Empirical Exploration of Perfect Phylogeny Haplotyping and Haplotypers

  • Ren Hua Chung
  • Dan Gusfield
Conference paper

DOI: 10.1007/3-540-45071-8_3

Part of the Lecture Notes in Computer Science book series (LNCS, volume 2697)
Cite this paper as:
Chung R.H., Gusfield D. (2003) Empirical Exploration of Perfect Phylogeny Haplotyping and Haplotypers. In: Warnow T., Zhu B. (eds) Computing and Combinatorics. COCOON 2003. Lecture Notes in Computer Science, vol 2697. Springer, Berlin, Heidelberg

Abstract

The next high-priority phase of human genomics will involve the development of a full Haplotype Map of the human genome 15. It will be used in large-scale screens of populations to associate specific haplotypes with specific complex genetic-influenced diseases. A key, perhaps bottleneck, problem is to computationally determine haplotype pairs from genotype data. An approach to this problem based on viewing it in the context of perfect phylogeny was introduced in 14 along with an efficient solution. A slower (in worst case) variation of that method was implemented 3. Two simpler methods for the perfect phylogeny approach that are also slower (in worst case) than the first algorithm were later developed 1,7. We have implemented and tested all three of these approachs in order to compare and explain the practical efficiencies of the three methods. We discuss two other empirical observations: a strong phase-transition in the frequency of obtaining a unique solution as a function of the number of individuals in the input; and results of using the method to find non-overlapping intervals where the haplotyping solution is highly reliable, as a function of the level of recombination in the data. Finally, we discuss the biological basis for the size of these tests.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • Ren Hua Chung
    • 1
  • Dan Gusfield
    • 1
  1. 1.Computer Science DepartmentUniversity of California, DavisDavisUSA

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