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Statistical analysis of DNA fingerprint data for ordered clone physical mapping of human chromosomes

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Abstract

A statistical framework is proposed for analysing DNA fingerprint data from experiments aimed at constructing ordered clone physical maps of chromosomes. The fingerprint data consists of the lengths and hybridization states of restriction digest fragments and the paper develops a solution to the fundamental problem of deciding whether or not two randomly selected clones overlap. Overlap probabilities are calculated using Bayes’ rule together with appropriate statistical descriptions of the chromosome and experimental procedure. The analysis is flexible, allowing a variety of assumptions to account for experimental errors and difficulties, such as unobserved fragments. The approach described here provides a basis for predicting the rate of progress of an experimental protocol and hence for comparing alternate protocols. It is readily generalized to related problems with a wide range of possible data. Results are presented for the clone mapping protocol currently being employed at Los Alamos National Laboratory on human chromosome 16

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Literature

  • Berger, J. O. 1980.Statistical Decision Theory. Berlin: Springer-Verlag

    Google Scholar 

  • Brenner, S. and K. J. Livak 1989. DNA fingerprinting by sampled sequencing.Proc. natl Acad. Sci. U.S.A. 86, 8902–8906.

    Article  Google Scholar 

  • Carrano, A. V., J. Lamerdin, L. K. Ashworth, B. Watkins, E. Branscomb, T. Slezak, M. Raff, P. J. de Jong, D. Keith, L. McBride, S. Meister and M. Kronick. 1989. A high resolution, fluorescence-based, semi-automated method of DNA fingerprinting.Genomics 4, 129–136.

    Article  Google Scholar 

  • Churchill, G. A. 1989. Stochastic models for heterogeneous DNA sequences.Bull. math. Biol. 51, 79–94.

    MATH  MathSciNet  Google Scholar 

  • Coulson, A., J. Sulston, S. Brenner and J. Karn. 1986. Toward a physical map of the genome of the nematodeCaenorhabditis elegans.Proc. natl. Acad. Sci. U.S.A. 83, 7821–7825.

    Article  Google Scholar 

  • Coulson, A., R. Waterstone, J. Kiff, J. Sulston and Y. Kohara. 1988. Genome linking with yeast artificial chromosome.Nature 335, 184–186.

    Article  Google Scholar 

  • Curnow, R. N. and T. B. L. Kirkwood. 1989. Statistical analysis of deoxyribonucleic acid sequence data—a review.J. R. Statist. Soc. A152, 199–220.

    Google Scholar 

  • Daniels, D. L. and F. R. Blattner. 1987. Mapping using gene encyclopaedias.Nature 325, 831–832.

    Article  Google Scholar 

  • Evans, G. A. and K. A. Lewis. 1989. Physical mapping of complex genomes by cosmid multiplex analysis.Proc. natl Acad. Sci. U.S.A. 86, 5030–5034.

    Article  Google Scholar 

  • Hall, P. 1988.An Introduction to the Theory of Coverage Processes, New York: Wiley.

    Google Scholar 

  • Kohara, Y., K. Akiyama and K. Isono. 1987. The physical map of the wholeE. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library.Cell 50, 495–508.

    Article  Google Scholar 

  • Lander, E. S. 1989. Analysis with restriction enzymes. In:Mathematical Methods for DNA Sequences, Ch. 2, M. S. Waterman (ed.), Florida: CRC Press.

    Google Scholar 

  • Lander, E. S. and M. S. Waterman. 1988. Genomic mapping by fingerprinting random clones.Genomics 2, 231–239.

    Article  Google Scholar 

  • Olson, M. V., J. E. Dutchik, M. Y. Graham, G. M. Brodeur, C. Helms, M. Frank, M. MacCollin, R. Scheinman and T. Frank. 1986. Random clone strategy for genomic restriction mapping in yeast.Proc. natl. Acad. Sci. U.S.A. 83, 7826–7830.

    Article  Google Scholar 

  • R. K. Moyzis, R. K., D. C. Torney, J. Meyne, J. M. Buckingham, J. R. Wu, C. Burks, K. M. Sirotkin and W. B. Goad. 1989. The distribution of interspersed repetitive DNA sequences in the human genome.Genomics 4, 273–289.

    Article  Google Scholar 

  • Poutska, A., T. Pohl, D. P. Barlow, G. Zehetner, A. Craig, F. Michaels, E. Erlich, A. M. Frischauf and H. Lehrauch. 1986. Molecular approaches to mammalian genetics.Cold Spring Harb. Symp. quant. Biol. 51, 131–139.

    Google Scholar 

  • Stallings, R. L., D. C. Torney, C. E. Hildebrand, J. L. Longmire, L. L. Deaven, J. H. Jett, N. A. Doggett and R. K. Moyzis. 1990. Physical mapping of human chromosomes by repetitive sequence fingerprinting.Proc. natl. Acad. Sci. U.S.A. 87, 6218–6222.

    Article  Google Scholar 

  • Wyman, A. R., L. B. Wolfe and D. Botstein. 1985. Propagation of some human DNA sequences in bacteriophage λ vectors requires mutantEscherichia coli hosts.Proc. natl Acad. Sci. U.S.A. 82, 2880–2884.

    Article  Google Scholar 

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Authors and Affiliations

  1. School of Mathematical Sciences, Queen Mary and Westfield College, University of London, Mile End Road, E1 4NS, London, UK

    David J. Balding

  2. Theoretical Biology and Biophysics, Group T-10, Mail Stop K-71-, Los Alamos National Laboratory, 87545, Los Alamos, NM, USA

    David C. Torney

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  1. David J. Balding
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  2. David C. Torney
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Balding, D.J., Torney, D.C. Statistical analysis of DNA fingerprint data for ordered clone physical mapping of human chromosomes. Bltn Mathcal Biology 53, 853–879 (1991). https://doi.org/10.1007/BF02461488

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