Deep sequencing of a genetically heterogeneous sample: Local haplotype reconstruction and read error correction

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 5541 LNBI, Issue , 2009, Pages 271-284

  Zagordi, Osvaldo ^a   Geyrhofer, Lukas ^a   Roth, Volker ^b   Beerenwinkel, Niko ^a  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITY OF BASEL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

BAYESIAN; CLUSTERING PROBLEMS; DIRICHLET PROCESS MIXTURE; ERROR RATE; GIBBS SAMPLERS; HAPLOTYPE; HAPLOTYPE STRUCTURE; HAPLOTYPES; POSTERIOR DISTRIBUTIONS; PRIOR DISTRIBUTION; PROBABILISTIC MODELS; SEQUENCING ERRORS; SIMULATED DATA; STATISTICAL SAMPLES;

BIOCHEMISTRY; ERROR CORRECTION; MOLECULAR BIOLOGY; MOLECULAR STRUCTURE; SAMPLING;

POPULATION STATISTICS;

EID: 67650337319     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-02008-7_21     Document Type: Conference Paper

References (17)

1. Mardis, E.R.: The impact of next-generation sequencing technology on genetics. Trends Genet. 24(3), 133-141 (2008)
2. Pop, M., Salzberg, S.L.: Bioinformatics challenges of new sequencing technology. Trends Genet. 24(3), 142-149 (2008)
3. Chi, K.R.: The year of sequencing. Nat. Methods 5(1), 11-14 (2008)
4. Nowak, M.A., Anderson, R.M., McLean, A.R., Wolfs, T.F., Goudsmit, J., May, R.M.: Antigenic diversity thresholds and the development of AIDS. Science 254(5034), 963-969 (1991)
5. Walker, B.D., Burton, D.R.: Toward an AIDS vaccine. Science 320(5877), 760-764 (2008)
6. Perrin, L., Telenti, A.: HIV treatment failure: testing for HIV resistance in clinical practice. Science 280(5371), 1871-1873 (1998)
7. Hoffmann, C., Minkah, N., Leipzig, J.,Wang, G., Arens,M.Q., Tebas, P., Bushman, F.D.: DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic Acids Res. 35(13), e91 (2007)
8. Wang, C., Mitsuya, Y., Gharizadeh, B., Ronaghi, M., Shafer, R.W.: Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res. 17(8), 1195-1201 (2007)
9. Wildenberg, A., Skiena, S., Sumazin, P.: Deconvolving sequence variation in mixed DNA populations. J. Comput. Biol. 10(3-4), 635-652 (2003)
10. Eriksson, N., Pachter, L., Mitsuya, Y., Rhee, S.Y., Wang, C., Gharizadeh, B., Ronaghi, M., Shafer, R.W., Beerenwinkel, N.: Viral population estimation using pyrosequencing. PLoS Computational Biology 4(4), e1000074 (2008)
11. Westbrooks, K., Astrovskaya, I., Campo, D., Khudyakov, Y., Berman, P., Zelikovsky, A.: HCV quasispecies assembly using network flows. In: Mǎndoiu, I., Sunderraman, R., Zelikovsky, A. (eds.) ISBRA 2008. LNCS (LNBI), vol. 4983, pp.159-170. Springer, Heidelberg (2008)284 O. Zagordi et al.
12. Xing, E.P., Jordan, M.I., Sharan, R.: Bayesian haplotype inference via the Dirichlet process. J. Comput. Biol. 14(3), 267-284 (2007)
13. Saeed, F., Khokhar, A., Zagordi, O., Beerenwinkel, N.: Multiple sequence alignment system for pyrosequencing reads. In: Bioinformatics and Computational Biology (BICoB) conference 2009, LNCS (in press, 2009)
14. Neal, R.: Markov chain sampling methods for Dirichlet process mixture models. Journal of Computational and Graphical Statistics 9(2), 249-265 (2000)
15. Schmid, R., Schuster, S., Steel, M., Huson, D.: Readsim- a simulator for sanger and 454 sequencing (unpublished) (2006)
16. Richter, D.C., Ott, F., Auch, A.F., Schmid, R., Huson, D.H., Field, D.: Metasim- a sequencing simulator for genomics and metagenomics. PLoS ONE 3(10), e3373 (2008)
17. Campbell, P.J., Pleasance, E.D., Stephens, P.J., Dicks, E., Rance, R., Goodhead, I., Follows, G.A., Green, A.R., Futreal, P.A., Stratton, M.R.: Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing. Proc. Natl. Acad. Sci. USA 105(35), 13081-13086 (2008)