Computational models and algorithms for the single individual haplotyping problem

Current Bioinformatics

Volumn 5, Issue 1, 2010, Pages 18-28

  Xie, Minzhu ^a,b   Wang, Jianxin ^a   Chen, Jianer ^a,c   Wu, Jingli ^a   Liu, Xucong ^a  

^a CENTRAL SOUTH UNIVERSITY   (China)

^b HUNAN NORMAL UNIVERSITY   (China)

^c Texas AandM University   (United States)

Author keywords

Computational model; Exact algorithm; Heuristic algorithm; Parameterized algorithm; Single individual haplotyping; SNP

Indexed keywords

GENOME;

COMPUTATIONAL ALGORITHM; COMPUTATIONAL MODELLING; EXACT ALGORITHMS; HAPLOTYPES; HAPLOTYPING; HEURISTICS ALGORITHM; MODEL AND ALGORITHMS; PARAMETERIZED ALGORITHM; SINGLE INDIVIDUAL HAPLOTYPING; SINGLE NUCLEOTIDE POLYMORPHISMS;

CONSENSUS ALGORITHM;

DNA FRAGMENT;

ALGORITHM; ANALYTICAL ERROR; DNA SEQUENCE; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; HAPLOTYPE; HUMAN; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; PRIORITY JOURNAL; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 77950175032     PISSN: 15748936     EISSN: None     Source Type: Journal    
DOI: 10.2174/157489310790596411     Document Type: Review

References (59)

1. Levy S, Sutton G, Ng PC, et al. The diploid genome sequence of an individual human. PLoS Biology 2007; 5: e254.
2. Wheeler DA, Srinivasan M, Egholm M, et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 2008; 452: 872-876.
3. The International SNP Map Working Group. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 2001; 409: 928-933.
4. The International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature 2007; 449: 851-861.
5. Tachmazidou I, Verzilli CJ, Iorio MD. Genetic association mapping via evolution-based clustering of haplotypes. PLoS Genet 2007; 3: e111.
6. Browning BL, Browning SR. Efficient multilocus association testing for whole genome association studies using localized haplotype clustering. Genet Epidemiol 2007; 31: 365-375.
7. Tzeng JY, Zhang D. Haplotype-based association analysis via variance-components score test. Am J Hum Genet 2007; 81: 927-938.
8. Arcaroli J, Sankoff J, Liu N, Allison DB, Maloney J, Abraham E. Association between urokinase haplotypes and outcome from infection-associated acute lung injury. Intensive Care Med 2008; 34: 300-307.
9. Clark AG. Inference of haplotypes from PCR-amplified samples of diploid populations. Mol Biol Evol 1990; 7: 111-122.
10. Gusfield D. An overview of combinatorial methods for haplotype inference. In Proc. the 1st RECOMB Satellite Workshop on Computational Methods for SNPs and Haplotype Inference. Springer-Verlag Berlin, Germany 2004; pp. 9-25.
11. Bonizzoni P, Della Vedova G, Dondi R, Li J. The haplotyping problem: an overview of computational models and solutions. J Comp Sci Technol 2003; 18: 675-88.
12. Zhang XS, Wang RS, Wu LY, Chen L. Models and algorithms for haplotyping problem. Curr Bioinformat 2006; 1: 105-14.
13. Bansal V, Bafna V. HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. Bioinformatics 2008; 24: i153-9.
14. Lancia G, Bafna V, Istrail S, Lippert R, Schwartz R. SNPs problems, complexity, and algorithms. In Proc. Ann. European Symp. on Algorithms (ESA). Springer: Berlin, Germany 2001; pp. 182-93.
15. Bubnoff A. Next-generation sequencing: the race is on. Cell 2008; 132: 721-3.
16. Siva N. 1000 Genomes project. Nat Biotechnol 2008; 26: 256.
17. Lippert R, Schwartz R, Lancia G, Istrail S. Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem. Brief Bioinform 2002; 3: 1-9.
18. Rizzi R, Bafna V, Istrail S, Lancia G. Algorithms and fixedparameter tractability for the single individual SNP haplotyping problem. In Proc. Ann.Workshop on Algorithms in Bioinformatics (WABI). Springer: Berlin, Germany 2002; pp. 29-43.
19. Li L, Kim JH, Waterman MS. Haplotype reconstruction from SNP alignment. In Proc Ann International Conference on Computational Molecular Biology (RECOMB). Association for Computing Machinery 2003; 207-16.
20. Wernicke S. On the algorithmic tractability of single nucleotide polymorphism (SNP) analysis and related problems. Ph. D. Thesis: Universität Tübingen 2003.
21. Panconesi A, Sozio M. Fast hare: a fast heuristic for single individual SNP haplotype reconstruction. In Proc of the 4th Int'l Workshop on Algorithms in Bioinformatics (WABI). Springer: Berlin, Germany 2004; pp. 266-77.
22. Zhao YY, Wu LY, Zhang JH, Wang RS, Zhang XS. Haplotype assembly from aligned weighted SNP fragments. Comput Biol Chem 2005; 29: 281-7.
23. Wang RS, Wu LY, Li ZP, Zhang XS. Haplotype reconstruction from SNP fragments by minimum error correction. Bioinformatics 2005; 21: 2456-62.
24. Bafna V, Istrail S, Lancia G, Rizzi R. Polynomial and APX-hard cases of the individual haplotyping problem. Theor Comp Sci 2005; 335: 109-25.
25. Cilibrasi R, Iersel L, Kelk S, Tromp J. On the complexity of several haplotyping problems. In 5th International Workshop of Algorithms in Bioinformatics (WABI 2005). Springer: Berlin, Germany 2005; pp. 128-39.
26. Kim JH, Waterman MS, Li LM. Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi. Genome Res 2007; 17: 1101-10.
27. Lindsay SJ, Bonfield JK, Hurles ME. Shotgun haplotyping: a novel method for surveying allelic sequence variation. Nucleic Acids Res 2005; 33: e152.
28. Zhang XS, Wang RS, Wu LY, Zhang W. Minimum conflict individual haplotyping from SNP fragments and related genotype. Evol Bioinform Online 2006; 2: 271-80.
29. Li Z, Wu L, Zhao Y, Zhang X. A dynamic programming algorithm for the k-haplotyping problem. Acta Math Appl Sinica (English Series) 2006; 22: 405-12.
30. Wang RS, Wu LY, Zhang XS, Chen L. A Markov chain model for haplotype assembly from SNP fragments. Genome Inform 2006; 17: 162-71.
31. Kim JH, Waterman MS, Li LM. Accuracy assessment of diploid consensus sequences. IEEE/ACM Trans Comput Biol Bioinform 2007; 4: 88-97.
32. Genovese L, Geraci F, Pellegrini M. A fast and accurate heuristic for the single individual SNP haplotyping problem with many gaps, high reading error rate and low coverage. In WABI 2007. Springer: Berlin, Germany 2007; pp. 49-60.
33. Xie M, Chen J, Wang J. Research on parameterized algorithms of the individual haplotyping problem. J Bioinform Comput Biol 2007; 5: 795-816.
