An MCMC algorithm for haplotype assembly from whole-genome sequence data

Genome Research

Volumn 18, Issue 8, 2008, Pages 1336-1346

  Bansal, Vikas ^a   Halpern, Aaron L ^b   Axelrod, Nelson ^b   Bafna, Vineet ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b J CRAIG VENTER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT;

ANALYTICAL ERROR; ARTICLE; DNA POLYMORPHISM; DNA SEQUENCE; GENE MAPPING; GENETIC VARIABILITY; HAPLOTYPE; MATHEMATICAL ANALYSIS; MONTE CARLO METHOD; PRIORITY JOURNAL;

ALGORITHMS; COMPUTER SIMULATION; GENOME, HUMAN; GENOMICS; HAPLOTYPES; HUMANS; MARKOV CHAINS; MONTE CARLO METHOD;

EID: 48949103013     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.077065.108     Document Type: Article

References (43)

1. Bafna, V., Istrail, S., Lancia, G., and Rizzi, R. 2005. Polynomial and APX-hard cases of individual haplotyping problems. Theor. Comput. Sci. 335: 109-125.
2. Bansal, V., Bashir, A., and Bafna, V. 2007. Evidence for large inversion polymorphisms in the human genome from HapMap data. Genome Res. 17: 219-230.
3. Bentley, D. 2006. Whole-genome re-sequencing. Curr. Opin. Genet. Dev. 16: 545-552.
4. Churchill, G.A. and Waterman, M.S. 1992. The accuracy of dna sequences: Estimating sequence quality. Genomics 14: 89-98.
5. Clark, A.G. 1990. Inference of haplotypes from PCR-amplified samples of diploid populations. Mol. Biol. Evol. 7: 111-122.
6. Easton, D., Pooley, K., Dunning, A., Pharoah, P., Thompson, D., Ballinger, D., Struewing, J., Morrison, J., Field, H., Luben, R., et al. 2007. Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 447: 1087-1093.
7. Ewing, B. and Green, P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8: 186-194.
8. Excoffier, L. and Slatkin, M. 1995. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol. Biol. Evol. 12: 921-927.
9. Gudmundsson, J., Sulem, P., Manolescu, A., Amundadottir, L., Gudbjartsson, D., Helgason, A., Rafnar, T., Bergthorsson, J., Agnarsson, B., Baker, A., et al. 2007. Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24. Nat. Genet. 39: 631-637.
10. Halldorsson, B.V., Bafna, V., Edwards, N., Lippert, R., Yooseph, S., and Istrail, S. 2003. Combinatorial problems arising in SNP and haplotype analysis. In DMTCS: Fourth International Conference on Discrete Mathematics and Theoretical Computer Science, pp. 26-47. Springer, Berlin.
11. Helgadottir, A., Thorleifsson, G., Manolescu, A., Gretarsdottir, S., Blondal, T., Jonasdottir, A., Jonasdottir, A., Sigurdsson, A., Baker, A., Palsson, A., et al. 2007. A common variant on chromosome 9p21 affects the risk of myocardial infarction. Science 316: 1491-1493.
12. The International HapMap Consortium. 2005. A haplotype map of the human genome. Nature 437: 1299-1320.
13. The International HapMap Consortium. 2007. A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851-861.
14. Kaiser, J. 2008. DNA sequencing: A plan to capture human diversity in 1000 genomes. Science 319: 395.
15. Kim, J., Waterman, M., and Li, L. 2007. Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi. Genome Res. 17: 1101.
16. Konfortov, B., Bankier, A., and Dear, P. 2007. An efficient method for multi-locus molecular haplotyping. Nucleic Acids Res. 35: e6.
17. Korlach, J., Marks, P.J., Cicero, R.L., Gray, J.J., Murphy, D.L., Roitman, D.B., Pham, T.T., Otto, G.A., Foquet, M., Turner, S.W., et al. 2008. Selective aluminum passivation for targeted immobilization of single dna polymerase molecules in zero-mode waveguide nanostructures. Proc. Natl. Acad. Sci. 105: 1176-1181.
18. Levy, S., Sutton, G., Ng, P.C., Feuk, L., Halpern, A.L., Walenz, B.P., Axelrod, N., Huang, J., Kirkness, E.F., Denisov, G., et al. 2007. The diploid genome sequence of an individual human. PLoS Biol. 5. doi: 10.1371/journal.pbio.0050254.
19. Li, L.M., Kim, J.H., and Waterman, M.S. 2004. Haplotype reconstruction from SNP alignment. J. Comput. Biol. 11: 505-516.
20. Lin, S., Cutler, D.J., Zwick, M.E., and Chakravarti, A. 2002. Haplotype inference in random population samples. Am. J. Hum. Genet. 71: 1129-1137.
