新一代DNA测序技术

近年来新型DNA测序平台454、Solexa、SOLiD、Polonator和HeliSeope等得到迅速推广,使测序成本下降了2-3个数量级.原先只能由大型测序中心完成的基因组项目,现在已经可以在个人实验室中实现.这些新技术大大加速了生物医学的研究步伐,因为全面分析基因组、转录物组和代谢组已不再是高不可攀,而将成为广泛运用的常规分析.本文介绍DNA测序新技术的原理、特点、现状和应用前景.     

唐氏综合征患儿线粒体基因组突变的分析

目的 研究唐氏综合征中线粒体DNA突变情况.方法 采用高通量测序和焦磷酸测序检测7个唐氏综合征(Down's syndrome,DS)家系中的患儿和母亲的线粒体基因组序列,分析线粒体基因组序列的变化情况.结果 ①DS患儿中检测到36个与其母亲中不同的线粒体DNA突变,其中14个位点是首次在唐氏综合征样本中发现;②36个线粒体DNA突变主要发生于D-Loop区和线粒体复合物Ⅰ中;③ 线粒体基因组13个编码基因中,有11个基因检测到线粒体DNA的突变;④ 焦磷酸测序对线粒体基因组杂合突变频率的检测结果和高通量测序结果吻合.结论 DS患儿中广泛存在线粒体DNA的突变,这些突变可能与唐氏综合征的线粒体功能异常相关.     

不同样本测序前处理方案对冠状病毒基因组高通量测序结果的影响

目的以基因组最大RNA病毒(冠状病毒)为代表,研究不同测序前样本处理模式对高通量测序获得病毒全基因组序列信息质量的影响。方法以细胞培养的人冠状病毒HCoV-OC43样本为代表,分为4种测序前样本处理模式,即:未处理组、核酸提取前DNase和RNase处理组、核酸提取后DNase处理组、核酸提取前DNase和RNase处理且核酸提取后DNase处理组。不同模式处理后的核酸分为两份,一份直接RNA测序(未扩增),另一份经序列非依赖的单引物扩增(SISPA)后DNA测序。结果尽管不同处理方式下获得的病毒基因组覆盖率差别不大,但是样本核酸提取后经DNase处理组直接测序获得了最高的基因覆盖度和测序准确性,而SISPA扩增可有效提高病毒测序读长(reads)比例与基因组各位点的测序深度。结论本研究为优化冠状病毒等RNA病毒全基因组测序策略提供了技术参考。     

全基因组外显子测序及其在遗传病研究中的应用

全基因组外显子测序是指利用序列捕获技术将全基因组外显子区域DNA捕捉并富集,然后进行高通量测序的基因组分析方法.与传统测序方式相比,该技术具有耗时短、成本低、通量大,对样品的要求量少等特点,已经成为人们研究某些疾病致病基因的重要方法.此文就全基因组外显子测序的优缺点及其在遗传病中的应用作简要综述.     

在光纤芯片上进行高速个体化全基因组测序

新近发展的在光纤芯片上做高通量测序的技术，可以将人类全基因组序列的测定时间由目前所用的10年时间缩短到100d。光纤芯片上的基因组测序结合了磁珠、乳液PCR和焦磷酸测序法等技术，利用光纤优良的表面性质和有效的加工工艺，将光纤制作成一种基因芯片。在芯片上用磁珠来耦联DNA、RNA等微量反应物。乳液PCR可以获得大量的不同的基因组DNA片段。乳液PCR和光纤芯片都是由于有了磁珠作为微量反应物的载体，从而可以将反应一再小型化。而这些技术的结合，工作效率是目前常规的测序方法的100多倍。成功实现了基因组测序反应小型化、高通量化的思想，大大降低了成本，减少了完成全基因组测序的时间。     

目标序列捕获测序技术及其在疾病相关基因研究中的作用

目标序列捕获测序是指将感兴趣的基因组区域定制成特异性探针与目标基因组DNA在序列捕获芯片(或溶液)进行杂交,将目标基因组区域的DNA片段进行富集后再利用新一代测序技术进行测序,以获得目标基因组序列的研究策略.该项技术具有高度灵活性、特异性及覆盖率,操作便捷等特点,该文就目标序列捕获测序技术的原理及其在疾病相关基因研究中的应用作一简要综述.     

目标序列捕获测序技术及其在疾病相关基因研究中的作用

目标序列捕获测序是指将感兴趣的基因组区域定制成特异性探针与目标基因组DNA在序列捕获芯片(或溶液)进行杂交,将目标基因组区域的DNA片段进行富集后再利用新一代测序技术进行测序,以获得目标基因组序列的研究策略.该项技术具有高度灵活性、特异性及覆盖率,操作便捷等特点,该文就目标序列捕获测序技术的原理及其在疾病相关基因研究中的应用作一简要综述.

Abstract：

Target sequence capture sequencing refers to a sequencing technology that uses the interested genomic region as specific probes, which are attached to chips or beads. The probes then hybridize with free target genomic DNA on sequence capture chip ( or in solution ) to enrich target genomic DNA. The enriched target genomic DNA fragments can then be amplified and studied using the next-generation sequencing technologies. The technology has a high degree of flexibility, specificity and coverage,and easy operation characteristics. The goal of this review is to outline the principle of target sequencing technology and its implication in disease-related gene research.     

三种测序DNA模板制备方法的比较○

背景：DNA模板质量对DNA序列测定起着至关重要的作用。 目的：为基因组DNA或甲基化DNA测序寻找一种经济,简便的方法。 方法：分别采用96管集合板及96孔板提取质粒,并且针对质粒设计一对包含目的片段的引物,扩增后纯化PCR产物,通过以上3种方法制备DNA测序模板进行测序。 结果与结论：实验所采用的3种方法对于基因组DNA测序效果无差异(P > 0.05)。对于甲基化DNA测序效果,96管集合板法优于其他2种方法(P < 0.05)。说明3种方法均适用于基因组DNA的测序,而96管集合板法更适用于甲基化DNA的测序。      

一例X-连锁无丙种球蛋白血症患者BTK基因新变异体的鉴定

目的 对一例X-连锁无丙种球蛋白血症(XLA)患者进行致病基因变异鉴定.方法 收集患者及家庭成员临床资料并采集外周血,从患者外周血中提取基因组DNA并进行全外显子组测序,筛查可疑致病变异,并对其父母基因组DNA进行Sanger测序验证及基因型-表型共分离分析,从患者外周血中提取RNA,反转录为cDNA后进行Sanger...     

应用全外显子结合全基因组低深度测序诊断2q37缺失综合征一例

目的探讨1例2q37缺失综合征患儿的临床及遗传学特征。方法采集患儿及其父母的外周血样,提取基因组DNA,进行全外显子组及全基因组低深度测序,并采用染色体核型分析及荧光定量PCR对基因组拷贝数异常区域进行验证。结果测序结果显示患儿在染色体2q37区存在6 Mb的杂合性缺失,涉及GBX2、LINC01881等98个基因。对其父母的检测提示,该缺失为新发变异。患儿染色体核型分析未发现异常。荧光定量PCR分析结果与测序结果一致。结论通过临床及基因测序分析,患儿被诊断为2q37缺失综合征。全外显子组测序结合全基因组低深度测序技术具有高分辨、高通量、高灵敏度等优点,能够显著提高智力障碍、多发畸形及临床疑似综合征患者的诊断率。     

Evaluation of clinical formalin-fixed paraffin-embedded tissue quality for targeted-bisulfite sequencing

Formalin-fixed paraffin-embedded (FFPE) tissues are promising biological resources for genetic research. Recent improvements in DNA extraction from FFPE samples allowed the use of these tissues for multiple sequencing methods. However, fundamental research addressing the application of FFPE-derived DNA for targeted-bisulfite sequencing (TB-seq) is lacking. Here, we evaluated the suitability of FFPE-derived DNA for TB-seq. We conducted TB-seq using FFPE-derived DNA and corresponding fresh frozen (FF) tissues of patients with kidney cancer and compared the quality of DNA, libraries, and TB-seq statistics between the two preservation methods. The approximately 600-bp average fragment size of the FFPE-derived DNA was significantly shorter than that of the FF-derived DNA. The sequencing libraries constructed using FFPE-derived DNA and the mapping ratio were approximately 10 times and 10% lower, respectively, than those constructed using FF-derived DNA. In the mapped data of FFPE-derived DNA, duplicated reads accounted for > 60% of the obtained sequence reads, with lower mean on-target coverage. Therefore, the standard TB-seq protocol is inadequate for obtaining high-quality data for epigenetic analysis from FFPE-derived DNA, and technical improvements are necessary for enabling the use of archived FFPE resources.     

Advances in Alport syndrome diagnosis using next-generation sequencing

Alport syndrome (ATS) is a hereditary nephropathy often associated with sensorineural hypoacusis and ocular abnormalities. Mutations in the COL4A5 gene cause X-linked ATS. Mutations in COL4A4 and COL4A3 genes have been reported in both autosomal recessive and autosomal dominant ATS. The conventional mutation screening, performed by DHPLC and/or Sanger sequencing, is time-consuming and has relatively high costs because of the absence of hot spots and to the high number of exons per gene: 51 (COL4A5), 48 (COL4A4) and 52 (COL4A3). Several months are usually necessary to complete the diagnosis, especially in cases with less informative pedigrees. To overcome these limitations, we designed a next-generation sequencing (NGS) protocol enabling simultaneous detection of all possible variants in the three genes. We used a method coupling selective amplification to the 454 Roche DNA sequencing platform (Genome Sequencer junior). The application of this technology allowed us to identify the second mutation in two ATS patients (p.Ser1147Phe in COL4A3 and p.Arg1682Trp in COL4A4) and to reconsider the diagnosis of ATS in a third patient. This study, therefore, illustrates the successful application of NGS to mutation screening of Mendelian disorders with locus heterogeneity.     

A long road/read to rapid high-resolution HLA typing: The nanopore perspective

Next-generation sequencing (NGS) has been widely adopted for clinical HLA typing and advanced immunogenetics researches. Current methodologies still face challenges in resolving cis–trans ambiguity involving distant variant positions, and the turnaround time is affected by testing volume and batching. Nanopore sequencing may become a promising addition to the existing options for HLA typing. The technology delivered by the MinION sequencer of Oxford Nanopore Technologies (ONT) can record the ionic current changes during the translocation of DNA/RNA strands through transmembrane pores and translate the signals to sequence reads. It features simple and flexible library preparations, long sequencing reads, portable and affordable sequencing devices, and rapid, real-time sequencing. However, the error rate of the sequencing reads is high and remains a hurdle for its broad application. This review article will provide a brief overview of this technology and then focus on the opportunities and challenges of using nanopore sequencing for high-resolution HLA typing and immunogenetics research.     

Critical points for an accurate human genome analysis

Next‐generation sequencing is radically changing how DNA diagnostic laboratories operate. What started as a single‐gene profession is now developing into gene panel sequencing and whole‐exome and whole‐genome sequencing (WES/WGS) analyses. With further advances in sequencing technology and concomitant price reductions, WGS will soon become the standard and be routinely offered. Here, we focus on the critical steps involved in performing WGS, with a particular emphasis on points where WGS differs from WES, the important variables that should be taken into account, and the quality control measures that can be taken to monitor the process. The points discussed here, combined with recent publications on guidelines for reporting variants, will facilitate the routine implementation of WGS into a diagnostic setting.     

Contribution of high‐throughput DNA sequencing to the study of primary immunodeficiencies

Primary immunodeficiencies (PIDs) are inborn errors of the immune system. PIDs have been characterized immunologically for the last 60 years and genetically, principally by Sanger DNA sequencing, over the last 30 years. The advent of next‐generation sequencing (NGS) in 2011, with the development of whole‐exome sequencing in particular, has facilitated the identification of previously unknown genetic lesions. NGS is rapidly generating a stream of candidate variants for an increasing number of genetically undefined PIDs. The use of NGS technology is ushering in a new era, by facilitating the discovery and characterization of new PIDs in patients with infections and other phenotypes, thereby helping to improve diagnostic accuracy. This review provides a historical overview of the identification of PIDs before NGS, and the advances and limitations of the use of NGS for the diagnosis and characterization of PIDs.     

人类白细胞抗原新等位基因DRB1*1219的确认及其序列分析

目的 鉴定分析1个白血病患者家庭HLA-DRB1位点1个新等位基因.方法 应用PCR-序列特异性引物及Luminex DNA杂交流式分型技术进行HLA分型,发现1个与HLA-DRB1*120201相关的未知基因.应用DNA测序技术进行鉴定分析并与已知序列比对分析.结果 先证者DRB1位点有1个等位基因的核苷酸序列与所有已知基因序列均不相同,与同源性最高的DRB1*120201相比,第2外显子第341位核苷酸碱基发生了C→T,结果导致相应85位密码子编码的丙氨酸变为缬氨酸.结论 测序表明被测样本含有1个HLA-DRB1新等位基因,被世界卫生组织HLA因子命名委员会正式命名为HLA-DRB1*1219(序列号EJ374889).

Abstract：

Objective To identify a novel HLA DRB1 allele in a Chinese leukemia family. Methods A new HLA-DRB1 allele was initially detected by polymerase chain reaction-sequence specific primer and unusual reaction pattern by Luminex RSSO, then DNA sequencing was performed to identify the sequence of the novel allele. Results The DNA sequencing revealed the presence of the new allele which differs from the closest macthing HLA- DRB1 * 120201 by a single nucleotide substitution at position (341 C→T in exon 2),resulting in an amino acid change from Ala to Val at coden 85. Conclusion A novel allele was confirmed by DNA sequencing and has been designated HLA-DRB1 * 1219 by the WHO Nomenclature Committee.     

外显子组测序是发现单基因病致病基因的捷径

新一代测序技术的产生和发展为疾病研究带来了新的机遇.作为一种高效、快速和高性价比的研究方法,外显子组测序技术已经开始应用于单基因疾病等遗传病的研究.该技术已经得到国际学术界的广泛认可,也将越来越多地应用于单基因疾病的研究中.这将对单基因病致病基因的发现产生巨大推动作用.作者对国内外近两年应用外显子测序技术检测疾病相关基因的一些研究进行文献综述.     

Xdrop: Targeted sequencing of long DNA molecules from low input samples using droplet sorting

Long‐read sequencing can resolve regions of the genome that are inaccessible to short reads, and therefore are ideal for genome‐gap closure, solving structural rearrangements and sequencing through repetitive elements. Here we introduce the Xdrop technology: a novel microfluidic‐based system that allows for targeted enrichment of long DNA molecules starting from only a few nanograms of DNA. Xdrop is based on the isolation of long DNA fragments in millions of droplets, where the droplets containing a target sequence of interest are fluorescently labeled and sorted using flow cytometry. The final product from the Xdrop procedure is an enriched population of long DNA molecules that can be investigated by sequencing. To demonstrate the capability of Xdrop, we performed enrichment of the human papilloma virus 18 integrated into the genome of human HeLa cells. Analysis of the sequencing reads resolved three HPV18‐chr8 integrations at base‐pair resolution, and the captured fragments extended up to 30 kb into the human genome at the integration sites. Further, we enriched the complete TP53 locus in a leukemia cell line and could successfully phase coexisting mutations using PacBio sequencing. In summary, our results show that Xdrop is an efficient enrichment technology for studying complex genomic regions.     

Simultaneous Whole Mitochondrial Genome Sequencing with Short Overlapping Amplicons Suitable for Degraded DNA Using the Ion Torrent Personal Genome Machine

Whole mitochondrial (mt) genome analysis enables a considerable increase in analysis throughput, and improves the discriminatory power to the maximum possible phylogenetic resolution. Most established protocols on the different massively parallel sequencing (MPS) platforms, however, invariably involve the PCR amplification of large fragments, typically several kilobases in size, which may fail due to mtDNA fragmentation in the available degraded materials. We introduce a MPS tiling approach for simultaneous whole human mt genome sequencing using 161 short overlapping amplicons (average 200 bp) with the Ion Torrent Personal Genome Machine. We illustrate the performance of this new method by sequencing 20 DNA samples belonging to different worldwide mtDNA haplogroups. Additional quality control, particularly regarding the potential detection of nuclear insertions of mtDNA (NUMTs), was performed by comparative MPS analysis using the conventional long‐range amplification method. Preliminary sensitivity testing revealed that detailed haplogroup inference was feasible with 100 pg genomic input DNA. Complete mt genome coverage was achieved from DNA samples experimentally degraded down to genomic fragment sizes of about 220 bp, and up to 90% coverage from naturally degraded samples. Overall, we introduce a new approach for whole mt genome MPS analysis from degraded and nondegraded materials relevant to resolve and infer maternal genetic ancestry at complete resolution in anthropological, evolutionary, medical, and forensic applications.