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Haplotype Inference for Pedigrees with Few Recombinations

  • B. KirkpatrickEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9683)

Abstract

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 \(\mathsf {NP}\)-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.

Keywords

Pedigrees Haplotype inference Minimum recombination haplotype configuration (MRHC) 

Notes

Acknowledgments

BK thanks M. Mnich at the Cluster of Excellence, Saarland University, Saarbrücken, Germany for critical reading of the manuscript. BK thanks arXiv for pre-print publication of the full manuscript [10].

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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  1. 1.Intrepid Net ComputingDillonUSA

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