Mutation Research/Mutation Research Genomics最新文献

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Predicted changes in pre-mRNA secondary structure vary in their association with exon skipping for mutations in exons 2, 4, and 8 of the Hprt gene and exon 51 of the fibrillin gene mrna前二级结构的预测变化与Hprt基因外显子2、4和8以及原纤维蛋白基因外显子51突变的外显子跳变有关
Mutation Research/Mutation Research Genomics Pub Date : 2000-02-01 DOI: 10.1016/S1383-5726(99)00011-4
Meihua Tu , Weida Tong , Roger Perkins , Carrie R Valentine
{"title":"Predicted changes in pre-mRNA secondary structure vary in their association with exon skipping for mutations in exons 2, 4, and 8 of the Hprt gene and exon 51 of the fibrillin gene","authors":"Meihua Tu ,&nbsp;Weida Tong ,&nbsp;Roger Perkins ,&nbsp;Carrie R Valentine","doi":"10.1016/S1383-5726(99)00011-4","DOIUrl":"10.1016/S1383-5726(99)00011-4","url":null,"abstract":"<div><p><span>Exon skipping<span> that accompanies exonic mutation might be caused by an effect of the mutation on pre-mRNA secondary structure. Previous attempts to associate predicted secondary structure of pre-mRNA with exon skipping have been hindered by either a small number of available mutations, sub-optimal structures, or weak effects on exon skipping. This report identifies more extensive sets of mutations from the human and hamster </span></span><span><em>Hprt</em></span><span> gene whose association with exon skipping is clear. Optimal secondary structures of the wild-type and mutant pre-mRNA surrounding each exon were predicted by energy minimization and were compared by energy dot plots. A significant association was found between the occurrence of exon skipping and the disruption of a stem containing the acceptor site consensus sequences of exon 8 of the human </span><em>Hprt</em> gene. However, no change in secondary structure was associated with skipping of exon 4 of the hamster <em>Hprt</em> gene. Using updated energy parameters we found a different structure than that previously reported for exon 2 of the hamster <em>Hprt</em> gene. In contrast to the previously reported structure, no significant association was found between predicted structural changes and skipping of exon 2. For all three <em>Hprt</em><span><span> exons studied, there was a significantly greater number of deoxythymidine substitutions among mutations accompanied by exon skipping than among mutations without exon skipping. For exon 8, deoxythymidine substitution was also associated with structural changes in the stem containing the acceptor site consensus sequences. For exon 51 of the human </span>fibrillin gene, structural differences from wild type were predicted for all four mutations accompanied by exon skipping that were not were predicted for a single mutation without exon skipping. Our results suggest that both primary and secondary pre-mRNA structure contribute to definition of </span><em>Hprt</em><span> exons, which may involve exonic splicing enhancers.</span></p></div>","PeriodicalId":100939,"journal":{"name":"Mutation Research/Mutation Research Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2000-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1383-5726(99)00011-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21580835","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 20
Human transcription factor SLUG: mutation analysis in patients with neural tube defects and identification of a missense mutation (D119E) in the Slug subfamily-defining region 人转录因子SLUG:在神经管缺陷患者中的突变分析和SLUG亚家族定义区错义突变(D119E)的鉴定
Mutation Research/Mutation Research Genomics Pub Date : 1999-08-01 DOI: 10.1016/S1383-5726(99)00002-3
Karolin Stegmann , Julia Boecker , Christian Kosan , August Ermert , Jürgen Kunz , Manuela C Koch
{"title":"Human transcription factor SLUG: mutation analysis in patients with neural tube defects and identification of a missense mutation (D119E) in the Slug subfamily-defining region","authors":"Karolin Stegmann ,&nbsp;Julia Boecker ,&nbsp;Christian Kosan ,&nbsp;August Ermert ,&nbsp;Jürgen Kunz ,&nbsp;Manuela C Koch","doi":"10.1016/S1383-5726(99)00002-3","DOIUrl":"10.1016/S1383-5726(99)00002-3","url":null,"abstract":"<div><p>Studies in mouse, chicken and <span><em>Xenopus</em></span> have shown that <em>Slug</em><span> is selectively expressed in the dorsal part of the developing neural tube. Ablation and antisense experiments in chicken suggest that </span><em>Slug</em> may be an important factor during neural tube closure. We therefore investigated the role of <em>Slug</em><span> as a possible candidate contributing to the aetiology of neural tube defects (NTD) in humans. We characterised the genomic structure of human </span><em>SLUG</em> including determination of the exon–intron boundaries. The coding sequence of <em>SLUG</em><span> was screened for mutations in 150 patients with NTD using single strand conformation analysis (SSCA). In one patient, we identified a missense mutation 1548C→A in exon 2 causing an exchange of a conserved amino acid (D119E) in the </span><em>Slug</em><span> subfamily-defining region preceding the first zinc finger. This is the first description of a human mutation in the </span><em>SLUG</em> gene. In accordance with the findings in model organisms, the <em>SLUG</em> mutation may be causally related to the development of NTD in our patient and could be considered as a predisposing factor.</p></div>","PeriodicalId":100939,"journal":{"name":"Mutation Research/Mutation Research Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1999-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1383-5726(99)00002-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21343076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 27
Gene expression in individual cells: analysis using global single cell reverse transcription polymerase chain reaction (GSC RT-PCR) 单细胞基因表达:全球单细胞逆转录聚合酶链反应(GSC RT-PCR)分析
Mutation Research/Mutation Research Genomics Pub Date : 1999-08-01 DOI: 10.1016/S1383-5726(98)00009-0
Leslie H Brail , Anne Jang , Filio Billia , Norman N Iscove , Henry J Klamut , Richard P Hill
{"title":"Gene expression in individual cells: analysis using global single cell reverse transcription polymerase chain reaction (GSC RT-PCR)","authors":"Leslie H Brail ,&nbsp;Anne Jang ,&nbsp;Filio Billia ,&nbsp;Norman N Iscove ,&nbsp;Henry J Klamut ,&nbsp;Richard P Hill","doi":"10.1016/S1383-5726(98)00009-0","DOIUrl":"10.1016/S1383-5726(98)00009-0","url":null,"abstract":"<div><p>The determination of the gene expression pattern of single cells has important implications for many areas of cellular and developmental biology including lineage determination, identification of primitive stem cells and temporal gene expression patterns induced by changes in the cellular microenvironment. Global Single Cell Reverse Transcription-Polymerase Chain Reaction (GSC RT-PCR) enables the study of single cell gene expression patterns. Initial observations of significant heterogeneity among single cells derived from a population of cells prompted us to determine how much of this observed heterogeneity was due to the intrinsic variation within the method. In this paper we discuss the sensitivity of GSC RT-PCR for analysis of differences in gene expression between single cells and, in particular, detail the amount of variation generated by the method itself. We found that most of the intrinsic variation in the method occurred in the PCR step. The total variation induced by the method was in the range of 5 fold. While we have determined that there is a five fold methodological variation in GSC RT-PCR, any method which use its components (including generation of cDNAs for microarray analysis) is likely to be affected by such experimental variability, which could limit the interpretation of the resulting data.</p></div>","PeriodicalId":100939,"journal":{"name":"Mutation Research/Mutation Research Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1999-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1383-5726(98)00009-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21343114","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 47
Inactivation of both alleles of the DPC4/SMAD4 gene in advanced colorectal cancers: identification of seven novel somatic mutations in tumors from Japanese patients 晚期结直肠癌DPC4/SMAD4基因两个等位基因失活:日本患者肿瘤中7个新的体细胞突变的鉴定
