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

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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.

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Authors and Affiliations

  1. School of Management, Xi’an Jiao Tong University, Xi’an, Shaanxi, 710049, China

    Yongxi Cheng

  2. Department of Computing Science, University of Alberta, Edmonton, Alberta, T6G 2E8, Canada

    Guohui Lin

Authors
  1. Yongxi Cheng
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  2. Guohui Lin
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Correspondence to Yongxi Cheng.

Additional information

Part of this work was done while Y. Cheng was at University of Alberta and University of Waterloo.

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Cheng, Y., Lin, G. Solving haplotype inference problem with non-genotyped founders via integer linear programming. J Comb Optim 23, 50–60 (2012). https://doi.org/10.1007/s10878-010-9340-8

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  • DOI: https://doi.org/10.1007/s10878-010-9340-8

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