Read length versus Depth of Coverage for Viral Quasispecies Reconstruction

PLoS ONE

Volumn 7, Issue 10, 2012, Pages

  Zagordi, Osvaldo ^a   Däumer, Martin ^b   Beisel, Christian ^c   Beerenwinkel, Niko ^c,d  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b Rheinland Pfälzische Technische Universität Kaiserslautern Landau   (Germany)

^c ETH ZURICH   (Switzerland)

^d SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL ERROR; ARTICLE; CLONE; COMPUTER PROGRAM; GENE SEQUENCE; GENETIC VARIABILITY; HAPLOTYPE; HUMAN IMMUNODEFICIENCY VIRUS; INTERMETHOD COMPARISON; NONHUMAN; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; VIRUS GENE;

ALGORITHMS; GENES, VIRAL; HAPLOTYPES; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84867060060     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0047046     Document Type: Article

References (34)

1. Vrancken B, Lequime S, Theys K, Lemey P, (2010) Covering all bases in HIV research: unveiling a hidden world of viral evolution. AIDS Rev 12: 89-102.
2. Beerenwinkel N, Zagordi O, (2011) Ultra-deep sequencing for the analysis of viral populations. Current Opinion in Virology 1: 413-418.
3. Metzker ML, (2010) Sequencing technologies- the next generation. Nat Rev Genet 11: 31-46.
4. Barzon L, Lavezzo E, Militello V, Toppo S, Palù G, (2011) Applications of next-generation sequencing technologies to diagnostic virology. Int J Mol Sci 12: 7861-7884.
5. Hoffmann C, Minkah N, Leipzig J, Wang G, Arens MQ, et al. (2007) DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic Acids Res 35: e91.
6. 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.
7. Powdrill MH, Tchesnokov EP, Kozak RA, Russell RS, Martin R, et al. (2011) Contribution of a mutational bias in hepatitis C virus replication to the genetic barrier in the development of drug resistance. Proc Natl Acad Sci U S A 108: 20509-20513.
8. Solmone M, Vincenti D, Prosperi MCF, Bruselles A, Ippolito G, et al. (2009) Use of massively parallel ultradeep pyrosequencing to characterize the genetic diversity of hepatitis B virus in drug-resistant and drug-naive patients and to detect minor variants in reverse transcriptase and hepatitis B S antigen. J Virol 83: 1718-1726.
9. Bull RA, Luciani F, McElroy K, Gaudieri S, Pham ST, et al. (2011) Sequential bottlenecks drive viral evolution in early acute hepatitis C virus infection. PLoS Pathog 7: e1002243.
10. Henn MR, Boutwell CL, Charlebois P, Lennon NJ, Power KA, et al. (2012) Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLoS Pathog 8: e1002529.
11. Bruselles A, Rozera G, Bartolini B, Prosperi M, Nonno FD, et al. (2009) Use of massive parallel pyrosequencing for near full-length characterization of a unique HIV Type 1 BF recombinant associated with a fatal primary infection. AIDS Res Hum Retroviruses 25: 937-942.
12. Poon AFY, McGovern RA, Mo T, Knapp DJHF, Brenner B, et al. (2011) Dates of HIV infection can be estimated for seroprevalent patients by coalescent analysis of serial next-generation sequencing data. AIDS.
13. Macalalad AR, Zody MC, Charlebois P, Lennon NJ, Newman RM, et al. (2012) Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data. PLoS Comput Biol 8: e1002417.
14. Flaherty P, Natsoulis G, Muralidharan O, Winters M, Buenrostro J, et al. (2012) Ultrasensitive detection of rare mutations using next-generation targeted resequencing. Nucleic Acids Res 40: e2.
15. Gerstung M, Beisel C, Rechsteiner M, Wild P, Schraml P, et al. (2012) Reliable detection of subclonal single-nucleotide variants in tumor cell populations. Nat Comm 3: 811.
16. Zagordi O, Klein R, Däumer M, Beerenwinkel N, (2010) Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies. Nucleic Acids Res 38: 7400-7409.
17. Eriksson N, Pachter L, Mitsuya Y, Rhee S-Y, Wang C, et al. (2008) Viral population estimation using pyrosequencing. PLoS Comput Biol 4: e1000074.
18. Zagordi O, Geyrhofer L, Roth V, Beerenwinkel N, (2010) Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction. J Comput Biol 17: 417-428.
19. Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ, (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12: 38.
20. Astrovskaya I, Tork B, Mangul S, Westbrooks K, M?ndoiu I, et al. (2011) Inferring viral quasispecies spectra from 454 pyrosequencing reads. BMC Bioinformatics 12 (Suppl 6):: S1.
21. Huang A, Kantor R, DeLong A, Schreier L, Istrail S. QColors: An algorithm for conservative viral quasispecies reconstruction from short and non-contiguous next generation sequencing reads; 2011 nov. pp. 130-136.
22. Westbrooks K, Astrovskaya I, Campo D, Khudyakov Y, Berman P, et al. (2009)HCV quasispecies assembly using network flows. In: Mandoiu II, Sunderraman R, Zelikovsky A, editors. Lecture Notes in Computer Science; 2008. Springer. pp. 159-170.
23. Prosperi MCF, Prosperi L, Bruselles A, Abbate I, Rozera G, et al. (2011) Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing. BMC Bioinformatics 12: 5.
24. Prabhakaran S, Rey M, Zagordi O, Beerenwinkel N, Roth V, (2010) HIV haplotype inference using a constraint-based Dirichlet process mixture model.
25. Jojic V, Hertz T, Jojic N (2008) Population sequencing using short reads: HIV as a case study. In: Altman RB, Dunker AK, Hunter L, Murray T, Klein TE, editors; 2008. World Scientific. pp. 114-125.
26. Zagordi O, Töpfer A, Prabhakaran S, Roth V, Halperin E, et al. (2012) Probabilistic inference of viral quasispecies subject to recombination. In: Chor B, editor. Lecture Notes in Bioinformatics; 2012. Springer. pp. 342-354.
27. 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.
28. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53-59.
29. Archer J, Baillie G, Watson SJ, Kellam P, Rambaut A, et al. (2012) Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II. BMC Bioinformatics 13: 47.
30. Zagordi O, Bhattacharya A, Eriksson N, Beerenwinkel N, (2011) ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. BMC Bioinformatics 12: 119.
31. Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, et al. (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol 10: R32.
32. Vandenbroucke I, Marck HV, Verhasselt P, Thys K, Mostmans W, et al. (2011) Minor variant detection in amplicons using 454 massive parallel pyrosequencing: experiences and considerations for successful applications. Biotechniques 51: 167-177.
33. Prosperi MCF, Salemi M, (2012) QuRe: software for viral quasispecies reconstruction from next-generation sequencing data. Bioinformatics 28: 132-133.
34. Skums P, Dimitrova Z, Campo DS, Vaughan G, Rossi L, et al. (2012) Efficient error correction for next-generation sequencing of viral amplicons. BMC Bioinformatics 13 (Suppl 10):: S6.