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Gaster J, Rangam G, Marx A. Increased single nucleotide discrimination in arrayed primer elongation by 4'C-modified primer probes. Chem Commun (Camb) 2007:1692-4. [PMID: 17457410 DOI: 10.1039/b616129d] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Herein we describe the beneficial impact of immobilized 4'C-modified primer probes on detecting single nucleotide variations in arrayed primer extension by a DNA polymerase.
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Affiliation(s)
- Jens Gaster
- Universität Konstanz, Fachbereich Chemie, Universitätsstr. 10, 78457 Konstanz, Germany
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2
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Järvelä IE. Molecular diagnosis of adult-type hypolactasia (lactase non-persistence). Scandinavian Journal of Clinical and Laboratory Investigation 2006; 65:535-9. [PMID: 16271984 DOI: 10.1080/00365510500208316] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- I E Järvelä
- Laboratory of Molecular Genetics, Helsinki University Central Hospital and Department of Medical Genetics, University of Helsinki, Helsinki, Finland.
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3
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Rasinpera H, Saarinen K, Pelkonen A, Jarvela I, Savilahti E, Kolho KL. Molecularly defined adult-type hypolactasia in school-aged children with a previous history of cow’s milk allergy. World J Gastroenterol 2006; 12:2264-8. [PMID: 16610034 PMCID: PMC4087659 DOI: 10.3748/wjg.v12.i14.2264] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To assess the role of lactase non-persistence/persistence in school-aged children and their milk-related symptoms.
METHODS: The genotypes for the C/T-13910 variant associated with lactase non-persistence/ persistence were determined using PCR-minisequencing in a group of 172 children with a mean age of 8.6 years (SE = 0.02, 93 boys) participating in a follow-up study for cow’s milk allergy. The parents were asked to assess their children’s milk consumption and abdominal symptoms.
RESULTS: The presence of allergy to cow’s milk was not associated with the C/C-13910 genotype related with a decline of lactase enzyme activity during childhood (lactase non-persistence). The frequency of the C/C-13910 genotype (16%) was similar to published figures for the prevalence of adult-type hypolactasia in Finland. The majority of the children (90%) in this series consumed milk but 26% of their families suspected that their children had milk-related symptoms. Forty-eight percent of the children with the C/C-13910 genotype did not drink milk at all or consumed a low lactose containing diet prior to the genotyping (P < 0.004 when compared to the other genotypes).
CONCLUSION: Analysis of the C/T-13910 polymorphism is an easy and reliable method for excluding adult-type hypolactasia in children with milk-related symptoms. Genotyping for this variant can be used to advise diets for children with a previous history of cow’s milk allergy.
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Affiliation(s)
- Heli Rasinpera
- Department of Medical Genetics, University of Helsinki, Finland
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4
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Rudi K, Holck AL. Real-time closed tube single nucleotide polymorphism (SNP) quantification in pooled samples by quencher extension (QEXT). Nucleic Acids Res 2003; 31:e117. [PMID: 14500845 PMCID: PMC206483 DOI: 10.1093/nar/gng118] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Quencher extension (QEXT) is a novel single step closed tube real-time method to quantify SNPs using reporters and quenchers in combination with primer extension. A probe with a 5'-reporter dye is single base extended with a dideoxy nucleotide containing a quencher dye if the target SNP allele is present. The extension is recorded from the quenching (reduced fluorescence) of the reporter dye. This avoids the influence of the unincorporated dye-labeled nucleotides, resulting in high accuracy and a high signal-to-noise ratio. The relative amount of a specific SNP allele is determined from the nucleotide incorporation rate in a thermo-cycling reaction. We tested the QEXT assay using five SNPs in the Listeria monocytogenes inlA gene as a model system. The presence of the target SNP alleles was determined with high statistical confidence (P < 0.0005). The quantitative detection limits were between 0 and 5% for the targeted SNP alleles on a background of other SNP alleles (P < 0.05). The QEXT method is directly adaptable to current real-time PCR equipment and is thus suited for high throughput and a wide application range.
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Affiliation(s)
- Knut Rudi
- MATFORSK Norwegian Food Research Institute, Osloveien 1, 1430 As, Norway.
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5
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Brennan MD. High throughput genotyping technologies for pharmacogenomics. AMERICAN JOURNAL OF PHARMACOGENOMICS : GENOMICS-RELATED RESEARCH IN DRUG DEVELOPMENT AND CLINICAL PRACTICE 2002; 1:295-302. [PMID: 12083961 DOI: 10.2165/00129785-200101040-00006] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Genetic differences between individuals play a role in determining susceptibility to diseases as well as in drug response. The challenge today is first to discover the range of genetic variability in the human population and then to define the particular gene variants, or alleles, that contribute to clinically important outcomes. Consequently, high throughput, automated methods are being developed that allow rapid scoring of microsatellite alleles and single nucleotide polymorphisms (SNPs). Many detection technologies are being used to accomplish this goal, including electrophoresis, standard fluorescence, fluorescence polarization, fluorescence resonance energy transfer, and mass spectrometry. SNP alleles may be distinguished by any one of several methods, including single nucleotide primer extension, allele-specific hybridization, allele-specific primer extension, oligonucleotide ligation assay, and invasive signal amplification. Newer methods require less sample manipulation, increase sensitivity, allow more flexibility, and decrease reagent costs. Recent developments show promise for continuing these trends by combining amplification and detection steps and providing flexible, miniaturized platforms for genotyping.
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Affiliation(s)
- M D Brennan
- Department of Biochemistry and Molecular Biology, University of Louisville School of Medicine, Louisville, Kentucky 40292, USA.
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6
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Nicewarner Peña SR, Raina S, Goodrich GP, Fedoroff NV, Keating CD. Hybridization and enzymatic extension of au nanoparticle-bound oligonucleotides. J Am Chem Soc 2002; 124:7314-23. [PMID: 12071740 DOI: 10.1021/ja0177915] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have investigated the impact of steric effects on the hybridization and enzymatic extension of oligonucleotides bound to 12-nm colloidal Au particles. In these experiments, a nanoparticle-bound 12-mer sequence is hybridized either to its solution phase 12-mer complement or to an 88-mer template sequence. The particle-bound oligonucleotide serves as a primer for enzymatic extension reactions, in which covalent incorporation of nucleotides to form the complement of the template is achieved by the action of DNA polymerase. Primers were attached via-C(6)H(12)SH, -C(12)H(24)SH, and -TTACAATC(6)H(12)SH linkers attached at the 5' end. Primer coverage on the nanoparticles was varied by dilution with (5')HSC(6)H(12)AAA AAA(3'). Hybridization efficiencies were determined as a function of linker length, primer coverage, complement length (12-mer vs 88-mer), and primer:complement concentration ratio. In all cases, hybridization for the 88-mer was less efficient than for the 12-mer. Low primer surface coverage, greater particle-primer separation, and higher primer:complement ratios led to optimal hybridization. Hybridization efficiencies as high as 98% and 75% were observed for the 12-mer and 88-mer, respectively. Enzymatic extension of particle-bound primers was observed under all conditions tested; however, the efficiency of the reaction was strongly affected by linker length and primer coverage. Extension of primers attached by the longest linker was as efficient as the solution-phase reaction.
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Affiliation(s)
- Sheila R Nicewarner Peña
- Department of Chemistry and Life Sciences Consortium, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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7
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Enattah NS, Sahi T, Savilahti E, Terwilliger JD, Peltonen L, Järvelä I. Identification of a variant associated with adult-type hypolactasia. Nat Genet 2002; 30:233-7. [PMID: 11788828 DOI: 10.1038/ng826] [Citation(s) in RCA: 649] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Adult-type hypolactasia, also known as lactase non-persistence (lactose intolerance), is a common autosomal recessive condition resulting from the physiological decline in activity of the lactase-phlorizin hydrolase (LPH) in intestinal cells after weaning. LPH hydrolyzes lactose into glucose and galactose. Sequence analyses of the coding and promoter regions of LCT, the gene encoding LPH, has revealed no DNA variations correlating with lactase non-persistence. An associated haplotype spanning LCT, as well as a distinct difference in the transcript levels of 'non-persistence' and 'persistence' alleles in heterozygotes, suggest that a cis-acting element contributes to the lactase non-persistence phenotype. Using linkage disequilibrium (LD) and haplotype analysis of nine extended Finnish families, we restricted the locus to a 47-kb interval on 2q21. Sequence analysis of the complete region and subsequent association analyses revealed that a DNA variant, C/T-13910, roughly 14 kb upstream from the LCT locus, completely associates with biochemically verified lactase non-persistence in Finnish families and a sample set of 236 individuals from four different populations. A second variant, G/A-22018, 8 kb telomeric to C/T-13910, is also associated with the trait in 229 of 236 cases. Prevalence of the C/T-13910 variant in 1,047 DNA samples is consistent with the reported prevalence of adult-type hypolactasia in four different populations. That the variant (C/T-13910) occurs in distantly related populations indicates that it is very old.
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Affiliation(s)
- Nabil Sabri Enattah
- Department of Molecular Medicine, National Public Health Institute, Haartmaninkatu 8, PO Box 104, FIN-00251 Helsinki, Finland
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8
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Pirrung MC, Worden JD, Labriola JP, Montague-Smith MP, Weislo LJ. Solid-phase, single nucleotide primer extension of DNA/RNA hybrids by reverse transcriptases. Bioorg Med Chem Lett 2001; 11:2437-40. [PMID: 11549441 DOI: 10.1016/s0960-894x(01)00465-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A method for RNA analysis based on primer extension by reverse transcriptase is described.
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Affiliation(s)
- M C Pirrung
- Department of Chemistry, Levine Science Research Center, Duke University, Durham, NC 27708-0317, USA.
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9
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Stoerker J, Mayo JD, Tetzlaff CN, Sarracino DA, Schwope I, Richert C. Rapid genotyping by MALDI-monitored nuclease selection from probe libraries. Nat Biotechnol 2000; 18:1213-6. [PMID: 11062445 DOI: 10.1038/81226] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Data on five single-nucleotide polymorphisms (SNPs) per gene are estimated to allow association of disease risks or pharmacogenetic parameters with individual genes. Efficient technologies for rapidly detecting SNPs will therefore facilitate the mining of genomic information. Known methods for SNP analysis include restriction-fragment-length polymorphism polymerase chain reaction (PCR), allele-specific oligomer hybridization, oligomer-specific ligation assays, minisequencing, direct sequencing, fluorescence-detected 5'-exonuclease assays, and hybridization with PNA probes. Detection by mass spectrometry (MS) offers speed and high resolution. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS) can detect primer extension products, mass-tagged oligonucleotides, DNA created by restriction endonuclease cleavage, and genomic DNA. We have previously reported MALDI-TOF-monitored nuclease selections of modified oligonucleotides with increased affinity for targets. Here we use nuclease selections for genotyping by treating DNA to be analyzed with oligonucleotide probes representing known genotypes and digesting probes that are not complementary to the DNA. With phosphodiesterase I, the target-bound, complementary probe is largely refractory to nuclease attack and its peak persists in mass spectra (Fig. 1A). In optimized assays, both alleles of a heterozygote were genotyped with six nonamer DNA probes (> or = 125 fmol each) and asymmetrically amplified DNA from exon 10 of the cystic fibrosis transmembrane regulatory gene (CFTR).
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Affiliation(s)
- J Stoerker
- Department of Chemistry, Tufts University, Medford, MA 02155, USA
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10
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Favis R, Day JP, Gerry NP, Phelan C, Narod S, Barany F. Universal DNA array detection of small insertions and deletions in BRCA1 and BRCA2. Nat Biotechnol 2000; 18:561-4. [PMID: 10802632 DOI: 10.1038/75452] [Citation(s) in RCA: 168] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Array-based mutation detection methodology typically relies on direct hybridization of the fluorescently labeled query sequence to surface-bound oligonucleotide probes. These probes contain either small sequence variations or perfect-match sequence. The intensity of fluorescence bound to each oligonucleotide probe is intended to reveal which sequence is perfectly complementary to the query sequence. However, these approaches have not always been successful, especially for detection of small frameshift mutations. Here we describe a multiplex assay to detect small insertions and deletions by using a modified PCR to evenly amplify each amplicon (PCR/PCR), followed by ligase detection reaction (LDR). Mutations were identified by screening reaction products with a universal DNA microarray, which uncouples mutation detection from array hybridization and provides for high sensitivity. Using the three BRCA1 and BRCA2 founder mutations in the Ashkenazi Jewish population (BRCA1 185delAG; BRCA1 5382insC; BRCA2 6174delT) as a model system, the assay readily detected these mutations in multiplexed reactions. Our results demonstrate that universal microarray analysis of PCR/PCR/LDR products permits rapid identification of small insertion and deletion mutations in the context of both clinical diagnosis and population studies.
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Affiliation(s)
- R Favis
- Department of Microbiology, Hearst Microbiology Research Center and Strang Cancer Prevention Center, Joan and Sanford I. Weill Medical College of Cornell University, 1300 York Ave., Box 62, New York, NY 10021, USA
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11
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Pirrung MC, Connors RV, Odenbaugh AL, Montague-Smith MP, Walcott NG, Tollett JJ. The Arrayed Primer Extension Method for DNA Microchip Analysis. Molecular Computation of Satisfaction Problems. J Am Chem Soc 2000. [DOI: 10.1021/ja992392j] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael C. Pirrung
- Contribution from the Department of Chemistry, Levine Science Research Center, Duke University, Durham, North Carolina 27708-0317, and the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Richard V. Connors
- Contribution from the Department of Chemistry, Levine Science Research Center, Duke University, Durham, North Carolina 27708-0317, and the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Amy L. Odenbaugh
- Contribution from the Department of Chemistry, Levine Science Research Center, Duke University, Durham, North Carolina 27708-0317, and the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Michael P. Montague-Smith
- Contribution from the Department of Chemistry, Levine Science Research Center, Duke University, Durham, North Carolina 27708-0317, and the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Nathan G. Walcott
- Contribution from the Department of Chemistry, Levine Science Research Center, Duke University, Durham, North Carolina 27708-0317, and the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Jeff J. Tollett
- Contribution from the Department of Chemistry, Levine Science Research Center, Duke University, Durham, North Carolina 27708-0317, and the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
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12
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Hatch A, Sano T, Misasi J, Smith CL. Rolling circle amplification of DNA immobilized on solid surfaces and its application to multiplex mutation detection. GENETIC ANALYSIS : BIOMOLECULAR ENGINEERING 1999; 15:35-40. [PMID: 10191983 DOI: 10.1016/s1050-3862(98)00014-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A new method of amplifying short DNA molecules immobilized on a solid support has been developed. This method uses a solid-phase rolling circle replication reaction, termed rolling circle amplification (RCA). The probe consists of a single-stranded DNA primer anchored at the 5' terminus to a solid support and a single stranded DNA template hybridized to the immobilized primer. Here, DNA ligase was used to circularize the template, and DNA polymerase I was used to extend the immobilized primer in a rolling circle replication reaction. This method was used to identify a known polymorphism in BRCA1 exon 5. These results demonstrate that RCA offers considerable promise to facilitate effective mutation screening of DNA using a solid-phase format.
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Affiliation(s)
- A Hatch
- Center for Advanced Biotechnology, Boston University, MA 02215, USA
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13
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Abstract
A rapidly expanding number of genetic mechanisms contributing to disease can be accessed via molecular analysis. In order to take full advantage of this potential for genetic diagnostics, and to monitor treatment by gene therapy and other emerging methods, a new generation of diagnostic techniques will be required. Of central importance in future analyses is the possibility to perform very large numbers of simultaneous genetic analyses in analytical devices of small linear dimensions. We have developed a new molecular probe design that is amenable to highly multiplex, specific analyses of total genomic DNA or of RNA molecules expressed in tissue samples. Here, a brief history of gene analytical procedures is presented, followed by a discussion of the properties, means of synthesis and applications of this new class of gene analytic reagents, padlock probes.
