SpringerLink
Log in

Haplotype Inference

  • Protocol
  • First Online:
Statistical Human Genetics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 850))

  • 4494 Accesses

Abstract

Haplotypes, as they specify linkage patterns between individual nucleotide variants, confer critical information for understanding the genetics of human diseases. However, haplotype information is not directly obtainable from high-throughput genoty** platforms. In this chapter, we introduce two representative methods to reconstruct haplotypes from unphased genotype data, one method is for unrelated individuals and the other is for families.

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

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Bonizzoni, P., Della Vedova, G., Dondi, R., and Li, J. (2003) The haploty** problem: an overview of computational models and solutions. Journal of Computer Science and Technology 18:675–688.

    Article  Google Scholar 

  2. Gusfield, D. (2004) An overview of combinatorial methods for haplotype inference. Computational Methods for SNPs and Haplotype Inference. 599–600.

    Google Scholar 

  3. Halldorsson, B., Bafna, V., Edwards, N., Lippert, R., Yooseph, S., and Istrail, S. (2004) A survey of computational methods for determining haplotypes. Computational Methods for SNPs and Haplotype Inference. 613–614.

    Google Scholar 

  4. Zhang, X., Wang, R., Wu, L., and Chen, L. (2006) Models and algorithms for haploty** problem. Current Bioinformatics 1:105–114.

    Article  CAS  Google Scholar 

  5. Li, J. and T. Jiang. (2008) A survey on haploty** algorithms for tightly linked markers. Journal of Bioinformatics and Computational Biology 6:241–259.

    Article  PubMed  CAS  Google Scholar 

  6. Scheet, P. and Stephens, M. (2006) A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. The American Journal of Human Genetics 78:629–644.

    Article  CAS  Google Scholar 

  7. Li, X. and Li, J. (2009) An almost linear time algorithm for a general haplotype solution on tree pedigrees with no recombination and its extensions. Journal of Bioinformatics and Computational Biology 7:521–545.

    Article  PubMed  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  9. The International HapMap Consortium. (2003) The international HapMap project. Nature 426: 789–796.

    Article  Google Scholar 

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

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  13. Qin, Z., Niu, T., and Liu, J. (2002) Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms. American journal of human genetics 71:1242–1247.

    Article  PubMed  CAS  Google Scholar 

  14. Sun, S., Greenwood, C., and Neal, R. (2007) Haplotype inference using a Bayesian hidden Markov model. Genetic Epidemiology 31:937–948.

    Article  PubMed  Google Scholar 

  15. Browning, S. and Browning, B. (2007) Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. The American Journal of Human Genetics 81:1084–1097.

    Article  CAS  Google Scholar 

  16. O’Connell, J. (2000) Zero-recombinant haploty**: applications to fine map** using SNPs. Genetic Epidemiology 19:S64–S70.

    Article  PubMed  Google Scholar 

  17. Qian, D. and Beckmann, L. (2002) Minimum-recombinant haploty** in pedigrees. The American Journal of Human Genetics 70:1434–1445.

    Article  CAS  Google Scholar 

  18. Tapadar, P., Ghosh, S., and Majumder, P. (2000) Haploty** in pedigrees via a genetic algorithm. Human Heredity 50:43–56.

    Article  PubMed  CAS  Google Scholar 

  19. Zhang, K., Sun, F., and Zhao, H. (2005) HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination. Bioinformatics 21:90–103

    Article  PubMed  CAS  Google Scholar 

  20. Chan, M., Chan, W., Chin, F., Fung, S., and Kao, M. (2006) Linear-time haplotype inference on pedigrees without recombinations. Algorithms in Bioinformatics. 56–67.

    Google Scholar 

  21. **ao, J., Liu, L., **a, L., and Jiang, T. (2007) Fast elimination of redundant linear equations and reconstruction of recombination-free Mendelian inheritance on a pedigree. Proceedings of the eighteenth annual ACM-SIAM symposium on Discrete algorithm spp. 655–664.

