Laboratory techniques for the detection of mutations in DNA

Brazilian Journal of Genetics

Volumn 20, Issue 2, 1997, Pages 339-344

  Vago, Annamaria R ^a   Pena, Sérgio D J ^a  

^a FEDERAL UNIVERSITY OF MINAS GERAIS   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

DENATURING GRADIENT GEL ELECTROPHORESIS; DNA DETERMINATION; DNA FINGERPRINTING; DNA SEQUENCE; GENE MUTATION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; LABORATORY TEST; POLYMERASE CHAIN REACTION; RESTRICTION MAPPING; REVIEW; SINGLE STRAND CONFORMATION POLYMORPHISM;

EID: 0030751892     PISSN: 01008455     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (56)

1. Abravaya, K., Carrino, J.J. and Muldon, S. (1995). Detection of point mutations with a modified ligase chain reaction (Gap-LCR). Nucleic Acids Res. 23: 675-682.
2. Barany, F. (1991). Genetic disease detection and DNA amplification using cloned thermostable ligase. Proc. Natl. Acad. Sci. USA 88: 189-193.
3. Barreto, G., Vago, A.R., Ginther, C., Simpson, J.G. and Pena, S.D.J. (1996). Mitochondrial D-loop "signatures" produced by low-stringency single specific primer PCR constitute a simple comparative human identity test. Am. J. Hum. Genet. 58: 1-8.
4. Chee, M., Yang, R., Hubbell, E., Berno, A., Huang, X.C., Stern, D., Winkler, J., Lockhart, D.J., Morris, M.S. and Fodor, S.P.A. (1996) Accessing genetic information with high-density DNA arrays. Science 274: 610-614.
5. Conner, B.J., Reyes, A.A. and Morin, C. (1983). Detection of sickle cell β-globin allele by hybridization with synthetic oligonucleotides. Proc. Natl. Acad. Sci. USA 80: 278-282.
6. Cotton, R.G.H. (1989). Detection of single base changes in nucleic acids. Biochem. J. 263: 1-10.
7. Cotton, R.G.H. (1997). Slowly but surely towards better scanning for mutations. Trends Genet. 13: 43-46.
8. De Risi, J., Penland, L., Brown, P.O., Bittner, M.L., Meltzer, P.S., Ray, M., Chen, Y., Su, Y.A. and Trent, J.M. (1996). Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat. Genet. 14: 457-460.
9. Editorial (1996). To affinity ... and beyond! Nat. Genet. 14: 367-370.
10. Ellis, L.A., Taylor G.R. and Banks, R. (1994). MutS protects heteroduplex DNA from exonuclease digestion in vitro: a simple method for detecting mutations. Nucleic Acids Res 22: 2710-2711.
11. Gomes, M.A., Silva, E.F., Macedo, A.M., Vago, A.R. and Melo, M.N. LSSP-PCR for characterization of strains of Entamoeba histolytica isolated in Brazil. Exp. Parasitol. (in press).
12. Green, P.M., Rowley, G. and Saad, S. (1996). Multiplex solid phase fluorescent chemical cleavage. In: Laboratory Protocols for Mutation Detection (Landegren, U., ed.). Oxford University Press, Walton Street, Oxford, pp. 61-64.
13. Grompe, M., Muzny, D.M. and Caskey, C.T. (1989). Scanning detection of mutations in human ornithine transcarbamoylase by chemical mismatch cleavage. Proc. Natl. Acad Sci. USA 86: 5888-5892.
14. Gyllenstein, U. and Allen, M. (1996). SSO-genetic typing with sequence-specific oligonucleotides. In: Laboratory Protocols for Mutation Detection (Landegren, U., ed.). Oxford University Press, Walton Street, Oxford, pp. 78-81.
15. Hacia, J.G., Brody, L.C., Chee, M.S., Fodor, S.P. and Collins, F.S. (1996). Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays. Nat. Genet. 14: 441-447.
16. Harris, I.I., Green, P.M. and Bentley, D.R. (1994). Mutation, detection by fluorescent chemical cleavage: application to hemophilia B. PCR Meth. Appl. 3: 268-271.
17. Hayashi, K. (1996). PCR SSCP: single strand conformation polymorphism analysis of PCR products. In: Laboratory Protocols for Mutation Detection (Landegren, U., ed.). Oxford University Press, Walton Street, Oxford, pp. 14-22.
