Skip to main content
SpringerLink
Log in

A Survey of Computational Methods for Determining Haplotypes

  • Conference paper
Computational Methods for SNPs and Haplotype Inference (RSNPsH 2002)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 2983))

Abstract

It is widely anticipated that the study of variation in the human genome will provide a means of predicting risk of a variety of complex diseases. Single nucleotide polymorphisms (SNPs) are the most common form of genomic variation. Haplotypes have been suggested as one means for reducing the complexity of studying SNPs. In this paper we review some of the computational approaches that have been taking for determining haplotypes and suggest new approaches.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Abecasis, G.R., Martin, R., Lewitzky, S.: Estimation of haplotype frequencies from diploid data. American Journal of Human Genetics 69(4 suppl. 1), 114 (2001)

    Google Scholar 

  2. Bafna, V., Gusfield, D., Lancia, G., Yooseph, S.: Haplotyping as a perfect phylogeny. A direct approach. Journal of Computational Biology 10(3), 323–340 (2003)

    Article  Google Scholar 

  3. Bodlaender, H., Fellows, M., Warnow, T.: Two strikes against perfect phylogeny. In: Kuich, W. (ed.) ICALP 1992. LNCS, vol. 623, pp. 273–283. Springer, Heidelberg (1992)

    Google Scholar 

  4. Broder, A.: Generating random spanning trees. In: Proceedings of the IEEE 30th Annual Symposium on Foundations of Computer Science, pp. 442–447 (1989)

    Google Scholar 

  5. Chaiken, S.: A combinatorial proof of the all-minors matrix tree theorem. SIAM Journal on Algebraic and Discrete Methods 3, 319–329 (1982)

    Article  MATH  MathSciNet  Google Scholar 

  6. Chen, E.Y.: Methods and products for analyzing polymers. U.S. Patent 6,355,420

    Google Scholar 

  7. Clark, G.: Inference of haplotypes from PCR-amplified samples of diploid populations. Molecular Biology and Evolution 7(2), 111–122 (1990)

    Google Scholar 

  8. Cohn, H., Pemantle, R., Propp, J.: Generating a random sink-free orientation in quadratic time. Electronic Journal of Combinatorics 9(1) (2002)

    Google Scholar 

  9. Daly, M.J., Rioux, J.D., Schaffner, S.F., Hudson, T.J., Lander, E.S.: Highresolution haplotype structure in the human genome. Nature Genetics 29, 229–232 (2001)

    Article  Google Scholar 

  10. Damaschke, P.: Fast perfect phylogeny haplotype inference. In: Lingas, A., Nilsson, B.J. (eds.) FCT 2003. LNCS, vol. 2751, pp. 183–194. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  11. Day, W.H.E., Sankoff, D.: Computational complexity of inferring phylogenies by compatibility. Systematic Zoology 35(2), 224–229 (1986)

    Article  Google Scholar 

  12. Halperin, R.M.K.E.: Perfect phylogeny and haplotype assignement. In: Proceedings of the Eigth Annual International Conference on Computational Molecular Biology, RECOMB (to appear, 2004)

    Google Scholar 

  13. Eronen, L., Geerts, F., Toivonen, H.: A markov chain approach to reconstruction of long haplotypes. In: Pacific Symposium on Biocomputing (PSB 2004) (to appear, 2004)

    Google Scholar 

  14. Eskin, E., Halperin, E., Karp, R.M.: Large scale reconstruction of haplotypes from genotype data. In: Proceedings of the Seventh Annual International Conference on Computational Molecular Biology (RECOMB), pp. 104–113 (2003)

    Google Scholar 

  15. Excoffier, L., Slatkin, M.: Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Molecular Biology and Evolution 12(5), 921–927 (1995)

    Google Scholar 

  16. Fallin, D., Schork, N.J.: Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data. American Journal of Human Genetics 67(4), 947–959 (2000)

    Article  Google Scholar 

  17. Frisse, L., Hudson, R., Bartoszewicz, A., Wall, J., Donfalk, T., Di Rienzo, A.: Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels. American Journal of Human Genetics 69, 831–843 (2001)

    Article  Google Scholar 

  18. Greenspan, G., Geiger, D.: Model-based inference of haplotype block variation. In: Proceedings of the Seventh Annual International Conference on Computational Molecular Biology (RECOMB), pp. 131–137 (2003)

    Google Scholar 

  19. Gusfield, D.: A practical algorithm for optimal inference of haplotypes from diploid populations. In: Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology (ISMB), pp. 183–189 (2000)

    Google Scholar 

  20. Gusfield, D.: Inference of haplotypes from samples of diploid populations: Complexity and algorithms. Journal of Computational Biology 8(3), 305–324 (2001)

