Analysis of high-depth sequence data for studying viral diversity: A comparison of next generation sequencing platforms using Segminator II

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Archer, John ^a   Baillie, Greg ^b   Watson, Simon J ^b   Kellam, Paul ^b,c   Rambaut, Andrew ^d,e   Robertson, David L ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c UNIVERSITY COLLEGE LONDON   (United Kingdom)

^d UNIVERSITY OF EDINBURGH   (United Kingdom)

^e NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL VARIATION; DRUG-RESISTANCE; GENOMIC LOCATIONS; HOMOPOLYMERIC STRETCHES; INSERTIONS AND DELETIONS; NEXT-GENERATION SEQUENCING; PLATFORM ERROR; RESEARCH COMMUNITIES;

ARTICLE; CLASSIFICATION; COMPARATIVE STUDY; COMPUTER LANGUAGE; COMPUTER PROGRAM; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; INDEL MUTATION; INFLUENZA; INFLUENZA VIRUS A H1N1; METHODOLOGY; VIROLOGY; VIRUS GENOME;

GENOME, VIRAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INDEL MUTATION; INFLUENZA A VIRUS, H1N1 SUBTYPE; INFLUENZA, HUMAN; PROGRAMMING LANGUAGES; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84858739096     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-47     Document Type: Article

References (39)

