1887

Chapter 15 : DNA Sequencing for Clinical and Public Health Virology: Some Assembly Required

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $30.00

Preview this chapter:
Zoom in
Zoomout

DNA Sequencing for Clinical and Public Health Virology: Some Assembly Required, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555819156/9781555819149.ch15-1.gif /docserver/preview/fulltext/10.1128/9781555819156/9781555819149.ch15-2.gif

Abstract:

Recent advances in sequencing technology, coupled with the relatively small genomes of viruses, make routine sequencing of entire genomes in clinical and public health settings increasingly feasible. The first two widely adopted DNA sequencing methodologies described, the chemical cleavage method of Maxam and Gilbert (1) and the chain termination method of Sanger et al., were both published in the 1970s (2, 3). Coincidental to the subject of this chapter, the first full genome to be sequenced by Sanger was that of a virus, albeit a bacteriophage, PhiX 174 (4). The Sanger method proved to be the more durable sequencing technology and, especially after the process was automated in 1996, was the most widely used method for DNA sequencing for more than a decade. Beginning in 2005, however, advances in sequencing technology, the so-called next generation sequencing (NGS) methodologies, resulted in a dramatic increase in the amount of sequence that can be generated and a concomitant dramatic decrease in the cost of sequencing. These factors have led to the widespread implementation of NGS in place of the Sanger method for typical sequencing applications and also for some novel purposes, for example, replacing microarrays to study gene expression. The increased use of NGS technologies has, not surprisingly, resulted in a rapid increase in the number of sequences submitted to the National Center for Biotechnology Information's (NCBI) Genbank database. In particular, the number of viral sequences submitted since 2012 has increased 22.9% as measured in nucleotide base pairs (5), and the number of publications based on NGS is increasing at an impressively rapid pace (6).

Citation: Bartkus J. 2016. DNA Sequencing for Clinical and Public Health Virology: Some Assembly Required, p 173-199. In Loeffelholz M, Hodinka R, Young S, Pinsky B (ed), Clinical Virology Manual, Fifth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819156.ch15
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of FIGURE 1
FIGURE 1

Illumina Sequencing Technology. A) Libraries for Illumina sequencing are prepared by ligation of adaptors to both ends of random fragments of DNA. DNA fragments are attached to the Illumina flow cell by hybridization of the adaptors to complimentary linker oligonucleotides on the surface of the flow cell. The hybridized DNA fragments are next amplified by a process referred to as solid phase bridge amplification. Each DNA strand has an attached and a free terminus. The strands are then denatured, resulting in the generation of millions of single-stranded DNA clusters. B) The reverse strands are released from the flow cell by cleavage and washed away, leaving only the forward strands for sequencing. Sequencing of these DNA clusters is done simultaneously by adding a sequencing primer and fluorescently labeled nucleotides. Laser excitation results in fluorescence of the last base incorporated, the label and a blocking group are removed and washed away, and the cycle is repeated. Fluorescence is detected by way of CCD camera image capture.

Citation: Bartkus J. 2016. DNA Sequencing for Clinical and Public Health Virology: Some Assembly Required, p 173-199. In Loeffelholz M, Hodinka R, Young S, Pinsky B (ed), Clinical Virology Manual, Fifth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819156.ch15
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2
FIGURE 2

Libraries for Ion Torrent sequencing are prepared by ligating adaptors onto DNA fragments. Fragments are clonally amplified by emulsion PCR. The particles are applied to the Ion Torrent chip for sequencing. Sequencing is accomplished by addition of a sequencing primer, DNA polymerase, and the sequential addition of dNTPs. The Ion Torrent chip is a semiconductor, and each microwell contains millions of copies of the amplified DNA template. Incorporation of a nucleotide results in the release of a proton, which results in a detectable change in pH in the microwell, which is converted to digital information. If no base is incorporated, then there is no voltage change. When multiple sequential nucleotides with the same base are present in the sequence, the result is an increase in the voltage that is proportional to the number of identical bases in the homopolymer run. So for two bases the voltage is doubled, for three it is tripled, and so on. Signals are processed and bases are called by the Ion Torrent software.

Citation: Bartkus J. 2016. DNA Sequencing for Clinical and Public Health Virology: Some Assembly Required, p 173-199. In Loeffelholz M, Hodinka R, Young S, Pinsky B (ed), Clinical Virology Manual, Fifth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819156.ch15
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555819156.ch15
1. Maxam AM, Gilbert W. 1977. A new method for sequencing DNA. Proc Natl Acad Sci USA 74:560564.[PubMed]
2. Sanger F, Coulson AR. 1975. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol 94:441448.[PubMed]
3. Sanger F, Nicklen S, Coulson AR. 1977. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:54635467.[PubMed]
4. Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M. 1977. Nucleotide sequence of bacteriophage phi X174 DNA. Nature 265:687695.[PubMed]
5. Benson DA, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. 2014. GenBank. Nucleic Acids Res 42(D1):D32D37.[PubMed]
6. Quiñones-Mateu ME, Avila S, Reyes-Teran G, Martinez MA. 2014. Deep sequencing: becoming a critical tool in clinical virology. J Clin Virol 61:919.[PubMed]
7. Ronaghi M, Karamohamed S, Pettersson B, Uhlén M, Nyrén P. 1996. Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem 242:8489.[PubMed]
8. Deyde VM, Nguyen T, Bright RA, Balish A, Shu B, Lindstrom S, Klimov AI, Gubareva LV. 2009. Detection of molecular markers of antiviral resistance in influenza A (H5N1) viruses using a pyrosequencing method. Antimicrob Agents Chemother 53:10391047.[PubMed]
9. Chantratita W, Sukasem C, Sirinavin S, Sankuntaw N, Srichantaratsamee C, Pasomsub E, Malathum K. 2011. Simultaneous detection and subtyping of H274Y-positive influenza A (H1N1) using pyrosequencing. J Infect Dev Ctries 5:348352.[PubMed]
10. Deng Y-M, Caldwell N, Barr IG. 2011. Rapid detection and subtyping of human influenza A viruses and reassortants by pyrosequencing. PLoS One 6:e23400.[PubMed]
11. Bright RA, Shay DK, Shu B, Cox NJ, Klimov AI. 2006. Adamantane resistance among influenza A viruses isolated early during the 2005–2006 influenza season in the United States. JAMA 295:891894.[PubMed]
12. Glenn TC. 2011. Field guide to next-generation DNA sequencers. Mol Ecol Resour 11:759769.[PubMed]
13. Schadt EE, Turner S, Kasarskis A. 2010. A window into third-generation sequencing. Hum Mol Genet 19(R2):R227R240.[PubMed]
14. Metzker ML. 2010. Sequencing technologies–the next generation. Nat Rev Genet 11:3146.[PubMed]
15. van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C. 2014. Ten years of next-generation sequencing technology. Trends Genet 30:418426.[PubMed]
16. Pareek CS, Smoczynski R, Tretyn A. 2011. Sequencing technologies and genome sequencing. J Appl Genet 52:413435.[PubMed]
17. Mardis ER. 2011. A decade's perspective on DNA sequencing technology. Nature 470:198203.[PubMed]
18. Caruccio N. 2011. Preparation of next-generation sequencing libraries using Nextera™ technology: simultaneous DNA fragmentation and adaptor tagging by in vitro transposition. Methods Mol Biol 733:241255.[PubMed]
19. Illumina. Application Note. Culture-free detection and identification of unknown RNA viruses. https://www.illumina.com/content/dam/illumina-marketing/documents/products/appnotes/appnote_afrims_rna_viruses.pdf
20. Rutvisuttinunt W, Chinnawirotpisan P, Simasathien S, Shrestha SK, Yoon I-K, Klungthong C, Fernandez S. 2013. Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform. J Virol Methods 193:394404.[PubMed]
21. Hang J, Forshey BM, Kochel TJ, Li T, Solórzano VF, Halsey ES, Kuschner RA. 2012. Random amplification and pyrosequencing for identification of novel viral genome sequences. J Biomol Tech 23:410.[PubMed]
22. Malboeuf CM, Yang X, Charlebois P, Qu J, Berlin AM, Casali M, Pesko KN, Boutwell CL, DeVincenzo JP, Ebel GD, Allen TM, Zody MC, Henn MR, Levin JZ. 2013. Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification. Nucleic Acids Res 41(1):e13.[PubMed]
