基于锁核酸及等位位点特异性扩增技术的KRAS基因突变检测荧光定量PCR方法研究

基于等位位点特异性扩增的原理,设计锁核酸修饰KRAS基因突变特异性扩增引物,结合封阻探针技术,建立检测KRAS基因突变的荧光定量PCR方法。结果发现,锁核酸修饰的引物及探针可显著提高等位位点特异性扩增技术用于复杂样本中的微量基因突变检测的敏感度,该技术检测KRAS基因突变的敏感性可达0.01%~0.1%。进一步用建立的荧光定量PCR方法检测52例结直肠癌患者血浆标本,并用DNA测序法作为对照,同时用健康人血浆标本建立阴性检测结果判读标准,以初步评价该方法应用于循环DNA中KRAS基因突变检测的可行性。结果发现结直肠癌患者KRAS基因突变主要是G12C、G12A和G12R,而且q PCR法的阳性检出率为46.15%,高于DNA测序法(13.46%),阴性结果与DNA测序法的符合率为100%。此外,结直肠癌患者外周血KRAS基因的突变检出率与文献报道组织标本中的突变检出率及常见突变类型基本相符。上述结果说明该方法检测循环肿瘤DNA(circulating tumor DNA,ct DNA)具有较高的可靠性,可以用于肿瘤患者循环血液中KRAS基因突变的检测。     

荧光定量PCR精确检测人胚胎干细胞线粒体DNA拷贝数方法的建立

建立一种精确定量人胚胎干细胞线粒体DNA拷贝数的方法。构建包含线粒体DNANDl和核单拷贝基β-globin基因序列的重组质粒作为标准品;收集无饲养层培养体系下人胚胎干细胞DNA样本,结合2个单独的Taqman探针实时荧光定量PCR对待测样本中线粒体NDl和核β-globin基因分别进行定量,从而对人胚胎干细胞线粒体DNA的含量进行了精确定量。结果提示,人胚胎干细胞线粒体DNA的平均拷贝数／细胞为1321±228。研究表明,该技术可对人胚胎干细胞线粒体DNA拷贝数进行准确的测定,为研究培养条件对人胚胎干细胞线粒体DNA拷贝数的影响及优化体外培养条件奠定了基础。     

MELAS和MERRF综合征相关mtDNA突变位点检测集成芯片的建立

摘要: 文中建立了一种新型的寡核苷酸芯片, 用于线粒体脑肌病伴高乳酸血症和卒中样发作(Mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes, MELAS)和肌阵挛性癫痫伴发不规整红纤维(Myoclonic epilepsy with ragged red fibers, MERRF)线粒体DNA所有已知突变位点的集成检测。将31对allele位点特异性的寡核苷酸探针包被在醛基修饰的载玻片表面, 以多重不对称PCR方法制备Cy5荧光标记靶基因。利用此芯片对5例MELAS患者、5例MERRF患者及20例健康对照进行筛查, 结果发现, MELAS患者均为MT-T1基因A3243G突变; 在MERRF患者组, MT-TK基因A8344G突变4例, T8356C突变1例; 健康对照组均未发现31种相关mtDNA突变。芯片检测与DNA测序结果完全一致。结果表明, 这种寡核苷酸芯片可以对MELAS和MERRF综合征已知突变位点进行同步快速检测, 具有较高的灵敏度和特异性。这一模式的基因芯片经过适当改装后也可用于其他人类线粒体疾病的基因诊断。     