    Article  MathSciNet  Google Scholar 

  21. Gusfield, D.: Haplotyping as perfect phylogeny: Conceptual framework and efficient solutions (Extended abstract). In: Proceedings of the Sixth Annual International Conference on Computational Molecular Biology (RECOMB), pp. 166–175 (2002)

    Google Scholar 

  22. Gusfield, D.: Haplotyping by pure parsimony. In: Baeza-Yates, R., Chávez, E., Crochemore, M. (eds.) CPM 2003. LNCS, vol. 2676, pp. 144–155. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  23. Hartl, D.L., Clark, A.G.: Principles of Population Genetics. Sinauer Associates (1997)

    Google Scholar 

  24. Hawley, M.E., Kidd, K.K.: HAPLO: A program using the EM algorithm to estimate the frequencies of multi-site haplotypes. Journal of Heredity 86, 409–411 (1995)

    Google Scholar 

  25. Helmuth, L.: Genome research: Map of the human genome 3.0. Science 293(5530), 583–585 (2001)

    Article  Google Scholar 

  26. Hubbell, E.: Finding a maximum likelihood solution to haplotype phases is difficult. Personal communication

    Google Scholar 

  27. Hubbell, E.: Finding a parsimony solution to haplotype phase is NP-hard. Personal communication

    Google Scholar 

  28. Hudson, R.R.: Gene genealogies and the coalescent process. In: Futuyma, D., Antonovics, J. (eds.) Oxford surveys in evolutionary biology, vol. 7, pp. 1–44. Oxford University Press, Oxford (1990)

    Google Scholar 

  29. Jeffreys, J., Kauppi, L., Neumann, R.: Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nature Genetics 29(2), 217–222 (2001)

    Article  Google Scholar 

  30. Kim, L., Kim, J.H., Waterman, M.S.: Haplotype reconstruction from SNP alignment. In: Proceedings of the Seventh Annual International Conference on Computational Molecular Biology (RECOMB), pp. 207–216 (2003)

    Google Scholar 

  31. Kimmel, G., Shamir, R.: Maximum likelihood resolution of multi-block genotypes. In: Proceedings of the Eigth Annual International Conference on Computational Molecular Biology, RECOMB (to appear, 2004)

    Google Scholar 

  32. Kirchhoff, G.: Über die auflösung der gleichungen, auf welche man bei der untersuchung der linearen verteilung galvanischer ströme geführt wird. Annalen für der Physik und der Chemie 72, 497–508 (1847)

    Article  MATH  Google Scholar 

  33. Kong, A., Gudbjartsson, D.F., Sainz, J., Jonsdottir, G.M., Gudjonsson, S.A., Richardsson, B., Sigurdardottir, S., Barnard, J., Hallbeck, B., Masson, G., Shlien, A., Palsson, S.T., Frigge, M.L., Thorgeirsson, T.E., Gulcher, J.R., Stefansson, K.: A high-resolution recombination map of the human genome. Nature Genetics 31(3), 241–247 (2002)

    Google Scholar 

  34. Lancia, G., Bafna, V., Istrail, S., Lippert, R., Schwartz, R.: SNPs problems, complexity and algorithms. In: Meyer auf der Heide, F. (ed.) ESA 2001. LNCS, vol. 2161, pp. 182–193. Springer, Heidelberg (2001)

    Chapter  Google Scholar 

  35. Li, J., Jiang, T.: Efficient rule based haplotyping algorithms for pedigree data. In: Proceedings of the Seventh Annual International Conference on Computational Molecular Biology (RECOMB), pp. 197–206 (2003)

    Google Scholar 

  36. Li, J., Jiang, T.: An exact solution for finding minimum recombinant haplotype configurations on pedigrees with missing data by integer linear programming. In: Proceedings of the Eigth Annual International Conference on Computational Molecular Biology (RECOMB) (to appear, 2004)

    Google Scholar 

  37. Lin, S., Cutler, D.J., Zwick, M.E., Chakravarti, A.: Haplotype inference in random population samples. American Journal of Human Genetics 71, 1129–1137 (2002)

    Article  Google Scholar 

  38. Lippert, R., Schwartz, R., Lancia, G., Istrail, S.: Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem. Briefings in Bioinformatics 3(1), 23–31 (2002)

    Article  Google Scholar 

  39. Long, J.C., Williams, R.C., Urbanek, M.: An E-M algorithm and testing strategy for multiple-locus haplotypes. American Journal of Human Genetics 56(2), 799–810 (1995)

    Google Scholar 

  40. Mitra, R., Butty, V., Shendure, J., Williams, B.R., Housman, D.E., Church, G.M.: Digital genotyping and haplotyping with polymerase colonies. Proceedings of the National Academy of Sciences 100(10), 5926–5931 (2003)

    Article  Google Scholar 

  41. Mitra, R., Church, G.M.: In situ localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Research 27(e34), 1–6 (1999)

