CSDL Home IEEE/ACM Transactions on Computational Biology and Bioinformatics 2008 vol.5 Issue No.01 - January-March

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Issue No.01 - January-March (2008 vol.5)

pp: 101-109

ABSTRACT

A haplotype is an m-long binary vector. The xor-genotype of two haplotypes is the m-vector of their coordinate-wise xor. We study the following problem: Given a set of xor-genotypes, reconstruct their haplotypes so that the set of resulting haplotypes can be mapped onto a perfect phylogeny tree. The question is motivated by studying population evolution in human genetics, and is a variant of the perfect phylogeny haplotyping problem that has received intensive attention recently. Unlike the latter problem, in which the input is "full" genotypes, here we assume less informative input, and so may be more economical to obtain experimentally.Building on ideas of Gusfield, we show how to solve the problem in polynomial time, by a reduction to the graph realization problem. The actual haplotypes are not uniquely determined by that tree they map onto, and the tree itself may or may not be unique. We show that tree uniqueness implies uniquely determined haplotypes, up to inherent degrees of freedom, and give a sufficient condition for the uniqueness. To actually determine the haplotypes given the tree, additional information is necessary. We show that two or three full genotypes suffice to reconstruct all the haplotypes, and present a linear algorithm for identifying those genotypes.

INDEX TERMS

XOR-genotypes, Haplotypes, Perfect Phylogeny, Graph Realization

CITATION

Tamar Barzuza, Jacques S. Beckmann, Ron Shamir, Itsik Pe'er, "Computational Problems in Perfect Phylogeny Haplotyping: Typing without Calling the Allele",

*IEEE/ACM Transactions on Computational Biology and Bioinformatics*, vol.5, no. 1, pp. 101-109, January-March 2008, doi:10.1109/TCBB.2007.1063REFERENCES