1. Droege M, Hill B. The Genome Sequencer FLX System-longer reads, more applications, straight forward bioinformatics and more complete data sets. J Biotechnol 2008, 136:3-10. 10.1016/j.jbiotec.2008.03.021, 18616967.
2. Bennett S. Solexa Ltd. Pharmacogenomics 2004, 5:433-438. 10.1517/14622416.5.4.433, 15165179.
3. Archer J, Rambaut A, Taillon BE, Harrigan PR, Lewis M, Robertson DL. The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time-an ultra-deep approach. PLoS Comput Biol 2010, 6:e1001022. 10.1371/journal.pcbi.1001022, 3002995, 21187908.
4. Holt KE, Parkhill J, Mazzoni CJ, Roumagnac P, Weill FX, Goodhead I, Rance R, Baker S, Maskell DJ, Wain J, et al. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet 2008, 40:987-993. 10.1038/ng.195, 2652037, 18660809.
5. Kuroda M, Katano H, Nakajima N, Tobiume M, Ainai A, Sekizuka T, Hasegawa H, Tashiro M, Sasaki Y, Arakawa Y, et al. Characterization of quasispecies of pandemic 2009 influenza A virus (A/H1N1/2009) by de novo sequencing using a next-generation DNA sequencer. PLoS One 2010, 5:e10256. 10.1371/journal.pone.0010256, 2859049, 20428231.
6. Poon AF, Swenson LC, Dong WW, Deng W, Kosakovsky Pond SL, Brumme ZL, Mullins JI, Richman DD, Harrigan PR, Frost SD. Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1. Mol Biol Evol 2009, 27:819-832. 2877536, 19955476.
7. Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer RW. Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res 2007, 17:1195-1201. 10.1101/gr.6468307, 1933516, 17600086.
8. ten Bosch JR, Grody WW. Keeping up with the next generation: massively parallel sequencing in clinical diagnostics. J Mol Diagn 2008, 10:484-492. 10.2353/jmoldx.2008.080027, 2570630, 18832462.
9. Binladen J, Gilbert MT, Bollback JP, Panitz F, Bendixen C, Nielsen R, Willerslev E. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One 2007, 2:e197. 10.1371/journal.pone.0000197, 1797623, 17299583.
10. Meyer M, Stenzel U, Hofreiter M. Parallel tagged sequencing on the 454 platform. Nat Protoc 2008, 3:267-278. 10.1038/nprot.2007.520, 18274529.
11. Lal RB, Chakrabarti S, Yang C. Impact of genetic diversity of HIV-1 on diagnosis, antiretroviral therapy & vaccine development. Indian J Med Res 2005, 121:287-314.
12. Luciani F, Alizon S. The evolutionary dynamics of a rapidly mutating virus within and between hosts: the case of hepatitis C virus. PLoS Comput Biol 2009, 5:e1000565. 10.1371/journal.pcbi.1000565, 2768904, 19911046.
13. Tazi L, Imamichi H, Hirschfeld S, Metcalf JA, Orsega S, Perez-Losada M, Posada D, Lane HC, Crandall KA. HIV-1 infected monozygotic twins: a tale of two outcomes. BMC Evol Biol 2011, 11:62. 10.1186/1471-2148-11-62, 3070645, 21385447.
14. Westby M, Lewis M, Whitcomb J, Youle M, Pozniak AL, James IT, Jenkins TM, Perros M, van der Ryst E. Emergence of CXCR4-using human immunodeficiency virus type 1 (HIV-1) variants in a minority of HIV-1-infected patients following treatment with the CCR5 antagonist maraviroc is from a pretreatment CXCR4-using virus reservoir. J Virol 2006, 80:4909-4920. 10.1128/JVI.80.10.4909-4920.2006, 1472081, 16641282.
15. Bushman FD, Hoffmann C, Ronen K, Malani N, Minkah N, Rose HM, Tebas P, Wang GP. Massively parallel pyrosequencing in HIV research. AIDS 2008, 22:1411-1415. 10.1097/QAD.0b013e3282fc972e, 18614863.
16. Shendure J, Hanlee J. Next-generation DNA sequencing. Nat Biotech 2008, 26:1135-1145.
17. Tsibris AM, Korber B, Arnaout R, Russ C, Lo CC, Leitner T, Gaschen B, Theiler J, Paredes R, Su Z, et al. Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo. PLoS One 2009, 4:e5683. 10.1371/journal.pone.0005683, 2682648, 19479085.
18. Rozera G, Abbate I, Bruselles A, Vlassi C, D'Offizi G, Narciso P, Chillemi G, Prosperi M, Ippolito G, Capobianchi MR. Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations. Retrovirology 2009, 6:15. 10.1186/1742-4690-6-15, 2660291, 19216757.
19. Hinkley T, Martins J, Chappey C, Haddad M, Stawiski E, Whitcomb JM, Petropoulos CJ, Bonhoeffer S. A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase. Nat Genet 2011, 43:487-489. 10.1038/ng.795, 21441930.
20. Korber B, Gaschen B, Yusim K, Thakallapally R, Kesmir C, Detours V. Evolutionary and immunological implications of contemporary HIV-1 variation. Br Med Bull 2001, 58:19-42. 10.1093/bmb/58.1.19, 11714622.
21. Shafer RW, Schapiro JM. HIV-1 drug resistance mutations: an updated framework for the second decade of HAART. AIDS Rev 2008, 10:67-84. 2547476, 18615118.
22. Barouch DH, O'Brien KL, Simmons NL, King SL, Abbink P, Maxfield LF, Sun YH, La Porte A, Riggs AM, Lynch DM, et al. Mosaic HIV-1 vaccines expand the breadth and depth of cellular immune responses in rhesus monkeys. Nat Med 2010, 16:319-323. 10.1038/nm.2089, 2834868, 20173752.
23. Fischer W, Perkins S, Theiler J, Bhattacharya T, Yusim K, Funkhouser R, Kuiken C, Haynes B, Letvin NL, Walker BD, et al. Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants. Nat Med 2007, 13:100-106. 10.1038/nm1461, 17187074.
24. Pop M, Salzberg SL. Bioinformatics challenges of new sequencing technology. Trends Genet 2008, 24:142-149. 10.1016/j.tig.2007.12.006, 2680276, 18262676.
25. Gilles A, Meglecz E, Pech N, Ferreira S, Malausa T, Martin JF. Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 2011, 12:245. 10.1186/1471-2164-12-245, 3116506, 21592414.
26. Nakamura K, Oshima T, Morimoto T, Ikeda S, Yoshikawa H, Shiwa Y, Ishikawa S, Linak MC, Hirai A, Takahashi H, et al. Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res 2011, 39:e90. 10.1093/nar/gkr344, 3141275, 21576222.
27. Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, Beeson KY, Schork NJ, Murray SS, Topol EJ, Levy S, et al. Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol 2009, 10:R32. 10.1186/gb-2009-10-3-r32, 2691003, 19327155.
28. Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 2008, 9:387-402. 10.1146/annurev.genom.9.081307.164359, 18576944.
29. Brockman W, Alvarez P, Young S, Garber M, Giannoukos G, Lee WL, Russ C, Lander ES, Nusbaum C, Jaffe DB. Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res 2008, 18:763-770. 10.1101/gr.070227.107, 2336812, 18212088.
30. Bao S, Jiang R, Kwan W, Wang B, Ma X, Song YQ. Evaluation of next-generation sequencing software in mapping and assembly. J Hum Genet 2011, 56:406-414. 10.1038/jhg.2011.43, 21525877.
31. Oshlack A, Robinson MD, Young MD. From RNA-seq reads to differential expression results. Genome Biol 2010, 11:220. 10.1186/gb-2010-11-12-220, 3046478, 21176179.
32. Geneious v5.4. , http://www.geneious.com/
33. Zhou B, Donnelly ME, Scholes DT, St George K, Hatta M, Kawaoka Y, Wentworth DE. Single-reaction genomic amplification accelerates sequencing and vaccine production for classical and Swine origin human influenza a viruses. J Virol 2009, 83:10309-10313. 10.1128/JVI.01109-09, 2748056, 19605485.
34. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797. 10.1093/nar/gkh340, 390337, 15034147.
35. Archer J, Braverman MS, Taillon BE, Desany B, James I, Harrigan PR, Lewis M, Robertson DL. Detection of low-frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-using HIV-1 with ultra-deep pyrosequencing. AIDS 2009, 23:1209-1218. 10.1097/QAD.0b013e32832b4399, 2857961, 19424056.
36. Li H. Improving SNP discovery by base alignment quality. Bioinformatics 2011, 27:1157-1158. 10.1093/bioinformatics/btr076, 21320865.
37. Quinlan AR, Stewart DA, Stromberg MP, Marth GT. Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Nat Methods 2008, 5:179-181. 10.1038/nmeth.1172, 18193056.
38. Salmela L, Schroder J. Correcting errors in short reads by multiple alignments. Bioinformatics 2011, 27:1455-61. 10.1093/bioinformatics/btr170, 21471014.
39. Zagordi O, Klein R, Daumer M, Beerenwinkel N. Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies. Nucleic Acids Res 2010, 38:7400-7409. 10.1093/nar/gkq655, 2995073, 20671025.