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Affiliation(s)
- U Landegren
- Department of Medical Genetics, Uppsala University, Sweden.
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14
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Piggee CA, Muth J, Carrilho E, Karger BL. Capillary electrophoresis for the detection of known point mutations by single-nucleotide primer extension and laser-induced fluorescence detection. J Chromatogr A 1997; 781:367-75. [PMID: 9368396 DOI: 10.1016/s0021-9673(97)00637-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Capillary electrophoresis (CE) with laser-induced fluorescence (LIF) was used to detect known point mutations using the method of single-nucleotide primer extension (SNuPE). Three different point mutations in human mitochondrial DNA associated with Leber's hereditary optic neuropathy (LHON) were detected by annealing a primer immediately 5' to the mutation on the template and extending the primer by one fluorescently labeled dideoxy terminator complementary to the mutation. By using two or more differently labeled terminators, both the mutant and wild type could be simultaneously detected. The advantages of using CE-LIF for detecting SNuPE reactions include speed and ease of analysis, absence of radioactivity, and potential for automation.
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Affiliation(s)
- C A Piggee
- Barnett Institute, Northeastern University, Boston, MA 02115, USA
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15
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Bellanné-Chantelot C, Beaufils S, Hourdel V, Lesage S, Morel V, Dessinais N, Le Gall I, Cohen D, Dausset J. Search for DNA sequence variations using a MutS-based technology. Mutat Res 1997; 382:35-43. [PMID: 9360636 DOI: 10.1016/s1383-5726(97)00007-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The search for DNA sequence variations (DSV) is emphasized with genetic studies of a large number of multifactorial diseases. Saturation of regions of interest with diallelic polymorphisms will be an essential step to pinpoint, through association studies, predisposing genes. We have developed a solid-phase method based on the ability of mismatch binding protein MutS to recognize single nucleotide mismatches. This approach was applied to the study of 83 sequence-tagged sites (STSs) extracted from an eight centimorgans (cM) chromosome 21 region. One-third of tested STSs were found to be polymorphic leading to a frequency of one DSV every 822 base pairs (bp). Sequencing of analyzed STSs showed the high reliability of the MutS-based technology for mismatches up to 2 bp in DNA fragments ranging in size from 200 bp to 1 kilobase (kb). The entire assay which is performed in a solid-phase format without the need of electrophoresis or sequencing, will provide an efficient tool for new polymorphism detection.
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16
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Abstract
Complete sequences of genomes and comprehensive sets of cDNA sequences open the way to a hugh range of biological problems. There is a need for analytical methods that can deal with the large number of sequences in the data banks and, ideally, we would like to analyse all sequences together. Gel-based sequencing is a serial process that analyses one sequence at a time. Oligonucleotide arrays, or 'DNA chips', are miniature, parallel analytical devices, which could bring to sequence analysis and molecular genetics many of the advantages that semiconductor devices brought to computing.
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Affiliation(s)
- E M Southern
- Department of Biochemistry, University of Oxford, UK.
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17
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[2]Detection of point mutations by solid-phase minisequencing. Hum Mol Genet 1996. [DOI: 10.1016/s1067-2389(96)80035-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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18
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Abstract
A mutation analysis method based upon a wild-type DNA sequence is presented. Oligonucleotides were utilized for primer extension by T7 DNA polymerase to discriminate between wild-type and mutant sequences in two solid phase approaches. 1. Oligonucleotides were annealed to an immobilized template, extended with fluorescent dideoxynucleotides (ddNTPs), and analyzed on an automated fluorescent DNA sequencer. The oligonucleotide length identified the known mutation site, and the fluorescence emission of the ddNTP identified the mutation. 2. Template DNA was annealed to an oligonucleotide array, extended with alpha-32P dNTPs, and analyzed with a Phosphor Imager. The grid position of the oligonucleotide identified the mutation site and the extended base identified the mutation.
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Affiliation(s)
- J M Shumaker
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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