Mutation Research/Mutation Research Genomics Pub Date : 1999-08-01 DOI: 10.1016/S1383-5726(99)00003-5
Masaaki Koyama , Masahide Ito , Hisaki Nagai , Mitsuru Emi , Yuukichi Moriyama
{"title":"Inactivation of both alleles of the DPC4/SMAD4 gene in advanced colorectal cancers: identification of seven novel somatic mutations in tumors from Japanese patients","authors":"Masaaki Koyama ,&nbsp;Masahide Ito ,&nbsp;Hisaki Nagai ,&nbsp;Mitsuru Emi ,&nbsp;Yuukichi Moriyama","doi":"10.1016/S1383-5726(99)00003-5","DOIUrl":"10.1016/S1383-5726(99)00003-5","url":null,"abstract":"<div><p><span><span>Loss of heterozygosity<span> (LOH) of loci on chromosome 18q occurs in a majority of </span></span>colorectal cancers. The </span><em>DPC4</em>/<em>SMAD4</em> gene, lying in close proximity to the <em>DCC</em><span><span> gene at 18q21.1, was recently identified as a candidate tumor suppressor for the genesis of pancreatic cancer as well as a predisposing gene for Juvenile </span>Polyposis<span> Syndrome (JPS). The gene product functions as a cytoplasmic mediator in the signaling pathway<span> of transforming growth factor beta (TGF-β). To investigate the potential role of </span></span></span><em>DPC4</em>/<em>SMAD4</em> gene in colorectal cancers, we examined 73 tumors of clinical stages II or III from Japanese patients, for LOH at 18q21 and also for subtle mutations anywhere within the coding region of <em>DPC4</em>/<em>SMAD4</em><span><span>. LOH was identified in 50 (78%) of the 64 tumors that were informative for polymorphic markers in the region. Somatic mutations<span><span> were identified in seven of those tumors: two frameshift mutations, a 1-bp deletion (326 del T) in exon 8 and a 1-bp insertion (50–51 ins A) in exon 1; two </span>nonsense mutations, Arg445Ter in exon 10 and Glu538Ter in exon 11; and three </span></span>missense mutations, Asn129Lys in exon 2, Tyr95Asn in exon 2, and Asp355Glu in exon 8. Three of the seven mutations were observed in the mad homology 1 (MH1) domain encoded by exons 1 and 2. In all of the tumors carrying intragenic mutations of one allele, LOH analysis had shown that the other allele was missing. The results demonstrated that inactivation of both alleles of the </span><em>DPC4</em>/<em>SMAD4</em> gene occurs in a substantial proportion of advanced colorectal cancers, and that the <em>DPC4</em>/<em>SMAD4</em><span><span> gene probably exerts a tumor-suppressor effect for colorectal carcinogenesis that fulfills the criterion of the two-hit concept proposed by Knudson [A.G. Knudson, Hereditary cancer, </span>oncogenes, and anti-oncogenes, Cancer Res. 45 (1985) 1437–1443.].</span></p></div>","PeriodicalId":100939,"journal":{"name":"Mutation Research/Mutation Research Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1999-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1383-5726(99)00003-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21343077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 62
Polymorphisms in the human DNA repair gene XPF 人类DNA修复基因XPF的多态性
Mutation Research/Mutation Research Genomics Pub Date : 1999-08-01 DOI: 10.1016/S1383-5726(99)00008-4
Fan Fan, Cheng-pin Liu, Simon Tavaré, Norman Arnheim
{"title":"Polymorphisms in the human DNA repair gene XPF","authors":"Fan Fan,&nbsp;Cheng-pin Liu,&nbsp;Simon Tavaré,&nbsp;Norman Arnheim","doi":"10.1016/S1383-5726(99)00008-4","DOIUrl":"10.1016/S1383-5726(99)00008-4","url":null,"abstract":"<div><p><span><span>DNA sequence polymorphisms were sought in the coding region and at the exon–intron boundaries of the human XPF gene, which plays a role in nucleotide excision repair. Based on a survey of 38 individuals, we found six single nucleotide polymorphisms, one in the 5′ non-coding region of the XPF gene, and five in the 2751 bp coding region. At each site, the frequency of the rarer allele varies from about 0.01 to over 0.38. Except for the 5′ non-coding and one coding sequence polymorphism, the rarer alleles for the remaining four polymorphisms were found only in heterozygotes. Of the five polymorphisms in the coding region, one is silent, one results in a conserved amino acid difference, and the remaining three result in non-conserved amino acid differences. Because of its biological function in nucleotide excision repair, functionally significant XPF </span>gene polymorphisms<span> are candidates for influencing cancer susceptibility and overall genetic stability. Nucleotide sequence diversity estimates for XPF are similar to the </span></span>lipoprotein lipase and beta-globin genes.</p></div>","PeriodicalId":100939,"journal":{"name":"Mutation Research/Mutation Research Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1999-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1383-5726(99)00008-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21343081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 47
Restriction fragment analysis as a source of error in detection of heteroplasmic mtDNA mutations 限制性内切片段分析是检测异质mtDNA突变的错误来源
Mutation Research/Mutation Research Genomics Pub Date : 1999-08-01 DOI: 10.1016/S1383-5726(99)00007-2
Saara Finnilä , Ilmo E Hassinen , Kari Majamaa
{"title":"Restriction fragment analysis as a source of error in detection of heteroplasmic mtDNA mutations","authors":"Saara Finnilä ,&nbsp;Ilmo E Hassinen ,&nbsp;Kari Majamaa","doi":"10.1016/S1383-5726(99)00007-2","DOIUrl":"10.1016/S1383-5726(99)00007-2","url":null,"abstract":"<div><p><span>The transition from A to G at nt 5656 (5656A→G) in mitochondrial DNA has been suggested to be a pathogenic mutation and, furthermore, a heteroplasmic one. We found that the mutation was present in 14 out of 83 healthy controls from northern Finland and that 5656A→G was exclusively associated with mtDNA haplogroup U. Interestingly, 5656A→G appeared to be heteroplasmic in </span><em>Nhe</em><span>I digestion of PCR fragments that were amplified by using a mismatched oligonucleotide<span> primer creating a digestion site in the presence of the mutant variant. However, we did not detect the wild type genome in clones from such a sample and subsequent experiments revealed that the apparent heteroplasmy was due to inhibition of </span></span><em>Nhe</em>I by NaCl. Our results suggest that 5656A→G is a polymorphism and it may be highly characteristic for Finns. Furthermore, new heteroplasmic mutations identified by restriction fragment analysis should be adequately controlled for any false positive results that may be due to incomplete digestion.</p></div>","PeriodicalId":100939,"journal":{"name":"Mutation Research/Mutation Research Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1999-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1383-5726(99)00007-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21343080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 15
Differential sensitivity of double minute chromosomes to hydroxyurea treatment in cultured methotrexate-resistant mouse cells 培养的甲氨蝶呤耐药小鼠细胞双分钟染色体对羟基脲处理的差异敏感性
Mutation Research/Mutation Research Genomics Pub Date : 1999-08-01 DOI: 10.1016/S1383-5726(98)00010-7
Barbara H. Nevaldine, Rabia Rizwana, Peter J. Hahn
{"title":"Differential sensitivity of double minute chromosomes to hydroxyurea treatment in cultured methotrexate-resistant mouse cells","authors":"Barbara H. Nevaldine,&nbsp;Rabia Rizwana,&nbsp;Peter J. Hahn","doi":"10.1016/S1383-5726(98)00010-7","DOIUrl":"10.1016/S1383-5726(98)00010-7","url":null,"abstract":"<div><p><span><span>Treating mammalian cells with continuous sub-lethal doses of </span>Hydroxyurea (HU) causes the loss of </span>double minute chromosomes<span><span><span> (DMs) containing amplified oncogenes in culture. Recently, we have shown that treating </span>glioblastoma multiforme<span> cells in culture with low doses of HU causes the loss of DMs containing epidermal growth factor receptor<span> genes. Loss of amplified EGFR genes was accompanied by cessation of growth, and greatly decreased tumorigenicity. To further study HU-induced elimination of DMs we have now followed the fate of </span></span></span>dihydrofolate reductase gene (DHFR) amplifying DMs in methotrexate-resistant mouse cells during simultaneous treatment with both MTX and HU. We report that in the presence of both HU and MTX, the amplified genes decreased to 25% of starting levels in the first week of treatment, but that ultimately the cells become resistant to HU and reamplify the DHFR gene. We also report that some DHFR amplifying DMs are much more sensitive to HU than others. This study demonstrates that HU does not simply increase the rate of passive loss of DMs.</span></p></div>","PeriodicalId":100939,"journal":{"name":"Mutation Research/Mutation Research Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1999-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1383-5726(98)00010-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21343115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 7
Screening of the human tumor necrosis factor-alpha (TNF-α) gene promoter polymorphisms by PCR–DGGE analysis PCR-DGGE分析筛选人肿瘤坏死因子-α基因启动子多态性
Mutation Research/Mutation Research Genomics Pub Date : 1999-08-01 DOI: 10.1016/S1383-5726(99)00004-7
A Patiño-Garcı́a , E Sotillo-Piñeiro , C Modesto , L Sierrasesúmaga
{"title":"Screening of the human tumor necrosis factor-alpha (TNF-α) gene promoter polymorphisms by PCR–DGGE analysis","authors":"A Patiño-Garcı́a ,&nbsp;E Sotillo-Piñeiro ,&nbsp;C Modesto ,&nbsp;L Sierrasesúmaga","doi":"10.1016/S1383-5726(99)00004-7","DOIUrl":"https://doi.org/10.1016/S1383-5726(99)00004-7","url":null,"abstract":"<div><p>We have designed a new PCR–DGGE technique that enables detection of base changes in the TNF-α gene promoter. Screening of 130 samples from Spanish children has shown that this technique accurately detects the altered band patterns induced by the presence of the polymorphisms at positions −376, −308, −238 and −163 of the promoter sequence. Although further analysis are needed to fully characterise the alterations detected, we believe that this PCR–DGGE technique is a rapid and sensitive first approach to the genetic characterisation of the TNF-α promoter.</p></div>","PeriodicalId":100939,"journal":{"name":"Mutation Research/Mutation Research Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1999-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1383-5726(99)00004-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72064079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 11
Needle-in-a-haystack detection and identification of base substitution mutations in human tissues 人体组织中碱基取代突变的大海捞针检测和鉴定
Mutation Research/Mutation Research Genomics Pub Date : 1999-08-01 DOI: 10.1016/S1383-5726(99)00005-9
Vincent L Wilson , Qi Wei , Kerry R Wade , Midori Chisa , Deidre Bailey , Christopher M Kanstrup , Xiuqin Yin , Chad M Jackson , Barbara Thompson , William R Lee
{"title":"Needle-in-a-haystack detection and identification of base substitution mutations in human tissues","authors":"Vincent L Wilson ,&nbsp;Qi Wei ,&nbsp;Kerry R Wade ,&nbsp;Midori Chisa ,&nbsp;Deidre Bailey ,&nbsp;Christopher M Kanstrup ,&nbsp;Xiuqin Yin ,&nbsp;Chad M Jackson ,&nbsp;Barbara Thompson ,&nbsp;William R Lee","doi":"10.1016/S1383-5726(99)00005-9","DOIUrl":"10.1016/S1383-5726(99)00005-9","url":null,"abstract":"<div><p><span><span><span>Background and induced germline<span> mutagenesis<span> and other genotoxicity studies have been hampered by the lack of a sufficiently sensitive technique for detecting mutations in a small cluster of cells or a single cell in a tissue sample composed of millions of cells. The most frequent type of </span></span></span>genetic alteration<span> is intragenic. The vast majority of oncogenic mutations in human and mammalian cancer involves only single base substitutions. We have developed universally applicable techniques that not only provide the necessary sensitivity and specificity for </span></span>site specific mutagenesis<span><span> studies, but also identify the point mutation<span>. The exponential amplification procedures of polymerase chain reaction (PCR) and ligase chain reaction (LCR) have been combined with </span></span>restriction endonuclease (RE) digestion to enable the selective enrichment and detection of single base substitution mutations in human oncogenic loci at a sensitivity of one mutant in more than 10</span></span><sup>7</sup> wild type alleles. These PCR/RE/LCR procedures have been successfully designed and used for codons 12 and 248 of the Ha-<em>ras</em> and p53 genes, respectively, both of which contain a natural <em>Msp</em>I restriction endonuclease recognition sequence. These procedures have also been adapted for the detection and identification of mutations in oncogenic loci that do not contain a natural restriction endonuclease recognition sequence. Using PCR techniques, a <em>Hph</em>I site was incorporated into the codons 12/13 region of the human N-<em>ras</em> gene, which was then used for the selective enrichment of mutants at this oncogenic locus. These PCR/RE/LCR procedures for base substitution mutations in codon 12 of the N-<em>ras</em> gene were found to have the sensitivity of detection of at least one mutant allele in the presence of the DNA equivalent of 10<sup>6</sup> wild type cells. Only one peripheral blood leukocyte DNA specimen out of nine normal individuals displayed an observable Ha-<em>ras</em> mutation that was present at frequency between 10<sup>−5</sup> and 10<sup>−6</sup>. These PCR/RE/LCR techniques for detecting and identifying base substitution mutations are universally applicable to almost any locus or base site within the human or animal genome. With the added advantage of the adjustability of both the amount of DNA (number of genomes) to be tested and the sensitivity (10<sup>−2</sup> to 10<sup>−7</sup>) of the assay selection or enrichment procedures, these PCR/RE/LCR techniques will be useful in addressing a broad range of important questions in mutagenesis and carcinogenesis.</p></div>","PeriodicalId":100939,"journal":{"name":"Mutation Research/Mutation Research Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1999-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1383-5726(99)00005-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21343078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 35
A characterization of genetic variants in BRCA1 intron 8 identifies a mutation and a polymorphism BRCA1内含子8基因变异的特征确定了突变和多态性
Mutation Research/Mutation Research Genomics Pub Date : 1999-08-01 DOI: 10.1016/S1383-5726(99)00006-0
Michael T Pyne, Dimtry Pruss, Brian E Ward, Thomas Scholl
{"title":"A characterization of genetic variants in BRCA1 intron 8 identifies a mutation and a polymorphism","authors":"Michael T Pyne,&nbsp;Dimtry Pruss,&nbsp;Brian E Ward,&nbsp;Thomas Scholl","doi":"10.1016/S1383-5726(99)00006-0","DOIUrl":"10.1016/S1383-5726(99)00006-0","url":null,"abstract":"<div><p>The biochemical and genetic characterizations of two variants that occur in <span><em>BRCA1</em></span><span><span> intron 8 are presented. The variant IVS8+2T→C induces an aberrant transcript that deletes exon 8. This exon-skipping deletion disrupts the open reading frame by juxtaposing exon 7 and exon 9 in the aberrant splice product. Theoretically, 50 abnormal residues from reading frame 2 are translated following exon 7 before a </span>stop codon<span> is encountered. The chromosomal contribution to the relevant RNA species was tracked using a silent polymorphism at codon 694 (serine AGC or AGT). Nucleotide sequencing of this polymorphic codon demonstrated that the aberrant transcript was derived solely from the chromosome encoding AGT. The normally spliced productive transcript also displayed loss of heterozygosity<span> and was derived solely from the chromosome encoding AGC at codon 694. Also, a haplotype analysis using a breast cancer patient database showed that the chromosome bearing serine 694-AGT carried IVS8+2T→C. A second more common variant, IVS8-58delT, was characterized as a polymorphism. Analysis of RNA from patient samples used the same silent polymorphism at codon 694 and showed that the normal message was derived from both chromosomes.</span></span></span></p></div>","PeriodicalId":100939,"journal":{"name":"Mutation Research/Mutation Research Genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1999-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1383-5726(99)00006-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"21343079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 11
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