34. Xie M, Chen J, Wang J. Parameterized algorithm of the individual haplotyping MSR problem with Mate-Pairs. J Software 2007; 18: 2070-82.
35. Wang Y, Feng E, Wang R. A clustering algorithm based on two distance functions for MEC model. Comput Biol Chem 2007; 31: 148-50.
36. Cilibrasi R, van Iersel L, Kelk S, Tromp J. The complexity of the single individual SNP haplotyping problem. Algorithmica 2007; 49(1): 13-36.
37. Konfortov BA, Bankier AT, Dear PH. An efficient method for multi-locus molecular haplotyping. Nucleic Acids Res 2007; 35: e6.
38. Wang Y, Feng E, Wang R, Zhang D. The haplotype assembly model with genotype information and iterative local-exhaustive search algorithm. Comput Biol Chem 2007; 31: 288-93.
39. Moeinzadeh MH, Asgarian E. Najafi-Ardabili A, Sharifian-R S, Sheikhaei, MS, Mohammadzadeh J. Three heuristic clustering methods for haplotype reconstruction problem with genotype information. In Proc of the 4th IEEE International Conference on Innovations in Information Technology (IIT). IEEE Computer Society: New York 2007; pp. 402-6.
40. Qian W, Yang Y, Yang N, Li C. Particle swarm optimization for SNP haplotype reconstruction problem. Appl Math Comput 2008; 196: 266-72.
41. Chen Z, Fu B, Schweller R, Yang B, Zhao Z, Zhu B. Linear time probabilistic algorithms for the singular haplotype reconstruction problem from SNP fragments. J Comput Biol 2008; 15(5): 535-46.
42. Xie M, Wang J, Chen J. A model of higher accuracy for the individual haplotyping problem based on weighted SNP fragments and genotype with errors. In Proc of ISMB 2008, Bioinformatics 2008; 24(13): i105-13.
43. Xie M, Wang J. An improved (and practical) parameterized algorithm of the individual haplotyping problem MFR with mate-pairs. Algorithmica 2008; 52: 250-66.
44. Xie M, Wang J, Chen J. A practical exact algorithm for the individual haplotyping problem MEC/GI. In Proc of COCOON 2008, Volume 5092 of Lecture Notes in Computer Science. Springer: Berlin, Germany 2008: pp. 342-51.
45. Xie M, Wang J, Chen J. A practical parameterized algorithm for the individual haplotyping problem MLF. In Proc of TAMC 2008, Volume 4978 of Lecture Notes in Computer Science. Springer; Berlin, Germany pp. 439-50.
46. Xie M, Wang J, Zhou W, Chen J. A practical parameterized algorithm for weighted minimum letter flips model of the individual haplotyping problem. In Proc of 2nd International Frontiers in Algorithmic Workshop (FAW), Volume 5059 of Lecture Notes in Computer Science. Springer: Berlin, Germany 2008; pp. 16-27.
47. Wu J, Wang J, Chen J. A particle swarm optimization algorithm based on optimal result set for haplotyping a single individual. In Proceedings of the 2008 International Conference on Bio-Medical Engineering and Informatics (BMEI). IEEE press: New York 2008; 395-99.
48. Xie M, Wang J, Chen J. A practical exact algorithm for the individual haplotyping problem MEC. In Proceedings of the 2008 International Conference on Bio-Medical Engineering and Informatics (BMEI). IEEE press: New York 2008; pp. 72-76.
49. Moeinzadeh MH, Asgarian E, Sharifian-R S, Najafi-Ardabili A, Mohammadzadeh J. Neural network based approaches, solving haplotype reconstruction in MEC and MEC/GI models. In Proc of Second Asia International Conference on Modelling and Simulation (AMS). IEEE Computer Society 2008; 934-9.
50. Genovese LM, Geraci F, Pellegrini M. SpeedHap: an accurate heuristic for the single individual SNP haplotyping problem with many gaps, high reading error rate and low coverage. IEEE/ACM Trans Comput Biol Bioinformatics 2008; 5: 492-502.
51. Vinson JP, Jaffe DB, O'Neill K, et al. Assembly of polymorphic genomes: algorithms and application to Ciona savignyi. Genome Res 2005; 15: 1127-35.
52. Halldórsson B, Bafna V, Edwards N, et al. A survey of computational methods for determining haplotypes. In Proc of the First RECOMB Satellite on Computational Methods for SNPs and Haplotype Inference: DIMACS/RECOMB Satellite Workshop. Volume 2938 of Lecture Notes in Computer Science, Springer: Berlin, Germany 2004: pp. 26-47.
53. Halldórsson B, Bafna V, Edwards N, Lippert R, Yooseph S, Istrail S. Combinatorial problems arising in SNP and haplotype analysis. Discrete Math Theor Comput Sci 2003: 26-47.
54. Greenberg H, Hart W, Lancia G. Opportunities for combinatorial optimization in computational biology. INFORMS J Comput 2004; 16: 211-31.
55. Kang H, Qin ZS, Niu T, Liu JS. Incorporating genotyping uncertainty in haplotype inference for single-nucleotide polymorphisms. Am J Human Genet 2004; 74(3): 495-10.
56. Chen J. Parameterized computation and complexity: a new approach dealing with NP-hardness. J Comput Sci Technol 2005; 20: 18-37.
57. Xie M. Research on parameterized models and algorithms for the haplotype assembly problem. Ph. D. Thesis, Central South University: P. R. China, 2008.
58. Bansal V, Halpern AL, Axelrod N, Bafna V. An MCMC algorithm for haplotype assembly from whole-genome sequence data. Genome Res 2008; 18: 1336-46.
59. The BioAlgo Group. http://bioalgo.iit.cnr.it/rehap/. Sep. 2, 2009.