Viral population estimation using pyrosequencing

PLoS Computational Biology

Volumn 4, Issue 5, 2008, Pages

  Eriksson, Nicholas ^a   Pachter, Lior ^b   Mitsuya, Yumi ^c   Rhee, Soo Yon ^c   Wang, Chunlin ^c   Gharizadeh, Baback ^d   Ronaghi, Mostafa ^d   Shafer, Robert W ^c   Beerenwinkel, Niko ^e  

^a University of Chicago   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c STANFORD UNIVERSITY MEDICAL CENTER   (United States)

^d STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

COST EFFECTIVENESS; DISEASE CONTROL; DISEASES; INFERENCE ENGINES; MAXIMUM PRINCIPLE; POPULATION STATISTICS; VIRUSES;

ANTI-VIRAL DRUGS; DRUG-RESISTANT VIRUS; HAPLOTYPES; HIV POPULATIONS; IMMUNE RESPONSE; POPULATION ESTIMATIONS; SEQUENCE DATA; TECHNOLOGY DATA; ULTRA DEEPS; VIRUS POPULATION;

ERROR CORRECTION;

PYROPHOSPHATE;

ALGORITHM; ARTICLE; DATA ANALYSIS; HAPLOTYPE; HUMAN IMMUNODEFICIENCY VIRUS; MATHEMATICAL MODEL; MICROBIAL DIVERSITY; POPULATION STRUCTURE; PYROSEQUENCING; SIMULATION; STATISTICAL ANALYSIS; VIRUS EXAMINATION; VIRUS STRAIN;

ALGORITHMS; BASE SEQUENCE; CHROMOSOME MAPPING; DNA, VIRAL; GENETIC VARIATION; HIV; MOLECULAR SEQUENCE DATA; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 44949250815     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000074     Document Type: Article

References (46)

1. Fakhrai-Rad H, Pourmand N, Ronaghi M (2002) Pyrosequencing: An accurate detection platform for single nucleotide polymorphisms. Hum Mutat 19: 479-485.
2. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
3. Malet I, Belnard M, Agut H, Cahour A (2003) From RNA to quasispecies: A DNA polymerase with proofreading activity is highly recommended for accurate assessment of viral diversity. J Virol Methods 109: 161-170.
4. Huse S, Huber J, Morrison H, Sogin M, Welch D (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8: R143.
5. Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer RW (2007) Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res 17: 1195-1201.
6. Eigen M, McCaskill J, Schuster P (1989) The molecular quasi-species. Adv Chem Phys 75: 149-263.
7. Domingo E, Holland JJ (1997) RNA virus mutations and fitness for survival. Annu Rev Microbiol 51: 151-178.
8. Nowak MA, Anderson RM, McLean AR, Wolfs TF, Goudsmit J, et al. (1991) Antigenic diversity thresholds and the development of AIDS. Science 254: 963-969.
9. Shankarappa R, Margolick JB, Gange SJ, Rodrigo AG, Upchurch D, et al. (1999) Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J Virol 73: 10489-10502.
10. Gaschen B, Taylor J, Yusim K, Foley B, Gao F, et al. (2002) Diversity considerations in HIV-1 vaccine selection. Science 296: 2354-2360.
11. Douek DC, Kwong PD, Nabel GJ (2006) The rational design of an AIDS vaccine. Cell 124: 677-681.
12. Beerenwinkel N, Sing T, Lengauer T, Rahnenfuehrer J, Roomp K, et al. (2005) Computational methods for the design of effective therapies against drug resistant HIV strains. Bioinformatics 21: 3943-3950.
13. Rhee S-Y, Liu TF, Holmes SP, Shafer RW (2007) HIV-1 Subtype B Protease and Reverse Transcriptase Amino Acid Covariation. PLoS Comput Biol 3: e87. doi:10.1371/journal.pcbi.0030087.
14. O'Meara D, Wilbe K, Leitner T, Hejdeman B, Albert J, et al. (2001) Monitoring resistance to human immunodeficiency virus type 1 protease inhibitors by pyrosequencing. J Clin Microbiol 39: 464-473.
15. Simons JF, Egholm M, Lanza J, Desany B, Turenchalk G, et al. (2005) Ultra-deep sequencing of HIV from drug resistant patients. Antivir Ther 10: S157.
16. Tsibris AMN, Russ C, Lee W, Paredes R, Arnaout R, et al. (2006) Detection and quantification of minority HIV-1 env V3 loop sequences by ultra-deep sequencing: Preliminary results. Antivir Ther 11: S74.
17. Roche Applied Sciences (2006) GS20 Data Processing Software Manual. Penzberg (Germany): Roche Diagnostics GmbH.
18. Bacheler L, Jeffrey S, Hanna G, D'Aquila R, Wallace L, et al. (2001) Genotypic correlates of phenotypic resistance to efavirenz in virus isolates from patients failing nonnucleoside reverse transcriptase inhibitor therapy. J Virol 75: 4999-5008.
19. Johnson VA, Brun-Vezinet F, Clotet B, Kuritzkes DR, Pillay D, et al. (2006) Update of the drug resistance mutations in HIV-1: Fall 2006. Top HIV Med 14: 125-130.
20. Pevzner PA, Tang H, Waterman MS (2001) An Eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci U S A 98: 9748-9753.
21. Tyson GW, Banfield JF (2005) Cultivating the uncultivated: a community genomics perspective. Trends Microbiol 13: 411-415.
22. Chen K, Pachter L (2005) Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities. PLoS Comput Biol 1: e24. doi:10.1371/journal.pcbi.0010024.
23. The International HapMap C (2005) A haplotype map of the human genome. Nature 437: 1299-1320.
24. Jenkins P, Lyngsø RB, Hein J (2006) How Many Transcripts Does It Take to Reconstruct the Splice Graph? In: Bucher P, Moret BME, eds. Lect Notes Comput Sci Springer. pp 103-114.
25. Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, et al. (2002) Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci U S A 99: 14250-14255.
26. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, et al. (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A 103: 12115-12120.
27. Kececioglu J, Ju J (2001) Separating repeats in DNA sequence assembly. New York: ACM Press. pp 176-183.
28. Tammi MT, Arner E, Britton T, Andersson B (2002) Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs. Bioinformatics 18: 379-388.
29. Lander ES, Waterman MS (1988) Genomic mapping by fingerprinting random clones: A mathematical analysis. Genomics 2: 231-239.
30. Dilworth RP (1950) A decomposition theorem for partially ordered sets. Ann Math (2) 51: 161-166.
31. Excoffier L, Slatkin M (1995) Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 12: 921-927.
32. Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68: 978-989.
33. Halperin E, Hazan E (2006) HAPLOFREQ-Estimating haplotype frequencies efficiently. J Comput Biol 13: 481-500.
34. Schmid R, Schuster SC, Steel MA, Huson DH (2006) ReadSim - A simulator for Sanger and 454 sequencing.
35. Rhee S-Y, Gonzales MJ, Kantor R, Betts BJ, Ravela J, et al. (2003) Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res 31: 298-303.
36. Gonzales MJ, Johnson E, Dupnik KM, Imamichi T, Shafer RW (2003) Colinearity of reverse transcriptase inhibitor resistance mutations detected by population-based sequencing. J Acquir Immune Defic Syndr 34: 398-402.
37. Doukhan L, Delwart E (2001) Population genetic analysis of the protease locus of human immunodeficiency virus type 1 quasispecies undergoing drug selection, using a denaturing gradient-heteroduplex tracking assay. J Virol 75: 6729-6736.
38. Metzner KJ, Rauch P, Walter H, Boesecke C, Zöllner B, et al. (2005) Detection of minor populations of drug-resistant HIV-1 in acute seroconverters. AIDS 19: 1819-1825.
39. Gottlieb GS, Nickle DC, Jensen MA, Wong KG, Grobler J, et al. (2004) Dual HIV-1 infection associated with rapid disease progression. Lancet 363: 619-622.
40. Rambaut A, Posada D, Crandall KA, Holmes EC (2004) The causes and consequences of HIV evolution. Nat Rev Genet 5: 52-61.
41. Rouzine IM, Rodrigo A, Coffin JM (2001) Transition between stochastic evolution and deterministic evolution in the presence of selection: General theory and application to virology. Microbiol Mol Biol Rev 65: 151-185.
42. Ford LR, Fulkerson DR (1962) Flows in networks. Princeton: Princeton University Press.
43. Hopcroft JE, Karp RM (1973) An n5/2 algorithm for maximum matchings in bipartite graphs. SIAM J Comput 2: 225-231.
44. Dempster A, Laird N, Rubin D (1977) Maximum likelihood from incomplete data via the EM algorithm (with discussions). J R Statist Soc B 39: 1-38.
45. Simpson EH (1949) Measurement of diversity. Nature 163: 688.
46. Collins ML, Irvine B, Tyner D, Fine E, Zayati C, et al. (1997) A branched DNA signal amplification assay for quantification of nucleic acid targets below 100 molecules/ml. Nucleic Acids Res 25: 2979-2984.