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2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS) (2012)
Las Vegas, NV, USA
Feb. 23, 2012 to Feb. 25, 2012
ISBN: 978-1-4673-1320-9
pp: 1-6
Yuri Pirola , DISCo, Univ. degli Studi di Milano-Bicocca, Milan, Italy
Gianluca Della Vedova , Dip. Statistica, Univ. degli Studi di Milano-Bicocca, Milan, Italy
Stefano Biffani , CeRSA, Parco Tecnologico Padano, Lodi, Italy
Alessandra Stella , CeRSA, Parco Tecnologico Padano, Lodi, Italy
Paola Bonizzoni , DISCo, Univ. degli Studi di Milano-Bicocca, Milan, Italy
ABSTRACT
In this work, we propose the MIN-RECOMBINANT HAPLOTYPE CONFIGURATION WITH BOUNDED ERRORS problem (MRHCE), which extends the original MIN-RECOMBINANT HAPLOTYPE CONFIGURATION formulation by incorporating two common characteristics of real data: errors and missing genotypes (including untyped individuals). We describe a practical algorithm for MRHCE that is based on a reduction to the Satisfiability problem (SAT) and exploits recent advances in the constraint programming literature. An experimental analysis demonstrates the soundness of our model and the effectiveness of the algorithm under several scenarios. The analysis on real data and the comparison with state-of-the-art programs reveals that our approach couples better scalability to large and complex pedigrees with the explicit inclusion of genotyping errors into the model.
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CITATION

Y. Pirola, S. Biffani, A. Stella, G. D. Vedova and P. Bonizzoni, "A fast and practical approach to genotype phasing and imputation on a pedigree with erroneous and incomplete information," 2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS), Las Vegas, NV, USA, 2012, pp. 1-6.
doi:10.1109/ICCABS.2012.6182643
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