CollHaps: A heuristic approach to haplotype inference by parsimony

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 7, Issue 3, 2010, Pages 511-523

  Tininini, Leonardo ^a   Bertolazzi, Paola ^a   Godi, Alessandra ^a   Lancia, Giuseppe ^b  

^a CNR   (Italy)

^b UNIVERSITY OF UDINE   (Italy)

Author keywords

Biology and genetics; discrete mathematics; heuristic methods; Heuristic methods; Miscellaneous

Indexed keywords

BIOLOGY AND GENETICS; COMPLEX DISEASE; DATA SETS; DISCRETE MATHEMATICS; DRUG DESIGN; EXPERIMENTAL DETERMINATION; GENETIC STUDIES; HAPLOTYPE INFERENCE; HAPLOTYPES; HEURISTIC APPROACH; LARGE DATASETS; MAXIMUM PARSIMONY; NP-HARD; PARSIMONY PRINCIPLE; PROCESSING TIME; SMALL DATA SET; THEORETICAL ARGUMENTS;

CHROMOSOMES; HEURISTIC ALGORITHMS; INFERENCE ENGINES; POPULATION STATISTICS;

HEURISTIC METHODS;

ALGORITHM; ARTICLE; BIOLOGY; COMPUTER PROGRAM; DNA SEQUENCE; GENETICS; GENOTYPE; HAPLOTYPE; HUMAN; METHODOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; COMPUTATIONAL BIOLOGY; GENOTYPE; HAPLOTYPES; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 77955467595     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2008.130     Document Type: Article

References (30)

