Haplotyping as Perfect Phylogeny: A Direct Approach

Journal of Computational Biology

Volumn 10, Issue 3-4, 2003, Pages 323-340

  Bafna, Vineet ^a   Gusfield, Dan ^b   Lancia, Giuseppe ^c   Yooseph, Shibu ^d  

^a Ctr for the Advancement of Genomics   (United States)

^b University of California   (United States)

^c UNIVERSITY OF PADOVA   (Italy)

^d Informatics Research   (United States)

Author keywords

Algorithms; Haplotypes; Perfect phylogeny; Phasing

Indexed keywords

CONFERENCE PAPER; GENE MAPPING; GENETIC RECOMBINATION; GENOTYPE; HAPLOTYPE; HEALTH CARE ORGANIZATION; MODEL; PERFECT PHYLOGENY HAPLOTYPING PROBLEM; PHYLOGENY; POPULATION GENETICS; PRIORITY JOURNAL;

ALGORITHMS; DATA INTERPRETATION, STATISTICAL; GENETIC PREDISPOSITION TO DISEASE; HAPLOTYPES; PHYLOGENY;

EID: 0038219512     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/10665270360688048     Document Type: Conference Paper

References (23)

1. Bafna, V., Gusfield, D., Lancia, G., and Yooseph, S. 2002. Haplotyping as perfect phylogeny: A direct approach. Technical report, Department of Computer Science, University of California, Davis.
2. Clark, A. 1990. Inference of haplotypes from PCR-amplified samples of diploid populations. Mol. Biol. Evol. 1, 111-122.
3. Clark, A., Weiss, K., Nickerson, D., Taylor, S., Buchanan, A., and Stengard, J. 1998. Haplotype structure and population genetic inferences from nucleotide-sequence variation in human lipoprotein lipase. Am. J. Human Genet. 63, 595-612.
4. Daly, M., Rioux, J., Schaffner, S., Hudson, T., and Lander, E. 2001. High-resolution haplotype structure in the human genome. Nature Genet. 29, 229-232.
5. Eskin, E., Halperin, E., and Karp, R. 2002a. Efficient reconstruction of haplotype structure via perfect phylogeny. Technical report, Computer Science Division (EEDS), University of California, Berkeley.
6. Eskin, E., Halperin, E., and Karp, R.M. 2002b. Efficient reconstruction of haplotype structure via perfect phylogeny. Technical report, Columbia University. Updated version of the UCB technical report of that title available at www.cs.columbia.edu/compbio/hap/.
7. Eskin, E., Halperin, E., and Karp, R. 2003. Large scale reconstruction of haplotypes from genotype data. In Proc. 7th Int. Conf. Computational Biology, 104-113.
8. Excoffier, L., and Slatkin, M. 1995. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol. Bio. Evol. 12, 921-927.
9. Friss, L., Hudson, R., Bartoszewicz, A., Wall, J., Donfalk, T., and Di Rienzo, A. 2001. Gene conversion and differential population histories may explain the contrast between polymorphism and linkage disequilibrium levels. Am. J. Human Genet. 69, 831-843.
10. Fullerton, M., Clark, A., Weiss, K., Nickerson, D., Taylor, S., Stengard, J., et al. 2000. Apolipoprotein E variation at the sequence haplotype level: Implications for the origin and maintenance of a major human polymorphism. Am. J. Human Genet. 67, 881-900.
11. Gusfield, D. 1991. Efficient algorithms for inferring evolutionary history. Networks 21, 19-28.
12. Gusfield, D. 1997. Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology, Cambridge University Press, London.
13. Gusfield, D. 2001. Inference of haplotypes from samples of diploid populations: complexity and algorithms. J. Comp. Biol. 8(3).
14. Gusfield, D. 2002. Haplotyping as perfect phylogeny: Conceptual framework and efficient solutions (extended abstract). Proc. 6th Int. Conf. Computational Biology, 166-175.
15. Hawley, M., and Kidd, K. 1995. HAPLO: A program using the EM algorithm to estimate the frequencies of multi-site haplotypes. J. Heredity 86, 409-411.
16. Helmuth, L. 2001. Genome research: Map of the human genome 3.0. Science 293(5530), 583-585.
17. Lin, S., Cutler, D., Zwick, M., and Chakravarti, A. 2003. Haplotype inference in random population samples. Am. J. Hum. Genet. 71, 1129-1137.
18. Niu, T., Qin, Z., Xu, X., and Liu, J.S. 2002. Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. Am. J. Hum. Genet. 70, 157-169.
19. Orzack, S., Gusfield, D., and Stanton, V. 2001. The absolute and relative accuracy of haplotype inferral methods and a consensus approach to haplotype inferral. Am. Soc. Human Genet. Suppl., Abstract No. 115.
20. Piccolboni, A., and Gusfield, D. 2003. Haplotyping by pure parsimony. Technical report, Department of Computer Science, University of California, Davis.
21. Stephens, J.C., Schneider, J.A., Tanguay, D.A., Choi, J., Acharya, T., Stanley, S.E., et al. 2001. Haplotype variation and linkage disequilibrium in 313 human genes. Science 293, 489-493.
22. Stephens, M., Smith, N., and Donnelly, P. 2001. A new statistical method for haplotype reconstruction from population data. Am. J. Human Genet. 68, 978-989.
23. Tavare, S. 1995. Calibrating the clock: Using stochastic processes to measure the rate of evolution, in E. Lander and M. Waterman, eds., Calculating the Secretes of Life, National Academy Press.