定量多重PCR-高效液相色谱分析错配修复基因大片段缺失

目的 建立一种以多重PCR-高效液相色谱(high performance liquid chromatography，HPLC)分析为基础的错配修复基因DNA大片段缺失检测技术。方法 设计合成35对引物，分8个多重PCR反应扩增MSH2和MLHl基因的35个外显子，PCR产物经高效液相色谱半定量分析，确定各外显子拷贝数。(1)双盲法分析阴性和阳性对照样本，完成方法学可靠性检验。(2)分析14例遗传性非息肉性大肠癌患者外周血细胞DNA和13例散发性大肠癌患者癌组织细胞DNA样本，筛查MSH2和．MLHl基因DNA大片段缺失。结果 (1)稳定检出阳性对照样本的DNA大片段缺失；(2)在筛查样本检出2例新的MSH2基因DNA大片段缺失，分别为MSH2基因外显子7遗传性缺失和MSH2基因外显子1～6体细胞性缺失。结论 多重PCR—HPLC分析系统可以作为突变基因分析系统的一个重要补充，在基因DNA大片段缺失检测中发挥作用。     

应用多重PCR-变性高效液相色谱技术检测大片段重复或缺失突变

目的 探讨多重PCR-变性高效液相色谱(PCR-denature high performance liquid chromatography,PCR-DHPLC)技术在假肥大型肌营养不良症和脊肌萎缩症外显子拷贝数异常检测中的应用价值.方法 应用多重PCR-DHPLC方法筛查35例假肥大型肌营养不良症患者和6例脊肌萎缩症患者.选择阳性对照和阴性对照进行方法学可靠性检验.结果 多重PCR-DHPLC可完全检测出全部阳性对照中重复或缺失片段.35例假肥大型肌营养不良症样本中检测出5例大片段重复,20例大片段缺失,突变检出率为71.4%.6例脊肌萎缩症患者均检测到第7外显子缺失.结论 多重PCR-DHPLC分析系统可作为有效筛查大片段重复或缺失突变的检测方法.     

中国人家族性结直肠癌错配修复基因大片段变异分析

目的分析中国人家庭性结直肠癌错配修复基因大片段变异的特点。方法 采用多重连接探针扩增技术，分析32例具有家庭史结直肠癌、20例散发性结直肠癌患者错配修复基因MSH2的16个外显子、MLH1的19个外显子及7个其它基因外显子的拷贝数。研究工作包括：（1）双盲法分析阴性和阳性对照样本，完成方法学可靠性检验；（2）分析结直肠癌患者外周血细胞DNA，筛查MSH2和MLH1基因大片段变异。结果 多重连接探针扩增技术分析系统稳定检出阳性对照样本的DNA大片段缺失；在3/32（9.4%）具有家庭聚集性结直肠癌患者中检出遗传性MSH2基因DNA大片段缺失。而在20例散发性结直肠癌患者未检出这类突变。结论 中国人家族性结直肠癌患者中错配修复基因的大片段变异是频发事件，对此类患者的遗传检测应包含错配修复基因大片段变异的筛查。     

PINK1基因外显子拷贝数分析方法的建立及应用

目的 建立PINK1(PTEN-induced kinase 1)基因外显子拷贝数分析方法 ,并应用该方法 分析常染色体隐性遗传性早发型帕金森综合征(autosomal recessive early onset Parkinsonism,AREP)PINK1基因拷贝数变异(copy-number variation,CNV)的特点.方法 应用实时荧光定量聚合酶链反应(polymerase chain reaction,PCR)技术分析方法 ,对30个正常对照和22个中国AREP汉族家系先证者的PINK1基因进行外显子拷贝数分析.结果 应用实时荧光定量PCR技术完成了PINK1基因第1～8外显子拷贝数分析,获得了扩增效率和特异性均满意的反应条件及各外显子引物.所检测的AREP先证者未发现PINK1基因的外显子拷贝数变异.结论 建立了PINK1基因外显子拷贝数分析方法 .中国人AREP患者PINK1基因外显子拷贝数变异可能罕见.     

PINK1基因外显子拷贝数分析方法的建立及应用

目的 建立PINK1(PTEN-induced kinase 1)基因外显子拷贝数分析方法 ,并应用该方法 分析常染色体隐性遗传性早发型帕金森综合征(autosomal recessive early onset Parkinsonism,AREP)PINK1基因拷贝数变异(copy-number variation,CNV)的特点.方法 应用实时荧光定量聚合酶链反应(polymerase chain reaction,PCR)技术分析方法 ,对30个正常对照和22个中国AREP汉族家系先证者的PINK1基因进行外显子拷贝数分析.结果 应用实时荧光定量PCR技术完成了PINK1基因第1～8外显子拷贝数分析,获得了扩增效率和特异性均满意的反应条件及各外显子引物.所检测的AREP先证者未发现PINK1基因的外显子拷贝数变异.结论 建立了PINK1基因外显子拷贝数分析方法 .中国人AREP患者PINK1基因外显子拷贝数变异可能罕见.     

PINK1基因外显子拷贝数分析方法的建立及应用

目的 建立PINK1(PTEN-induced kinase 1)基因外显子拷贝数分析方法 ,并应用该方法 分析常染色体隐性遗传性早发型帕金森综合征(autosomal recessive early onset Parkinsonism,AREP)PINK1基因拷贝数变异(copy-number variation,CNV)的特点.方法 应用实时荧光定量聚合酶链反应(polymerase chain reaction,PCR)技术分析方法 ,对30个正常对照和22个中国AREP汉族家系先证者的PINK1基因进行外显子拷贝数分析.结果 应用实时荧光定量PCR技术完成了PINK1基因第1～8外显子拷贝数分析,获得了扩增效率和特异性均满意的反应条件及各外显子引物.所检测的AREP先证者未发现PINK1基因的外显子拷贝数变异.结论 建立了PINK1基因外显子拷贝数分析方法 .中国人AREP患者PINK1基因外显子拷贝数变异可能罕见.     

小头畸形-骨发育不良-原基性侏儒症Ⅱ型家系的临床及遗传学分析

目的 小头畸形-骨发育不良-原基性侏儒症Ⅱ型（MOPDⅡ）罕见病家系的中心粒周蛋白基因（PCNT）新发变异的鉴定,以及流产胚胎的PCNT基因突变筛查。方法 对两名MOPDⅡ疑似患儿及其父母进行全外显子测序（WES）的家系分析,并通过一代测序和实时荧光相对定量PCR验证。同时,对流产组织进行全外显子测序分析以筛查PCNT基因的突变情况。结果 通过全外显子测序发现先证者及其弟弟的PCNT基因外显子34存在c.7469＿7472del杂合突变,以及17～21号外显子杂合缺失。经过父母的验证,c.7469＿7472del缺失遗传自父亲,17～21号外显子缺失遗传自母亲。对30例流产组织进行筛查,发现有4例突变,其中有3例为杂合突变且均为新的突变位点,1例为复合杂合突变。结论 在先证者及家系中发现了一个新的插入缺失突变（InDel）变异和一个新的拷贝数变异（CNV）,复合杂合突变是导致MOPDⅡ发生的主要原因。对流产组织的检测,进一步揭示了PCNT基因突变在流产患儿中的携带率。     

644例肺癌中HER-220外显子插入突变阳性率及临床病理分析

目的探讨肺癌中HER-2 20外显子插入突变的阳性率,分析其与临床病理特征的相关性。方法采用荧光定量PCR法检测644例肺癌标本中HER-2 20外显子插入、EGFR、ALK、MET、ROS1、BRAF、KRAS、NRAS和PIK3CA基因状态。采用免疫组化法检测HER-2 20外显子插入阳性肺癌标本中PD-L1的表达,分析HER-2 20外显子插入与肺癌患者年龄、性别、分期、分化程度等的相关性。结果肺癌中HER-2 20外显子插入突变的阳性率为4.97%(32/644),且均为腺癌,HER-2 20外显子插入突变与患者年龄、性别、分化程度及分期均相关。HER-2 20外显子插入突变肺癌患者PD-L1阳性率为50%(9/18)。结论利用荧光定量PCR法检测肺癌标本中HER-2 20插入突变,可能对未来临床指导肺癌精准靶向治疗有积极作用。     

RB1基因突变的筛查技术和发病风险评估

RB1基因早已被确认为视网膜母细胞瘤的唯一致病基因,也是人类第一个被分离的肿瘤抑制基因。视网膜母细胞瘤（RB）是婴幼儿最常见的眼科肿瘤,也是一种致死性肿瘤。RB1基因的突变检测,对RB患者及家系成员的分子诊断、筛查、产前诊断、植入前遗传学诊断及早期治疗均具有重要意义。迄今为止,RB1基因中所发现的突变类型包括点突变、缺失、插入、易位、剪接突变以及各种复杂突变,几乎遍布基因的启动子和27个外显子,甚至还有部分内含子突变。但RB1基因不存在突变热点,这大大增加了RB1基因突变筛查的难度。RB1基因的突变不仅存在于视网膜母细胞瘤患者中,而且见于许多恶性肿瘤。本文对RB1基因突变筛查技术和发病风险评估的最新研究进展作一简单综述。     

Direct genomic multiplex PCR for BRCA1 and application to mutation detection by single-strand conformation and heteroduplex analysis

Most mutation detection methods are based on analysis of PCR amplified segments and the application of multiplex PCR is one central approach to improving screening efficiency. Genes like the breast-ovarian cancer susceptibility gene BRCA1 pose a difficult challenge to efficient mutation screening because of large coding regions, numerous exons, and complex mutational spectra. The application to BRCA1 of a general approach to effective multiplex PCR is described here. Fifteen triplex PCRs and a single PCR reaction condition were used for amplification of all BRCA1 coding regions and the BRCA1-specific segments from the duplicated promoter region. SSCP/HDX gel analysis of the multiplex products detected mobility distinctions for 34/34 sets of allelic BRCA1 fragments. A novel polymorphism was found, CTTCT(4)CT(10)CT(12) >CT(4)CT(11), a compound deletion in a region beginning at the +33 position of IVS7 and resulting in a net deletion of 15 bp. This change was shown to be one of the common polymorphisms that define the two major haplotypes of the BRCA1-RNU2 region in a large proportion of the world population. A triplex PCR for SSCP detection of this deletion and two other distantly located common polymorphisms may be used to screen haplotype content and facilitate comparison of samples with similar haplotypes in subsequent mutation screening. The approach for robust multiplex amplification is generally applicable and allows rapid development of efficient testing for a wide variety of mutations in any gene(s) encompassing a large coding region or numerous exons and including as many as 50 different genomic PCR products.     

Rapid detection by fluorescent multiplex PCR of exon deletions and duplications in the C1 inhibitor gene of hereditary angioedema patients

Hereditary angioedema (HAE) is due to a variety of defects in the C1 inhibitor gene (C1NH gene), including approximately 20% of partial deletions/duplications whose boundaries are usually within Alu repeats. To ensure complete molecular characterization of C1 inhibitor deficiencies a fluorescent multiplex assay was constructed to amplify simultaneously five exons of C1NH and an exon of the BRCA1 gene. PCR protocols were optimized for these amplicons (size range between 300 and 700 bp). Forward and reverse chimeric primers that carry strand-specific 5' tags of 16 nucleotides were used to ensure similar levels of PCR products for each amplicon in the multiplex. Data were analyzed by superposing fluorescent profiles of test and control DNA and by visually comparing the normalized peak levels of corresponding amplicons, rather than by calculating the ratios of peak areas. Tests on a collection of known defects, including five different Alu-mediated deletions and a partial duplication have validated this approach. In a study of 19 sporadic cases of HAE, of which four had failed to reveal mutations upon screening all exons by fluorescent chemical cleavage, three de novo deletions were diagnosed by using this multiplex PCR approach: a deletion of exon 4, a deletion of exons 5 and 6, and an apparently complete gene deletion. Besides being suitable for the initial DNA screening of the C1NH gene in HAE patients prior to screening for point mutations, this method can be easily adapted to complex genes for the screening of rearrangements.     

