The LightTyper™: High-throughput genotyping using fluorescent melting curve analysis

BioTechniques

Volumn 34, Issue 6, 2003, Pages 1288-1295

  Bennett, C D ^a   Campbell, M N ^a   Cook, C J ^a   Eyre, D J ^a   Nay, L M ^a   Nielsen, D R ^a   Rasmussen, R P ^a   Bernard, Philipe Seth ^b,c  

^a Idaho Technology Inc   (United States)

^b UNIVERSITY OF UTAH   (United States)

^c UNIVERSITY OF UTAH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMEDICAL ENGINEERING; COMPUTER SOFTWARE; DNA SEQUENCES; ENERGY TRANSFER; FLUORESCENCE; MELTING; MUTAGENESIS;

GENOTYING;

GENE TRANSFER;

BLOOD CLOTTING FACTOR 5 LEIDEN; TRANSMEMBRANE CONDUCTANCE REGULATOR;

ARTICLE; COMPUTER PROGRAM; ENERGY TRANSFER; FLUORESCENCE; GENE AMPLIFICATION; GENE MUTATION; GENOTYPE; HEATING; MELTING POINT; TECHNIQUE;

EID: 0037838867     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/03346pf01     Document Type: Article

References (31)

1. Shastry, B.S. 2002. SNP alleles in human disease and evolution. J. Hum. Genet. 47:561-566.
2. Sanger, F., S. Nicklen, and A.R. Coulson. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74:5463-5467.
3. Ronaghi, M., S. Karamohamed, B. Pettersson, M. Uhlen, and P. Nyren. 1996. Real-time DNA sequencing using detection of pyrophosphate release. Anal. Biochem. 242:84-89.
4. Ahmadian, A., B. Gharizadeh, A.C. Gustafsson, F. Sterky, P. Nyren, M. Uhlen, and J. Lundeberg. 2000. Single-nucleotide polymorphism analysis by pyrosequencing. Anal. Biochem. 280:103-110.
5. Wenham, P.R., C.R. Newton, and W.H. Price. 1991. Analysis of apolipoprotein E genotypes by the amplification refractory mutation system. Clin. Chem. 37:241-244.
6. Okimoto, R. and J.B. Dodgson. 1996. Improved PCR amplification of multiple specific alleles (PAMSA) using internally mismatched primers. BioTechniques 21:20-26.
7. Syvanen, A.C., K. Aalto-Setala, L. Harju, K. Kontula, and H.A. Soderlund. 1990. Primer-guided nucleotide incorporation assay in the genotyping of apolipoprotein E. Genomics 8:684-692.
8. Yershov, G., V. Barsky, A. Belgovskiy, E. Kirillov, E. Kreindlin, I. Ivanov, S. Parinov, D. Guschin, et al. 1996. DNA analysis and diagnostics on oligonucleotide microchips. Proc. Natl. Acad. Sci. USA 93:4913-4918.
9. Goto, S., A. Takahashi, K. Kamisango, and K. Matsubara. 2002. Single-nucleotide polymorphism analysis by hybridization protection assay on solid support. Anal. Biochem. 307:25-32.
10. Foy, C.A. and H.C. Parkes. 2001. Emerging homogeneous DNA-based technologies in the clinical laboratory. Clin. Chem. 47:990-1000.
11. Wittwer, C.T., M.G. Herrmann, A.A. Moss, and R.P. Rasmussen. 1997. Continuous fluorescence monitoring of rapid cycle DNA amplification. BioTechniques 22:130-138.
12. Bernard, P.S., R.S. Ajioka, J.P. Kushner, and C.T. Wittwer. 1998. Homogeneous multiplex genotyping of hemochromatosis mutations with fluorescent hybridization probes. Am. J. Pathol. 153:1055-1061.
13. Bernard, P.S., M.J. Lay, and C.T. Wittwer. 1998. Integrated amplification and detection of the C677T point mutation in the methylenetetrahydrofolate reductase gene by fluorescence resonance energy transfer and probe melting curves. Anal. Biochem. 255:101-107.
