Salvatore A.E. Marras, Fred Russell Kramer, Sanjay Tyagi
{"title":"Multiplex detection of single-nucleotide variations using molecular beacons","authors":"Salvatore A.E. Marras, Fred Russell Kramer, Sanjay Tyagi","doi":"10.1016/S1050-3862(98)00018-7","DOIUrl":"10.1016/S1050-3862(98)00018-7","url":null,"abstract":"<div><p>We demonstrate that single-nucleotide differences in a DNA sequence can be detected in homogeneous assays using molecular beacons. In this method, the region surrounding the site of a sequence variation is amplified in a polymerase chain reaction and the identity of the variant nucleotide is determined by observing which of four differently colored molecular beacons binds to the amplification product. Each of the molecular beacons is perfectly complementary to one variant of the target sequence and each is labeled with a different fluorophore. To demonstrate the specificity of these assays, we prepared four template DNAs that only differed from one another by the identity of the nucleotide at one position. Four amplification reactions were prepared, each containing all four molecular beacons, but each initiated with only one of the four template DNAs. The results show that in each reaction a fluorogenic response was elicited from the molecular beacon that was perfectly complementary to the amplified DNA, but not from the three molecular beacons whose probe sequence mismatched the target sequence. The color of the fluorescence that appeared in each tube during the course of the amplification indicated which nucleotide was present at the site of variation. These results demonstrate the extraordinary specificity of molecular beacons. Furthermore, the results illustrate how the ability to label molecular beacons with differently colored fluorophores enables simple multiplex assays to be carried out for genetic analysis.</p></div>","PeriodicalId":77142,"journal":{"name":"Genetic analysis, techniques and applications","volume":"14 5","pages":"Pages 151-156"},"PeriodicalIF":0.0,"publicationDate":"1999-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1050-3862(98)00018-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20956118","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}
{"title":"Glycosylase mediated polymorphism detection (GMPD)—a novel process for genetic analysis","authors":"Patrick Vaughan, Tommie V. McCarthy","doi":"10.1016/S1050-3862(98)00025-4","DOIUrl":"10.1016/S1050-3862(98)00025-4","url":null,"abstract":"<div><p>A process for mutation and polymorphism detection is described here that offers significant advances over current mutation detection systems and that has the potential to significantly enhance molecular genetic analysis of human disease. This novel process is referred to as glycosylase mediated polymorphism detection (GMPD) and exploits the use of highly specific DNA glycosylase enzymes to excise substrate bases incorporated into amplified DNA. Action of the glycosylase leaves the DNA with one or more specific abasic sites which can be cleaved by enzymatic or chemical means. The GMPD process permits detection of polymorphisms and mutations using fragment size analysis or solid phase formats. GMPD is particularly suitable for genotyping of single nucleotide polymorphism (SNP) based markers and also permits efficient scanning of genes for unknown polymorphisms and mutations.</p></div>","PeriodicalId":77142,"journal":{"name":"Genetic analysis, techniques and applications","volume":"14 5","pages":"Pages 169-175"},"PeriodicalIF":0.0,"publicationDate":"1999-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1050-3862(98)00025-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20956121","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}
{"title":"Recent enhancements in SSCP","authors":"Kenshi Hayashi","doi":"10.1016/S1050-3862(98)00017-5","DOIUrl":"10.1016/S1050-3862(98)00017-5","url":null,"abstract":"<div><p>High sensitivity, robustness and scalability are the three criteria which influence whether techniques for rapid mutation detection will be used in the future. PCR-SSCP, one of the most popular methods for detecting mutation, especially in the field of medical genetics, is being improved (1) to efficiently detect mutations in long stretches of PCR products; (2) to simplify data interpretation by removing PCR artifacts and (3) to minimize human involvement in the process of mutation detection by a simple post-PCR fluorescence labeling followed by separation using automated DNA sequencers.</p></div>","PeriodicalId":77142,"journal":{"name":"Genetic analysis, techniques and applications","volume":"14 5","pages":"Pages 193-196"},"PeriodicalIF":0.0,"publicationDate":"1999-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1050-3862(98)00017-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20957544","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}
Joel H. Graber, Cassandra L. Smith, Charles R. Cantor
{"title":"Differential sequencing with mass spectrometry","authors":"Joel H. Graber, Cassandra L. Smith, Charles R. Cantor","doi":"10.1016/S1050-3862(98)00020-5","DOIUrl":"10.1016/S1050-3862(98)00020-5","url":null,"abstract":"<div><p>Differential or genetic sequencing requires searching sample DNA for variations with respect to a reference sequence. Conventional detection techniques are too labor and cost expensive for use in diagnostic applications, therefore new technologies will be required. Measurement techniques based on mass spectrometry (MS) possess the potential for high-throughput, high fidelity measurement of sequence variation. Unambiguous detection of polymorphic sequences has been demonstrated, even in heterozygous samples. Automated reproducible measurements of microscopic arrays of samples will enable the high-throughput detection required for large-scale applications. Computational simulation and analysis of experimental parameters prior to experimentation will provide the optimization necessary for development of robust, reproducible measurements.