The use of real-time PCR methods in DNA sequence variation analysis

Clinica Chimica Acta

Volumn 363, Issue 1-2, 2006, Pages 32-47

  Gibson, Neil J ^a  

^a ASTRAZENECA   (United Kingdom)

Author keywords

Genotyping; Mutations; Real time PCR; SNP discovery; SNPs

Indexed keywords

ALLELE; ANALYTIC METHOD; CARCINOGENESIS; DNA SEQUENCE; FLUORESCENCE ANALYSIS; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; HEREDITY; INSTRUMENTATION; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; REVIEW; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; SOMATIC MUTATION;

ANIMALS; DNA MUTATIONAL ANALYSIS; GENOTYPE; HUMANS; MUTATION; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA;

EID: 28544449472     PISSN: 00098981     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cccn.2005.06.022     Document Type: Review

References (61)

1. L.T. Franca, E. Carrilho, and T.B. Kist A review of DNA sequencing techniques Q Rev Biophys 35 2002 169 200
2. A. Maitra, Y. Cohen, and S.E. Gillespie The Human MitoChip: a high-throughput sequencing microarray for mitochondrial mutation detection Genome Res 14 2004 812 819
3. B. Schroell-Metzger, M. Dicato, M. Bosseler, and G. Berchem Comparison of standard PCR and the LightCycler technique to determine the thrombophilic mutations: an efficiency and cost study Clin Chem Lab Med 41 2003 482 485
4. D.T. Newby, T.L. Hadfield, and F.F. Roberto Real-time PCR detection of Brucella abortus: a comparative study of SYBR green I, 5′-exonuclease, and hybridization probe Appl Environ Microbiol 69 2003 4753 4759
5. L. Zhou, A.N. Myers, J.G. Vandersteen, L. Wang, and C.T. Wittwer Closed-tube genotyping with unlabeled oligonucleotide probes and a saturating DNA dye Clin Chem 50 2004 1328 1335
6. M. Bengtsson, H.J. Karlsson, G. Westman, and M. Kubista A new minor groove binding asymmetric cyanine reporter dye for real-time PCR Nucleic Acids Res 31 2003 e45
7. M. Gupta, P. Song, C.R. Yates, and B. Meibohm Real-time PCR-based genotyping assay for CXCR2 polymorphisms Clin Chim Acta 341 2004 93 100
8. S. Dall'Ozzo, C. Andres, P. Bardos, H. Watier, and G. Thibault Rapid single-step FCGR3A genotyping based on SYBR Green I fluorescence in real-time multiplex allele-specific PCR J Immunol Methods 277 2003 185 192
9. J. Brownie, S. Shawcross, and J. Theaker The elimination of primer-dimer accumulation in PCR Nucleic Acids Res 25 1997 3235 3241
10. M. Urata, Y. Wada, and S.H. Kim High-sensitivity detection of the A3243G mutation of mitochondrial DNA by a combination of allele-specific PCR and peptide nucleic acid-directed PCR clamping Clin Chem 50 2004 2045 2051
11. N. Marziliano, E. Bevilacqua, D. Pirulli, A. Span, A. Amoroso, and S. Crovella Single tube melting temperature assay for rapid and sensitive detection of the most frequent hemocromatosis mutations, C282Y and H63D Haematologica 85 2000 990 991
12. W. Shengqi, W. Xiaohong, C. Suhong, and G. Wei A new fluorescent quantitative polymerase chain reaction technique Anal Biochem 309 2002 206 211
13. A.M. Rickert, T.A. Borodina, E.J. Kuhn, H. Lehrach, and S. Sperling Refinement of single-nucleotide polymorphism genotyping methods on human genomic DNA: amplifluor allele-specific polymerase chain reaction versus ligation detection reaction-TaqMan Anal Biochem 330 2004 288 297
14. P.M. Holland, R.D. Abramson, R. Watson, and D.H. Gelfand Detection of specific polymerase chain reaction product by utilizing the 5′-3′ exonuclease activity of Thermus aquaticus DNA polymerase Proc Natl Acad Sci U S A 88 1991 7276 7280
15. D. Whitcombe, J. Theaker, S.P. Guy, T. Brown, and S. Little Nat Biotechnol 17 1999 804 807
16. M.J. Lay, and C.T. Wittwer Real-time fluorescence genotyping of factor V Leiden during rapid-cycle PCR Clin Chem 43 1997 2262 2267
17. G.H. Reed, and C.T. Wittwer Sensitivity and specificity of single-nucleotide polymorphism scanning by high-resolution melting analysis Clin Chem 50 2004 1748 1754
18. M. Liew, R. Pryor, and R. Palais Genotyping of single-nucleotide polymorphisms by high-resolution melting of small amplicons Clin Chem 50 2004 1156 1164