1. J.C. Venter et al., "The Sequence of the Human Genome," Science, vol.291, pp. 1304-1351, 2001.
2. L. Jin, P.A. Underhill, V. Doctor, R.W. Davis, P. Shen, L.L. Cavalli- Sforza, and P.J. Oefner, "Distribution of Haplotypes from a Chromosome 21 Region Distinguishes Multiple Prehistoric Human Migiration," Proc. Nat'l Academy of Sciences USA, vol.96, pp. 3796-3800, 1999.
3. M.R. Hoehe, K. Köpke, B. Wendel, K. Rohde, C. Flachmeier, K.K. Kidd, W.H. Berrettini, and C.G. M, "Sequence Variability and Candidate Gene Analysis in Complex Disease: Association ofμ Opioid Receptor Gene Variation with Substance Dependence," Human Molecular Genetics, vol.9, pp. 2895-2908, 2000.
4. D. Gusfield and S.H. Orzack, "Haplotype Inference," Handbook of Computational Molecular Biology, S. Aluru, ed., pp. 18-1-18-28, CRC Press, 2005.
5. B.V. Halldorsson, V. Bafna, N. Edwards, R. Lippert, S. Yooseph, and S. Istrail, "A Survey of Computational Methods for Determining Haplotypes," Proc. DIMACS/RECOMB Satellite Workshop Computational Methods for SNPs and Haplotype Inference, pp. 26-47, 2002.
6. G. Lancia, M.C. Pinotti, and R. Rizzi, "Haplotyping Populations by Pure Parsimony: Complexity of Exact and Approximation Algorithms," INFORMS J. Computing, vol.16, pp. 348-359, 2004.
7. S. Clark, "Inference of Haplotypes from Pcr-Amplified Samples of Diploid Populations," Molecular Biology and Evolution, vol.7, pp. 111-122, 1990.
8. E. Hubbell, "Finding a Maximum Parsimony Solution to Haplotype Phase Is NP-Hard," personal comm., 2000.
9. R. Sharan, B.V. Halldorsson, and S. Istrail, "Islands of Tractability for Parsimony Haplotyping," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol.3, no.3, pp. 303-311, July-Sept. 2006.
10. L. Wang and Y. Xu, "Haplotype Inference by Maximum Parsimony," Bioinformatics, vol.19, pp. 1773-1780, 2003.
11. D. Gusfield, "Haplotype Inference by Pure Parsimony," Proc. 14th Ann. Symp. Combinatorial Pattern Matching (CPM '03), pp. 144-155, 2003.
12. D.G. Brown and I.M. Harrower, "Integer Programming Approaches to Haplotype Inference by Pure Parsimony," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol.3, no.2, pp. 141-154, Apr.-June 2006.
13. I. Lynce and J. Marques-Silva, "Sat in Bioinformatics: Making the Case with Haplotype Inference," Proc. Int'l Conf. Theory and Applications of Satisfiability Testing (SAT), pp. 283-296, 2006.
14. I. Lynce and J. Marques-Silva, "Haplotype Inference with Boolean Satisfiability," Int'l J. Artificial Intelligence Tools, vol.17, pp. 355- 387, 2008.
15. L. Excoffier and M. Slatkin, "Maximum-Likelihood Estimation of Molecular Haplotype Frequencies in a Diploid Population," Molecular Biology and Evolution, vol.12, pp. 921-927, 1995.
16. M.E. Hawley and K.K. Kidd, "Haplo: A Program Using the EM Algorithm to Estimate the Frequencies of Multi-Site Haplotypes," J. Heredity, vol.86, pp. 409-411, 1995.
17. J.C. Long, R.C. Williams, and M. Urbanek, "An E-M Algorithm and Testing Strategy for Multiple-Locus Haplotypes," Am. J. Human Genetics, vol.56, pp. 799-810, 1995.
18. G. Kimmel and R. Shamir, "Gerbil: Genotype Resolution and Block Identification Using Likelihood," Proc. Nat'l Academy of Sciences USA, vol.102, pp. 158-162, 2005.
19. M. Stephens and P. Donnelly, "A Comparison of Bayesian Methods for Haplotype Reconstruction from Population Genotype Data," Am. J. Human Genetics, vol.73, pp. 1162-1169, 2003.
20. R.R. Hudson, "Gene Genealogies and the Coalescent Process," Oxford Surveys in Evolutionary Biology, D.J. Futuyma and J. Antonovics, eds., vol.7, pp. 1-44, Oxford Univ. Press, 2006.
21. P. Scheet and M. Stephens, "A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic Phase," Am. J. Human Genetics, vol.78, pp. 629-644, 2006.
22. T. Niu, Z.S. Qin, X. Xu, and J.S. Liu, "Bayesian Haplotype Inference for Multiple Linked Single-Nucleotide Polymorphisms," Am. J. Human Genetics, vol.70, pp. 157-169, 2002.
23. G. Lancia and P. Serafini, "A Covering Approach with Column- Generation for Parsimony Haplotyping," Technical Report 4-07, Dip. di Matematica e Informatica, Univ. of Udine, 2007.
24. R.R. Hudson, "Generating Samples under aWright-Fisher Neutral Model of Genetic Variation," Bioinformatics, vol.18, pp. 337-338, 2002.
25. M. Stephens, N. Smith, and P. Donnelly, "A New Statistical Method for Haplotype Reconstruction from Population Data," Am. J. Human Genetics, vol.68, pp. 978-989, 2001.
26. S. Lin, D.J. Cutler, E. Zwick, and A. Chakravarti, "Haplotype Inference in Random Population Samples," Am. J. Human Genetics, vol.71, pp. 1129-1137, 2002.
27. M.J. Rieder, S.L. Taylor, A.G. Clark, and D.A. Nickerson, "Sequence Variation in the Human Angiotensin Converting Enzyme," Nature Genetics, vol.22, pp. 59-62, 1999.
28. B. Kerem, J.M. Rommens, J.A. Buchanan, D. Marliewicz, T.K. Cox, A. Chakravarti, M. Buchwald, and L. Tsui, "Identification of the Cystic Fibrosis Gene: Genetic Analysis," Science, vol.245, pp. 1073- 1080, 1989. (Pubitemid 19231815)
29. D. Fallin and N.J. Schork, "Accuracy of Haplotype Frequency Estimation for Biallelic Loci, via the Expectation-Maximization Algorithm for Unphased Diploid Genotype Data," Am. J. Human Genetics, vol.67, pp. 947-959, 2000.
30. M.J. Daly, J.D. Rioux, S.F. Schaffner, T.J. Hudson, and E.S. Lander, "High-Resolution Haplotype Structure in the Human Genome," Nature Genetics, vol.29, pp. 229-232, 2001.