</p></div>","PeriodicalId":77142,"journal":{"name":"Genetic analysis, techniques and applications","volume":"14 5","pages":"Pages 215-219"},"PeriodicalIF":0.0,"publicationDate":"1999-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1050-3862(98)00020-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20957547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Enzymatic methods for mutation scanning","authors":"Graham R. Taylor , Jayne Deeble","doi":"10.1016/S1050-3862(98)00029-1","DOIUrl":"10.1016/S1050-3862(98)00029-1","url":null,"abstract":"<div><p>Enzymatic methods for mutation scanning still lack the sensitivity and specificity of the chemical cleavage of mismatch method. However developments in our understanding of the mismatch recognition process should lead to improvements. Several promising candidates exist with potential for more specific and sensitive mutation detection.</p></div>","PeriodicalId":77142,"journal":{"name":"Genetic analysis, techniques and applications","volume":"14 5","pages":"Pages 181-186"},"PeriodicalIF":0.0,"publicationDate":"1999-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1050-3862(98)00029-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20956123","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}
Ronald J. Sapolsky , Linda Hsie , Anthony Berno , Ghassan Ghandour , Michael Mittmann , Jian-Bing Fan
{"title":"High-throughput polymorphism screening and genotyping with high-density oligonucleotide arrays","authors":"Ronald J. Sapolsky , Linda Hsie , Anthony Berno , Ghassan Ghandour , Michael Mittmann , Jian-Bing Fan","doi":"10.1016/S1050-3862(98)00026-6","DOIUrl":"10.1016/S1050-3862(98)00026-6","url":null,"abstract":"<div><p>A highly reliable and efficient technology has been developed for high-throughput DNA polymorphism screening and large-scale genotyping. Photolithographic synthesis has been used to generate miniaturized, high-density oligonucleotide arrays. Dedicated instrumentation and software have been developed for array hybridization, fluorescent detection, and data acquisition and analysis. Specific oligonucleotide probe arrays have been designed to rapidly screen human STSs, known genes and full-length cDNAs. This has led to the identification of several thousand biallelic single-nucleotide polymorphisms (SNPs). Meanwhile, a rapid and robust method has been developed for genotyping these SNPs using oligonucleotide arrays. Each allele of an SNP marker is represented on the array by a set of perfect match and mismatch probes. Prototype genotyping chips have been produced to detect 400, 600 and 3000 of these SNPs. Based on the preliminary results, using oligonucleotide arrays to genotype several thousand polymorphic loci simultaneously appears feasible.</p></div>","PeriodicalId":77142,"journal":{"name":"Genetic analysis, techniques and applications","volume":"14 5","pages":"Pages 187-192"},"PeriodicalIF":0.0,"publicationDate":"1999-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1050-3862(98)00026-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20957543","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}
{"title":"Application of constant denaturant capillary electrophoresis (CDCE) to mutation detection in humans","authors":"Brindha P. Muniappan, William G. Thilly","doi":"10.1016/S1050-3862(98)00032-1","DOIUrl":"10.1016/S1050-3862(98)00032-1","url":null,"abstract":"<div><p>Constant denaturant electrophoresis is a DNA separation technique based on the principle of cooperative melting equilibrium. DNA sequences with distinct high and low melting domains can be utilized to separate and identify molecules differing by only one base pair in the lower melting domain. Combined with capillary gel electrophoresis and when coupled with high fidelity DNA amplification, this approach can detect mutants at a fraction of 10<sup>−6</sup>. Modifications to the capillary elecctrophoretic system have also increased DNA loading capacity which allows for analysis of rare mutations in a large, heterogeneous population such as DNA samples derived from human tissues. Employment of this technology has determined the first mutational spectrum in human cells and tissues in a mitochondrial sequence without phenotypic selection of mutants.</p></div>","PeriodicalId":77142,"journal":{"name":"Genetic analysis, techniques and applications","volume":"14 5","pages":"Pages 221-227"},"PeriodicalIF":0.0,"publicationDate":"1999-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1050-3862(98)00032-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20957548","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}
Tina Hernandez-Boussard, Ruggero Montesano, Pierre Hainaut
{"title":"Sources of bias in the detection and reporting of p53 mutations in human cancer: analysis of the IARC p53 mutation database","authors":"Tina Hernandez-Boussard, Ruggero Montesano, Pierre Hainaut","doi":"10.1016/S1050-3862(98)00030-8","DOIUrl":"10.1016/S1050-3862(98)00030-8","url":null,"abstract":"<div><p>p53 gene encodes a transcription factor with tumor suppressive properties and to date, somatic mutation of this gene is the most common genetic event in human cancer. A relational database has been developed to facilitate the retrieval and analysis of these mutations at the International Agency for Research on Cancer (IARC) and it currently contains information on over 8000 individual tumors and cell lines. Many factors may influence the detection and reporting of mutations, including selection of tumor samples, study design, choice of methods, and quality control. There is also concern that several biases may affect the way data appear in the literature. Minimizing these biases is an essential methodological issue in the development of mutation databases. In this paper, we review and discuss these main sources of bias and make recommendations to authors in order to minimize bias in mutation detection and reporting.</p></div>","PeriodicalId":77142,"journal":{"name":"Genetic analysis, techniques and applications","volume":"14 5","pages":"Pages 229-233"},"PeriodicalIF":0.0,"publicationDate":"1999-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S1050-3862(98)00030-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20957549","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}