Linear-Time haplotype inference on pedigrees without recombinations

Authors:
M. Y. Chan;Wun-Tat Chan;Francis Y. L. Chin;Stanley P. Y. Fung;Ming-Yang Kao
Affiliations:
Department of Computer Science, University of Hong Kong, Hong Kong;Department of Computer Science, University of Hong Kong, Hong Kong;Department of Computer Science, University of Hong Kong, Hong Kong;Department of Computer Science, University of Leicester, Leicester, UK;Department of Electrical Engineering and Computer Science, Northwestern University
Venue:
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Year:
2006

Citing 2
Cited 6

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An exact solution for finding minimum recombinant haplotype configurations on pedigrees with missing data by integer linear programming

RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology

Fast elimination of redundant linear equations and reconstruction of recombination-free mendelian inheritance on a pedigree

SODA '07 Proceedings of the eighteenth annual ACM-SIAM symposium on Discrete algorithms
Beyond evolutionary trees

Natural Computing: an international journal
Xor perfect phylogeny haplotyping in pedigrees

ICIC'10 Proceedings of the Advanced intelligent computing theories and applications, and 6th international conference on Intelligent computing
Fixed-parameter algorithm for haplotype inferences on general pedigrees with small number of sites

WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
Solving haplotype inference problem with non-genotyped founders via integer linear programming

Journal of Combinatorial Optimization
Fixed-parameter algorithm for general pedigrees with a single pair of sites

ISBRA'10 Proceedings of the 6th international conference on Bioinformatics Research and Applications

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Abstract

In this paper, a linear-time algorithm, which is optimal, is presented to solve the haplotype inference problem for pedigree data when there are no recombinations and the pedigree has no mating loops. The approach is based on the use of graphs to capture SNP, Mendelian and parity constraints of the given pedigree.