Different denaturation rates between methylated and non-methylated genomic DNA can result in allele-specific PCR amplification

We analysed a DNA sample from a father and child who were both heterozygous for a 7 base pair insertion in the MEST gene differentially-methylated promoter region, previously shown by PCR analysis of bisulphite-treated DNA to be on the methylated allele in the unaffected father and the unmethylated allele in the affected child. PCR from genomic DNA was then carried out using a commercial PCR kit with its recommended initial DNA denaturation step of 2 minutes. Subsequent sequence analysis showed that only the non-methylated allele had been amplified, the father appearing to be homozygous normal and the child appearing to have a homozygous 7 b.p. insertion. The PCR protocol was then modified in order to use a longer DNA denaturation stage prior to the addition of the polymerase enzyme. Upon doing so, both the methylated and non-methylated alleles were then identifiable by sequencing with the mutation appearing in its expected heterozygous form. These results highlight the fact that the methylation status of DNA can affect the denaturation rate prior to PCR and result in allele drop-out, showing that the standard protocols of commercial kits should be used with caution when working with methylated regions of DNA.

高分子量麦谷蛋白1Bx14亚基AS-PCR标记

根据已发表的1Bx14亚基的基因序列在不同位点设计了10对特异引物,从中筛选出1对引物,对HMW-GS在Glu-1Bx位点已知的10个小麦品种进行了PCR扩增.结果表明,具有1Bx14亚基的4个品种都能扩增出1条1 256 bp左右的特异带.用这一特异标记对山东省种植面积较大的40个品种进行PCR扩增(即等位专一PCR,AS-PCR),发现仅有5个品种携带1Bx14亚基.该AS-PCR标记可用于检测小麦品种在该位点的亚基组成,与SDS-PAGE相比,可显著提高检测的准确性和效率,可为种质鉴定和育种工作提供参考.

簇毛麦HMW-GS基因的位点特异PCR(AS-PCR)标记及其多态性

簇毛麦含有丰富的HMW-GS基因变异。本研究旨在建立簇毛麦HMW-GS基因的位点特异PCR(AS-PCR)标记,并对18个居群簇毛麦HMW-GS基因遗传多样性进行系统评价,为开发和利用簇毛麦HMW-GS改良普通小麦品质奠定基础。根据先前克隆的3个簇毛麦HMW-GS基因序列(1Va、1Vb和1Vc)和已发表的普通小麦HMW-GS基因序列,经过同源性比较后设计了簇毛麦HMW-GS基因的位点特异性引物P6+P7。对中国春及其簇毛麦附加系、6个不同来源簇毛麦的扩增结果表明,该对引物能在普通小麦背景下特异扩增簇毛麦HMW-GS基因,可以鉴别簇毛麦之间的HMW-GS等位基因变异,且其长度变异主要存在于中部重复结构区。利用该标记对来自美国国家种质库的18份材料的108个单株进行了研究,结果发现,每个单株均能扩增出1条或2条片段,共检测出7种等位基因变异的类型。不同等位基因类型的频率也不一样,等位基因b存在于除W6 7288外的所有簇毛麦居群中,占检测单株总数的59.55%,其次为等位基因d,占25.19%,等位基因a和等位基因f频率最低,仅出现在1个单株中。说明由于簇毛麦为异花受粉植物,同一居群不同单株间出现了不同的等位基因。

Identification of <i>JAK2</i>(V617F) Mutation in Myeloproliferative Neoplasms by Using Allele Specific Polymerase Chain Reaction (AS-PCR)

