Computing and Combinatorics

Volume 2697 of the series Lecture Notes in Computer Science pp 5-19


Empirical Exploration of Perfect Phylogeny Haplotyping and Haplotypers

  • Ren Hua ChungAffiliated withComputer Science Department, University of California, Davis
  • , Dan GusfieldAffiliated withComputer Science Department, University of California, Davis

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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.