    Google Scholar 

  22. Li, X., Chen, Y., and Li, J. (2010) Detecting genome-wide haplotype polymorphism by combined use of Mendelian constraints and local population structure. Pacific Symposium on Biocomputing 15:348–358.

    Google Scholar 

  23. Liu, L., **, C., **ao, J., and Jiang, T. (2007) Complexity and approximation of the minimum recombinant haplotype configuration problem. Theoretical Computer Science 378:316–330.

    Article  Google Scholar 

  24. Elston, R. and Stewart, J. (1971) A general model for the genetic analysis of pedigree data. Human Heredity 21:523–542.

    Article  PubMed  CAS  Google Scholar 

  25. Lander, E. and Green, P. (1987) Construction of multilocus genetic linkage maps in humans. Proceedings of the National Academy of Sciences 84:2363–2367.

    Article  CAS  Google Scholar 

  26. Sobel, E. and Lange, K. (1996) Descent graphs in pedigree analysis: applications to haploty**, location scores, and marker-sharing statistics. American Journal of Human Genetics 58:1323–1327.

    PubMed  CAS  Google Scholar 

  27. Kruglyak, L., Daly, M., Reeve-Daly, M., and Lander, E. (1996) Parametric and nonparametric linkage analysis: a unified multipoint approach. American Journal of Human Genetics 58:1347–1363.

    PubMed  CAS  Google Scholar 

  28. Gudbjartsson, D., Jonasson, K., Frigge, M., and Kong, A. (2000) Allegro, a new computer program for multipoint linkage analysis. Nature Genetics 25:12–13.

    Article  PubMed  CAS  Google Scholar 

  29. Abecasis, G., Cherny, S., Cookson, W., and Cardon, L. (2001) Merlin – rapid analysis of dense genetic maps using sparse gene flow trees. Nature genetics 30:97–101.

    Article  PubMed  Google Scholar 

  30. Abecasis, G. and Wigginton, J. (2005) Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers. The American Journal of Human Genetics 77:754–767.

    Article  CAS  Google Scholar 

  31. Li, J. and Jiang, T. (2003) Efficient inference of haplotypes from genotypes on a pedigree. International Journal of Bioinformatics and Computational Biology 1:41–70.

    Article  CAS  Google Scholar 

  32. Doi, K., Li, J., and Jiang, T. (2003) Minimum recombinant haplotype configuration on tree pedigrees. Algorithms in Bioinformatics. 339–353.

    Google Scholar 

  33. Li, J. and Jiang, T. (2005) Computing the minimum recombinant haplotype configuration from incomplete genotype data on a pedigree by integer linear programming. Journal of Computational Biology 12:719–739.

    Article  PubMed  CAS  Google Scholar 

  34. Li, X. and Li, J. (2007) Comparison of haploty** methods using families and unrelated individuals on simulated rheumatoid arthritis data. BMC proceedings 1, S55.

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported in part by NIH R01 LM008991.

Author information

Authors and Affiliations

  1. Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH, USA

    **n Li & **g Li

Authors
  1. **n Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. **g Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to **g Li .

Editor information

Editors and Affiliations

  1. School of Medicine, Dept. Epidemiology & Biostatistics, Case Western Reserve University, Cornell Road 2103, Cleveland, 44106, Ohio, USA

    Robert C. Elston

  2. Dept. Epidemiology & Biostatistics, Memorial Sloan-Kettering Cancer Center, East 63rd Street 307, New York, 10021, New York, USA

    Jaya M. Satagopan

  3. School of Medicine, Dept. Epidemiology & Biostatistics, Case Western Reserve University, Cornell Road 2103, Cleveland, 44106, Ohio, USA

    Shuying Sun

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Li, X., Li, J. (2012). Haplotype Inference. In: Elston, R., Satagopan, J., Sun, S. (eds) Statistical Human Genetics. Methods in Molecular Biology, vol 850. Humana Press. https://doi.org/10.1007/978-1-61779-555-8_22

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-555-8_22

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-554-1

  • Online ISBN: 978-1-61779-555-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation