DNA diagnostics by surface-bound melt-curve reactions

Journal of Molecular Diagnostics

Volumn 9, Issue 1, 2007, Pages 30-41

  Meuzelaar, Linda Strömqvist ^a   Hopkins, Katie ^b   Liebana, Ernesto ^c   Brookes, Anthony J ^a  

^a UNIVERSITY OF LEICESTER   (United Kingdom)

^b PUBLIC HEALTH ENGLAND   (United Kingdom)

^c Veterinary Laboratory Agency   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; DNA TOPOISOMERASE (ATP HYDROLYSING) A; GENOMIC DNA; DNA; DNA TOPOISOMERASE (ATP HYDROLYSING); PRIMER DNA;

ACCURACY; ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; CONTROLLED STUDY; DNA DENATURATION; DNA HYBRIDIZATION; DNA PROBE; DNA SEQUENCE; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; FEMALE; GENE MUTATION; GENETIC VARIABILITY; HUMAN; MUTATIONAL ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; SALMONELLA; SINGLE NUCLEOTIDE POLYMORPHISM; WILD TYPE; DIAGNOSTIC PROCEDURE; EVALUATION; GENETICS; METHODOLOGY; MOLECULAR GENETICS; NUCLEIC ACID HYBRIDIZATION; SEQUENCE ALIGNMENT; TRANSITION TEMPERATURE;

SALMONELLA;

BASE SEQUENCE; DNA; DNA GYRASE; DNA MUTATIONAL ANALYSIS; DNA PRIMERS; EVALUATION STUDIES; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; MOLECULAR SEQUENCE DATA; NUCLEIC ACID DENATURATION; NUCLEIC ACID HYBRIDIZATION; POLYMORPHISM, SINGLE NUCLEOTIDE; SALMONELLA; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; TRANSITION TEMPERATURE;

EID: 34548254489     PISSN: 15251578     EISSN: None     Source Type: Journal    
DOI: 10.2353/jmoldx.2007.060057     Document Type: Article

References (33)