    Google Scholar 

  42. Niu, T., Qin, Z.S., Xu, X., Liu, J.S.: Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. American Journal of Human Genetics 70, 157–169 (2002)

    Article  Google Scholar 

  43. Nordborg, M.: Handbook of Statistical Genetics, chapter Coalescent Theory. John Wiley & Sons, Ltd., Chichester (2001)

    Google Scholar 

  44. Patil, N., Berno, A.J., Hinds, D.A., Barrett, W.A., Doshi, J.M., Hacker, C.R., Kautzer, C.R., Lee, D.H., Marjoribanks, C., McDonough, D.P., Nguyen, B.T.N., Norris, M.C., Sheehan, J.B., Shen, N., Stern, D., Stokowski, R.P., Thomas, D.J., Trulson, M.O., Vyas, K.R., Frazer, K.A., Fodor, S.P.A., Cox, D.R.: Blocks of limited haplotype diversity revealed by high resolution scanning of human chromosome 21. Science 294, 1719–1723 (2001)

    Article  Google Scholar 

  45. Rizzi, R., Bafna, V., Istrail, S., Lancia, G.: Practical algorithms and fixedparameter tractability for the single individual SNP haplotyping problem. In: Proceedings of the Second International Workshop on Algorithms in Bioinformatics (WABI), pp. 29–43 (2002)

    Google Scholar 

  46. Steel, M.A.: The complexity of reconstructing trees from qualitative characters and subtrees. Journal of Classification 9, 91–116 (1992)

    Article  MATH  MathSciNet  Google Scholar 

  47. Stephens, J.C., Schneider, J.A., Tanguay, D.A., Choi, J., Acharya, T., Stanley, S.E., Jiang, R., Messer, C.J., Chew, A., Han, J.-H., Duan, J., Carr, J.L., Lee, M.S., Koshy, B., Kumar, A.M., Zhang, G., Newell, W.R., Windemuth, A., Xu, C., Kalbfleisch, T.S., Shaner, S.L., Arnold, K., Schulz, V., Drysdale, C.M., Nandabalan, K., Judson, R.S., Ruano, G., Vovis, G.F.: Haplotype variation and linkage disequilibrium in 313 human genes. Science 293(5529), 489–493 (2001)

    Article  Google Scholar 

  48. Stephens, M., Donnelly, P.: Inference in molecular population genetics. Journal of the Royal Statistical Society, Series B 62(4), 605–635 (2000)

    Article  MATH  MathSciNet  Google Scholar 

  49. Stephens, M., Donnelly, P.: A comparison of bayesian methods for haplotype reconstruction from population genotype data. American Journal of Human Genetics 73, 1162–1169 (2003)

    Article  Google Scholar 

  50. Stephens, M., Smith, N.J., Donnelly, P.: A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics 68, 978–989 (2001)

    Article  Google Scholar 

  51. Wang, L., Zhang, K., Zhang, L.: Perfect phylogenetic networks with recombination. Journal of Computational Biology 8(1), 69–78 (2001)

    Article  Google Scholar 

  52. Zhang, P., Sheng, H., Morabia, A., Gilliam, T.C.: Optimal step length EM algorithm (OSLEM) for the estimation of haplotype frequency and its application in lipoprotein lipase genotyping. BMC Bioinformatics 4(3) (2003)

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Informatics Research, Celera Genomics/Applied Biosystems, 45 W. Gude Drive, Rockville, MD, 20850

    Bjarni V. Halldórsson, Vineet Bafna, Nathan Edwards, Ross Lippert, Shibu Yooseph & Sorin Istrail

Authors
  1. Bjarni V. Halldórsson
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Vineet Bafna
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Nathan Edwards
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ross Lippert
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Shibu Yooseph
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Sorin Istrail
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Center for Molecular Biology and Computer Sciecne Department, Brown University, 115 Waterman St., RI 02912, Providence, USA

    Sorin Istrail

  2. Program in Computational Biology, Department of Biological Sciences, University of Southern California, 90089, Los Angeles, CA, USA

    Michael Waterman

  3. Information Security Institute, Queensland University of Technology, QLD 4001, Brisbane, Australia

    Andrew Clark

Rights and permissions

Reprints and permissions

Copyright information

© 2004 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Halldórsson, B.V., Bafna, V., Edwards, N., Lippert, R., Yooseph, S., Istrail, S. (2004). A Survey of Computational Methods for Determining Haplotypes. In: Istrail, S., Waterman, M., Clark, A. (eds) Computational Methods for SNPs and Haplotype Inference. RSNPsH 2002. Lecture Notes in Computer Science(), vol 2983. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-24719-7_3

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-24719-7_3

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-21249-2

  • Online ISBN: 978-3-540-24719-7

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation