An FPT haplotyping algorithm on pedigrees with a small number of sites

Doan, Duong D.; Evans, Patricia

doi:10.1186/1748-7188-6-8

Cited by 3 publications

(2 citation statements)

References 14 publications

(24 reference statements)

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“…rations for pedigrees with all genotyped individuals, with only polynomial dependence on the number m of sites (which can be very large in practice) and small exponential dependence on the minimum number k of recombinations. This algorithm significantly improves, and corrects, earlier results by Doan and Evans[4],[5]. An open question is how this algorithm performs when implemented and applied to data.…”

supporting

confidence: 72%

Haplotype Inference for Pedigrees with Few Recombinations

Kirkpatrick¹

2016

Bioinformatics Research and Applications

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Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with n individuals genotyped at every site, a set of Mendelian-consistent haplotypes that have the minimum number of recombinations. This is an NP-hard problem and some pedigrees can have thousands of individuals and hundreds of thousands of sites. This paper formulates this problem as a optimization on a graph and introduces a tailored algorithm with a running time of O(n (k+2) m 6k ) for n individuals, m sites, and k recombinations.Since there are generally only 1-2 recombinations per chromosome in each meiosis, k is small enough to make this algorithm practically relevant.

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confidence: 72%

Haplotype Inference for Pedigrees with Few Recombinations

Kirkpatrick¹

2016

Bioinformatics Research and Applications

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“…Li and Jiang [17] presented an O(m 3 n 3 ) time algorithm and a computer program PedPhase which solves ZRHC, by reducing the problem to solving a system of linear equations over the cyclic group Z 2 , where m is the number of loci and n is the number of members in the pedigree. Doan and Evans [23] presented another O(2 m 2 m 3 n 2 ) time algorithm for ZRHC, a consequence of a fixed-parameter tractable algorithm for the general minimization problem.…”

Section: Introductionmentioning

confidence: 99%

Whole Genome Identity-by-Descent Determination

Sabaa

Cai

Goebel

et al. 2013

J. Bioinform. Comput. Biol.

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High-throughput single nucleotide polymorphism genotyping assays conveniently produce genotype data for genome-wide genetic linkage and association studies. For pedigree datasets, the unphased genotype data is used to infer the haplotypes for individuals, according to Mendelian inheritance rules. Linkage studies can then locate putative chromosomal regions based on the haplotype allele sharing among the pedigree members and their disease status. Most existing haplotyping programs require rather strict pedigree structures and return a single inferred solution for downstream analysis. In this research, we relax the pedigree structure to contain ungenotyped founders and present a cubic time whole genome haplotyping algorithm to minimize the number of zero-recombination haplotype blocks. With or without explicitly enumerating all the haplotyping solutions, the algorithm determines all distinct haplotype allele identity-by-descent (IBD) sharings among the pedigree members, in linear time in the total number of haplotyping solutions. Our algorithm is implemented as a computer program iBDD. Extensive simulation experiments using 2 sets of 16 pedigree structures from previous studies showed that, in general, there are trillions of haplotyping solutions, but only up to a few thousand distinct haplotype allele IBD sharings. iBDD is able to return all these sharings for downstream genome-wide linkage and association studies.

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Parameterized Algorithmics for Finding Exact Solutions of NP-Hard Biological Problems

Hüffner

Komusiewicz

Niedermeier

et al. 2016

Methods in Molecular Biology

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Fixed-parameter algorithms are designed to efficiently find optimal solutions to some computationally hard (NP-hard) problems by identifying and exploiting "small" problem-specific parameters. We survey practical techniques to develop such algorithms. Each technique is introduced and supported by case studies of applications to biological problems, with additional pointers to experimental results.

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An FPT haplotyping algorithm on pedigrees with a small number of sites

Cited by 3 publications

References 14 publications

Haplotype Inference for Pedigrees with Few Recombinations

Haplotype Inference for Pedigrees with Few Recombinations

Whole Genome Identity-by-Descent Determination

Parameterized Algorithmics for Finding Exact Solutions of NP-Hard Biological Problems

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