Myeloproliferative neoplasms (MPNs) are a group of clonal haematopoietic stem cell disorders characterized by the proliferation of one or more myeloid cell lineages. According to WHO classification, the Janus associated kinase 2 (JAK2) V617F mutation is one of the major diagnostic criteria in BCR-ABL1 negative myeloproliferative neoplasms. The aim of this study is to detect the JAK2 (V617F) mutation in patients with myeloproliferative neoplasms to get accurate diagnosis and proper management. A total of 90 clinically diagnosed MPN patients attending to Department of Clinical Haematology, Yangon General Hospital were enrolled in this study. The mean age was 53.4 ± 14 years which ranged from 16 to 81 years old and male and female ratio was 2.4:1. The identification of JAK2 (V617F) point mutation was found to be positive in 44/90 MPN patients (48.9%). According to MPN subtypes, the JAK2 mutation positivity was found in 19 out of 46 polycythemia vera patients (41.3%), 17 out of 25 essential thrombocythemia patients (68%), 8 out of 15 primary myelofibrosis patients (53.3%), 0 of 4 others myeloproliferative neoplasms (0%). Confirmation of each of nine JAK2 mutation positive and negative samples was done by Sanger sequencing. The arterial or venous thrombotic attack was found in 32/44 JAK2 mutation positive cases (72.7%) and 12/44 JAK2 mutation negative cases (27.3%). The association between thrombotic attack and presence of JAK2 mutation was statistically significance with p = 0.000. The diagnosis of myeloproliferative neoplasms mainly relies on the molecular genetics according to WHO classification. The Allele specific PCR reaction is sensitive, simple test and relatively cost-effective. Therefore, the identification of JAK2 (V617F) somatic point mutation by AS-PCR should be implemented as a routine diagnosis procedure for patients with chronic and suspected myeloproliferative neoplasms.

利用等位基因特异性PCR检测水稻可溶性淀粉合酶基因的单核苷酸多态性

单核苷酸多态性(SNP)广泛分布于水稻基因组中,SNP分型已成为水稻遗传作图、关联分析、资源鉴定和分子标记辅助选择等研究的重要技术。本文选择水稻可溶性淀粉合酶基因SSIIIa的12个SNP位点,研究了利用等位基因特异性PCR法检测SNP的可行性。按照等位基因特异性PCR原理设计引物3'末端碱基,并根据每个SNP位点引物3'端的错配类型,在上游引物3'末端第3位引入不同的错配碱基,结果均获得了很好的扩增特异性,PCR检测结果与测序结果吻合。表明,等位基因特异性PCR是一种简便、快捷、可靠和低成本的SNP分型方法,可有效应用于水稻可溶性淀粉合酶基因的种质资源鉴定和分子标记辅助选择育种等相关研究。

三种肺炎支原体PCR耐药检测方法的临床意义探讨

目的探讨PCR测序法、AS-PCR法、多重荧光PCR法检测肺炎支原体(MP)及大环内酯类耐药肺炎支原体(MRMP)的临床意义。方法采集呼吸道感染患儿的咽拭子样本116例,使用PCR测序法、AS-PCR法、多重荧光PCR法检测MP和MRMP,探讨三种方法的特点和临床价值。结果共采集116份咽拭子样本,PCR测序法检测MP阳性69例,阳性率59.48%,其中耐药株67例,包含1株耐药株与敏感株混合感染,耐药率97.1%,均为A2063G点突变,敏感株2例。AS-PCR法检测MP阳性63例,阳性率54.31%,其中耐药株58例,耐药率92.06%,敏感株5例,58例耐药株中混合感染21例,混合感染率33.33%(21/63),混合感染中18例耐药株比例超过50%。与PCR测序法比较,对MP阳性检测结果一致性极好(Kappa=0.86),对MRMP检测结果有较高的一致性(Kappa=0.652)。多重荧光PCR法检测MP阳性共67例,阳性率57.76%,其中耐药株61例,耐药率91.04%,敏感株6例,与PCR测序法相比,对MP阳性检测结果有极好的一致性(Kappa=0.929),对MRMP检测结果中度一致(Kappa=0.476)。结论PCR测序法、AS-PCR法和多重荧光PCR法检测敏感性和特异性均较高,三种方法均可同时进行MP和MRMP检测。AS-PCR法和多重荧光PCR法操作简单,适合临床应用,能为临床诊疗快速提供MP和MRMP检测结果。AS-PCR法能检测MP耐药株和敏感株混合感染,检测敏感性好。三种检测方法可为临床医生合理用药提供数据支持。

Allele-specific real-time PCR testing for minor HIV-1 drug resistance mutations： assay preparation and application to reveal dynamic of mutations in vivo

Background It is very important for the clinical management to test for minor HIV-1 resistance mutations accurately and sensitively. The conventional genotypic assays of HIV drug resistance detection based on sequencing can only discriminate the mutations which present in more than 20%-30%. The aim of this study was to evaluate allele-specific real-time PCR （ASPCR） to detect the resistance-related mutations located at positions 103, 184 and 215.Methods We developed the allele-specific PCR assay, using the most common drug resistance mutations in Chinese AIDS patients, K103N, M184V/I, T215F/Y as a model system. The standards were constructed by cloning the wild-type and mutant DNA fragments into the T-vector. We designed specific primers to discriminate mutant templates in the real-time PCR using SYBR green as a fluorescence reporter. And then we evaluated the ASPCR assay and tested 140clinical samples using this method.Results The sensitivities of ASPCR assay were 0.04% for K103N, 0.30% for M1841, 0.40% for M184V, 0.03% for T215F and 0.02% for T215Y. The intra-assay and inter-assay coefficients of variation were less than 0.42. One hundred and forty plasma samples were tested by ASPCR and dynamic resistance curves of ten patients were obtained.Conclusions Drug resistance emerged half a year after the start of antiretroviral therapy. The mutation of T215Yemerged 1 to 1.5 years after starting treatment and then increased rapidly. The ASPCR assay we developed was a sensitive, accurate and rapid method to detect the minor HIV-1 variants and it can provide earlier and more drug-resistance information for HIV research and AIDS antiretroviral therapy.

A single tube modified allele-specific-PCR for rapid detection of erythromycin-resistant Mycoplasma pneumoniae in Beijing

Background Mycoplasma pneumoniae （M. pneumoniae） is one of the common pathogens causing atypical pneumonia. In recent years, resistance to macrolides has become more common, especially in China. Previous studies have confirmed that the mutation at position 2063 in domain V of the 23S rRNA is the most prevalent, followed by the mutation at position 2064. Reported molecular detection methods for the identification of these mutations include direct sequencing, restriction fragment length polymorphism analysis, real-time polymerase chain reaction （PCR） with high-resolution melt analysis, and nested PCR-linked with capillary electrophoresis, etc. The most commonly used method for monitoring resistance-conferring mutations in M. pneumoniae is direct DNA sequencing of PCR or nested PCR products. However, these methods are time-consuming, labor-intensive or need expensive equipments. Therefore the development of rapid and sensitive methods is very important for monitoring the resistance globally. Methods In this study, we reported a fast and cost-effective method for detecting 2063 and/or 2064 macrolide resistant mutations from specimens using a modified allele-specific PCR analysis, and all results were compared with the sequencing data. We also analyzed the clinical courses of these samples to confirm the modified allele-specific PCR results. Results Among 97 M. pneumoniae specimens, 88 were found to possess mutations by this method, and all modified allele-specific PCR analysis results were consistent with the sequencing data. The data of the clinical courses of these 97 cases showed that they suffered from severe pneumonia. Erythromycin showed better efficacy on cases from which no macrolide resistance mutation was found on their specimens. However, in some cases from which mutations were detected, erythromycin monotherapy had poor efficacy, and on these patients severe symptoms improved only when azithromycin was added to the treatment. Conclusions The drug-resistant M. pneumoniae is very common in Beijing, China. Our modified allele-specific PCR analysis can identify erythromycin resistant mutations more rapidly from specimens than any other method currently available. Erythromycin is still effective for treating patients infected with the mutation negative M. pneumoniae, but this treatment fails to work on mutant organisms. This method can facilitate clinicians in selecting appropriate therapy within short timescales.

RNA-primed allele-specific PCR

RNA/DNA primer pairs and two polymerases were used to efficiently amplify DNA sequences using the conventional polymerase chain reaction(PCR).The reaction required the use of both DNA polymerase and reverse transcriptase during each thermal cycle and formed a double-stranded DNA in which one terminus was an RNA/DNA hybrid.Because there is a higher sensitivity of the DNA polymerase to the mismatch at the 3?-end in the RNA/DNA hybrid duplex than in the DNA/DNA duplex,the RNA-primed PCR reveals much better specificity in the allele-specific PCR to detect single-nucleotide mutation.

Establish an allele-specific real-time PCR for Leishmania species identification

Background:Leishmaniasis is a serious neglected tropical disease that may lead to life-threatening outcome, which species are closely related to clinical diagnosis and patient management. The current Leishmania species determination method is not appropriate for clinical application. New Leishmania species identification tool is needed using clinical samples directly without isolation and cultivation of parasites.Methods:A probe-based allele-specific real-time PCR assay was established for Leishmania species identification between Leishmania donovani and L. infantum for visceral leishmaniasis (VL) and among L. major, L. tropica and L. donovani/L. infantum for cutaneous leishmaniasis (CL), targeting hypoxanthine-guanine phosphoribosyl transferase (HGPRT) and spermidine synthase (SPDSYN) gene with their species-specific single nucleotide polymorphisms (SNPs). The limit of detection of this assay was evaluated based on 8 repeated tests with intra-assay standard deviation < 0.5 and inter-assay coefficients of variability < 5%. The specificity of this assay was tested with DNA samples obtained from Plasmodium falciparum, Toxoplasma gondii, Brucella melitensis and Orientia tsutsugamushi. Total 42 clinical specimens were used to evaluate the ability of this assay for Leishmania species identification. The phylogenetic tree was constructed using HGPRT and SPDSYN gene fragments to validate the performance of this assay.Results:This new method was able to detect 3 and 12 parasites/reaction for VL and CL respectively, and exhibited no cross-reaction with P. falciparum, T. gondii, B. melitensis, O. tsutsugamushi and non-target species of Leishmania. Twenty-two samples from VL patients were identified as L. donovani (n = 3) and L. infantum (n = 19), and 20 specimens from CL patients were identified as L. major (n = 20), providing an agreement of 100% compared with sequencing results. For further validation, 29 sequences of HGPRT fragment from nine Leishmania species and 22 sequences from VL patients were used for phylogenetic analysis, which agreed with the results of this new method. Similar results were obtained with 43 sequences of SPDSYN fragment from 18 Leishmania species and 20 sequences from CL patients.Conclusions:Our assay provides a rapid and accurate tool for Leishmania species identification which is applicable for species-adapted therapeutic schedule and patient management.

番茄Mi-1基因的SNP分型

SNP分型是SNP分子标记辅助育种,以及分子遗传作图等研究的重要基础技术。试验利用在番茄Mi-1基因中开发出的一个A/T型SNP位点,应用等位基因聚合酶链式反应技术,成功的对438个F2群体进行了SNP分型。结果表明,这一F2群体中有72个纯合T/T基因型,175个杂合A/T基因型,70个纯合A/A基因型,以及121个不明原因缺失的F2单株,已得基因型经卡方测验符合1:2:1分离比例;同时,试验通过在下游引物3′末端第二、三位点引入错配碱基,以及优化PCR反应体系为Mg2+1.875 mmol.L-1,dNTP 100μmol.L-1,提高了反应的准确性,为番茄抗根结线虫辅助育种打下了基础。

番茄抗枯萎病I-2基因的SNP分型

利用直接测序方法检测番茄抗感品种I-2基因的DNA序列,发现了2个SNPs。以其为3′端,设计等位基因特异引物及其互补引物,研究了特异引物3′端碱基错配类型和位置对等位基因特异PCR的影响,并对52份种质资源进行了SNP分型。结果表明在下游引物3′末端第1、2位引入错配碱基可以提高反应的准确性;引入C-T碱基错配的引物,退火温度在58℃时能把I-2基因的突变位点和感病品种的对应位点区分开来,为番茄抗枯萎病辅助育种提供了有力工具。

百日咳鲍特菌23S rRNA位点变异AS-PCR检测方法建立

目的根据allele-specific PCR(AS-PCR)原理,建立具有良好敏感性与特异性的百日咳鲍特菌23S r RNA位点变异检测方法。方法基于百日咳鲍特菌23S r RNA A2047G位点突变与其对红霉素耐药的相关性,设计包含特异变异位点的引物进行两阶段PCR反应,根据电泳有无特异大小目的片段的出现,确定百日咳鲍特菌23S r RNA A2047G位点是否有变异。结果以基因序列测定法为金标准的评价结果显示,AS-PCR法检测突变型菌株的灵敏度为96%(144/150),特异度为100%(100/100),kappa=0.95(P<0.01);检测野生型菌株的灵敏度为100%(18/18),特异度为100%(100/100),kappa=1(P<0.01)。结论 AS-PCR方法检测百日咳鲍特菌23S r RNA A2047G位点变异具有较高灵敏度和特异度,适用于普通微生物实验室开展百日咳鲍特菌对红霉素耐药性的快速检测。

Identification of SNPs in barley(Hordeum vulgare L.)by deep sequencing of six reduced representation libraries

High-density genetic markers are required for genotyping and linkage mapping in identifying genes from crops with complex genomes, such as barley. As the most common variation, single nucleotide polymorphisms(SNPs) are suitable for accurate genotyping by using the next-generation sequencing(NGS) technology. Reduced representation libraries(RRLs) of five barley accessions and one mutant were sequenced using NGS technology for SNP discovery. Twenty million short reads were generated and the proportion of repetitive sequences was reduced by more than 56%. A total of 6061 SNPs were identified, and 451 were mapped to the draft sequence of the barley genome with pairing reads. Eleven SNPs were validated using length polymorphic allele-specific PCR markers.

Creating New Germplasm by Distant Hybridization in Stone Fruits:Ⅱ-Embryo Rescue and Hybrid Identification Between Plum and Apricot

Embryo abortion stage and rescue system of hybrids were studied in the distant hybridizationbetween plum and apricot. Identification of the hybrids was also made. The resultsshowed: (1) Embryo abortion started from three weeks after pollination. (2) The germinationand growth of embryos were different at different growth stages, which could germinateand grow with PF value>0.5, but failed with PF value<0.5. In embryo rescue system ofhybrids, the best germination and differentiation medium was MS+6-BA 2mgL-1+IAA 0.3mgL-1,the rate of germination and differentiation reached up to 80%, bud induction andmultiplication medium was MS+6-BA 1.5mgL-1+IAA 0.3mgL-1, rooting medium was 1/2 MS+IAA0.8mgL-1. Some hybrids were transplanted into the field successfully. (3) Leaf shapeinvestigation and identification by S allele-specific PCR and RAPDs showed that thehybrids were true ones.

Discrimination of mitochondrial DNA 10400 locus by SNP-operated on/off Switch

Objective：To apply reformed AS-PCR, which combined phosphorothioate-modified primers with exo^＋ polymerase, in single nucleotide polymorphism discrimination of mitochondrial DNA 10400 locus. Methods： We used the mtDNA 10400 locus to design unrnodifled and 3 ＇ phosphorothioate-modified allele-specific primers for PCR, which was performed using polymerases with and without 3 ＇ exonuclease activities. The effects of these primers on primer-extension were evaluated by agarose gel electrophoresis. Results： The unmodified primers were extended by both exo and exo^＋ polymerase irrespective of whether the primers were matched or mismatched with the templates. However, the 3＇ phosphorothioate-modified primers with a terminal mismatch triggered an ＂off-switch＂ of exo~ polymerase when compared to exopolymerase. Conclusion： The＂ on/off＇switch constituted by the combination of 3 ＇ phosphorothioatemodified primers with exo^＋ polymerase is a cost-effective, high-throughput and reliable method for SNP typing, which will be of enormous application in association studies by single nucleotide polymorphism screening.