支原体检测多重定量PCR方法的建立及应用

目的:建立一种快速、准确的方法检测支原体,这不仅可以有效地减少和预防支原体污染,还能为科研工作者提供一定的指导价值。方法:利用荧光定量PCR(TaqMan探针法)检测支原体,反应体系中同时存在标记两种颜色TaqMan探针及相关引物,分别检测支原体DNA和参考基因模板。根据支原体16S核糖体RNA保守区和参考基因TOP3A保守区设计引物和探针。通过对引物浓度、探针浓度和退火温度等反应条件的优化,建立了TaqMan探针多重定量PCR方法,并对该方法的特异性、敏感性和重复性进行了验证。结果:建立的双色荧光探针定量PCR方法的标准曲线相关系数r2和扩增效率分别为0.995和113.36%;该方法最低检测限为10 copies/μL;组内及组间变异系数均小于1%,证明该检测方法高效。利用该方法对随机挑选90例细胞抽提DNA样本进行检测,结果有60例为支原体阳性样本,阳性率67%,阳性率与相关研究报道一致。检测3个细胞培养上清样本,结果 1例支原体阳性,2例支原体阴性。从检测的样本中随机选择3个阳性样本及2个阴性样本使用普通PCR支原体检测试剂盒检测,结果一致;将其测序,测序结果比对正确。结论:本研究建立的多重定量PCR支原体检测方法能够应用于细胞抽提DNA及细胞培养上清的支原体检测,可以实现高效、快速检测支原体污染。     

一个2型糖尿病家系中新发现的线粒体DNA G7444A 突变分析

应用PCR-RFLP和测序对一个2型糖尿病家系的线粒体DNA G7444A的突变进行检测, 并分析其临床资料的特点。结果发现, 27例家系成员中, 11例母系亲属均存在线粒体DNA G7444A突变, 而配偶及父系亲属中未发现该突变。11例突变者中确诊为2型糖尿病患者5例, 糖耐量受损1例, 均表现为乳酸和血糖增高。因此, 线粒体DNA G7444A突变是该家系中糖尿病的遗传易感因素, 是导致2型糖尿病的一个新的突变位点。     

应用LNA-PCR法检测乙型肝炎病毒阿德福韦酯耐药位点基因突变

目的:建立简便、快速、灵敏的锁核酸(locked nucleic acid,LNA)探针实时荧光聚合酶链反应(PCR)检测方法,检测乙型肝炎病毒(hepatitis B virus,HBV)阿德福韦酯(Adefovir dipivoxil,ADV)耐药相关位点(rtA181V、rtN236T)突变。方法:通过基因测序筛选阳性样本,进而构建ADV rt181和rt236位点野生株和突变株重组质粒,设计包含扩增阿德福韦酯rtA181V和rtN236T耐药位点在内的特异性引物和LNA荧光探针,以构建的重组质粒为标准品建立实时荧光PCR反应体系,并通过与基因测序平行检测血清样本以判断检测方法的可行性与准确性。结果:所建立的LNA-PCR法能够检测102copies/ml的HBV中ADV基因突变,同时具备较高的特异性。通过对89例ADV治疗一年后HBV阳性临床样本进行检测,有8例(8.98%)rtA181V突变、5例(5.61%)rtN236T突变、2例(2.24%)rtA181V和rtN236T混合突变,检测结果与测序结果一致。结论:所建立的LNA-PCR法是一种简便、快速、灵敏的基因突变检测方法,能有效的区分单碱基突变,对慢性乙型肝炎患者德福韦治疗过程中耐药突变的监控和抗病毒药物的调整具有指导意义。     

肝癌患者体内乙型肝炎病毒基因组BCP/Pre C区基因突变多样性分析

为研究肝癌患者组织样本中HBV DNA核心启动子区(BCP区)和前C区(Pre C区)的基因突变多样性及其突变规律。收集第四军医大学附属西京医院2015年收治的192例HBV阳性的肝癌患者组织样本,PCR扩增HBV BCP/Pre C区DNA片段并进行测序分析,从测序失败的样本中随机抽取21例,采用构建单克隆文库后测序的方法进行分析。结果显示37.89%(72/190)的HBV阳性肝癌患者体内HBV病毒因呈现多种突变株混合感染的特点而导致PCR产物直接测序失败,经单克隆测序揭示,每一例失败样本的HBV DNA准种池中至少有2~11种突变株共同存在;突变株中缺失突变和插入突变的发生率高达80.95%;其它突变形式按照频率从高到低分别为A1762T/G1764A双突变90.48%,G1756C/T1803A/Δ(1 757~1 765)/Δ(1 824~1 832)四联突变80.95%,T1753C/A1762T/G1764A三联突变57.14%,A1762T/G1764A/G1896A三联突变42.86%,G1756C/Δ(1 757~1 765)双突变28.57%,T1753C/A1762T/G1764A/G1896A四联突变23.81%。由此可见,肝癌患者体内HBV病毒具有BCP/Pre C区DNA突变的多样性,这些缺失与插入突变是导致序列移码与PCR产物测序失败的直接原因。研究结果为HBV持续感染及基因突变检测、相关机制研究和个体化防治奠定了基础。     

