Solving haplotype inference problem with non-genotyped founders via integer linear programming

Authors:
Yongxi Cheng;Guohui Lin
Affiliations:
School of Management, Xi'an Jiao Tong University, Xi'an, China 710049;Department of Computing Science, University of Alberta, Edmonton, Canada T6G 2E8
Venue:
Journal of Combinatorial Optimization
Year:
2012

Citing 3
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Efficient rule-based haplotyping algorithms for pedigree data

RECOMB '03 Proceedings of the seventh annual international conference on Research 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
Linear-Time haplotype inference on pedigrees without recombinations

WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics

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Abstract

In Cheng et al. (Acta Math. Appl. Sin. (English Ser.), 25:475---486, 2009), the authors present a cubic time zero-recombination haplotyping algorithm that can handle some incomplete pedigrees. More specifically, the algorithm can handle pedigrees with non-genotyped founders, provided that for each nuclear family at least one parent is genotyped and each non-genotyped founder appears in at most one nuclear family. The importance of this lies in that such cases frequently happen in real data, because some founders may have passed away and their genotype data can no longer be collected. In this paper, we further generalize the above algorithm by removing the first restriction. We present a new integer linear programming based algorithm that handles pedigrees with non-genotyped founders. The new algorithm allows the pedigrees to have nuclear families where both parents are non-genotyped founders, provided that each non-genotyped founder appears in at most one nuclear family.