23. Kuersten S. 2012. A transposable approach to RNA-seq from total RNA. Nat Methods 9:i-ii.
24. Merriman B, Ion Torrent R&D Team, Rothberg JM. 2012. Progress in ion torrent semiconductor chip based sequencing. Electrophoresis 33:33973417.[PubMed]
25. McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, Zhang Z, Ranade SS, Dimalanta ET, Hyland FC, Sokolsky TD, Zhang L, Sheridan A, Fu H, Hendrickson CL, Li B, Kotler L, Stuart JR, Malek JA, Manning JM, Antipova AA, Perez DS, Moore MP, Hayashibara KC, Lyons MR, Beaudoin RE, Coleman BE, Laptewicz MW, Sannicandro AE, Rhodes MD, Gottimukkala RK, Yang S, Bafna V, Bashir A, MacBride A, Alkan C, Kidd JM, Eichler EE, Reese MG, De La Vega FM, Blanchard AP. 2009. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res 19:15271541.[PubMed]
26. Ozsolak F, Milos PM. 2011. Single-molecule direct RNA sequencing without cDNA synthesis. Wiley Interdiscip Rev RNA 2:565570.[PubMed]
27. Branton D, Deamer DW, Marziali A, Bayley H, Benner SA, Butler T, Di Ventra M, Garaj S, Hibbs A, Huang X, Jovanovich SB, Krstic PS, Lindsay S, Ling XS, Mastrangelo CH, Meller A, Oliver JS, Pershin YV, Ramsey JM, Riehn R, Soni GV, Tabard-Cossa V, Wanunu M, Wiggin M, Schloss JA. 2008. The potential and challenges of nanopore sequencing. Nat Biotechnol 26:11461153.[PubMed]
28. Check Hayden E. 2014. Data from pocket-sized genome sequencer unveiled. Nature 521.
29. Suzuki S, Ono N, Furusawa C, Ying B-W, Yomo T. 2011. Comparison of sequence reads obtained from three next-generation sequencing platforms. PLoS One 6:e19534.[PubMed]
30. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y. 2012. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 13:341.[PubMed]
31. Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M. 2012. Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012:251364.[PubMed]
32. Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, Pallen MJ. 2012. Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 30:434439[CrossRef].[PubMed]
33. Frey KG, Herrera-Galeano JE, Redden CL, Luu TV, Servetas SL, Mateczun AJ, Mokashi VP, Bishop-Lilly KA. 2014. Comparison of three next-generation sequencing platforms for metagenomic sequencing and identification of pathogens in blood. BMC Genomics 15:96.[PubMed]
34. Li JZ, Chapman B, Charlebois P, Hofmann O, Weiner B, Porter AJ, Samuel R, Vardhanabhuti S, Zheng L, Eron J, Taiwo B, Zody MC, Henn MR, Kuritzkes DR, Hide W, and the ACTG A5262 Study Team. 2014. Comparison of illumina and 454 deep sequencing in participants failing raltegravir-based antiretroviral therapy. PLoS One 9:e90485.[PubMed]
35. Archer J, Weber J, Henry K, Winner D, Gibson R, Lee L, Paxinos E, Arts EJ, Robertson DL, Mimms L, Quiñones-Mateu ME. 2012. Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism. PLoS One 7:e49602.[PubMed]