实时荧光PCR法检测肉制品中鸡、鸭源性成分

根据鸡、鸭线粒体DNA(mt DNA)序列设计了鸡、鸭特异性引物及Taqman探针,建立了肉制品中鸡、鸭源性成分的实时荧光聚合酶链式(real-time PCR)检测方法。结果发现:利用此方法,两种动物源性的最低检出限值(质量分数)分别为0.01%和0.001%。实时荧光PCR法能够作为肉制品中检测鸡、鸭源性成分的有效方法。     

肝癌患者体内乙型肝炎病毒基因组BCP/Pre C区基因突变多样性分析北大核心CSCD

为研究肝癌患者组织样本中HBV DNA核心启动子区(BCP区)和前C区(Pre C区)的基因突变多样性及其突变规律。收集第四军医大学附属西京医院2015年收治的192例HBV阳性的肝癌患者组织样本,PCR扩增HBV BCP/Pre C区DNA片段并进行测序分析,从测序失败的样本中随机抽取21例,采用构建单克隆文库后测序的方法进行分析。结果显示37.89%(72/190)的HBV阳性肝癌患者体内HBV病毒因呈现多种突变株混合感染的特点而导致PCR产物直接测序失败,经单克隆测序揭示,每一例失败样本的HBV DNA准种池中至少有2~11种突变株共同存在;突变株中缺失突变和插入突变的发生率高达80.95%;其它突变形式按照频率从高到低分别为A1762T/G1764A双突变90.48%,G1756C/T1803A/Δ(1 757~1 765)/Δ(1 824~1 832)四联突变80.95%,T1753C/A1762T/G1764A三联突变57.14%,A1762T/G1764A/G1896A三联突变42.86%,G1756C/Δ(1 757~1 765)双突变28.57%,T1753C/A1762T/G1764A/G1896A四联突变23.81%。由此可见,肝癌患者体内HBV病毒具有BCP/Pre C区DNA突变的多样性,这些缺失与插入突变是导致序列移码与PCR产物测序失败的直接原因。研究结果为HBV持续感染及基因突变检测、相关机制研究和个体化防治奠定了基础。     

应用基因芯片技术检测非综合征型耳聋基因突变

目的:应用遗传性耳聋基因芯片对散发性聋患者进行分子病因学检测,评估其在遗传性耳聋快速基因诊断中的可靠性。方法:门诊收集散发性聋患者10例,取外周血,提取基因组DNA,用遗传性耳聋基因芯片检测4个中国人中常见的耳聋相关基因中的9个热点突变,包括GJB2(35delG、176del16bp、235delC及299delAT)、GJB3(C538T)、SLC26A4(IVS7-2AG、A2168G)和线粒体DNA 12S rRNA(A1555G、C1494T)。同时,PCR扩增GJB2、线粒体12S rRNA基因全序列,DNA测序,以验证基因芯片检测结果的准确性。结果:在10名耳聋患者中,基因芯片方法检出1例携带线粒体DNA 12S rRNA C1494T突变;2例GJB2基因235delC纯合突变;2例235delC杂合突变;SLC26A4基因和GJB3基因未检出突变。基因芯片的结果与测序结果完全一致。结论:遗传性耳聋基因芯片技术对中国人常见耳聋相关基因热点突变的检出率高,结果准确、可靠,具有快速、高通量、高准确性、低成本等特点,能够满足临床耳聋基因检测的要求,同时结合产前诊断技术能有效预防耳聋患儿的出生,因而具有广阔的临床应用前景。     

The A1555G mitochondrial DNA mutation in Greek patients with non-syndromic, sensorineural hearing loss

Mitochondrial DNA mutations are undoubtedly a factor that contributes to sensorineural, non-syndromic deafness. One specific mutation, the A1555G, is associated with both aminoglycoside-induced and non-syndromic hearing impairment. The mutation is considered to be the most common of all mitochondrial DNA deafness-causing mutations but its frequency varies between different populations. Here we report on the first large screening of the A1555G mitochondrial DNA mutation in the Greek population. The aim of this study was to determine the frequency of the A1555G mutation in Greek sensorineural, non-syndromic deafness patients, with childhood onset. We screened 478 unrelated Greek patients with hearing loss of any degree and found two individuals harboring the A1555G mutation (0.42%). Both cases had been subjected to aminoglycosides. They were prelingual, familial and homoplasmic for the A1555G mutation. One of the cases was also found heterozygous for the frequent GJB2 35delG mutation, while the other case was negative. The A1555G mutation seems to be less common than in other European populations.     