结合多重链置换扩增和等位基因特异性PCR从单细胞中扩增脊髓性肌萎缩症运动神经元生存基因

目的:建立结合多重链置换扩增(multiple displacement amplification,MDA)全基因组扩增法和等位基因特异性PCR(allele-specific PCR,AS-PCR)对单细胞进行脊髓性肌萎缩(spinal muscular atrophy,SMA)诊断的方法。方法:对脊髓性肌萎缩症运动神经元生存基因(survival motor neuron gene1,smn1)7号外显子纯合缺失皮肤成纤维细胞及正常的皮肤成纤维细胞使用MDA法进行全基因组扩增,使用AS-PCR检测扩增产物的smn1和smn2基因,同时扩增D5S435、D5S351这2个微卫星位点,评估扩增效率、等位基因脱扣(allele dropout,ADO)率及污染检测。结果:对18个SMA细胞和21个smn1基因正常的细胞进行扩增。smn1和smn2基因扩增成功率分别为90.4%(19/21)和94.8%(37/39)。2个微卫星的扩增成功率为82.1%(32/39)和88.9%(16/18),ADO率分别为16.22%(6/37)和12.5%(2/16)。总扩增成功率为88.89%(104/117),总ADO率为15.09%(8/53)。结论:建立了结合MDA和等位基因特异性PCR对单个细胞进行smn1、smn2基因的扩增方法,为SMA单细胞植入前诊断奠定了基础。

猪IGF-1R基因启动子区单核苷酸多态性检测分析

本试验对猪混合基因池中胰岛素样生长因子-1受体基因(IGF-1R)启动子区进行克隆并测序,筛查不同猪种间的突变位点并对其转录因子结合位点进行预测。采用AS-PCR方法,对巴马香猪、西藏小型猪、军牧1号白猪、东北野猪和大白猪5个品种猪的IGF-1R启动子区进行了单核苷酸多态性分析。结果表明该基因启动子区上存在2个SNPs位点(G-1 440C,C-1 165T),但均未引起转录因子结合位点的变化。在G-1 440C位点,5个猪种出现3种基因型,分别为GG,GC,CC,其中巴马香猪的等位基因频率G%=C%,其余4个猪种优势等位基因为G;在C-1 165T处,存在CC,CT,TT 3种基因型,西藏小型猪的优势等位基因为T,其余4个猪种优势等位基因为C。2个突变位点的基因型分布差异极显著(P<0.01)。

花生AhFAD2的基因型与O/L值的相关性分析

花生(Arachis hypogaea L.)高油酸性状受2对同源非等位隐性基因ol1和ol2调控,分别编码Ah FAD2A和Ah FAD2B。本研究利用红外无损检测技术分析不同花生品种的油酸、亚油酸及粗脂肪含量,并设计等位基因特异引物,对不同油亚比值的12个花生品种进行AS-PCR检测分析。结果表明:对12个花生基因型均能准确分析出Ah FAD2基因型,其中1514、606、9102、614和1474的基因型为OL1OL1OL2OL2,其相应的O/L值位于0.971~1.759;花17、1513、1476和1586的基因型是ol1ol1/OL2OL2,其相应的O/L值位于2.252~3.679;1504、1505和1515的基因型为ol1ol1ol2ol2,其相应的O/L值位于8.204~12.79。综合12个花生品系籽粒O/L值和Ah FAD2基因型的相关性结果表明,基因型的改变直接导致O/L值的变化,但与含油量无特定相关性。