36. Ninomiya M, Ueno Y, Funayama R, Nagashima T, Nishida Y, Kondo Y, Inoue J, Kakazu E, Kimura O, Nakayama K, Shimosegawa T. 2012. Use of illumina deep sequencing technology to differentiate hepatitis C virus variants. J Clin Microbiol 50:857866.[PubMed]
37. Marston DA, McElhinney LM, Ellis RJ, Horton DL, Wise EL, Leech SL, David D, de Lamballerie X, Fooks AR. 2013. Next generation sequencing of viral RNA genomes. BMC Genomics 14:444.[PubMed]
38. Téllez-Sosa J, Rodríguez MH, Gómez-Barreto RE, Valdovinos-Torres H, Hidalgo AC, Cruz-Hervert P, Luna RS, Carrillo-Valenzo E, Ramos C, García-García L, Martínez-Barnetche J. 2013. Using high-throughput sequencing to leverage surveillance of genetic diversity and oseltamivir resistance: a pilot study during the 2009 influenza A(H1N1) pandemic. PLoS One 8:e67010.[PubMed]
39. Barzon L, Militello V, Lavezzo E, Franchin E, Peta E, Squarzon L, Trevisan M, Pagni S, Dal Bello F, Toppo S, Palù G. 2011. Human papillomavirus genotyping by 454 next generation sequencing technology. J Clin Virol 52:9397.[PubMed]
40. Sides TL, Akinsete O, Henry K, Wotton JT, Carr PW, Bartkus J. 2005. HIV-1 subtype diversity in Minnesota. J Infect Dis 192:3745.[PubMed]
41. Oberste MS, Maher K, Kilpatrick DR, Flemister MR, Brown BA, Pallansch MA. 1999. Typing of human enteroviruses by partial sequencing of VP1. J Clin Microbiol 37:12881293.[PubMed]
42. Cotten M, Lam TT, Watson SJ, Palser AL, Petrova V, Grant P, Pybus OG, Rambaut A, Guan Y, Pillay D, Kellam P, Nastouli E. 2013. Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus. Emerg Infect Dis 19:73642B.[PubMed]
43. Höper D, Hoffmann B, Beer M. 2009. Simple, sensitive, and swift sequencing of complete H5N1 avian influenza virus genomes. J Clin Microbiol 47:674679.[PubMed]
44. Gardner SN, Jaing CJ, Elsheikh MM, Peña J, Hysom DA, Borucki MK. 2014. Multiplex degenerate primer design for targeted whole genome amplification of many viral genomes. Adv Bioinforma 2014:101894.[PubMed]
45. Kapoor A, Simmonds P, Slikas E, Li L, Bodhidatta L, Sethabutr O, Triki H, Bahri O, Oderinde BS, Baba MM, Bukbuk DN, Besser J, Bartkus J, Delwart E. 2010. Human bocaviruses are highly diverse, dispersed, recombination prone, and prevalent in enteric infections. J Infect Dis 201:16331643.[PubMed]
46. Fan X, Xu Y, Di Bisceglie AM. 2006. Efficient amplification and cloning of near full-length hepatitis C virus genome from clinical samples. Biochem Biophys Res Commun 346:11631172.[PubMed]
47. Froussard P. 1992. A random-PCR method (rPCR) to construct whole cDNA library from low amounts of RNA. Nucleic Acids Res 20:2900.[PubMed]
48. Tan V, Van Doorn HR, Van der Hoek L, Minh Hien V, Jebbink MF, Quang Ha D, Farrar J, Van Vinh Chau N, de Jong MD. 2011. Random PCR and ultracentrifugation increases sensitivity and throughput of VIDISCA for screening of pathogens in clinical specimens. J Infect Dev Ctries 5:142148.[PubMed]
49. Victoria JG, Kapoor A, Dupuis K, Schnurr DP, Delwart EL. 2008. Rapid identification of known and new RNA viruses from animal tissues. PLoS Pathog 4:e1000163.[PubMed]
50. Nakamura S, Yang C-S, Sakon N, Ueda M, Tougan T, Yamashita A, Goto N, Takahashi K, Yasunaga T, Ikuta K, Mizutani T, Okamoto Y, Tagami M, Morita R, Maeda N, Kawai J, Hayashizaki Y, Nagai Y, Horii T, Iida T, Nakaya T. 2009. Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach. PLoS One 4:e4219.[PubMed]
51. Batty EM, Wong THN, Trebes A, Argoud K, Attar M, Buck D, Ip CLC, Golubchik T, Cule M, Bowden R, Manganis C, Klenerman P, Barnes E, Walker AS, Wyllie DH, Wilson DJ, Dingle KE, Peto TEA, Crook DW, Piazza P. 2013. A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples. PLoS One 8:e66129.[PubMed]
52. Jones MS, Kapoor A, Lukashov VV, Simmonds P, Hecht F, Delwart E. 2005. New DNA viruses identified in patients with acute viral infection syndrome. J Virol 79:82308236.[PubMed]
53. Karlsson OE, Belák S, Granberg F. 2013. The effect of preprocessing by sequence-independent, single-primer amplification (SISPA) on metagenomic detection of viruses. Biosecur Bioterror 11(Suppl 1):S227S234.[PubMed]
54. Li L, Victoria J, Kapoor A, Blinkova O, Wang C, Babrzadeh F, Mason CJ, Pandey P, Triki H, Bahri O, Oderinde BS, Baba MM, Bukbuk DN, Besser JM, Bartkus JM, Delwart EL. 2009. A novel picornavirus associated with gastroenteritis. J Virol 83:1200212006.[PubMed]
55. Johne R, Müller H, Rector A, van Ranst M, Stevens H. 2009. Rolling-circle amplification of viral DNA genomes using phi29 polymerase. Trends Microbiol 17:205211.[PubMed]
56. Meiring TL, Salimo AT, Coetzee B, Maree HJ, Moodley J, Hitzeroth II, Freeborough M-J, Rybicki EP, Williamson A-L. 2012. Next-generation sequencing of cervical DNA detects human papillomavirus types not detected by commercial kits. Virol J 9:164.[PubMed]
57. de Vries M, Oude Munnink BB, Deijs M, Canuti M, Koekkoek SM, Molenkamp R, Bakker M, Jurriaans S, van Schaik BDC, Luyf AC, Olabarriaga SD, van Kampen AHC, van der Hoek L. 2012. Performance of VIDISCA-454 in feces-suspensions and serum. Viruses 4:13281334.[PubMed]
58. Head SR, Komori HK, LaMere SA, Whisenant T, Van Nieuwerburgh F, Salomon DR, Ordoukhanian P. 2014. Library construction for next-generation sequencing: overviews and challenges. Biotechniques 56:6164, 66, 68 passim.[PubMed]
59. van Dijk EL, Jaszczyszyn Y, Thermes C. 2014. Library preparation methods for next-generation sequencing: tone down the bias. Exp Cell Res 322:1220.[PubMed]
60. Ross MG, Russ C, Costello M, Hollinger A, Lennon NJ, Hegarty R, Nusbaum C, Jaffe DB. 2013. Characterizing and measuring bias in sequence data. Genome Biol 14:R51.[PubMed]