Cochlear alterations in deaf and unaffected subjects carrying the deafness-associated A1555G mutation in the mitochondrial 12S rRNA gene

The A1555G mutation in the mitochondrial small ribosomal RNA gene (12S rRNA) has been associated with aminoglycoside-induced, nonsyndromic hearing loss. However, the clinical phenotype of A1555G carriers is extremely variable. In the present study, we have performed an audiological evaluation of a group of deaf patients and hearing carriers of mutation A1555G with the aim to assess the prevalence of the mutation and determine the associated cochlear alterations. Fifty-four patients affected of nonsyndromic hearing loss were screened for the presence of the A1555G mitochondrial mutation. Nine of the familial cases (21%) carried the A1555G mutation, whereas the mutation was not found in any of the sporadic cases. The positive cases and some of their family members underwent a clinical study consisting in a clinical evaluation and audiological testing. The phenotype of A1555G patients varied in age of onset and severity of hearing loss, ranging from profound deafness to completely normal hearing. The audiometric alterations showed bilateral hearing loss, being more severe at high frequencies. Otoacoustic emissions were absent in deaf A1555G carriers, and auditory brainstem response indicated a prolonged Wave I, suggesting a cochlear dysfunction without any effect of the auditory nerve. Moreover, all hearing carriers of A1555G also presented alterations in cochlear physiology. In conclusion, the A1555G mitochondrial mutation causes a cochlear form of deafness, characterized by a more severe loss of hearing at high frequencies. Although the expression of the mutation is variable, cochlear alterations are present in all carriers of mutation A1555G.     

Investigation of the A1555G mutation in mitochondrial DNA (MT-RNR1) in groups of Brazilian individuals with nonsyndromic deafness and normal-hearing

BACKGROUND:

Mutations of mitochondrial DNA were described into two genes: The mitochondrially encoded 12S RNA (MT-RNR1) and the mitochondrially encoded tRNA serine^ucn (MT-TS1). The A1555G mutation in MT-RNR1 gene is a frequent cause of deafness in different countries.

AIM:

The aim of this work was to investigate the frequency of the A1555G mutation in the MT-RNR1 gene in the mitochondrial DNA in Brazilians individuals with nonsyndromic deafness, and listeners.

MATERIALS AND METHODS:

DNA samples were submitted to polymerase chain reaction and to posterior digestion with the Hae III enzyme.

RESULTS:

Seventy eight (78) DNA samples of deaf individuals were analyzed; 75 showed normality in the region investigated, two samples (2.5%) showed the T1291C substitution, which is not related to the cause of deafness, and one sample (1.3%) showed the A1555G mutation. Among the 70 non-impaired individuals no A1555G mutation or T1291C substitution was found.

CONCLUSION:

We can affirm that A1555G mutation is not prevalent, or it must be very rare in normal-hearing subjects in the State of Paraná, the south region of Brazil. The A1555G mutation frequency (1.3%) found in individual with nonsyndromic deafness is similar to those found in other populations, with nonsyndromic deafness. Consequently, it should be examined in deafness diagnosis. The investigation of the A1555G mutation can contribute towards the determination of the nonsyndromic deafness etiology, hence, contributing to the correct genetic counseling process.     

