western breeds. The characters of CNVs in four Chinese normal size breeds (Luchuan, Tongcheng and Laiwu pigs) and two minipig breeds (Bama and Wuzhishan pigs) were also analyzed in this study. Functional annotation suggested that these CNVRs possess a great variety of molecular function and may play important roles in phenotypic and production traits between Chinese and western breeds. Our results are important complementary to the CNV map in pig genome, which provide new information about the diversity of Chinese and western pig breeds, and facilitate further research on porcine genome CNVs.     

Exploring copy number variation in the rabbit (Oryctolagus cuniculus) genome by array comparative genome hybridization

The European rabbit (Oryctolagus cuniculus) is relevant in a large spectrum of fields: it is a livestock, a pet, a biomedical model and a biotechnology tool, a wild resource and a pest. The sequencing of the rabbit genome has opened new perspectives to study this lagomorph at the genome level. We herein investigated for the first time the O. cuniculus genome by array comparative genome hybridization (aCGH) and established a first copy number variation (CNV) genome map in this species comprising 155 copy number variation regions (CNVRs; 95 gains, 59 losses, 1 with both gain and loss) covering ~0.3% of the OryCun2.0 version. About 50% of the 155 CNVRs identified spanned 139 different protein coding genes, 110 genes of which were annotated or partially annotated (including Major Histocompatibility Complex genes) with 277 different gene ontology terms. Many rabbit CNVRs might have a functional relevance that should be further investigated.     

Genome-Wide Detection of Copy Number Variations among Diverse Horse Breeds by Array CGH

Recent studies have found that copy number variations (CNVs) are widespread in human and animal genomes. CNVs are a significant source of genetic variation, and have been shown to be associated with phenotypic diversity. However, the effect of CNVs on genetic variation in horses is not well understood. In the present study, CNVs in 6 different breeds of mare horses, Mongolia horse, Abaga horse, Hequ horse and Kazakh horse (all plateau breeds) and Debao pony and Thoroughbred, were determined using aCGH. In total, seven hundred CNVs were identified ranging in size from 6.1 Kb to 0.57 Mb across all autosomes, with an average size of 43.08 Kb and a median size of 15.11 Kb. By merging overlapping CNVs, we found a total of three hundred and fifty-three CNV regions (CNVRs). The length of the CNVRs ranged from 6.1 Kb to 1.45 Mb with average and median sizes of 38.49 Kb and 13.1 Kb. Collectively, 13.59 Mb of copy number variation was identified among the horses investigated and accounted for approximately 0.61% of the horse genome sequence. Five hundred and eighteen annotated genes were affected by CNVs, which corresponded to about 2.26% of all horse genes. Through the gene ontology (GO), genetic pathway analysis and comparison of CNV genes among different breeds, we found evidence that CNVs involving 7 genes may be related to the adaptation to severe environment of these plateau horses. This study is the first report of copy number variations in Chinese horses, which indicates that CNVs are ubiquitous in the horse genome and influence many biological processes of the horse. These results will be helpful not only in mapping the horse whole-genome CNVs, but also to further research for the adaption to the high altitude severe environment for plateau horses.     

A genome-wide survey of copy number variation regions in various chicken breeds by array comparative genomic hybridization method

The discovery of copy number variation (CNV) in the genome has provided new insight into genomic polymorphism. Studies with chickens have identified a number of large CNV segments using a 385k comparative genomic hybridization (CGH) chip (mean length >140 kb). We present a detailed CNV map for local Chinese chicken breeds and commercial chicken lines using an Agilent 400k array CGH platform with custom-designed probes. We identified a total of 130 copy number variation regions (CNVRs; mean length = 25.70 kb). Of these, 104 (80.0%) were novel segments reported for the first time in chickens. Among the 104 novel CNVRs, 56 (53.8%) of the segments were non-coding sequences, 65 (62.5%) showed the gain of DNA and 40 (38.5%) showed the loss of DNA (one locus showed both loss and gain). Overlapping with the formal selective sweep data and the quantitative trait loci data, we identified four loci that might be considered to be high-confidence selective segments that arose during the domestication of chickens. Compared with the CNVRs reported previously, genes for the positive regulation of phospholipase A2 activity were discovered to be significantly over-represented in the novel CNVRs reported here by gene ontology analysis. Availability of our results should facilitate further research in the study of the genetic variability in chicken breeds.     

