Computational problems in perfect phylogeny haplotyping: typing without calling the allele.

Details

Serval ID
serval:BIB_A2E84AD187F8
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Computational problems in perfect phylogeny haplotyping: typing without calling the allele.
Journal
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM
Author(s)
Barzuza T., Beckmann J.S., Shamir R., Pe'er I.
ISSN
1545-5963
Publication state
Published
Issued date
2008
Peer-reviewed
Oui
Volume
5
Number
1
Pages
101-109
Language
english
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 (PP) 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.
Keywords
Algorithms, Evolution, Molecular, Genetics, Population, Genotype, Haplotypes, Heterozygote, Homozygote, Humans, Internet, Models, Genetic, Phylogeny, Polymorphism, Single Nucleotide, Software
Pubmed
Web of science
Create date
20/02/2009 14:29
Last modification date
20/08/2019 16:08
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