乙型肝炎病毒变异株研究进展

乙型肝炎病毒在其复制过程中需通过以 RNA 为中间体的逆转录过程,因而其突变率较一般的 DNA 病毒高,随着对 HBV 研究普遍和深入开展,最近几年发现了一些新的具有不同生物功能的变异株.文章综述了近年来对 HBV 变异株研究的进展,内容主要包括:表面抗原相关变异,e 抗原表达变异,核心抗原相关变异以及变异与肝癌的关系.     

1．3倍体HBV YIDD变异株真核表达载体构建及鉴定

构建HBV YIDD拉米夫定耐药株1．3倍全基因真核表达载体,为进一步探讨乙肝病毒变异株的生物学特性及筛选抗病毒药物奠定基础。参考GenBankHBV序列设计并合成一系列引物,以临床证实为拉米夫定耐药的病人HBV DNA为模板,通过PCR扩增得到HBV全基因组并克隆至pGEM—T Easy载体中,经测序证实聚合酶基因存在YIDD变异,然后以该病人的HBV全基因组为模板构建1．3倍全基因HBV—YIDD变异真核表达载体pcDNA3．1（＋）-1．3HBV。通过PCR扩增,酶切及测序证明pcDNA3．1（＋）-1．3HBV表达载体构建成功,该表达载体的构建为后期建立稳定表达HBV—YIDD变异的细胞模型提供材料。     

利用基因芯片分析拉米夫定治疗过程中HBV DNA的基因变异

依据乙型肝炎病毒(Hepatitis B virus; HBV)聚合酶基因序列研制HBV基因芯片,此芯片可分析HBV的7个基因型、4种血清型和HBV聚合酶基因rtV173、rtL180、rtM204和rtV207位点的突变.利用此芯片对A、B两组共计45例拉米夫定治疗12个月的患者进行服药前和服药后3、6、9、12个月的动态检测,其中C基因型39例,且血清型均为adr;B基因型6例,其血清型均为adw.在完成全程检测的38例患者中,17例ALT升高的A组出现1例拉米夫定耐药变异株,而21例ALT正常的B组出现4例变异株,且所有变异株均为rtM204 V/rtL180M,其中2例野生株和变异株共存.rtM204V变异最早在服药6个月时出现,随后出现rtL180M变异.10份PCR产物测序分析表明,芯片检测结果与测序结果基本一致,仅在rtL173位点出现1例差异.进一步分析HBV DNA变异与HBV DNA含量、ALT水平和HBeAg血清转换率的相关性,初步结果表明变异株的出现与治疗过程中的DNA反弹呈正相关,而与起始HBV DNA水平、ALT值无关联.HBV基因芯片可初步用于HBV DNA 检测,可能是临床追踪评价抗病毒治疗效果的较好方法之一.     

利用基因芯片分析拉米夫定治疗过程中HBV DNA的基因变异

依据乙型肝炎病毒(Hepatitis B virus;HBV)聚合酶基因序列研制HBV基因芯片,此芯片可分析HBV的7个基因型、4种血清型和HBV聚合酶基因rtV173、rtL180、rtM204和rtV207位点的突变。利用此芯片对A、B两组共计45例拉米夫定治疗12个月的患者进行服药前和服药后3、6、9、12个月的动态检测,其中C基因型39例,且血清型均为adr;B基因型6例,其血清型均为adw。在完成全程检测的38例患者中,17例ALT升高的A组出现1例拉米夫定耐药变异株,而21例ALT正常的B组出现4例变异株,且所有变异株均为rtM204 V／rtL180M,其中2例野生株和变异株共存。rtM204V变异最早在服药6个月时出现,随后出现rtL180M变异。10份PCR产物测序分析表明,芯片检测结果与测序结果基本一致,仅在rtL173位点出现1例差异。进一步分析HBV DNA变异与HBV DNA含量、ALT水平和HBeAg血清转换率的相关性,初步结果表明变异株的出现与治疗过程中的DNA反弹呈正相关,而与起始HBVDNA水平、ALT值无关联。HBV基因芯片可初步用于HBV DNA检测,可能是临床追踪评价抗病毒治疗效果的较好方法之一。     

未经抗病毒治疗慢乙肝患者YMDD变异检测及HBV基因分型

目的 :探讨未接受拉米呋啶及干扰素抗病毒治疗的慢性乙型肝炎患者中YMDD是否存在变异及HBV的基因亚型。方法 :采用PCR荧光分子信标探针检测技术及PCR微板核酸杂交 ELISA技术进行HBVYMDD变异株 (YIDD YVDD)及HBV基因分型检测。结果 :2 9例慢性乙肝患者HBVYMDD变异阳性 6例 ,阳性率为 2 0 6%。 5例变异阳性中 3例为YIDD阳性 ,2例为YVDD阳性 ,6例均为YMDD野生株和变异株同时存在 ;HBV基因亚型以C、B、D亚型为主 ,分别占41 3% ( 1 2 2 9)、2 4 1 % ( 7 2 9)、2 0 6% ( 6 2 9)。结论 :在未经抗病毒治疗的慢乙肝患者中存在YMDD变异株 ,临床上在应用拉米呋啶对慢性乙型肝炎患者进行抗病毒治疗前 ,应对患者是否存在YMDD变异加以重视 。     

乙肝病毒表面抗原和抗体双阳性者中病毒S区基因序列分析

为了解乙肝病毒(HBV)表面抗原和抗体双阳性患者中病毒的基因型及其HVB S区是否有变异.用放射免疫试剂检测HBsAg阳性样品中的抗-HBs抗体,用聚合酶链反应法检测双阳性样品中的HBV DNA,然后对阳性样品进行克隆和基因序列分析,并将所得序列与HBV不同基因型的代表株进行比较分析.结果显示389例HBsAg阳性样品中有10例为抗HBs抗体阳性;该10例双阳性样品中有5例为HBV DNA阳性;序列分析显示该5株HBV均为B基因型,其中4株为adw亚型,1株为adr亚型;其中有2株在S区的"a"决定簇的氨基酸发生了变异.     

乙肝病毒表面抗原的抗体双阳性者中病毒S区基因序列分析

为了解乙肝病毒（HBV）表面抗原和抗体双阳性患者中病毒的基因型及其HVB S区是否有变异。用放射免疫试剂检测HBsAg阳性样品中的抗－HBs抗体，用聚合酶链反应法检测双阳性样品中的HBV DNA，然后对阳性样品进行克隆和基因序列分析，并将所得序列与HBV不同基因型的代表株进行比较分析。结果显示389例HBsAg阳性样品中有10例为抗HBs抗体阳性；该10例双阳性样品中有5例为HBV DNA阳性；序列分析显示该5株HBV均为B基因型，其中4株为adw亚型，1株为adr亚型；其中有2株在S区的“a”决定簇的氨基酸发生了变异。     

乙肝病毒表面抗原和抗体双阳性者中病毒S区基因序列分析

为了解乙肝病毒 (HBV)表面抗原和抗体双阳性患者中病毒的基因型及其HVBS区是否有变异。用放射免疫试剂检测HBsAg阳性样品中的抗 HBs抗体 ,用聚合酶链反应法检测双阳性样品中的HBVDNA ,然后对阳性样品进行克隆和基因序列分析 ,并将所得序列与HBV不同基因型的代表株进行比较分析。结果显示 389例HBsAg阳性样品中有 10例为抗HBs抗体阳性 ;该 10例双阳性样品中有 5例为HBVDNA阳性 ;序列分析显示该 5株HBV均为B基因型 ,其中 4株为adw亚型 ,1株为adr亚型 ;其中有 2株在S区的“a”决定簇的氨基酸发生了变异     

一种联合检测乙型肝炎病毒前S1抗原与核心抗原方法的建立及其与病毒核酸检测结果的一致性

本研究以与血清中HBV DNA含量高度相关的两种HBV抗原(前S1抗原与核心抗原)为靶标,建立了联合检测这两种HBV核酸相关抗原(NRAg)的双抗体夹心法ELISA试剂.对系列稀释血清的检测表明,该试剂的平均分析灵敏度为103.2基因组拷贝/mL(95%可信限102.2-4.2基因组拷贝/mL),显著高于前S1抗原或核心抗原的单独检测.对994份HBsAg阴性血清的检测结果表明NRAg ELISA的特异性为99.7%(95%可信限:99.1%～99.9%).对271份临床慢性肝炎血清进行检测,结果NRAg ELISA与HBV DNA结果的总符合率达96.3%(95%可信限:93.3%～98.2%),NRAg ELISA的读值/临界值比(S/CO)与HBV基因组拷贝数呈正相关.利用NRAg试剂,发现了1例HBsAg"a"抗原表位突变的变异株.这些结果显示HBV NRAg ELISA与HBV DNA具有高度相关性,并能够检测出HBsAg抗原变异株,有望成为HBsAg变异株筛选的有力工具,并为广大基层医疗单位提供一种便捷的替代HBV DNA定性检测的手段.     

HBV感染免疫状态与HBV基因型关系研究思路

HBV感染免疫状态不同,临床意义不同;HBV基因型不同,导致病毒致病性、变异、抗病毒等临床疗效及预后不同.HBV感染临床意义的不同,是宿主与病毒共同作用的结果.将HBV感染免疫状态与HBV基因型结合在一起研究,探索广西桂北地区不同免疫状态下基因型的分布情况及HBV感染免疫状态与基因型的关系,并希期望能针对宿主免疫状态、病毒特性,为每一位HBV感染患者制订最好的治疗方案.     

Prioritization of regulatory variants with tissue-specific function in the non-coding regions of human genome

Understanding the functional consequences of genetic variation in the non-coding regions of the human genome remains a challenge. We introduce h ere a computational tool, TURF, to prioritize regulatory variants with tissue-specific function by leveraging evidence from functional genomics experiments, including over 3000 functional genomics datasets from the ENCODE project provided in the RegulomeDB database. TURF is able to generate prediction scores at both organism and tissue/organ-specific levels for any non-coding variant on the genome. We present that TURF has an overall top performance in prediction by using validated variants from MPRA experiments. We also demonstrate how TURF can pick out the regulatory variants with tissue-specific function over a candidate list from associate studies. Furthermore, we found that various GWAS traits showed the enrichment of regulatory variants predicted by TURF scores in the trait-relevant organs, which indicates that these variants can be a valuable source for future studies.     

Determining causality and consequence of expression quantitative trait loci

Expression quantitative trait loci (eQTLs) are currently the most abundant and systematically-surveyed class of functional consequence for genetic variation. Recent genetic studies of gene expression have identified thousands of eQTLs in diverse tissue types for the majority of human genes. Application of this large eQTL catalog provides an important resource for understanding the molecular basis of common genetic diseases. However, only now has both the availability of individuals with full genomes and corresponding advances in functional genomics provided the opportunity to dissect eQTLs to identify causal regulatory variants. Resolving the properties of such causal regulatory variants is improving understanding of the molecular mechanisms that influence traits and guiding the development of new genome-scale approaches to variant interpretation. In this review, we provide an overview of current computational and experimental methods for identifying causal regulatory variants and predicting their phenotypic consequences.     

小麦的比较基因组学和功能基因组学

小麦是异源多倍体植物,具有大的染色体组,并且基因组中重复序列所占比例较高,这些特征限制了小麦基因组研究的进展。比较基因组学方法为运用模式植物进行小麦基因组学研究提供了一个操作平台。功能基因组学的研究集中于基因组中转录表达的部分,基因功能的确定是功能基因组学研究的主要内容。对比较基因组学在小麦基因组研究中的应用和小麦功能基因组学的研究内容和方法进行了综述。     

TILLING技术在功能基因组学中的应用

TILLING(定向诱导基因组局部突变)技术是近年发展起来的一种高通量筛选化学诱变的点突变的技术,它利用专一识别点突变的核酸酶结合PCR来检测单核苷酸多态性(SNP)。TILLING技术起源于植物基因组研究,逐渐扩展到动物及人类功能基因组学的研究中。无论是筛选突变体还是研究特定基因的重要性,TILLING都具有高通量、自动化的优势。随着此项技术应用范围的扩展,从诱变剂和内切酶的选择到具体的操作方式,以及结果的识别和统计方法,都有了不少改进。在其他相关学科不断发展的大环境下,TILLING技术也在不断发展,其在功能基因组学研究中的作用也会更显著。     

Genetic variation in an individual human exome

There is much interest in characterizing the variation in a human individual, because this may elucidate what contributes significantly to a person's phenotype, thereby enabling personalized genomics. We focus here on the variants in a person's 'exome,' which is the set of exons in a genome, because the exome is believed to harbor much of the functional variation. We provide an analysis of the approximately 12,500 variants that affect the protein coding portion of an individual's genome. We identified approximately 10,400 nonsynonymous single nucleotide polymorphisms (nsSNPs) in this individual, of which approximately 15-20% are rare in the human population. We predict approximately 1,500 nsSNPs affect protein function and these tend be heterozygous, rare, or novel. Of the approximately 700 coding indels, approximately half tend to have lengths that are a multiple of three, which causes insertions/deletions of amino acids in the corresponding protein, rather than introducing frameshifts. Coding indels also occur frequently at the termini of genes, so even if an indel causes a frameshift, an alternative start or stop site in the gene can still be used to make a functional protein. In summary, we reduced the set of approximately 12,500 nonsilent coding variants by approximately 8-fold to a set of variants that are most likely to have major effects on their proteins' functions. This is our first glimpse of an individual's exome and a snapshot of the current state of personalized genomics. The majority of coding variants in this individual are common and appear to be functionally neutral. Our results also indicate that some variants can be used to improve the current NCBI human reference genome. As more genomes are sequenced, many rare variants and non-SNP variants will be discovered. We present an approach to analyze the coding variation in humans by proposing multiple bioinformatic methods to hone in on possible functional variation.     

Use of genome information for the study of the pathogenesis of fungal infections and the development of diagnostic tools

One of the most exciting advances in Mycology is the application of genomic approaches. The advent of genomics, together with post-genomic studies, promises to revolutionize the studies on the pathogenesis of fungal infections. Approaches include comparative genomics to identify sequences that contribute to infection and disease and functional genomics and proteomics to analyze global patterns of gene and protein expression involved in fungal pathogenesis.     

拟南芥基因组研究进展

拟南芥基因组全序列在2000年底已完全测定并公开发表,这是第一个经完全测序的开花植物.序列的获得为进行大规模高等植物基因的鉴定、基因结构与功能的分析、基因表达与调控的研究奠定了坚实物质基础,并将改进和发展一系列进行功能基因组研究的方法与技术.     

Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

Genome and exome sequencing yield extensive catalogues of human genetic variation. However, pinpointing the few phenotypically causal variants among the many variants present in human genomes remains a major challenge, particularly for rare and complex traits wherein genetic information alone is often insufficient. Here, we review approaches to estimate the deleteriousness of single nucleotide variants (SNVs), which can be used to prioritize disease-causal variants. We describe recent advances in comparative and functional genomics that enable systematic annotation of both coding and non-coding variants. Application and optimization of these methods will be essential to find the genetic answers that sequencing promises to hide in plain sight.