A survey on haplotyping algorithma for tightly linked markers

Journal of Bioinformatics and Computational Biology

Volumn 6, Issue 1, 2008, Pages 241-259

  Li, Jing ^a   Jiang, Tao ^b  

^a Case Western Reserve University   (United States)

^b University of California Riverside   (United States)

Author keywords

Haplotype inference; SNP

Indexed keywords

ACCURACY; CONFERENCE PAPER; DIPLOIDY; DRUG RESPONSE; GENETIC ALGORITHM; GENETIC ASSOCIATION; GENETIC MARKER; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOMICS; GENOTYPE; HAPLOTYPE; HEREDITY; HUMAN; HUMAN GENOME; MAXIMUM LIKELIHOOD METHOD; PEDIGREE; PHYLOGENY; SINGLE NUCLEOTIDE POLYMORPHISM; ALGORITHM; ARTICLE; CHROMOSOME MAP; DNA SEQUENCE; GENE LINKAGE DISEQUILIBRIUM; GENETICS; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

ALGORITHMS; BASE SEQUENCE; CHROMOSOME MAPPING; DNA MUTATIONAL ANALYSIS; GENETIC MARKERS; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MOLECULAR SEQUENCE DATA; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 44049100764     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720008003369     Document Type: Conference Paper

References (61)

1. International Human Genome Sequencing Consortium, Initial sequencing and analysis of the human genome, Nature 409(6822):860-921, 2001.
2. Venter JC et al., The sequence of the human genome, Science 291(5507):1304-1351, 2001.
3. The International HapMap Consortium, The International HapMap Project, Nature 426:789-796, 2003.
4. Sobel E, Lange K, O'Connell J, Weeks D, Haplotyping algorithms, in Speed T, Waterman M (eds.), Genetic Mapping and DNA Sequencing, IMA Volumes in Mathematics and Its Applications, Vol. 81, Springer-Verlag, New York, pp. 89-110, 1996.
5. Bonizzoni P, Della Vedova G, Dondi R, Li J, The haplotyping problem: An overview of computational models and solutions, J Comput Sci Technol 18(6):675-688, 2003.
6. Gusfield D, An overview of combinatorial methods for haplotype inference, in Istrail S, Waterman M, Clark A (eds.), Computational Methods for SNPs and Haplotype Inference, Lecture Notes in Computer Science, Vol. 2983, Springer-Verlag, Berlin, pp. 9-25, 2004.
7. Halldórsson BV, Bafna V, Edwards N, Lippert R, Yooseph S, Istrail S, A survey of computational methods for determining haplotypes, in Istrail S, Waterman M, Clark A (eds.), Computational Methods for SNPs and Haplotype Inference, Lecture Notes in Computer Science, Vol. 2983, Springer-Verlag, Berlin, pp. 26-47, 2004.
8. Zhang XS, Wang RS, Wu LY, Chen L, Models and algorithms for haplotyping problem, Curr Bioinformatics 1(1):105-114, 2006.
9. Sham P, Statistics in Human Genetics, Oxford University Press, New York, 1998.
10. Elston RC, Stewart J, A general model for the genetic analysis of pedigree data, Hum Hered 21:523-542, 1971.
11. Lander ES, Green P, Construction of multilocus genetic linkage maps in humans, Proc Natl Acad Sci USA 84:2363-2367, 1987.
12. Kruglyak L, Daly MJ, Reeve-Daly MP, Lander ES, Parametric and nonparametric linkage analysis: A unified multipoint approach, Am J Hum Genet 58:1347-1363, 1996.
13. Gudbjartsson DF, Jonasson K, Frigge ML, Kong A, Allegro, a new computer program for multipoint linkage analysis, Nat Genet 25 1):12-13, 2000.
14. Abecasis GR, Cherny SS, Cookson WO, Cardon LR, Merlin - Rapid analysis of dense genetic maps using sparse gene flow trees, Nat Genet 30(1):97-101, 2002.
15. Abecasis GR, Wigginton JE, Handling marker-marker linkage disequilibrium: Pedigree analysis with clustered markers, Am J Hum Genet 77:754-767, 2005.
16. O'Connell JR, Zero-recombinant haplotyping: Applications to fine mapping using SNPs, Genet Epidemiol 19(Suppl 1):S64-S70, 2000.
17. Qian D, Beckmann L, Minimum-recombinant haplotyping in pedigrees, Am J Hum Genet 70(6):1434-1445, 2002.
18. Tapadar P, Ghosh S, Majumder PP, Haplotyping in pedigrees via a genetic algorithm, Hum Hered 50(1):43-56, 2000.
19. Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES, High-resolution haplotype structure in the human genome, Nat Genet 29 2):229-232, 2001.
20. Gabriel SB et al., The structure of haplotype blocks in the human genome, Science 296(5576):2225-2229, 2002.
21. Helmuth L, Genome research: Map of the human genome 3.0, Science 293(5530):583-585, 2001.
22. Li J, Jiang T, Efficient rule-based haplotyping algorithms for pedigree data, in Proc RECOMB'03, pp. 197-206, 2003.
23. Li J, Jiang T, Efficient inference of haplotypes from genotypes on a pedigree, J Bioinform Comput Biol 1(1):41-69, 2003.
24. Doi K, Li J, Jiang T, Minimum recombinant haplotype configuration on pedigrees without mating loops, Proc Workshop on Algorithms in Bioinformatics (WABI), Budapest, Hungary, pp. 339-353, 2003.
25. Li J, Jiang T, An exact solution for finding minimum recombinant haplotype configurations on pedigrees with missing data by integer linear programming, in Proc RECOMB'04, pp. 101-110, 2004.
26. Li J, Jiang T, Computing the minimum recombinant haplotype configuration from incomplete genotype data on a pedigree by integer linear programming, J Comput Biol 12:719-739, 2005.
27. Zhang K, Sun F, Zhao H, HAPLORE: A program for haplotype reconstruction in general pedigrees without recombination, Bioinformatics 21 90-103, 2005.
28. Chin F, Zhang Q, Haplotype inference on tightly linked markers in pedigree data, unpublished manuscript, 2005.
29. Li X, Chen Y, Li J, An efficient algorithm for the zero-recombinant haplotype configuration problem, unpublished manuscript, 2006.
30. Chan MY, Chan W, Chin F, Fung S, Kao M, Linear-time haplotype inference on pedigrees without recombinations, Proc of the 6th Annual Workshop on Algorithms in Bioinformatics (WABI06), pp. 56-67, 2006.