19. C.N. Gundry, J.G. Vandersteen, G.H. Reed, R.J. Pryor, J. Chen, and C.T. Wittwer Amplicon melting analysis with labeled primers: a closed-tube method for differentiating homozygotes and heterozygotes Clin Chem 49 2003 396 406
20. H. Millward, W. Samowitz, C.T. Wittwer, and P.S. Bernard Homogeneous amplification and mutation scanning of the p53 gene using fluorescent melting curves Clin Chem 48 2002 1321 1328
21. P.S. Bernard, R.S. Ajioka, J.P. Kushner, and C.T. Wittwer Homogeneous multiplex genotyping of hemochromatosis mutations with fluorescent hybridization probes Am J Pathol 153 1998 1055 1061
22. P. Duck, G. Alvarado-Urbina, B. Burdick, and B. Collier Probe amplifier system based on chimeric cycling oligonucleotides Biotechniques 9 1990 142 148
23. J.J. Harvey, S.P. Lee, and E.K. Chan Characterization and applications of CataCleave probe in real-time detection assays Anal Biochem 333 2004 246 255
24. C.R. Newton, A. Graham, and L.E. Heptinstall Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS) Nucleic Acids Res 17 1989 2503 2516
25. S. Germer, and R. Higuchi Homogeneous allele-specific PCR in SNP genotyping Methods Mol Biol 212 2003 197 214
26. M.M. Huang, N. Arnheim, and M.F. Goodman Extension of base mispairs by Taq DNA polymerase: implications for single nucleotide discrimination in PCR Nucleic Acids Res 20 1992 4567 4573
27. K. Sylvain, H. Aurelie, M. Marc, and R. Christophe Rapid screening for HLA-B27 by a TaqMan-PCR assay using sequence-specific primers and a minor groove binder probe, a novel type of TaqMan™ probe J Immunol Methods 287 2004 179 186
28. D. Whitcombe, J. Brownie, and H.L. Gillard A homogeneous fluorescence assay for PCR amplicons: its application to real-time, single-tube genotyping Clin Chem 44 1998 918 923
29. B.L. Gaffney, and R.A. Jones Thermodynamic comparison of the base pairs formed by the carcinogenic lesion O6-methylguanine with reference both to Watson-Crick pairs and to mismatched pairs Biochemistry 28 1989 5881 5889
30. I.A. Afonina, S. Sanders, D. Walburger, and Y.S. Belousov Accurate SNP typing by real-time PCR. A comparison of minor groove binder-conjugated DNA probes Pharmagenomics 2 2002 48 54
31. M. Louis, A.F. Dekairelle, and J.L. Gala Rapid combined genotyping of factor V, prothrombin and methylenetetrahydrofolate reductase single nucleotide polymorphisms using minor groove binding DNA oligonucleotides (MGB probes) and real-time polymerase chain reaction Clin Chem Lab Med 42 2004 1364 1369
32. P. Sham, J.S. Bader, I. Craig, M. O'Donovan, and M. Owen DNA pooling: a tool for large-scale association studies Nat Rev Genet 3 2002 862 871
33. D.R. Hodgson, C.A. Foy, M. Partridge, S. Pateromichelakis, and N.J. Gibson Development of a facile fluorescent assay for the detection of 80 mutations within the p53 gene Mol Med 8 2002 227 237
34. V.J. Johnson, B. Yucesoy, and M.I. Luster Genotyping of single nucleotide polymorphisms in cytokine genes using real-time PCR allelic discrimination technology Cytokine 27 2004 135 141
35. R. Faner, N. Casamitjana, and R. Colobran HLA-B27 genotyping by fluorescent resonance emission transfer (FRET) probes in real-time PCR Hum Immunol 65 2004 826 838
36. C. Vrettou, J. Traeger-Synodinos, M. Tzetis, G. Palmer, C. Sofocleous, and E. Kanavakis Real-time PCR for single-cell genotyping in sickle cell and thalassemia syndromes as a rapid, accurate, reliable, and widely applicable protocol for preimplantation genetic diagnosis Hum Mutat 23 2004 513 521
37. K. Petersen, U. Vogel, and E. Rockenbauer Short PNA molecular beacons for real-time PCR allelic discrimination of single nucleotide polymorphisms Mol Cell Probes 18 2004 117 122
38. A. Simeonov, and T.T. Nikiforov Single nucleotide polymorphism genotyping using short, fluorescently labeled locked nucleic acid (LNA) probes and fluorescence polarization detection Nucleic Acids Res 30 2002 e91
39. P. Mouritzen, A.T. Nielsen, H.M. Pfundheller, Y. Choleva, L. Kongsbak, and S. Moller Single nucleotide polymorphism genotyping using locked nucleic acid (LNA) Expert Rev Mol Diagn 3 2003 27 38
40. D. Latorra, K. Campbell, A. Wolter, and J.M. Hurley Enhanced allele-specific PCR discrimination in SNP genotyping using 3′ locked nucleic acid (LNA) primers Hum Mutat 22 2003 79 85
41. Latorra D, Hopkins D, Campbell K, Hurley JM. Multiplex allele-specific PCR with optimized locked nucleic acid primers. Biotechniques 2003;34:1150-2, 1154, 1158.
42. L.A. Ugozzoli, D. Latorra, R. Pucket, K. Arar, and K. Hamby Real-time genotyping with oligonucleotide probes containing locked nucleic acids Anal Biochem 324 2004 143 152
43. B.J. Duggan, S.B. Gray, J.J. McKnight, C.J. Watson, S.R. Johnston, and K.E. Williamson Oligoclonality in bladder cancer: the implication for molecular therapies J Urol 171 2004 419 425
44. M.C. Brandon, M.T. Lott, and K.C. Nguyen MITOMAP: a human mitochondrial genome database-2004 update Nucleic Acids Res 33 Database Issue 2005 D611 D613 [URL: http://www.mitomap.org ]
45. D.R. Hodgson, S.J. Clayton, and F. Girdler ARMS allele-specific amplification-based detection of mutant p53 DNA and mRNA in tumors of the breast Clin Chem 47 2001 774 778
46. M.H. Hazbon, and D. Alland Hairpin primers for simplified single-nucleotide polymorphism analysis of Mycobacterium tuberculosis and other organisms J Clin Microbiol 42 2004 1236 1242
47. M. Boniotto, M.H. Hazbon, and W.J. Jordan Novel hairpin-shaped primer assay to study the association of the - 44 single-nucleotide polymorphism of the DEFB1 gene with early-onset periodontal disease Clin Diagn Lab Immunol 11 2004 766 769
48. T. Itabashi, C. Maesawa, M. Uchiyama, T. Higuchi, and T. Masuda Quantitative detection of mutant alleles of the K-ras gene with minor groove binder-conjugated fluorogenic DNA probes Int J Oncol 24 2004 687 696
49. H.K. Tabor, N.J. Risch, and R.M. Myers Opinion: candidate-gene approaches for studying complex genetic traits: practical considerations Nat Rev Genet 3 2002 391 397
50. S. Rollinson, J.M. Allan, and G.R. Law High-throughput association testing on DNA pools to identify genetic variants that confer susceptibility to acute myeloid leukemia Cancer Epidemiol Biomarkers Prev 13 2004 795 800
51. J. Chen, S. Germer, R. Higuchi, G. Berkowitz, J. Godbold, and J.G. Wetmur Kinetic polymerase chain reaction on pooled DNA: a high-throughput, high-efficiency alternative in genetic epidemiological studies Cancer Epidemiol Biomarkers Prev 11 2002 131 136
52. S. Germer, M.J. Holland, and R. Higuchi High-throughput SNP allele-frequency determination in pooled DNA samples by kinetic PCR Genome Res 10 2000 258 266
53. S.H. Yeh, C.Y. Tsai, and J.H. Kao Quantification and genotyping of hepatitis B virus in a single reaction by real-time PCR and melting curve analysis J Hepatol 41 2004 659 666
54. S. Payungporn, P. Tangkijvanich, P. Jantaradsamee, A. Theamboonlers, and Y. Poovorawan Simultaneous quantitation and genotyping of hepatitis B virus by real-time PCR and melting curve analysis J Virol Methods 120 2004 131 140
55. H. Esaki, K. Noda, and N. Otsuki Rapid detection of quinolone-resistant Salmonella by real time SNP genotyping J Microbiol Methods 58 2004 131 134
56. P.A. Campsall, N.H. Au, J.S. Prendiville, D.P. Speert, R. Tan, and E.E. Thomas Detection and genotyping of varicella-zoster virus by TaqMan allelic discrimination real-time PCR J Clin Microbiol 42 2004 1409 1413
57. J.T. McKinney, N. Longo, and S.H. Hahn Rapid, comprehensive screening of the human medium chain acyl-CoA dehydrogenase gene Mol Genet Metab 82 2004 112 120
58. L. Zhou, J. Vandersteen, and L. Wang High-resolution DNA melting curve analysis to establish HLA genotypic identity Tissue Antigens 64 2004 156 164
59. Y. Feng, T. Niu, and H. Xing A common haplotype of the nicotine acetylcholine receptor alpha 4 subunit gene is associated with vulnerability to nicotine addiction in men Am J Hum Genet 75 2004 112 121
60. G. Pont-Kingdon, and E. Lyon Direct molecular haplotyping by melting curve analysis of hybridisation probes: beta 2-adrenergic receptor hapotypes as an example Nucleic Acids Res 33 2005 e89
61. Hanna Pincas, Maneesh R. Pingle, and Jianmin Huang High sensitivity EndoV mutation scanning through real-time ligase proofreading Nucleic Acids Res 32 2004 e148