Candidate locus for a nuclear modifier gene for maternally inherited deafness

Maternally inherited deafness associated with the A1555G mutation in the mitochondrial 12S ribosomal RNA (rRNA) gene appears to require additional environmental or genetic changes for phenotypic expression. Aminoglycosides have been identified as one such environmental factor. In one large Arab-Israeli pedigree with congenital hearing loss in some of the family members with the A1555G mutation and with no exposure to aminoglycosides, biochemical evidence has suggested the role of nuclear modifier gene(s), but a genomewide search has indicated the absence of a single major locus having such an effect. Thus it has been concluded that the penetrance of the mitochondrial mutation appears to depend on additive effects of several nuclear genes. We have now investigated 10 multiplex Spanish and Italian families with 35 members with the A1555G mutation and sensorineural deafness. Parametric analysis of a genomewide screen again failed to identify significant evidence for linkage to a single autosomal locus. However, nonparametric analysis supported the role of the chromosomal region around marker D8S277. The combined maximized allele-sharing LOD score of 3.1 in Arab-Israeli/Spanish/Italian families represents a highly suggestive linkage result. We suggest that this region should be considered a candidate for containing the first human nuclear modifier gene for a mitochondrial DNA disorder. The locus operates in Arab-Israeli, Spanish, and Italian families, resulting in the deafness phenotype on a background of the mitochondrial A1555G mutation. No obvious candidate genes are located in this region.     

Multiple Origins of a Mitochondrial Mutation Conferring Deafness

A point mutation (1555G) in the smaller ribosomal subunit of the mitochondrial DNA (mtDNA) has been associated with maternally inherited traits of hypersensitivity to streptomycin and sensorineural deafness in a number of families from China, Japan, Israel, and Africa. To determine whether this distribution was the result of a single or multiple mutational events, we carried out genetic distance analysis and phylogenetic analysis of 10 independent mtDNA D-loop sequences from Africa and Asia. The mtDNA sequence diversity was high (2.21%). Phylogenetic analysis assigned 1555G-bearing haplotypes at very divergent points in the human mtDNA evolutionary tree, and the 1555G mutations occur in many cases on race-specific mtDNA haplotypes, both facts are inconsistent with a recent introgression of the mutation into these races. The simplest interpretation of the available data is that there have been multiple origins of the 1555G mutation. The genetic distance among mtDNAs bearing the pathogenic 1555G mutation is much larger than among mtDNAs bearing either evolutionarily neutral or weakly deleterious nucleotide substitutions (such as the 4336G mutation). These results are consistent with the view that pathogenic mtDNA haplotypes such as 1555G arise on disparate mtDNA lineages which because of negative natural selection leave relatively few related descendants. The co-existence of the same mutation with deafness in individuals with very different nuclear and mitochondrial genetic backgrounds confirms the pathogenicity of the 1555G mutation.     

线粒体DNA G7444A突变可能影响A1555G突变的表型表达

线粒体12S rRNA和tRNASer(UCN) 基因是导致非综合征型听力损失的两个突变热点区域。作者收集了1个母系遗传感音神经性聋家系, 该家系同时携带线粒体DNA (mtDNA) A1555G和G7444A突变。临床资料分析表明, 该家系包括药物致聋的耳聋外显率(所有耳聋患者/所有母系成员)为58%, 而非药物致聋的耳聋外显率(非药物性聋患者/所有母系成员)为25%, 明显高于其他携带A1555G突变的耳聋家系。先证者的线粒体全序列分析表明, 该线粒体基因组共有28个多态位点, 属于东亚人群B4c1单体型。在这些多态位点中, 除A1555G和G7444A突变外, 未发现其他有功能意义的突变。这表明mtDNA G7444A突变可能加重由A1555G突变造成的线粒体功能缺失, 从而增加耳聋的外显率。     

Myelocystocele-cloacal exstrophy in a pedigree with a mitochondrial 12S rRNA mutation, aminoglycoside-induced deafness, pigmentary disturbances, and spinal anomalies

A large Filipino-American family with progressive matrilineal hearing loss, premature graying, depigmented patches, and digital anomalies was ascertained through a survey of a spina bifida clinic for neural crest disorders. Deafness followed a matrilineal pattern of inheritance and was associated with the A1555G mutation in the 12S rRNA gene (MTRNR1) in affected individuals as well as unaffected maternal relatives. Several other malformations were found in carriers of the mutation. The proband had a myelocystocele, Arnold-Chiari type I malformation, cloacal exstrophy, and severe early-onset hearing loss. Several family members had premature graying, white forelock, congenital leukoderma with or without telecanthus, somewhat suggestive of a Waardenburg syndrome variant. In addition to the patient with myelocystocele, two individuals had scoliosis and one had segmentation defects of spinal vertebrae. The syndromic characteristics reported here are novel for the mitochondrial A1555G substitution, and may result from dysfunction of mitochondrial genes during early development. However, the mitochondrial A1555G mutation is only rarely associated with neural tube defects as it was not found in a screen of 218 additional individuals with spina bifida, four of whom had congenital hearing loss.     

