A mixed integer programming model for the parsimonious loss of heterozygosity problem

  • Authors:

  • Daniele Catanzaro;Martine Labbé;Bjarni V. Halldórsson

  • Affiliations:

  • Graphs and Mathematical Optimization Unit, Computer Science Department, Université Libre de Bruxelles (ULB), Belgium;Graphs and Mathematical Optimization Unit, Computer Science Department, Université Libre de Bruxelles (ULB), Belgium;School of Science and Engineering, Reykjavík University, Reykjavik, Iceland

  • Venue:
  • ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
  • Year:
  • 2012

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Abstract

We investigate the Parsimonious Loss of Heterozygosity Problem (PLOHP) , i.e., the problem of partitioning suspected polymorphisms of a set of individuals into the minimum number of deletion areas. We generalize the work of Halldórsson et al. ' by showing how one can incorporate prior knowledge about the location of deletion; we prove the general $\mathcal{NP}$ -hardness of the problem and we provide a state-of-the-art mixed integer programming formulation and a number of possible strengthening valid inequalities able to exactly solve practical instances of the PLHOP containing up to 9.000 individuals and 3000 SNPs within 12 hours compute time.