14. Lay, M.J. and C.T. Wittwer. 1997. Real-time fluorescence genotyping of factor V Leiden during rapid-cycle PCR. Clin. Chem. 43:2262-2267.
15. Crockett, A.O. and C.T. Wittwer. 2001. Fluorescein-labeled oligonucleotides for real-time pcr: using the inherent quenching of deoxyguanosine nucleotides. Anal. Biochem. 290:89-97.
16. Millward, H., W. Samowitz, C.T. Wittwer, and P.S. Bernard. 2002. Homogeneous amplification and mutation scanning of the p53 gene using fluorescent melting curves. Clin. Chem. 48:1321-1328.
17. Germer, S. and R. Higuchi. 1999. Single-tube genotyping without oligonucleotide probes. Genome Res. 9:72-78.
18. Livak, K.J., S.J. Flood, J. Marmaro, W. Giusti, and K. Deetz. 1995. Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. PCR Methods Appl. 4:357-362.
19. Happich, D., K. Madlener, R. Schwaab, P. Hanfland, and B. Potzsch. 2000. Application of the TaqMan-PCR for genotyping of the prothrombin G20210A mutation and of the thermolabile methylenetetrahydrofolate reductase mutation. Thromb. Haemost. 84:144-145.
20. Whitcombe, D., J. Theaker, S.P. Guy, T. Brown, and S. Little. 1999. Detection of PCR products using self-probing amplicons and fluorescence. Nat. Biotechnol. 17:804-807.
21. Thelwell, N., S. Millington, A. Solinas, J. Booth, and T. Brown. 2000. Mode of action and application of Scorpion primers to mutation detection. Nucleic Acids Res. 28:3752-3761.
22. Tyagi, S. and F.R. Kramer. 1996. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14:303-308.
23. Giesendorf, B.A., J.A. Vet, S. Tyagi, E.J. Mensink, F.J. Trijbels, and H.J. Blom. 1998. Molecular beacons: a new approach for semiautomated mutation analysis. Clin. Chem. 44:482-486.
24. Lane, D.A. and P.J. Grant. 2000. Role of hemostatic gene polymorphisms in venous and arterial thrombotic disease. Blood 95:1517-1532.
25. Nauck, M., W. Marz, and H. Wieland. 2000. Evaluation of the Roche Diagnostics LightCycler-Factor V Leiden mutation detection kit and the LightCycler-Prothrombin mutation detection kit. Clin. Biochem. 33:213-216.
26. Lyon, E., A. Millson, T. Phan, and C.T. Wittwer. 1998. Detection and identification of base alterations within the region of factor V Leiden by fluorescent melting curves. Mol. Diagn. 3:203-210.
27. Wine, J.J., E. Kuo, G. Hurlock, and R.B. Moss. 2001. Comprehensive mutation screening in a cystic fibrosis center. Pediatrics 107:280-286.
28. Gregg, A.R. and J.L. Simpson. 2002. Genetic screening for cystic fibrosis. Obstet. Gynecol. Clin. North Am. 29:329-340.
29. Grody, W.W., G.R. Cutting, K.W. Klinger, C.S. Richards, M.S. Watson, and R.J. Desnick. 2001. Laboratory standards and guidelines for population-based cystic fibrosis carrier screening. Genet. Med. 3:149-154.
30. SantaLucia, J., Jr., H.T. Allawi, and P.A. Seneviratne. 1996. Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35:3555-3562.
31. von Ahsen, N. and E. Schutz. 2001. Using the nearest neighbor model for the estimation of matched and mismatched hybridization probe melting points and selection of optimal probes on the LightCycler, p. 43-56. In S. Meuer, C.T. Wittwer, and K. Nakagawara (Eds.), Rapid Cycle Real-Time PCR: Methods and Applications. Springer-Verlag, Heidelberg, Germany.