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.
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Catanzaro, D., Labbé, M., Halldórsson, B.V. (2012). A Mixed Integer Programming Model for the Parsimonious Loss of Heterozygosity Problem. In: Bleris, L., Măndoiu, I., Schwartz, R., Wang, J. (eds) Bioinformatics Research and Applications. ISBRA 2012. Lecture Notes in Computer Science(), vol 7292. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30191-9_3
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DOI: https://doi.org/10.1007/978-3-642-30191-9_3
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