Comprehensive screening for constitutional RB1 mutations by DHPLC and QMPSF

Constitutional mutations of the RB1 gene are associated with a predisposition to retinoblastoma. It is essential to identify these mutations to provide appropriate genetic counseling in retinoblastoma patients, but this represents an extremely challenging task, as the vast majority of mutations are unique and spread over the entire coding sequence. Since 2001, we have implemented RB1 testing on a routine basis as part of the clinical management of retinoblastoma. As most screening techniques do not meet the requirements for efficient RB1 testing, we have devised a semi-automated denaturing high-performance liquid chromatography (DHPLC) method for point mutation detection combined with a quantitative multiplex PCR of short fluorescent fragments (QMPSF) approach to screen for gene rearrangements. We report the results of this comprehensive screening of all exons and promoter of RB1 in 192 unrelated patients, mostly of French origin. Among 102 bilateral and/or familial cases and 90 unilateral sporadic probands, mutations were identified in 83 (81.5%) and 5 (5.5%) cases, respectively. A total of 43 mutations have not been previously reported. The mutational spectrum was found to be significantly different from previous published series, displaying a surprising amount of splice mutations and large deletions. This study demonstrates the reliability of DHPLC for RB1 analysis, but also illustrates the need for a deletion scanning approach. Finally, considering the benefits to retinoblastoma patients, RB1 testing should be widely implemented in routine healthcare because our study clearly illustrates its feasibility.     

A modified multiplex PCR assay for detection of large deletions in MSH2 and MLH1

A method for detection of large genomic deletions in the MSH2 and MLH1 genes based on multiplex PCR and quantitative evaluation of PCR products is presented. All 35 exons of MSH2 and MLH1 were screened simultaneously in seven PCR reactions, each of them including primers for both genes. The method is reliable for uncovering large genomic deletions in patients suspected of HNPCC. With this method, six novel deletions were identified, two in MSH2: EX1_10del and EX1_16del (representing deletion of the entire MSH2 gene); and four in MLH1: EX1_10del in two unrelated patients, EX3_5del, and EX4del. The deletions were detected in 18 unrelated patients in whom no germline mutation had been identified by SSCP and DHPLC. These results indicate that our modified multiplex PCR assay is suited for the detection of large deletions both in the MSH2 and MLH1 gene and therefore represents an additional valuable tool for mutation screening in HNPCC families.     

反向点杂交快速诊断非缺失型α-地中海贫血

目的 建立一种简便快速筛查非缺失型α—地中海贫血点突变的反向点杂交(reverse dot blot,RDB)技术。方法 将生物素直接标记在引物上,选择性扩增人α2珠蛋白基因,将PCR产物与固化在膜条上的寡核苷酸探针杂交,洗膜、显色后分析结果。结果 采用生物素标记的引物：Bio—C1和Bio—C3可选择性扩增α2珠蛋白基因,PCR产物长度为1085bp,该标记片段与固相探针构成的反向点杂交检测体系,可以分辨出中国人群中已知的6种非缺失型α—地中海贫血点突变。结论 该反向点杂交检测体系无需巢式PCR扩增,一步选择性扩增的α2珠蛋白基因产物即可用于杂交;无需进行检测标记物(如生物素)反应,而将生物素直接标记在引物上;无需不同的洗膜条件,故较已报道的同类方法更为简单易行。RDB技术可用于快速诊断中国人非缺失型α—地中海贫血点突变。     

Sensitivity and frequencies of dystrophin gene mutations in Thai DMD/BMD patients as detected by multiplex PCR

Background: Duchenne muscular dystrophy (DMD), a lethal X-linked disease affecting 1 in 3500 male births, and its more benign variant, Becker muscular dystrophy (BMD), are caused by mutations in the dystrophin gene. Because of its large size, analysing the whole gene is impractical. Methods have been developed to detect the commonest mutations i.e. the deletions of the exons. Although these tests are highly specific, their sensitivity is inherently limited by the prevalence of deletions, which differs among different populations. Methods: We reviewed our database for the detection of Dystrophin gene mutation by means of 31-exon multiplex PCR in Thai males, diagnosed clinically and biochemically with DMD or BMD from July 1994 to November 2006. One index patient was chosen from each family for statistical analysis. The overall sensitivity of the test, the number of fragment deleted, and the deletion frequency of each fragment were calculated, along with their 95% confidence intervals (C.I.). Results: We found deletions in 99 out of the 202 index patients (49%; Bayesian 95% C.I. = 42%–56%). 51% of these had deletion in only one of the 31 exons tested, while the patient with the most extensive deletions had 14 exons deleted. The mean number of deleted exons were 2.84 (BC_a bootstrap 95% C.I. = 2.37–3.48), or 5.02 (3.81–6.85) if all the untested exons adjacent to the confirmed deleted exons were assumed to be deleted. The region spanning exons 44-52 was the most frequently deleted. These were similar to those reported in the Japanese. Conclusion: The multiplex PCR detected deletions only in about half of the Thai patients. The diseases therefore should not be excluded solely on the negative result if DMD/BMD is strongly suspected.     

Molecular nature of spontaneous mutations at the hypoxanthine-guanine phosphoribosyltransferase (hprt) locus in chinese hamster ovary cells

The hypoxanthine-guanine phosphoribosyltransferase (hprt) locus has been widely used as a selectable genetic marker for studies of mammalian cell mutagenesis. We report here the spontaneous mutation spectrum at the hprt locus in 64 independently isolated mutants of Chinese hamster ovary (CHO) cells. All nine hprt exons were simultaneously analyzed via multiplex polymerase chain reaction (PCR) for rapid detection of gene deletions or insertions. Structural point mutations were identified by direct sequence analysis of the PCR amplified cDNA. The molecular nature of RNA splicing errors and insertions was analyzed by solid-phase direct exon sequencing. Single base substitutions were found in 24 mutants (38%), of which 21 were missense and 3 were nonsense mutations. Transversions were about twice as frequent as transitions. Fifteen mutants (23%) had deletions involving either intragenic small fragments (2), single exons (9), or multiple exons (4). The majority of deletion breakpoints (71%) were located in regions surrounding exons 4, 5, and 6. RNA splicing mutations were observed in 15 mutants (23%) and affected exons 3–8; most (6/15) resulted in the loss of exon 7. Two insertion mutants, one with a 209 bp insert in exon 4 and the other with a 88 bp insert accompanied by a 24 bp deletion in exon 6, represent novel mutations reported for the first time in spontaneous mutants of the mammalian hprt gene. © 1995 Wiley-Liss, Inc.     

Screening for large rearrangements of the BRCA1 gene in German breast or ovarian cancer families using semi-quantitative multiplex PCR method

Since the identification of the breast and ovarian cancer susceptibility genes BRCA1 and BRCA2, a large number of different germline mutations in both genes have been found by conventional PCR-based mutation detection methods. Complex germline rearrangements such as those reported in the BRCA1 gene are often not detectable by these standard diagnostic techniques. To detect large deletions or duplications encompassing one or more exons of the BRCA1 gene and in order to estimate the frequency of BRCA1 rearrangements in German breast or ovarian cancer families, a semi-quantitative multiplex PCR method was developed and applied to DNA samples of patients from families negatively tested for disease causing mutations in the BRCA1 and BRCA2 coding regions by direct sequencing. Out of 59 families analysed, one family was found to carry a rearrangement in the BRCA1 gene (duplication of exon 13). The results indicate that the semi-quantitative multiplex PCR method is useful for the detection of large rearrangements in the BRCA1 gene and therefore represents an additional valuable tool for mutation analysis of BRCA1 and BRCA2.