31. Xiao J, Liu L, Xia L, Jiang T, Fast elimination of redundant linear equations and reconstruction of recombination-free Mendelian inheritance on a pedigree, Proc 18th ACM-SIAM Symposium on Discrete Algorithms (SODA), New Orleans, LA, pp. 655-664, 2007.
32. Elkin M, Emeky Y, Spielman DA, Teng S, Lower-stretch spanning trees, Proc 37th ACM Symposium on Theory of Computing (STOC'05), pp. 494-503, 2005.
33. Liu L, Chen X, Xiao J, Jiang T, Complexity and approximation of the minimum recombination haplotype configuration problem, Proc 16th International Symposium on Algorithms and Computation (ISAAC'05) pp. 370-379, 2005.
34. Liu L, Chen X, Xiao J, Jiang T, Complexity and approximation of the minimum recombination haplotype configuration problem, Theor Comput Sci 378:316-330, 2007.
35. Clark AG, Inference of haplotypes from PCR-amplified samples of diploid populations, Mol Biol Evol 7(2):111-122, 1990.
36. Gusfield D, Inference of haplotypes from samples of diploid populations: Complexity and algorithms, J Comput Biol 8:305-323, 2001.
37. Gusfield D, Haplotyping as perfect phylogeny: Conceptual framework and efficient solutions, in Proc RECOMB'02, pp. 166-175, 2002.
38. Gusfield D, Haplotype inference by pure parsimony, in Proc Combinatorial Pattern Matching Conference'03, pp. 144-155, 2003.
39. Wang L, Xu L, Haplotype inference by pure parsimony, Bioinformatics 19:1773-1780, 2003.
40. Lancia G, Pinotti MC, Rizzi R, Haplotyping populations by pure parsimony, INFORMS J Comput 16(4):C348-C359, 2004.
41. Excoffier L, Slatkin M, Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population, Mol Biol Evol 12 921-927, 1995.
42. Hawley ME, Kidd KK, HAPLO: A program using the EM algorithm to estimate the frequencies of multi-site haplotypes, J Hered 86 409-411, 1995.
43. Stephens M, Smith NJ, Donnelly P, A new statistical method for haplotype reconstruction from population data, Am J Hum Genet 68 4):978-989, 2001.
44. Niu T, Qin Z, Xu X, Liu JS, Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms, Am J Hum Genet 70 157-159, 2002.
45. Bafna V, Gusfield D, Lancia G, Yooseph S, Haplotyping as perfect phylogeny: A direct approach, Technical Report, University of California, Davis, Davis, CA, 2002.
46. Eskin E, Halperin E, Large scale recovery of haplotypes from genotype data using imperfect phylogeny, in Proc RECOMB 2003, pp. 104-113, 2003.
47. Ding Z, Filkov V, Gusfield D, A linear-time algorithm for perfect phylogeny haplotyping, in Proc RECOMB'05, pp. 585-600, 2005.
48. Stephens M, Donnelly P, A comparison of Bayesian methods for haplotype reconstruction from population genotype data, Am J Hum Genet 73 1162-1169, 2003.
49. Qin Z, Niu T, Liu J, Partitioning-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms, Am J Hum Genet 71:1242-1247, 2002.
50. Pfeiffer RM, Rutter JL, Gail MH, Struewing J, Gastwirth JL, Efficiency of DNA pooling to estimate joint allele frequencies and measure linkage disequilibrium, Genet Epidemiol 22(1):94-102, 2002.
51. Wang S, Kidd KK, Zhao H, On the use of DNA pooling to estimate haplotype frequencies, Genet Epidemiol 24(1):74-82, 2003.
52. Yang Y, Zhang J, Hoh J, Matsuda F, Xu P, Lathrop M, Ott J, Efficiency of single-nucleotide polymorphism haplotype estimation from pooled DNA, Proc Natl Acad Sci USA 100(12):7225-7230, 2003.
53. Quade SR, Elston RC, Goddard KA, Estimating haplotype frequencies in pooled DNA samples when there is genotyping error, BMC Genet 6 25, 2005.
54. de Bakker PI, Yelensky R, Pe'er I, Gabriel SB, Daly MJ, Altshuler D, Efficiency and power in genetic association studies, Nat Genet 37:1217-1223, 2005.
55. Patil N et al., Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21, Science 294 1719-1723, 2001.
56. Zhang K, Deng M, Chen T, Waterman M, Sun F, A dynamic programming algorithm for haplotype partitioning, Proc Natl Acad Sci USA 99 11):7335-7339, 2002.
57. McPeek MS, Strahs AH, Assessment of linkage disequilibrium by the decay of haplotype sharing, with application to fine-scale genetic mapping, Am J Hum Genet 65(3):858-875, 1999.
58. Liu JS, Sabatti C, Teng J, Keats BJ, Risch N, Bayesian analysis of haplotypes for linkage disequilibrium mapping, Genome Res 11 1716-1724, 2001.
59. Li J, Jiang T, Haplotype-based linkage disequilibrium mapping via direct data mining, Bioinformatics 21:4384-4393, 2005.
60. Tzeng JY, Wang CH, Kao JT, Hsiao CK, Regression-based association analysis with clustered haplotypes through use of genotypes, Am J Hum Genet 78(2):231-242, 2006.
61. S.A.G.E., Statistical Analysis for Genetic Epidemiology, http://darwin.cwru.edu/sage/, 2007.