Haplotype inferring via galled-tree networks is NP-complete

Journal of Computational Biology

Volumn 17, Issue 10, 2010, Pages 1317-1331

  Gupta, Arvind ^a   Karimi, Mohammad M ^a   Maňuch, Ján ^a,b   Stacho, Ladislav ^b   Zhao, Xiaohong ^c  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b SIMON FRASER UNIVERSITY   (Canada)

^c Siemans Corporate Research   (United States)

Author keywords

algorithms; combinatorial optimization; combinatorics; RNA

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; EVOLUTION; GENOTYPE; HAPLOTYPE; HUMAN; PHYLOGENY; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; BIOLOGICAL EVOLUTION; GENOTYPE; HAPLOTYPES; HUMANS; MODELS, GENETIC; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 77958065841     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2009.0117     Document Type: Article

References (27)

1. Bafna, V., Gusfield, D., Lancia, G., et al. 2003. Haplotyping as perfect phylogeny: a direct approach. J. Comput. Biol. 10:323-340.
2. Bordewich, M., and Semple, C. 2004. On the computational complexity of the rooted subtree prune and regraft distance. Ann. Combin. 8:409-423.
3. Clark, A. 1990. Inference of haplotypes from PCR-amplified samples of dipoid populations. Mol. Biol. Evol. 7:111-122.
4. Daly, M., Rioux, J., Schaffner, S., et al. 2001. High-resolution haplotype structure in the human genome. Nat. Genet. 29:229-232.
5. Gabriel, S., Schaffner, S., Nguyen, H., et al. 2002. The structure of haplotype blocks in the human genome. Science 296, 2225-2229.
6. Gupta, A., Maňuch, J., Stacho, L., et al. 2006. Characterization of the existence of galled-tree networks. J. Bioinform. Comput. Biol. 4:1309-1328.
7. Gupta, A., Maňuch, J., Stacho, L., et al. 2007. Algorithm for haplotype inferring via galled-tree networks with simple galls [extended abstract]. Lect. Notes Bioinform 4463, 121-132.
8. Gupta, A., Maňuch, J., Stacho, L., et al. 2008. Haplotype inferring via galled-tree networks is NP-complete. Lect. Notes Comput. Sci. 5902, 287-298.
9. Gupta, A., Maňuch, J., Stacho, L., et al. 2009. Haplotype inferring via galled-tree networks using a hypergraph covering problem for special genotype matrices. Discr. Appl. Math. 157:2310-2324.
10. Gusfield, D. 2001. Inference of haplotypes from samples of diploid populations: complexity and algorithms. J. Comput. Biol. 8:305-323.
11. Gusfield, D. 2002. Haplotyping as perfect phylogeny: conceptual framework and efficient solutions. Proc. RECOMB 2002 166-175.
12. Gusfield, D. 2003. Haplotype inference by pure parsimony. Lect. Notes Comput. Sci. 2676, 144-155.
13. Gusfield, D. 2005. Optimal, efficient reconstruction of root-unknown phylogenetic networks with constrained and structured recombination. J. Comput. Syst. Sci. 70:381-398.
14. Gusfield, D., and Orzack, S. H. 2006. Haplotype inference, 18-1-18-28. In: Handbook of Computational Molecular Biology. CRC Computer and Information Science Series. Chapman & Hall, New York (S. Aluru, editor).
15. Gusfield, D., Eddhu, S., and Langley, C. 2004a. The fine structure of galls in phylogenetic networks. INFORMS J. Comput. 16:459-469.
16. Gusfield, D., Eddhu, S., and Langley, C. 2004b. Optimal, efficient reconstruction of phylogenetic networks with constrained recombination. J. Bioinform. Comput. Biol. 2:173-213.
17. Helmuth, L. 2001. Genome research: map of the human genome 3.0. Science 293:583-585.
18. International HapMap Consortium. 2005. A haplotype map of the human genome. Nature 437:1299-1320.
19. Lancia, G., Pinotti, C., and Rizzi, R. 2002. Haplotyping populations: complexity and approximations [Dit-02-082]. University of Trento.
20. Mitra, R. D., Butty, V. L., Shendure, J., et al. 2003. Digital genotyping and haplotyping with polymerase colonies. Proc. Natl. Acad. Sci. USA 100, 5926-5931.
21. Papadimitriou, C. H. 1994. Computational Complexity. Addison-Wesley, New York.
22. Patil, N., Berno, A., Hinds, D., et al. 2001. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294:1719-1723.
23. Pennisi, E. 2007. Breakthrough of the year: human genetic variation. Science 318:1842-1843.
24. Song, Y. S. 2006. A concise, necessary and sufficient condition for the existence of a galled-tree. IEEE/ACM Trans. Comput. Biol. and Bioinform. 3:186-191.
25. Song, Y. S., Wu, Y., and Gusfield, D. 2005. Algorithms for imperfect phylogeny haplotyping (IPPH) with a single homoplasy or recombination event. Lect. Notes Comput. Sci. 3692, 152-164.
26. Thorisson, G., Smith, A., Krishnan, L., et al. 2005. The international HapMap project web site. Genome Res. 15:1591-1593.
27. Wang, L., Zhang, K., and Zhang, L. 2001. Perfect phylogenetic networks with recombination. J. Comput. Biol. 8:69-78.