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Resequencing and mutational analysis using oligonucleotide microarrays

Nature Genetics volume 21, pages 42–47 (1999)Cite this article

Abstract

Oligonucleotide microarray (DNA chip)–based hybridization analysis is a promising new technology which potentially allows rapid and cost–effective screens for all possible mutations and sequence variations in genomic DNA. Here, I review current strategies and uses for DNA chip–based resequencing and mutational analysis, the underlying principles of experimental designs, and future efforts to improve the sensitivity and specificity of chip–based assays.

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Figure 1: Three experimental strategies for array–based sequence analysis.
Figure 2: Typical oligonucleotide probes used in gain–of–signal sequence analysis.
Figure 3: Oligonucleotide probes used in loss of hybridization signal sequence analysis.
Figure 4: Hybridization patterns to BRCA1 oligonucleotide arrays.
Figure 5: Detection of the 185delAG BRCA1 mutation and sequence variations using loss of signal analysis.

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References

  1. Collins, F.S., Guyer, M.S. & Chakravarti, A. Variations on a theme: cataloging human DNA sequence variation. Science 278, 1580– 1581 (1997).

    Article  CAS  Google Scholar 

  2. Nickerson, D.A. et al. DNA sequence diversity in a 9.7–kb region of the human lipoprotein lipase gene. Nature Genet. 19, 233–240 (1998).

    Article  CAS  Google Scholar 

  3. Chakravarti, A. Population genetics—making sense out of sequence. Nature Genet. 21, 56–60 ( 1999).

    Article  CAS  Google Scholar 

  4. Moldin, S.O. & Gottesman, I.I. At issue: genes, experience and chance in schizophrenia—positioning for the 21st century. Schizophr. Bulletin 23, 547–561 (1997).

    Article  CAS  Google Scholar 

  5. Zhang, H., Zhao, H. & Merikangas, K. Strategies to identify genes for complex diseases. Ann. Med. 29, 493–498 ( 1998).

    Article  Google Scholar 

  6. Southern, E.M. DNA chips: analysing sequence by hybridization to oligonucleotides on a large scale. Trends Genet. 12, 110– 115 (1996).

    Article  CAS  Google Scholar 

  7. Ramsay, G. DNA chips: state–of–the art. Nature Biotechnol. 16, 40–44 (1998).

    Article  CAS  Google Scholar 

  8. Duggan, D.J., Bittner, M., Chen, Y., Meltzer, P. & Trent, J. Expression profiling using cDNA microarrays. Nature Genet. 21, 10–14 (1999).

    Article  CAS  Google Scholar 

  9. Schena, M., Shalon, D., Davis, R.W. & Brown, P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470 ( 1995).

    Article  CAS  Google Scholar 

  10. Lockhart, D.J. et al. Expression monitoring by hybridization to high–density oligonucleotide arrays. Nature Biotechnol. 14, 1675–1680 (1996).

    Article  CAS  Google Scholar 

  11. Bains, W. & Smith, G. A novel method for nucleic acid sequence determination. J. Theor. Biol. 135, 303– 307 (1988).

    Article  CAS  Google Scholar 

  12. Khrapko, K.R. et al. An oligonucleotide hybridization approach to DNA sequencing. FEBS Lett. 256, 118–122 (1989).

    Article  CAS  Google Scholar 

  13. Drmanac, R., Labat, I., Brukner, I. & Crkvenjakov, R. Sequencing of megabase plus DNA by hybridization: theory of the method. Genomics 4, 114–128 ( 1989).

    Article  CAS  Google Scholar 

  14. Southern, E.M., Maskos, U. & Elder, J.K. Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. Genomics 13, 1008–1017 ( 1992).

    Article  CAS  Google Scholar 

  15. Drmanac, S. et al. Accurate sequencing by hybridization for DNA diagnostics and individual genomics. Nature Biotechnol. 16, 54–58 (1998).

    Article  CAS  Google Scholar 

  16. Fodor, S.P.A. et al. Light–directed spatially addressable parallel chemical synthesis. Science 251, 767– 773 (1991).

    Article  CAS  Google Scholar 

  17. Lipshutz, R.J., Fodor, S.P.A., Gingeras, T.R. & Lockhart, D.J. High density synthetic oligonucleotide arrays. Nature Genet. 21, 20–24 (1999).

    Article  CAS  Google Scholar 

  18. Marshall, A. & Hodgson, J. DNA chips: an array of possibilities. Nature Biotechnol. 16, 27– 31 (1998).

    Article  CAS  Google Scholar 

  19. Schena, M. et al. Microarray: biotechnology's discovery platform for functional genomics. Trends Biotechnol. 16, 301– 306 (1998).

    Article  CAS  Google Scholar 

  20. Saiki, R.K., Walsh, P.S., Levenson, C.H. & Erlich, H.A., Genetic analysis of amplified DNA with immobilized sequence–specific oligonucleotide probes. Proc. Natl Acad. Sci. USA 86 , 6230–6234 (1989).

    Article  CAS  Google Scholar 

  21. Cronin M.T. et al. Cystic fibrosis mutation detection by hybridization to light–generated DNA probe arrays. Hum. Mutat. 7, 244– 255 (1996).

    Article  CAS  Google Scholar 

  22. Yershov, G. et al. DNA analysis and diagnostics on oligonucleotide microchips. Proc. Natl Acad. Sci. USA 93, 4913– 4918 (1996).

    Article  CAS  Google Scholar 

  23. Cooper, D.N., Smith, B.A., Cooke, H.J., Niemann, S. & Schmidtke, J. An estimate of unique DNA sequence heterozygosity in the human genome. Hum. Genet. 69, 201– 205 (1985).

    Article  CAS  Google Scholar 

  24. Hofker, M.H. et al. The X chromosome shows less genetic variation at restriction sites than the autosomes. Am. J. Hum. Genet. 39, 438–451 (1986).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Chee, M. et al. Accessing genetic information with high–density DNA arrays. Science 274, 610–614 (1996).

    Article  CAS  Google Scholar 

  26. Hacia, J.G., Brody, L.C., Chee, M.S., Fodor, S.P. & Collins, F.S. Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two–colour fluorescence analysis. Nature Genet. 14, 441– 447 (1996).

    Article  CAS  Google Scholar 

  27. Pastinen, T., Kurg, A., Metsapalu, A., Peltonen, L. & Syvanen, A.C. Minisequencing: a specific tool for DNA analysis and diagnostics on oligonucleotide arrays. Genome Res. 7, 606–614 (1997).

    Article  CAS  Google Scholar 

  28. Kozal, M. et al. Extensive polymorphisms observed in HIV–1 cladeB protease gene using high–density oligonucleotide arrays. Nature Med. 2, 753–759 ( 1996).

    Article  CAS  Google Scholar 

  29. Hacia, J. et al. Strategies for mutational analysis of the large multi–exon ATM gene using high–density oligonucleotide arrays. Genome Res. (in press).

  30. Wang, D.G. et al. Large–scale identification, mapping, and genotyping of single–nucleotide polymorphisms in the human genome. Science 280, 1077–1082 ( 1998).

    Article  CAS  Google Scholar 

  31. Shumaker, J.M., Metspalu, A. & Caskey, C.T. Mutation detection by solid phase primer extension. Hum. Mutat. 7, 346–354 (1996).

    Article  CAS  Google Scholar 

  32. Nikiforov, T.T. et al. Genetic bit analysis: a solid phase method for typing single nucleotide polymorphisms. Nucleic Acids Res. 22, 4167–4175 (1994).

    Article  CAS  Google Scholar 

  33. Head, S.R. et al. Nested genetic bit analysis (N–GBA) for mutation detection in the p53 tumor suppressor gene. Nucleic Acids Res. 25, 5065–5071 (1997).

    Article  CAS  Google Scholar 

  34. McGall, G. et al. Light–directed synthesis of high–density oligonucleotide arrays using semiconductor photoresists. Proc. Natl Acad. Sci. USA 93, 13555–13560 ( 1996).

    Article  CAS  Google Scholar 

  35. Blanchard, A.P., Kaiser, R.J. & Hood, L.E. High–density oligonucleotide arrays. Biosens. Bioelectron. 11, 687–690 (1996).

    Article  CAS  Google Scholar 

  36. Proudnikov, D., Timofeev, E. & Mirzabekov, A. Immobilization of DNA in polyacrylamide gel for the manufacture of DNA and DNA–oligonucleotide microchips. Anal. Biochem. 259, 34–41 ( 1998).

    Article  CAS  Google Scholar 

  37. Hacia, J.G. et al. Evolutionary sequence comparisons using high–density oligonucleotide arrays. Nature Genet. 18, 155–158 (1998).

    Article  CAS  Google Scholar 

  38. The Huntington's Disease Collaborative Research Group. A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes. Cell 72, 971–983 (1993).

  39. Milner, N., Mir, K.U. & Southern, E.M. Selecting effective antisense reagents on combinatorial oligonucleotide arrays. Nature Biotechnol. 15, 537–541 (1997).

    Article  CAS  Google Scholar 

  40. Southern, E. Mir, K. & Shchepinov, M. Molecular interactions on microarrays. Nature Genet. 21, 5–9 ( 1999).

    Article  CAS  Google Scholar 

  41. Simone, N.L., Bonner, R.F., Gillespie, J.W., Emmert–Buck, M.R. & Liotta, L.A. Laser–capture microdissection: opening the microscopic frontier to molecular analysis. Trends Genet. 14, 272–276 (1998).

    Article  CAS  Google Scholar 

  42. Hoheisel, J.D. Sequence–independent and linear variation of oligonucleotide DNA binding stabilities. Nucleic Acids Res. 24, 430– 432 (1996).

    Article  CAS  Google Scholar 

  43. Weiler, J., Gausepohl, H., Hauser, N., Jensen, O.N. & Hoheisel, J.D. Hybridisation based DNA screening on peptide nucleic acid (PNA) oligomer arrays. Nucleic Acids Res. 25, 2792–2799 ( 1997).

    Article  CAS  Google Scholar 

  44. Arlinghaus, H.F., Kwoka, M.N. & Jacobson, K.B. Analysis of biosensor chips for identification of nucleic acids. Anal. Chem. 15, 3747– 3753 (1997).

    Article  Google Scholar 

  45. Hacia, J.G. et al. Enhanced high density oligonucleotide array– based sequence analysis using modified nucleoside triphosphates. Nucleic Acids Res. 26, 4975–4982 ( 1998).

    Article  CAS  Google Scholar 

  46. Nguyen, H.K. et al. The stability of duplexes involving AT and/or G4EtC base pairs is not dependent on their AT/G4EtC ratio content. Implication for DNA sequencing by hybridization. Nucleic Acids Res. 26, 4249–4258 (1998).

    Article  CAS  Google Scholar 

  47. Hacia, J.G. et al. Two color hybridization analysis using high density oligonucleotide arrays and energy transfer dyes. Nucleic Acids Res. 26, 3865–3866 (1998).

    Article  CAS  Google Scholar 

  48. Lizardi, P.M. et al. Mutation detection and single–molecule counting using isothermal rolling–circle amplification. Nature Genet. 19, 225–232 (1998).

    Article  CAS  Google Scholar 

  49. Edman, C.F. et al. Electric field directed nucleic acid hybridization on microchips. Nucleic Acids Res. 25, 4907– 4914 (1997).

    Article  CAS  Google Scholar 

  50. Sosnowski, R.G., Tu, E., Butler, W.F., O'Connell, J.P. & Heller, M.J. Rapid determination of single base mismatch mutations in DNA hybrids by direct electric field control. Proc. Natl Acad. Sci. USA 94, 1119–1123 ( 1997).

    Article  CAS  Google Scholar 

  51. Broude, N.E., Sano, T., Smith, C.L. & Cantor, C.R. Enhanced DNA sequencing by hybridization. Proc. Natl Acad. Sci. USA 91, 3072–3076 (1994).

    Article  CAS  Google Scholar 

  52. Dubiley, S., Kirillov, E., Lysov, Y. & Mirzabekov, A. Fractionation, phosphorylation and ligation on oligonucleotide microchips to enhance sequencing by hybridization. Nucleic Acids Res. 25, 2259–2265 (1997).

    Article  CAS  Google Scholar 

  53. Parinov, S. et al. DNA sequencing by hybridization to microchip octa– and decanucleotides extended by stacked pentanucleotides. Nucleic Acids Res. 24, 2998–3004 ( 1996).

    Article  CAS  Google Scholar 

  54. Sanger, F., Nicklen, S. & Coulson, A.R. DNA sequencing with chain–terminating inhibitors. Proc. Natl Acad. USA 74, 5463– 5467 (1977).

    Article  CAS  Google Scholar 

  55. Wilson, R.K., Chen, C., Avdalovic, N., Burns, J. & Hood, L. Development of an automated procedure for fluorescent DNA sequencing. Genomics 6, 626–634 ( 1990).

    Article  CAS  Google Scholar 

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Acknowledgements

I thank L. Brody, F. Collins, K. Edgemon, A. Mayer and B. Sun from NIH for helpful suggestions and discussion. I also thank M. Chee at Illumina, M. Cronin at Protogene, S. Fodor at Affymetrix and N. Hunt at GeneTrace for comments and discussion.

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  1. Genetics and Molecular Biology Branch, National Human Genome Research Institute, Building 49/3A14, National Institutes of Health, Bethesda, 20892, Maryland, USA

    Joseph G. Hacia

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Hacia, J. Resequencing and mutational analysis using oligonucleotide microarrays . Nat Genet 21 (Suppl 1), 42–47 (1999). https://doi.org/10.1038/4469

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