Identification of copy number variations in three Chinese horse breeds using 70K single nucleotide polymorphism BeadChip array

Copy number variation (CNV), an essential form of genetic variation, has been increasingly recognized as one promising genetic marker in the analysis of animal genomes. Here, we used the Equine 70K single nucleotide polymorphism genotyping array for the genome‐wide detection of CNVs in 96 horses from three diverse Chinese breeds: Debao pony (DB), Mongolian horse (MG) and Yili horse (YL). A total of 287 CNVs were determined and merged into 122 CNV regions (CNVRs) ranging from 199 bp to 2344 kb in size and distributed in a heterogeneous manner on chromosomes. These CNVRs were integrated with seven existing reports to generate a composite genome‐wide dataset of 1558 equine CNVRs, revealing 69 (56.6%) novel CNVRs. The majority (69.7%) of the 122 CNVRs overlapped with 438 genes, whereas 30.3% were located in intergenic regions. Most of these genes were associated with common CNVRs, which were shared by divergent horse breeds. As many as 60, 42 and 91 genes overlapping with the breed‐specific ss were identified in DB, MG and YL respectively. Among these genes, FGF11, SPEM1, PPARG, CIDEB, HIVEP1 and GALR may have potential relevance to breed‐specific traits. These findings provide valuable information for understanding the equine genome and facilitating association studies of economically important traits with equine CNVRs in the future.     

An atlas of CNV maps in cattle,goat and sheep

Copy number variation(CNV) is the most prevalent type of genetic structural variation that has been recognized as an important source of phenotypic variation in humans, animals and plants. However, the mechanisms underlying the evolution of CNVs and their function in natural or artificial selection remain unknown. Here, we generated CNV region(CNVR) datasets which were diverged or shared among cattle, goat, and sheep, including 886 individuals from 171 diverse populations. Using 9 environmental factors for genome-wide association study(GWAS), we identified a series of candidate CNVRs, including genes relating to immunity, tick resistance, multi-drug resistance, and muscle development. The number of CNVRs shared between species is significantly higher than expected(P0.00001), and these CNVRs may be more persist than the single nucleotide polymorphisms(SNPs) shared between species. We also identified genomic regions under long-term balancing selection and uncovered the potential diversity of the selected CNVRs close to the important functional genes. This study provides the evidence that balancing selection might be more common in mammals than previously considered, and might play an important role in the daily activities of these ruminant species.     

Analyses of copy number variation of GK rat reveal new putative type 2 diabetes susceptibility loci

Large efforts have been taken to search for genes responsible for type 2 diabetes (T2D), but have resulted in only about 20 in humans due to its complexity and heterogeneity. The GK rat, a spontanous T2D model, offers us a superior opportunity to search for more diabetic genes. Utilizing array comparative genome hybridization (aCGH) technology, we identifed 137 non-redundant copy number variation (CNV) regions from the GK rats when using normal Wistar rats as control. These CNV regions (CNVRs) covered approximately 36 Mb nucleotides, accounting for about 1% of the whole genome. By integrating information from gene annotations and disease knowledge, we investigated the CNVRs comprehensively for mining new T2D genes. As a result, we prioritized 16 putative protein-coding genes and two microRNA genes (rno-mir-30b and rno-mir-30d) as good candidates. The catalogue of CNVRs between GK and Wistar rats identified in this work served as a repository for mining genes that might play roles in the pathogenesis of T2D. Moreover, our efforts in utilizing bioinformatics methods to prioritize good candidate genes provided a more specific set of putative candidates. These findings would contribute to the research into the genetic basis of T2D, and thus shed light on its pathogenesis.     

Genome‐wide copy number profiling using high‐density SNP array in chickens

Phenotypic diversity is a direct consequence resulting mainly from the impact of underlying genetic variation, and recent studies have shown that copy number variation (CNV) is emerging as an important contributor to both phenotypic variability and disease susceptibility. Herein, we performed a genome‐wide CNV scan in 96 chickens from 12 diversified breeds, benefiting from the high‐density Affymetrix 600 K SNP arrays. We identified a total of 231 autosomal CNV regions (CNVRs) encompassing 5.41 Mb of the chicken genome and corresponding to 0.59% of the autosomal sequence. The length of these CNVRs ranged from 2.6 to 586.2 kb with an average of 23.4 kb, including 130 gain, 93 loss and eight both gain and loss events. These CNVRs, especially deletions, had lower GC content and were located particularly in gene deserts. In particular, 102 CNVRs harbored 128 chicken genes, most of which were enriched in immune responses. We obtained 221 autosomal CNVRs after converting probe coordinates to Galgal3, and comparative analysis with previous studies illustrated that 153 of these CNVRs were regarded as novel events. Furthermore, qPCR assays were designed for 11 novel CNVRs, and eight (72.73%) were validated successfully. In this study, we demonstrated that the high‐density 600 K SNP array can capture CNVs with higher efficiency and accuracy and highlighted the necessity of integrating multiple technologies and algorithms. Our findings provide a pioneering exploration of chicken CNVs based on a high‐density SNP array, which contributes to a more comprehensive understanding of genetic variation in the chicken genome and is beneficial to unearthing potential CNVs underlying important traits of chickens.