18. Holloway, B., Erdman, D.D. and Durigon, E.L. (1993). An exonuclease-amplification coupled capture technique improves detection of PCR products. Nucleic Acids Res. 21: 3905-3906.
19. Ikonen, E., Manninen, T. and Peltonen, L. (1992). Quantitative determination of rare mRNA species by PCR and solid-phase minisequencing. PCR Meth. Appl. 1: 234-240.
20. Khrapko, K., Hanekamp, J.S. and Thilly, W.G. (1994). Constant denaturant capillary electrophoresis (CDCE): a high resolution approach to mutational analysis. Nucleic Acids Res. 22: 364-369.
21. Kuppuswamy, M.N., Hoffman, J.W. and Kasper, C.K. (1991). Single nucleotide primer extension to detect genetic diseases: experimental application to hemophilia B and cystic fibrosis genes. Proc. Natl. Acad. Sci. USA, 88: 1143-1147.
22. Landegren, U. (1996). Laboratory Protocols for Mutation Detection. Oxford University Press, Oxford.
23. Landegren, U., Kaiser, R. and Sanders, J. (1988). A ligase-mediated gene detection technique. Science 241: 1077-1080.
24. Lin, F.-H. and Lin, R. (1992). A comparison of single nucleotide primer extension with mispairing PCR-RFLP in detecting a point mutation. Biochem. Biophys. Res. Commun. 189: 1202-1206.
25. Lishanski, A., Ostrander, E.A. and Rine, J. (1994). Mutation detection by mismatch binding protein, MutS, in amplified DNA: application to the cystic fibrosis gene. Proc. Natl. Acad. Sci. USA 91: 2674-2678.
26. Liu, Q. and Sommer, S.S. (1995). Restriction endonuclease fingerprinting (REF): a sensitive method for screening mutations in long, contiguous segments of DNA. BioTechniques 18: 470-477.
27. Lu, A.-L. (1996). MREC: Mismatch repair enzyme cleavage. In: Laboratory Protocols for Mutation Detection (Landegren, U., ed.). Oxford University Press, Walton Street, Oxford, pp. 69-75.
28. Lu, A.-L. and Hsu, I.-C. (1992). Detection of single DNA base mutation with mismatch repair enzymes. Genomics 14: 249-255.
29. Myers, R.M., Lumelsky, N. and Lerman, L.S. (1985). Detection of single base substitutions in total genomic DNA. Nature 313: 495-498.
30. Newton, C.R., Graham, A. and Heptinstall, L.E. (1989). Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res. 17: 2503-2508.
31. Okayama, H., Curiel, D.T. and Brantly, M.L. (1989). Rapid non-radioactive detection of mutations in the human genome by allele-specific amplification. J. Lab. Clin. Med. 114: 105-113.
32. Orita, M., Iwahama, H. and Kanazana, H. (1989). Detection of polymorphisms of human DNA by gel electrophoresis and single-strand conformation polymorphisms. Proc. Natl. Acad. Sci. USA 6: 2766-2770.
33. Pena, S.D.J. and Simpson, A.J.G. (1996). LSSP-PCR: multiplex mutation detection using sequence-specific gene signatures. In: Laboratory Protocols for Mutation Detection (Landegren, U., ed.). Oxford University Press, Oxford, pp. 42-49.
34. Pena, S.D.J., Barreto, G., Vago, A.R., De Marco, L., Reinach, F.C., Dias Neto, E. and Simpson, A.J.G. (1994). Sequence-specific "gene signatures" can be obtained by PCR with single specific primers at low stringency. Proc. Natl. Acad. Sci. 91: 1946-1949.
35. Prosser, J. (1995). Detecting single-base mutations. Trends Biotech. 11: 238-246.
36. Ramus, S. and Cotton, R.G.H. (1996). CCM: chemical cleavage of mismatch. In: Laboratory Protocols for Mutation Detection (Landegren, U., ed.). Oxford University Press, Walton Street, Oxford, pp. 50-53.
37. Samiotaki, M., Kwiatkowski, M. and Parik, J.N. (1994). Dual-color detection of DNA sequence variants by ligase-mediated analysis. Genomics 20: 238-242.
38. Santos, F.R., Pena, S.D.J. and Tyler-Smith, C. (1995). PCR haplotypes for the human Y chromosome based on alphoid satellites variants and heteroduplex analysis. Gene 165: 191-198.
39. Sarkar, G., Yoon, H.-S. and Sommer, S.S. (1992). Dideoxy fingerprinting (ddF): a rapid and efficient screening for the presence of mutations. Genomics 13: 441-443.
40. Sheffield, V.C., Cox, D.R. and Lerman, L.S. (1989). Attachment of a 40-base-pair G+C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes. Proc. Natl. Acad. Sci. USA 86: 232-236.
41. Sheffield, V.C., Fishman, G.A. and Beck, J.S. (1991). Identification of novel rhodopsin mutations associated with retinitis pigmentosa by GC-clamped denaturing gradient gel electrophoresis. Am. J. Hum. Genet. 49: 699-706.
42. Shumaker, J.M., Metspalu, A. and Caskey, C.T. (1996). Multiplex solid-phase fluorescent primer-extension. In: Laboratory Protocols for Mutation Detection (Landegren, U., ed.). Oxford University Press, Walton Street, Oxford, pp. 93-95.
43. Simpson, A.J.G. and Pena, S.D.J. (1997) Sequence-specific gene signatures produced by LSSP-PCR. In: The Detection of DNA Sequence Polymorphisms and Mutations: Methods and Applications (G.R. Taylor, ed.). CRC Press, New York, pp. 132-148.
44. Sommer, S.S. (1996). PASA: PCR amplification of specific alleles. In: Laboratory Protocols for Mutation Detection (Landegren, U., ed.). Oxford University Press, Walton Street, Oxford, pp. 82-86.
45. Syvänen, A.-C. (1996). Solid-phase minisequencing. In: Laboratory Protocols for Mutation Detection (Landegren, U., ed.). Oxford University Press, Walton Street, Oxford, pp. 87-92.
46. Taylor, G.R. (1997). Laboratory Methods for the Detection of Mutations and Polymorphisms in DNA. CRC Press, New York.
47. Underhill, P.A., Jin, L., Zemans, R., Oefner, P.J. and Cavalli-Sforza, L. (1996). A pre-Columbian Y chromosome-specific transition and its implications for human evolutionary history. Proc. Natl. Acad. Sci. USA 93: 196-200.
48. Vago, A.R., Macedo, A.M., Oliveira, R.P., Andrade, L.O., Chiari, E., Galvão, L.M.C., Reis, D.A., Pereira, E.M.S., Tostes, S., Simpson, A.J.G. and Pena, S.D.J. (1996). Kinetoplast DNA signatures of Trypanosoma cruzi obtained directly from infected tissues. Am. J. Pathol. 149: 2153-2159.
49. Verpy, E., Biasotto, M. and Meo, T. (1994). Efficient detection of point mutations on color-coded strands of target DNA. Proc. Natl. Acad. Sci. USA 91: 1873-1877.
50. Villa, L.L., Caballero, O.L., Levi, J.O., Pena, S.D.J. and Simpson, A.J.G. (1995). An approach to human papillomavirus identification using low-stringency single specific primer PCR. Mol. Cell Probes 9: 45-48.
51. Wallace, B., Ugozolli, L. and Reyes, A.A. (1996). LCR: ligase chain reaction. In: Laboratory Protocols for Mutation Detection (Landegren, U., ed.). Oxford University Press, Walton Street, Oxford, pp. 101-104.
52. White, M.B., Carvalho, M. and Derse, D. (1992). Detecting single base substitutions as heteroduplex polymorphisms. Genomics 12: 301-306.
53. Wood, N.A.P. and Bidwell, J.L. (1996). UHG: heteroduplex and universal heteroduplex generator analysis. In: Laboratory Protocols for Mutation Detection (Landegren, U., ed.). Oxford University Press, Walton Street, Oxford, pp. 105-112.
54. Wood, N.A.P., Tyfield, L. and Bidwell, J. (1993). Rapid classification of phenylketonuria genotypes by analysis of heteroduplex generated by PCR-amplifiable synthetic DNA. Hum. Mut. 2: 131-137.
55. Wu, D.Y., Ugozzoli, L. and Pal, B.K. (1989). Allele-specific enzymatic amplification of β-globin genomic DNA for diagnosis of sickle cell anemia. Proc. Natl. Acad. Sci. USA 86: 2757-2760.
56. Youil, R. and Cotton, R.G.H. (1996). EMC: enzyme mismatch cleavage. In: Laboratory Protocols for Mutation Detection (Landegren, U., ed.). Oxford University Press, Walton Street, Oxford, pp. 65-68.