1. Underhill PA, Jin L, Lin AA, Mehdi SQ, Jenkins T, Vollrath D, Davis RW, Cavalli-Sforza LL, Oefner PJ: Detection of numerous Y chromosome biallelic polymorphisms by denaturing high performance liquid chromatography. Genome Res 1997, 7:996-1005
2. O'Donovan MC, Oefner PJ, Roberts SC, Austin J, Hoogendoorn B, Guy C, Speight G, Upadhyaya M, Sommer SS, McGuffin P: Blind analysis of denaturing high-performance liquid chromatography as a tool for mutation detection. Genomics 1998, 52:44-49
3. Myers RM, Lumelsky N, Lerman LS, Maniatis T: Detection of single base substitutions in total genomic DNA. Nature 1985, 313:495-498
4. Noll WW, Collins M: Detection of human DNA polymorphisms with a simplified denaturing gradient gel electrophoresis technique. Proc Natl Acad Sci USA 1987, 84:3339-3343
5. Riesner D, Steger G, Zimmat R, Owens RA, Wagenhofer M, Hillen W, Vollbach S, Henco K: Temperature-gradient gel electrophoresis of nucleic acids: analysis of conformational transitions, sequence variations, and protein-nucleic acid interactions. Electrophoresis 1989, 10:377-389
6. Orita M, Iwahana H, Kanazawa H, Hayashi K, Sekiya T: Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc Natl Acad Sci USA 1989, 86:2766-2770
7. Makino R, Yazyu H, Kishimoto Y, Sekiya T, Hayashi K: F-SSCP: fluorescence-based polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) analysis. PCR Methods Appl 1992, 2:10-13
8. Wittwer CT, Reed GH, Gundry CN, Vandersteen JG, Pryor RJ: High-resolution genotyping by amplicon melting analysis using LCGreen. Clin Chem 2003, 49:853-860
9. Gundry CN, Vandersteen JG, Reed GH, Pryor RJ, Chen J, Wittwer CT: Amplicon melting analysis with labeled primers: a closed-tube method for differentiating homozygotes and heterozygotes. Clin Chem 2003, 49:396-406
10. Lay MJ, Wittwer CT: Real-time fluorescence genotyping of factor V Leiden during rapid-cycle PCR. Clin Chem 1997, 43:2262-2267
11. Vrettou C, Traeger-Synodinos J, Tzetis M, Malamis G, Kanavakis E: Rapid screening of multiple β-globin gene mutations by real-time PCR on the LightCycler: application to carrier screening and prenatal diagnosis of thalassemia syndromes. Clin Chem 2003, 49:769-776
12. Millward H, Samowitz W, Wittwer CT, Bernard PS: Homogeneous amplification and mutation scanning of the p53 gene using fluorescent melting curves. Clin Chem 2002, 48:1321-1328
13. Afonina IA, Reed MW, Lusby E, Shishkina IG, Belousov YS: Minor groove binder-conjugated DNA probes for quantitative DNA detection by hybridization-triggered fluorescence. Biotechniques 2002, 32:940-949
14. Belousov Y, Welch RA, Sanders S, Mills A, Kulchenko A, Dempcy R, Afonina IA, Walburger DA, Glaser CL, Yadavalli S, Vermeulen NMJ, Mahoney W: Single nucleotide polymorphism genotyping by two colour melting curve analysis using the MGB Eclipse probe system in challenging sequence environment. Hum Genomics 2004, 1:209-217
15. Kafatos FC, Jones CW, Efstratiadis A: Determination of nucleic acid sequence homologies and relative concentrations by a dot hybridization procedure. Nucleic Acids Res 1979, 7:1541-1552
16. Saiki RK, Walsh PS, Levenson CH, Erlich HA: Genetic analysis of amplified DNA with immobilized sequence-specific oligonucleotide probes. Proc Natl Acad Sci USA 1989, 86:6230-6234
17. Kennedy GC, Matsuzaki H, Dong S, Liu WM, Huang J, Liu G, Su X, Cao M, Chen W, Zhang J, Liu W, Yang G, Di X, Ryder T, He Z, Surti U, Phillips MS, Boyce-Jacino MT, Fodor SP, Jones KW: Large-scale genotyping of complex DNA. Nat Biotechnol 2003, 21:1233-1237
18. Matsuzaki H, Dong S, Loi H, Di X, Liu G, Hubbell E, Law J, Berntsen T, Chadha M, Hui H, Yang G, Kennedy GC, Webster TA, Cawley S, Walsh PS, Jones KW, Fodor SP, Mei R: Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat Methods 2004, 1:109-111
19. Hacia JG: Resequencing and mutational analysis using oligonucleotide microarrays. Nat Genet 1999, 21:42-47
20. Mockler TC, Ecker JR: Applications of DNA tiling arrays for whole-genome analysis. Genomics 2005, 85:1-15
21. Howell WM, Jobs M, Gyllensten U, Brookes AJ: Dynamic allele-specific hybridization. A new method for scoring single nucleotide polymorphisms. Nat Biotech 1999, 17:87-88
22. Prince JA, Feuk L, Howell WM, Jobs M, Emahazion T, Blennow K, Brookes AJ: Robust and accurate single nucleotide polymorphism genotyping by dynamic allele-specific hybridization (DASH): design criteria and assay validation. Genome Res 2001, 11:152-162
23. Jobs M, Howell WM, Strömqvist L, Mayr T, Brookes AJ: DASH-2: flexible, low-cost, and high-throughput SNP genotyping by dynamic allele-specific hybridization on membrane arrays. Genome Res 2003, 13:916-924
24. Sosnowski RG, Tu E, Butler WF, O'Connell JP, Heller MJ: Rapid determination of single base mismatch mutations in DNA hybrids by direct electric field control. Proc Natl Acad Sci USA 1997, 94:1119-1123
25. Gilles PN, Wu DJ, Foster CB, Dillon PJ, Chanock SJ: Single nucleotide polymorphic discrimination by an electronic dot blot assay on semiconductor microchips. Nat Biotechnol 1999, 17:365-370
26. Sawyer SE, Howell WM, Brookes AJ: Scoring insertion-deletion polymorphisms by dynamic allele-specific hybridization. Biotechniques 2003, 35:292-298
27. Fredman D, White SJ, Potter S, Eichler EE, Den Dunnen JT, Brookes AJ: Complex SNP-related sequence variation in segmental genome duplications. Nat Genet 2004, 36:861-866
28. Hopkins KL, Davies RH, Threlfall EJ: Mechanisms of quinolone resistance in Escherichia coli and Salmonella: recent developments. Int J Antimicrob Agents 2005, 25:358-373
29. Randall LP, Woodward MJ: Multiple antibiotic resistance (mar) locus in Salmonella enterica serovar typhimurium DT104. Appl Environ Microbiol 2001, 67:1190-1197
30. Giraud E, Cloeckaert A, Kerboeuf D, Chaslus-Dancla E: Evidence for active efflux as the primary mechanism of resistance to ciprofloxacin in Salmonella enterica serovar typhimurium. Antimicrob Agents Chemother 2000, 44:1223-1228
31. Griggs DJ, Gensberg K, Piddock LJ: Mutations in gyrA gene of quinolone-resistant Salmonella serotypes isolated from humans and animals. Antimicrob Agents Chemother 1996, 40:1009-1013
32. Jobs M, Howell WM, Brookes AJ: Creating arrays by centrifugation. Biotechniques 2002, 32:1322-1329
33. Howell WM, Jobs M, Brookes AJ: iFRET: an improved fluorescence system for DNA-melting analysis. Genome Res 2002, 12:1401-1407