Resolving power of isothermic DNA sequencing chips

• Autorzy: Formanowicz P.
• Języki publikacji: EN

Abstrakty

EN

DNA sequencing remains one of the most important problems in molecular and computational biology. One of the methods used for this purpose is sequencing by hybridization. In this approach usually DNA chips composed of a flul library of oligonucleotides of a given length are used, but in principle it is possible to use another types of chips. Isothermic DNA chips, being one of them, when used for sequencing may reduce hybridization error rate. However, it was not clear if a number of errors following from subsequence repetitions is also reduced in this case. In this paper a method for estimating resolving power of isothermic DNA chips is described which allows for a comparison of such chips and the classical ones. The analysis of the resolving power shows that the probability of sequencing errors caused by subsequence repetitions is greater in the case of isothermic chips in comparison to their classical counterparts of a similar cardinality. This result suggests that isothermic chips should be chosen carefully since in some cases they may not give better results than the classical ones.

Słowa kluczowe

EN

computational biology; DNA sequencing; DNA chips; sequencing errors; resolving power

• Wydawca: Polska Akademia Nauk, Wydział IV Nauk Technicznych
• Czasopismo: Bulletin of the Polish Academy of Sciences. Technical Sciences
• Rocznik: 2004
• Tom: Vol. 52, nr 3
• Strony: 231--237
• Opis fizyczny: Bibliogr. 13 poz., 6 tab.

Twórcy

autor

Formanowicz P.

• Institute of Computing Science, Poznan University of Technology, 3A Piotrowo St., 60-965 Poznan, Poland, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14 Noskowskiego St., 61-704 Poznan, Poland

Bibliografia

• [1] R. Drmanac, I. Labat, I. Brukner and R. Crkvenjakov, “Sequencing of megabase plus DNA by hybridization: theory and the method”, Genomics 4, 114–128 (1989).
• [2] K. R. Khrapko, Y. P. Lysov, A. A. Khorlin, V. V. Shik, V. L. Florentiev and A. D. Mirzabekov, “An oligonucleotide approach to DNA sequencing”, FEBS Lett. 256, 118–122 (1989).
• [3] E. M. Sou thern, U. Maskos and J. K. Elder, “Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models”, Genomics 13, 1008–1017 (1992).
• [4] S. P. A. Fodor, J. L. Read, M. C. Pirru ng, L. Stryer and A. Lu, D. Solas, “Light-directed, spatially addressable parallel chemical synthesis”, Science 251, 767–773 (1991).
• [5] E. M. Southern, United Kingdom patent application GB8 810400 (1988).
• [6] A. C. Pease, D. Solas, E. Sullivan, M. Cronin, C. Holmes and S. Fodor, “Light-generated oligonucleotide arrays for rapid DNA sequence analysis”, Proc. Natl. Acad. Sci. USA 91, 5022–5026 (1994).
• [7] P. A. Pevzner and R. J. Lipshu tz, “Towards DNA sequ encing chips”, in Proceedings of 9th International Symposium MFCS’94, ed. I. Pr´ıvara, B. Rovan, P. Ruˇziˇcka, pp. 143–151, August 22–26 (1994).
• [8] J. D. Watson and F. H. C. Crick, “Genetic implications of the structure of deoxyribonucleic acid”, Nature 171, 964–967 (1953).
• [9] J. BNla˙zewicz, P. Formanowicz, M. Kasprzak, W. T. Markiewicz and J. W¸eglarz, “DNA sequencing with positive and negative errors”, J. Comp. Biol. 6, 113–123 (1999).
• [10] J. BNla˙zewicz, P. Formanowicz, M. Kasprzak and W. T. Markiewicz, “Sequencing by hybridization with isothermic oligonucleotide libraries”, Disc. Appl. Math. 145, 40–51 (2004).
• [11] R. B. Wallace, M. J. Johnson, T. Hirose, T. Miyake, E. H. Kawashima and K. Itakura, “The use of synthetic oligonucleotides as hybridization probes. ii. hybridization of oligonucleotides of mixed sequence to rabbit beta-globin DNA”, Nucleic Acids Res. 9, 879–894 (1981).
• [12] F. P. Preparata, A. M. Frieze and E. Upfal, “On the power of universal bases in sequencing by hybridization”, in Proceedings of the Third Annual International Conference on Computational Molecular Biology, ed. S. Istrail, P. Pevzner, M. Waterman, Lyon, France, pp. 295–301, April 11–14 (1999).
• [13] P. Sachadyn and J. Kur, “Reducing the number of microlocations in oligonucleotide microchip matrices by the application of degenerate oligonucleotides”, J. Theor. Biol. 197, 393–401 (1999).