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A Modified Mutation Detection Method for Large-scale Cloning of the Possible Single Nucleotide Polymorphism Sequences

  • Published : 2005.03.31

Abstract

Although the human genome has been nearly completely sequenced, the functions and the roles of the vast majority of the genes, and the influences of single nucleotide polymorphisms (SNPs) in these genes are not entirely known. A modified mutation detection method was developed for large-scale cloning of the possible SNPs between tumor and normal cells for facilitating the identification of genetic factors that associated with cancer formation and progression. The method involves hybridization of restriction enzyme-cut chromosomal DNA, cleavage and modification of the sites of differences by enzymes, and differential cloning of sequence variations with a designed vector. Experimental validations of the presence and location of sequence variations in the isolated clones by PCR and DNA sequencing support the capability of this method in identifying sequence differences between tumor cells and normal cells.

Keywords

References

  1. Becker, N., Nieters, A. and Rittgen, W. (2003) Single nucleotide polymorphism-disease relationships: statistical issues for the performance of association studies. Mutat. Res. 525, 11-18 https://doi.org/10.1016/S0027-5107(02)00283-X
  2. Cantor, C. R. (1999) Pharmacogenetics becomes pharmacogenomics: wake up and get ready. Mol. Diagn. 4, 287-288 https://doi.org/10.1016/S1084-8592(99)80004-6
  3. Chaudhry, M. and Weinfeld, M. (1995) Induction of double-strand breaks by S1 nuclease, mung bean nuclease and nuclease P1 in DNA containing abasic sites and nicks. Nucleic Acids Res. 23, 3805-3809 https://doi.org/10.1093/nar/23.19.3805
  4. Chen, X. and Sullivan, P. F. (2003) Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput. Pharmacogenomics J. 3, 77-96 https://doi.org/10.1038/sj.tpj.6500167
  5. Goodstadt, L. and Ponting, C. P. (2001) Sequence variation and disease in the wake of the draft human genome. Hum. Mol. Genet. 10, 2209-2214 https://doi.org/10.1093/hmg/10.20.2209
  6. Elahi, E., Kumm, J. and Ronaghi, M. (2004) Global genetic analysis. J. Biochem. Mol. Biol. 37, 11-27 https://doi.org/10.5483/BMBRep.2004.37.1.011
  7. Kelley, W. and Stump, K. (1979) A rapid procedure for isolation of large quantities of Escherichia coli DNA polymerase I utilizing a lambdapol A transducing phage. J. Biol. Chem. 254, 3206-3210
  8. Kleff, S. and Kemper, B. (1988) Initiation of heteroduplex-loop repair by T4-encoded endonuclease VII in vitro. EMBO J. 7, 1527-1535
  9. Kosak, H. and Kemper, B. (1990) Large-scale preparation of T4 endonuclease VII from over-expressing bacteria. Eur. J. Biochem. 194, 779-784 https://doi.org/10.1111/j.1432-1033.1990.tb19469.x
  10. Kwok, P. (2003) Single Nucleotide Polymorphisms: Methods and Protocols, Humana Press, New Jersey, USA
  11. Jiang, M. C. and Liao, C. F. (2004) CAS overexpression inhibits the tumorigenicity of HT-29 colon cancer cells. J. Exp. Clin. Cancer Res. 23, 325-332
  12. Mashal, R., Koontz, J. and Sklar, J. (1995) Detection of mutations by cleavage of DNA heteroduplexes with bacteriophage resolvases. Nat. Genet. 23, 177-183
  13. Mir, K. U. and Southern, E. M. (200) Sequence variation in genes and genomic DNA: methods for large-scale analysis. Annu. Rev. Genomics Hum. Genet. 1, 329-360 https://doi.org/10.1146/annurev.genom.1.1.329
  14. Nelson, M. R., Marnellos, G., Kammerer, S., Hoyal, C. R., Shi, M. M., Cantor, C. R. and Braun, A. (2004) Large-scale validation of single nucleotide polymorphisms in gene regions. Genome Res. 14, 1664-1668 https://doi.org/10.1101/gr.2421604
  15. Parkinson, M. and Lilley, D. (1997) The junction-resolving enzyme T7 endonuclease I: quaternary structure and interaction with DNA. J. Mol. Biol. 270, 169-178 https://doi.org/10.1006/jmbi.1997.1128
  16. Parsons, C., Kemper, B. and West, S. (1990) Interaction of a fourway junction in DNA with T4 endonuclease VII. J. Biol. Chem. 265, 9285-9289
  17. Sambrook, J., Fritsch, E. and Maniatis, T. (1989) Molecular Cloning, 2nd ed. Cold Spring Harbor Laboratory Press, New York, USA
  18. Sinden, R. R. and Wells, R. D. (1992) DNA structure, mutations, and human genetic disease. Curr. Opin. Biotechnol. 3, 612-622 https://doi.org/10.1016/0958-1669(92)90005-4
  19. Solaro, P., Birkenkamp, K., Pfeiffer, P. and Kemper, B. (1993) Endonuclease VII of phage T4 triggers mismatch correction in vitro. J. Mol. Biol. 230, 868-877 https://doi.org/10.1006/jmbi.1993.1207
  20. The International HapMap Consortium (2003) The international HapMap project. Nature 426, 789-796 https://doi.org/10.1038/nature02168
  21. The International SNP Map Working Group (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928-933 https://doi.org/10.1038/35057149
  22. Youil, R., Kemper, B. and Cotton, R. (1995) Screening for mutations by enzyme mismatch cleavage with T4 endonuclease VII. Proc. Natl. Acad. Sci. USA 92, 87-91 https://doi.org/10.1073/pnas.92.1.87