Mitochondrial 12S rRNA gene mutations affect RNA secondary structure and lead to variable penetrance in hearing impairment

Mutations in the mitochondrial DNA are one of the most important causes of sensorineural hearing loss, especially in the 12S ribosomal RNA (rRNA) gene. We have analyzed the mtDNA 12S rRNA gene in a cohort of 443 families with hearing impairment, and have identified the A1555G mutation in 69 unrelated cases. A1555G is not a fully penetrant change, since only 63% of subjects with this change have developed hearing impairment. In addition, only 22% of the 183 A1555G deaf subjects were treated with aminoglycosides. Two novel nucleotide changes (T1291C and T1243C) were identified. T1243C was found in five deafness cases and one control sample. Mutation T1291C was detected in all maternally related individuals of a pedigree and in none of 95 control samples. Conservation analysis and comparison of the 12S rRNA structure with the 16S rRNA of Escherichia coli showed that the T at nucleotide 1243 and A at nucleotide 1555 are conserved positions. Prediction of RNA secondary structure showed changes in all 12S rRNA variants, the most severe being for T1291C. The reported data confirm the high prevalence of mutation A1555G in deafness cases and the major role of the 12S rRNA gene in hearing. The two novel changes reported here might have different contributions as deafness-related variants. T1291C fulfills the criteria of a disease-causing change. As in the case of mutation A1555G, the underlying phenotype of T1291C is not homogeneous for all family members, providing evidence for the implication of environmental and/or additional genetic factors.     

一个母系遗传非综合征耳聋大家系mtDNA序列分析

通过分析本家mtDNA序列,探讨淮阴一非综合耳聋大家患病的分子遗传学机制。采用聚合酶链反应（PCR）扩增mtDNA与非综合征耳聋相关位点nt1555,nt7445的区域和人类种群研究的D－loop区,PCR－异源双链分析,PCR－RFLP、PCR产物克隆序列测定等技术对该家系进行了系统的研究。发现该家系中全部母系亲属有mtDNAA1555G突变,而家系中非母 个体,对照组（100例正常个体）的mtDNA1555位点均为A。该家系mtDNA7445位点无突变;该系属于Ⅱ型线性体;发现家系D－loop区存在未见报道的碱基插入。提示mtDNAA1555G位点突变可能是导致该家系患致聋的主要因素之一。遗传背景可能对家系疾病的表现存在一定程度的影响。     

Screening of common mitochondrial mutations in Chinese patients with mitochondrial encephalomyopathies

To investigate the spectrum of common mitochondrial mutations in Northern China during the years of 2000-2005, 552 patients of mitochondrial encephalomyopathies clinically diagnosed as MELAS, MERRF or Leigh's syndrome, 14 cases of LHON and 46 cases of aminoglycoside induced deafness along with their family members, accepted routine point mutation tests at nucleotide positions 3243, 8344, 8993, 11778 or 1555 in mitochondrial genome. PCR-RFLP analysis, site-specific PCR and PCR-sequencing methods were used to identify the mutations. Fifty-seven cases with A3243G mutation, 4 cases with A8344G, 2 cases with T8993C and 1 case with T8993G were identified from the 552 encephalomyopathy patients. In addition, one case with G11778A was found from the 14 cases of LHON, and 5 cases with A1555G from the 46 cases of aminoglycoside ototoxicity patients. Additional screening for T8356G and T3271C merely had limited significance for the diagnosis of MERRF and MELAS. Differential diagnosis among mitochondrial encephalomyopathies was often complicated due to many similar clinical manifestations. For A3243G mutation, the proportion of mutant mtDNA was not related to severity of the disease but to the age of onset.