21. Lippert, R., Schwartz, R., Lancia, G., and Istrail, S. 2002. Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem. Brief. Bioinform. 3: 23-31.
22. Marchini, J., Cutler, D., Patterson, N., Stephens, M., Eskin, E., Halperin, E., Lin, S., Qin, Z., Munro, H., Abecasis, G., et al. 2006. A comparison of phasing algorithms for trios and unrelated individuals. Am. J. Hum. Genet. 78: 437-450.
23. Marchini, J., Howie, B., Myers, S., McVean, G., and Donnelly, P. 2007. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat. Genet. 39: 906-913.
24. Mardis, E.R. 2008. The impact of next-generation sequencing technology on genetics. Trends Genet. 24: 133-141.
25. McPherson, R., Pertsemlidis, A., Kavaslar, N., Stewart, A., Roberts, R., Cox, D., Hinds, D., Pennacchio, L., Tybjaerg-Hansen, A., Folsom, A., et al. 2007. A common allele on chromosome 9 associated with coronary heart disease. Science 316: 1488-1491.
26. Metropolis, N., Rosenbluth, A.W., Rosenbluth, M.N., Teller, A.H., and Teller, E. 1953. Equations of state calculations by fast computing machine. J. Chem. Phys. 21: 1087-1091.
27. Niu, T., Qin, Z.S., Xu, X., and Liu, J.S. 2002. Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. Am. J. Hum. Genet. 70: 157-169.
28. Pe'er, I., de Bakker, P., Maller, J., Yelensky, R., Altshuler, D., and Daly, M. 2006. Evaluating and improving power in whole-genome association studies using fixed marker sets. Nat. Genet. 38: 663-667.
29. Randall, D. 2006. Rapidly mixing markov chains with applications in computer science and physics. Comput. Sci. Eng. 8: 30-41.
30. Rizzi, R., Bafna, V., Istrail, S., and Lancia, G. 2002. Practical algorithms and fixed-parameter tractability for the single individual SNP haplotyping problem. In Proceedings of the Second International Workshop on Algorithms in Bioinformatics (WABI), pp. 29-43. Springer, Berlin.
31. Sabeti, P., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., Xie, X., and Byrne, E. 2007. Genome-wide detection and characterization of positive selection in human populations. Nature 449: 913-918.
32. Schuster, S. 2008. Next-generation sequencing transforms today's biology. Nat. Methods 5: 16-18.
33. Shaffer, C. 2007. Next-generation sequencing outpaces expectations. Nat. Biotechnol. 25: 149.
34. Sherry, S.T., Ward, M.H., Kholodov, M., Baker, J., Phan, L., Smigielski, E.M., and Sirotkin, K. 2001. DBSNP: The NCBI database of genetic variation. Nucleic Acids Res. 29: 308-311.
35. Sladek, R., Rocheleau, G., Rung, J., Dina, C., Shen, L., Serre, D., Boutin, P., Vincent, D., Belisle, A., Hadjadj, S., et al. 2007. A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 445: 881-885.
36. Stephens, M. and Donnelly, P. 2003. A comparison of bayesian methods for haplotype reconstruction from population genotype data. Am. J. Hum. Genet. 73: 1162-1169.
37. Stephens, M., Smith, N.J., and Donnelly, P. 2001. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68: 978-989.
38. Stoer, M. and Wagner, F. 1994. A simple min cut algorithm. In ESA: Second Annual European Symposium on Algorithms, pp. 141-147. Springer, Berlin.
39. Vinson, J.P., Jaffe, D.B., O'Neill, K., Karlsson, E.K., Stange-Thomann, N., Anderson, S., Mesirov, J.P., Satoh, N., Satou, Y., Nusbaum, C., et al. 2005. Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi. Genome Res. 15: 1127-1135.
40. von Bubnoff, A. 2008. Next-generation sequencing: the race is on. Cell 132: 721-723.
41. The Wellcome Trust Case Control Consortium. 2007. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661-678.
42. Wheeler, D.A., Srinivasan, M., Egholm, M., Shen, Y., Chen, L., McGuire, A., He, W., Chen, Y.J., Makhijani, V., Roth, G.T., et al. 2008. The complete genome of an individual by massively parallel dna sequencing. Nature 452: 872-876.
43. Zaitlen, N., Kang, H., Eskin, E., and Halperin, E. 2007. Leveraging the HapMap correlation structure in association studies. Am. J. Hum. Genet. 80: 683-691.