脑胶质瘤IDH1基因突变HRM检测方法的初步建立

在大多数弥漫性人脑胶质瘤中常伴随着异柠檬酸脱氢酶基因(isocitrate dehydrogenase gene)1(IDH1)的突变.有着此突变的胶质瘤患者在临床上有良好的预后效果,因此可以作为胶质瘤患者的分子标记.通过提取石蜡切片中的胶质瘤组织DNA,优化条件以初步建立IDH1基因突变高分辨率熔解曲线分析法(high resolution melting,HRM)检测方法.用HRM对胶质瘤石蜡包埋组织标本中IDH1基因检测突变,并用直接测序法对比,观察反应体系和反应条件的可行性.正交试验结果证明引物最适退火温度为53℃,20μL HRM反应体系中,0.6μmol/L引物,2.5 mmol/L Mg2+,60 ng DNA模板为最佳.HRM IDH1基因突变的结果和直接测序法结果一致,但灵敏度更高.说明此HRM方法简单,特异性强,准确可靠,可为IDH1突变检测的临床应用提供借鉴依据.     

高分辨率熔解曲线分析法检测结直肠癌KRAS基因突变

目的:采用高分辨率熔解曲线分析法检测结直肠癌中KRAS基因突变,探讨其用于临床检测的可行性。方法:首先用高分辨率熔解曲线分析法检测64例结直肠癌患者KRAS基因第2外显子的突变情况,再用直接测序法对结果进行验证。结果:通过高分辨率熔解曲线分析法检测,发现有23例KRAS基因突变(35.9%),经直接测序法验证,证实所有患者的突变情况与高分辨率熔解曲线法的结果完全一致;共检测出6种KRAS突变类型,G12D(GGT>GAT)的突变率最高(47.8%),G12D、G12V和G13D等3种常见突变型占总突变数的78.3%。结论:与直接测序法相比,应用高分辨率熔解曲线分析法检测KRAS基因突变具有操作简单快捷、结果准确、成本低的优点,适合应用于临床检测。     

应用高分辨率熔解曲线分析石蜡标本中KRAS基因突变

目的:KRAS基因在结直肠癌患者突变率为30％～50％,并且KRAS基因状态与抗EGFR抗体疗效的密切相关.常用的直接测序法其检测灵敏度低、容易出现假阴性结果.采用高分辨率溶解曲线分析法检测结直肠癌中KRAS基因突变,探索其应用于临床检测的可行性.方法:本文收集20例结直肠癌患者石蜡包埋组织标本,应用高分辨率熔解曲线方法检测KRAS基因突变(2,3号外显子).将KRAS基因突变型DNA(p.G12D)和野生型DNA梯度混合稀释,突变型DNA浓度分别为40％、20％、10％、2％,进行高分辨率熔解曲线方法进行检测,并将扩增产物进行直接测序,比较两种方法的灵敏度.结果:在20例结直肠癌患者中检出5例2号外显子突变,p.G12D 2例,p.G12V 2例,p.G13D 1例,3号外显子未检出突变.HRM方法检测基因突变的检出限可达2％,直接测序法检测基因突变的检出限为20％.结论:HRM法比直接测序法灵敏度高,能精确检测出结直肠癌石蜡标本中低浓度的KRAS突变,有望应用于临床基因突变检测.     

高分辨率熔解曲线法检测CYP4A118590T＞C单核苷酸多态性

目的 建立CYP4A11 8590T＞C单核苷酸多态性（single nucleotide polymorphism,SNP）的高分辨率熔解曲线（high resolution melting,HRM）检测方法.方法先采用温度梯度PCR,确定适宜的退火温度;再利用正交试验,优化引物、DNA模板量和Mg2＋量,最终确定PCR反应体系和反应条件.通过对607例无血缘关系的受试者基因组DNA进行HRM分析,并随机选择50例产物测序.结果 引物最适退火温度为57.8 ℃;PCR最佳反应体系为20 μl,包括2×conc dNTP mix 10 μl,上下游引物（10 μmol/L）各0.5 μl,DNA溶液（30 ng/μl）1.0 μl,Mg2＋（2.5 mmol/L）1.5 μl和灭菌水6.5 μl.607例受试者中CYP4A11 8590TT、TC和CC基因型频率分别为54.7 %、37.6 %和7.7 %.结论该正交试验优化的HRM技术可用于检测CYP4A11 8590T＞C单核苷酸多态性,且其分析结果和测序结果一致.     

一种用于优化PCR引物设计的短链DNA熔点分析方法

目前,PCR引物设计主要依赖于软件对引物熔点的模拟计算,而PCR退火条件的优化需进行不同条件下的扩增实验。为开发一种可高效、精确评价引物和确定退火条件的方法,本研究采用高分辨率熔解曲线（high resolution melting,HRM）测定技术直接分析短链DNA的熔点,用于引物优劣性的评价,并为退火条件的优化提供参考。本文用HRM法直接测定了非完全互补的双链DNA以及DNA发卡结构的熔点,结果显示：（1）与完全互补的双链DNA相比,较为稳定的单碱基错配A?G、G?G和T?G的熔点只降低2℃ ~ 3℃,部分双碱基错配的熔点只降低4℃ ~ 6℃,单碱基突出熔点只降低4℃~ 5℃。因此,如果采用的退火温度不当,部分错配的非目的模板可能会被扩增。（2）即使发卡结构的茎干区只有6 bp,当其环区碱基少于10 nt时,其熔点也可达到60℃以上。此外,环区的长度对发卡熔点也有较大影响。根据本研究结果发现,引物设计时应尽量避免模板引物结合区同其邻近的30 nt碱基有6 bp以上的互补部分。综上所述,本研究证明HRM熔点法是一种高效评价引物及确定退火温度的方法。     

利用HRM技术区分ob糖尿病小鼠不同基因型

ob/ob小鼠是糖尿病相关研究中使用最广泛的动物模型之一,近年来,市场需求呈上升趋势。与野生型小鼠相比,其瘦素蛋白基因105号密码子发生CT点突变,导致不能产生正常的瘦素蛋白。该模型4周前外观表型与野生型无异,而ob/ob纯合子不育,因而在繁殖建系过程中,需要通过基因型鉴定纯合、杂合和野生三种基因型。该文建立了基于高分辨率溶解曲线分析(high resolution melting analysis,HRM)的基因型鉴定方法,基因型分型结果与常规PCR加酶切方法一致,也与DNA测序结果吻合;通过该方法分型后获得纯合子小鼠外观表型、血糖浓度参数符合预期。该方法较常规方法省时、高效、节省实验成本,可用于大规模ob小鼠繁殖中的基因型鉴定。     

高分辨率熔解曲线分析技术检测结核分枝杆菌的耐药性

目的:探讨高分辨率熔解曲线分析(High resolution melting,HRM)技术检测结核分枝杆菌耐药突变位点的可行性。方法:对218株结核分枝杆菌进行利福平(RFP)和异烟肼(INH)的药物敏感性测定,并进行耐药基因位点的PCR扩增和测序,同时采用HRM方法检测RFP和INH耐药基因位点情况,分析HRM的敏感性和特异性。结果:218株结核分枝杆菌药敏试验结果显示,有106株(48.6%)对RFP耐药,100株(45.9%)对INH耐药,81株(37.4%)对RFP和INH均耐药。测序发现,101株(46.3%)存在RFP耐药基因的突变,107株(49.1%)存在INH耐药基因的突变。HRM检测结果显示,100株(45.9%)存在RFP耐药基因的突变,103株(47.2%)存在INH耐药基因的突变。分别以药敏试验和测序结果为标准,HRM检测RFP耐药的敏感性为94.3%(100/106)和99.0%(100/101);特异性为97.3%(109/112)和100%(117/117);INH耐药的敏感性为97.0%(97/100)和98.1%(103/105);特异性为97.3%(109/112)和100%(113/113)。结论:HRM快速检测结核分枝杆菌耐药具有较高的特异性和灵敏度,能够满足临床需求。     

高分辨率熔解曲线及其应用

饱和荧光染料、未标记探针与实时荧光PCR结合产生的高分辨率熔解曲线(HRM)是一种新的实时定量技术,在检测速度、灵敏度和准确性上具有突出的优点,近几年来在突变扫描、DNA甲基化和基因分型等医学检测中发展迅速.就HRM的原理、应用以及在HRM基础上发展起来的未标记探针(unlabled probe)HMR、弹回探针(snap probe)HMR技术作一介绍.     

反向斑点杂交法检测HBV基本核心启动子区A1762T／G1764A突变的实验研究

目的建立一种基于尼龙膜的反向斑点杂交法,用于检测乙型肝炎病毒（HBV）基本核心启动子区（BCP）A1762T／G1764A突变。方法根据我国HBV主要流行的基因型为B和C,从GenBank上查出4种HBVBCP序列。利用在线工具ClustalW进行比对,针对该突变位点设计引物和检测探针。探针经合成和修饰后点在带正电的尼龙膜上。将反向斑点杂交法结合地高辛检测试剂盒用于检测A1762T／G1764A突变,以测序法确定该区域序列的标本为检测对象。结果反向斑点杂交法分别检测5例A1762／G1764病毒株、2例T1762／G1764病毒株、5例A1762／A1764病毒株和4例T1762／A1764病毒株,结果与测序完全相同。结论应用本方法可以快速、准确地HBV相关的热点突变。     

利用CRISPR/Cas系统快速高效构建血友病乙小鼠模型

血友病乙是由凝血因子Ⅸ(Factor Ⅸ,FⅨ)缺乏或功能缺陷导致的出血性疾病,为伴X染色体隐性遗传病。小鼠模型对于血友病乙的研究具有十分重要的意义,而基因组编辑技术又为小鼠模型的构建提供了一种快捷而且高效的途径。本文利用CRISPR/Cas系统,在小鼠FⅨ基因第8外显子上选择靶位点,将Cas9 mRNA和带有靶位点的sgRNA显微注射到C57BL/6品系小鼠的受精卵中,获得基因修饰的小鼠。利用高分辨率熔解曲线分析(High resolution melting, HRM)技术进行精确基因分型,并通过测序验证,在60只小鼠中,总共有51只小鼠的靶位点发生了突变,突变率高达85%,其中雄鼠的突变率为79.5%,雌鼠的突变率为95.2%;未检测到非目标位置的基因编辑脱靶。凝血活性实验显示,突变小鼠的FⅨ活性值(Factor Ⅸ coagulant activity, FⅨ: C)是非突变小鼠的6.82%,大大低于非突变小鼠,表明突变小鼠的凝血活性缺失。本研究表明,利用CRISPR/Cas系统成功构建了人类血友病乙遗传病小鼠模型。     

Applications of the method of high resolution melting analysis for diagnosis of Leber's disease and the three primary mutation spectrum of LHON in the Han Chinese population

Current screening methods, such as single strand conformational polymorphism (SSCP), denaturing high performance liquid chromatography (dHPLC) and direct DNA sequencing that are used for detecting mutation in Leber's hereditary optic neuropathy (LHON) subjects are time consuming and costly. Here we tested high-resolution melt (HRM) analysis for mtDNA primary mutations in LHON patients. In this study, we applied the high resolution melting (HRM) technology to screen mtDNA primary mutations in 50 LHON patients from their peripheral blood. In order to evaluate the reliability of this technique, we compared the results obtained by HRM and direct mtDNA sequencing. We also investigated the spectrum of three most common mtDNA mutations implicated in LHON in the Han Chinese population. The results showed HRM analysis differentiated all of the mtDNA primary mutations and identified 4 additional mtDNA mutations from 50 patients in the blind study. The prevalence of three primary mutations were 11778G>A (87.9%), 14484T>C (6.5%) and 3460G>A (1.7%) in the Han Chinese population. In conclusion, HRM analysis is a rapid, reliable, and low-cost tool for detecting mtDNA primary mutations and has practical applications in molecular genetics.     

Glucose-6-phosphate dehydrogenase (G6PD) gene mutations detection by improved high-resolution DNA melting assay

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is a common inherited disorder worldwide including southern China. G6PD gene mutations cause deficiency of the enzyme and a large spectrum of diseases. High-resolution DNA melting (HRM) assay was recently introduced as a rapid, inexpensive and effective method for genotyping. But there was a shortcoming of this method that hemizygous and homozygous genotypes were not easily distinguished from wild-types. Here we used improved HRM method for a small-scale screening of G6PD-deficient variants among people of Meizhou region. Then all amplicons were ascertained by direct DNA sequencing. These results indicated that HRM method was a major technical advance for G6PD mutations screening.     

High-Resolution Melting Curve Analysis for Identification of Pasteurellaceae Species in Experimental Animal Facilities

Pasteurellaceae are among the most prevalent bacterial pathogens isolated from mice housed in experimental animal facilities. Reliable detection and differentiation of Pasteurellaceae are essential for high-quality health monitoring. In this study, we combined a real-time PCR assay amplifying a variable region in the 16S rRNA sequence with high-resolution melting curve analysis (HRM) to identify and differentiate among the commonly isolated species Pasteurella pneumotropica biotypes “Jawetz” and “Heyl”, Actinobacillus muris, and Haemophilus influenzaemurium. We used a set of six reference strains for assay development, with the melting profiles of these strains clearly distinguishable due to DNA sequence variations in the amplicon. For evaluation, we used real-time PCR/HRM to test 25 unknown Pasteurellaceae isolates obtained from an external diagnostic laboratory and found the results to be consistent with those of partial 16S rRNA sequencing. The real-time PCR/HRM method provides a sensitive, rapid, and closed-tube approach for Pasteurellaceae species identification for health monitoring of laboratory mice.     

Detection and classification of SARS-CoV-2 using high-resolution melting analysis

Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has recently posed a significant threat to global public health. The objective of this study was to develop and evaluate a rapid, expandable and sequencing-free high-resolution melting (HRM) approach for the direct detection and classification of SARS-CoV-2. Thirty-one common pathogens that can cause respiratory tract infections were used to evaluate the specificity of the method. Synthetic RNA with serial dilutions was utilized to determine the sensitivity of the method. Finally, the clinical performance of the method was assessed using 290 clinical samples. The one-step multiplex HRM could accurately identify SARS-CoV-2 and differentiate mutations in each marker site within approximately 2 h. For each target, the limit of detection was lower than 10 copies/reaction, and no cross-reactivity was observed among organisms within the specificity testing panel. The method showed good uniformity for SARS-CoV-2 detection with a consistency of 100%. Regarding the clade classification performance, the results showed good concordance compared with sequencing, with the rate of agreement being 95.1% (78/82). The one-step multiplex HRM method is a rapid method for SARS-CoV-2 detection and classification.     

In silico single nucleotide polymorphism discovery and application to marker-assisted selection in soybean

The general approach to discovering single nucleotide polymorphisms (SNPs) requires locus-specific PCR amplification. To enhance the efficiency of SNP discovery in soybean, we used in silico analysis prior to re-sequencing as it is both rapid and inexpensive. In silico analysis was performed to detect putative SNPs in expressed sequence tag (EST) contigs assembled using publicly available ESTs from 18 different soybean genotypes. SNP validation by direct sequencing of six soybean cultivars and a wild soybean genotype was performed with PCR primers designed from EST contigs aligned with at least 5 out of 18 soybean genotypes. The efficiency of SNP discovery among the confirmation genotypes was 81.2%. Furthermore, the efficiency of SNP discovery between Pureunkong and Jinpumkong 2 genotypes was 47.4%, a great improvement on our previous finding based on direct sequencing (22.3%). Using SNPs between Pureunkong and Jinpumkong 2 in EST contigs, which were linked to target traits, we were able to genotype 90 recombinant inbred lines by high-resolution melting (HRM) analysis. These SNPs were mapped onto the expected locations near quantitative trait loci for water-logging tolerance and seed pectin concentration. Thus, our protocol for HRM analysis can be applied successfully not only to genetic diversity studies, but also to marker-assisted selection (MAS). Our study suggests that a combination of in silico analysis and HRM can reduce the cost and labor involved in developing SNP markers and genotyping SNPs. The markers developed in this study can also easily be applied to MAS if the markers are associated with the target traits.     

基于高分辨率熔解曲线的常见五种皮肤癣菌分子鉴定

皮肤癣菌是浅表真菌感染的重要致病菌,常见致病菌种包括红色毛癣菌、趾间毛癣菌、絮状表皮癣菌、犬小孢子菌和内弯小孢子菌。本研究基于实时荧光PCR的高分辨率熔解曲线分析技术,以几丁质合成酶1为目标基因设计扩增引物,对经测序鉴定的上述5种皮肤癣菌进行熔解曲线分析,并在方法建立后,对已鉴定的临床菌株进行验证。实验结果表明,使用该方法上述5种皮肤癣菌均能扩增,并表现出不同的熔解曲线和熔解温度值,可有效区分;对其余对照菌及人基因均无法扩增,特异性为100%;临床菌株的熔解曲线分析结果与DNA测序结果一致。本研究提供了一种快速、准确鉴别5种常见皮肤癣菌的方法,可为临床应用和分子流行病学研究提供参考。     

Analysis of HIV Using a High Resolution Melting (HRM) Diversity Assay: Automation of HRM Data Analysis Enhances the Utility of the Assay for Analysis of HIV Incidence

Background

HIV diversity may be a useful biomarker for discriminating between recent and non-recent HIV infection. The high resolution melting (HRM) diversity assay was developed to quantify HIV diversity in viral populations without sequencing. In this assay, HIV diversity is expressed as a single numeric HRM score that represents the width of a melting peak. HRM scores are highly associated with diversity measures obtained with next generation sequencing. In this report, a software package, the HRM Diversity Assay Analysis Tool (DivMelt), was developed to automate calculation of HRM scores from melting curve data.

Methods

DivMelt uses computational algorithms to calculate HRM scores by identifying the start (T1) and end (T2) melting temperatures for a DNA sample and subtracting them (T2–T1 = HRM score). DivMelt contains many user-supplied analysis parameters to allow analyses to be tailored to different contexts. DivMelt analysis options were optimized to discriminate between recent and non-recent HIV infection and to maximize HRM score reproducibility. HRM scores calculated using DivMelt were compared to HRM scores obtained using a manual method that is based on visual inspection of DNA melting curves.

Results

HRM scores generated with DivMelt agreed with manually generated HRM scores obtained from the same DNA melting data. Optimal parameters for discriminating between recent and non-recent HIV infection were identified. DivMelt provided greater discrimination between recent and non-recent HIV infection than the manual method.

Conclusion

DivMelt provides a rapid, accurate method of determining HRM scores from melting curve data, facilitating use of the HRM diversity assay for large-scale studies.     

Application of high-resolution DNA melting for genotyping in lepidopteran non-model species: Ostrinia furnacalis (Crambidae)

Development of an ideal marker system facilitates a better understanding of the genetic diversity in lepidopteran non-model organisms, which have abundant species, but relatively limited genomic resources. Single nucleotide polymorphisms (SNPs) discovered within single-copy genes have proved to be desired markers, but SNP genotyping by current techniques remain laborious and expensive. High resolution melting (HRM) curve analysis represents a simple, rapid and inexpensive genotyping method that is primarily confined to clinical and diagnostic studies. In this study, we evaluated the potential of HRM analysis for SNP genotyping in the lepidopteran non-model species Ostrinia furnacalis (Crambidae). Small amplicon and unlabeled probe assays were developed for the SNPs, which were identified in 30 females of O. furnacalis from 3 different populations by our direct sequencing. Both assays were then applied to genotype 90 unknown female DNA by prior mixing with known wild-type DNA. The genotyping results were compared with those that were obtained using bi-directional sequencing analysis. Our results demonstrated the efficiency and reliability of the HRM assays. HRM has the potential to provide simple, cost-effective genotyping assays and facilitates genotyping studies in any non-model lepidopteran species of interest.