61. Depledge DP, Palser AL, Watson SJ, Lai IY-C, Gray ER, Grant P, Kanda RK, Leproust E, Kellam P, Breuer J. 2011. Specific capture and whole-genome sequencing of viruses from clinical samples. PLoS One 6:e27805.[PubMed]
62. Duncavage EJ, Magrini V, Becker N, Armstrong JR, Demeter RT, Wylie T, Abel HJ, Pfeifer JD. 2011. Hybrid capture and next-generation sequencing identify viral integration sites from formalin-fixed, paraffin-embedded tissue. J Mol Diagn 13:325333.[PubMed]
63. Szpara ML, Parsons L, Enquist LW. 2010. Sequence variability in clinical and laboratory isolates of herpes simplex virus 1 reveals new mutations. J Virol 84:53035313.[PubMed]
64. Kapranov P, Chen L, Dederich D, Dong B, He J, Steinmann KE, Moore AR, Thompson JF, Milos PM, Xiao W. 2012. Native molecular state of adeno-associated viral vectors revealed by single-molecule sequencing. Hum Gene Ther 23:4655.[PubMed]
65. Breitbart M, Rohwer F. 2005. Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing. Biotechniques 39:729736.[PubMed]
66. Prachayangprecha S, Schapendonk CME, Koopmans MP, Osterhaus ADME, Schürch AC, Pas SD, van der Eijk AA, Poovorawan Y, Haagmans BL, Smits SL. 2014. Exploring the potential of next-generation sequencing in detection of respiratory viruses. J Clin Microbiol 52:37223730.[PubMed]
67. Hall RJ, Wang J, Todd AK, Bissielo AB, Yen S, Strydom H, Moore NE, Ren X, Huang QS, Carter PE, Peacey M. 2014. Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery. J Virol Methods 195:194204.[PubMed]
68. Lam TT-Y, Hon C-C, Tang JW. 2010. Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections. Crit Rev Clin Lab Sci 47:549.[PubMed]
69. Gogol-Döring A, Chen W. 2012. An overview of the analysis of next generation sequencing data. Methods Mol Biol 802:249257.[PubMed]
70. Gilbert D. 2004. Bioinformatics software resources. Brief Bioinform 5:300304.[PubMed]
71. Kerr A. 2011. Desktop Sequence Analysis: software review. Bioinforma Knowledgeblog.
72. Lauck M, Alvarado-Mora MV, Becker EA, Bhattacharya D, Striker R, Hughes AL, Carrilho FJ, O'Connor DH, Pinho JRR. 2012. Analysis of hepatitis C virus intrahost diversity across the coding region by ultradeep pyrosequencing. J Virol 86:39523960.[PubMed]
73. Lei H, Li T, Hung G-C, Li B, Tsai S, Lo S-C. 2013. Identification and characterization of EBV genomes in spontaneously immortalized human peripheral blood B lymphocytes by NGS technology. BMC Genomics 14:804.[PubMed]
74. Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.[PubMed]
75. Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J. 2009. SNP detection for massively parallel whole-genome resequencing. Genome Res 19:11241132.[PubMed]
76. Gurtowski J, Schatz MC, Langmead B,. 2012. Genotyping in the Cloud with Crossbow. Curr Protoc Bioinforma Ed Board Baxevanis A, CHAPTER: 15. Unit: 15.3.
77. Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL. 2009. Searching for SNPs with cloud computing. Genome Biol 10:R134.[PubMed]
78. Sadedin SP, Pope B, Oshlack A. 2012. Bpipe: a tool for running and managing bioinformatics pipelines. Bioinformatics 28:15251526.[PubMed]
79. Afgan E, Baker D, Coraor N, Chapman B, Nekrutenko A, Taylor J. 2010. Galaxy CloudMan: delivering cloud compute clusters. BMC Bioinformatics 11(Suppl 12):S4.[PubMed]
80. Cock PJA, Grüning BA, Paszkiewicz K, Pritchard L. 2013. Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology. PeerJ 1:e167.[PubMed]
81. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. 2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:12971303.[PubMed]
82. Dai L, Gao X, Guo Y, Xiao J, Zhang Z. 2012. Bioinformatics clouds for big data manipulation. Biol Direct 7:43, discussion 43.[PubMed]
83. Angiuoli SV, Matalka M, Gussman A, Galens K, Vangala M, Riley DR, Arze C, White JR, White O, Fricke WF. 2011. CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinformatics 12:356.[PubMed]
84. Krampis K, Booth T, Chapman B, Tiwari B, Bicak M, Field D, Nelson KE. 2012. Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community. BMC Bioinformatics 13:42.[PubMed]
85. Naccache SN, Federman S, Veeraraghavan N, Zaharia M, Lee D, Samayoa E, Bouquet J, Greninger AL, Luk K-C, Enge B, Wadford DA, Messenger SL, Genrich GL, Pellegrino K, Grard G, Leroy E, Schneider BS, Fair JN, Martínez MA, Isa P, Crump JA, DeRisi JL, Sittler T, Hackett J Jr, Miller S, Chiu CY. 2014. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res 24:11801192.[PubMed]
86. Liu B, Madduri RK, Sotomayor B, Chard K, Lacinski L, Dave UJ, Li J, Liu C, Foster IT. 2014. Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses. J Biomed Inform 49:119133.[PubMed]
87. Marz M, Beerenwinkel N, Drosten C, Fricke M, Frishman D, Hofacker IL, Hoffmann D, Middendorf M, Rattei T, Stadler PF, Töpfer A. 2014. Challenges in RNA virus bioinformatics. Bioinformatics 30:17931799.[PubMed]
88. Mokili JL, Rohwer F, Dutilh BE. 2012. Metagenomics and future perspectives in virus discovery. Curr Opin Virol 2:6377.[PubMed]
89. Yan Q. 2008. Bioinformatics databases and tools in virology research: an overview. In Silico Biol 8:7185.[PubMed]
90. Zhao G, Krishnamurthy S, Cai Z, Popov VL, Travassos da Rosa AP, Guzman H, Cao S, Virgin HW, Tesh RB, Wang D. 2013. Identification of novel viruses using VirusHunter—an automated data analysis pipeline. PLoS One 8:e78470.[PubMed]
91. Pickett BE, Sadat EL, Zhang Y, Noronha JM, Squires RB, Hunt V, Liu M, Kumar S, Zaremba S, Gu Z, Zhou L, Larson CN, Dietrich J, Klem EB, Scheuermann RH. 2012. ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Res 40(D1):D593D598.[PubMed]
92. Pickett BE, Greer DS, Zhang Y, Stewart L, Zhou L, Sun G, Gu Z, Kumar S, Zaremba S, Larsen CN, Jen W, Klem EB, Scheuermann RH. 2012. Virus pathogen database and analysis resource (ViPR): a comprehensive bioinformatics database and analysis resource for the coronavirus research community. Viruses 4:32093226.[PubMed]
93. Fancello L, Raoult D, Desnues C. 2012. Computational tools for viral metagenomics and their application in clinical research. Virology 434:162174.[PubMed]
94. Takeuchi F, Sekizuka T, Yamashita A, Ogasawara Y, Mizuta K, Kuroda M. 2014. MePIC, metagenomic pathogen identification for clinical specimens. Jpn J Infect Dis 67:6265.[PubMed]
95. Petty TJ, Cordey S, Padioleau I, Docquier M, Turin L, Preynat-Seauve O, Zdobnov EM, Kaiser L. 2014. Comprehensive human virus screening using high-throughput sequencing with a user-friendly representation of bioinformatics analysis: a pilot study. J Clin Microbiol 52:33513361.[PubMed]
96. Underwood A, Green J. 2011. Call for a quality standard for sequence-based assays in clinical microbiology: necessity for quality assessment of sequences used in microbial identification and typing. J Clin Microbiol 49:2326.[PubMed]
97. Zhao S, Prenger K, Smith L, Messina T, Fan H, Jaeger E, Stephens S. 2013. Rainbow: a tool for large-scale whole-genome sequencing data analysis using cloud computing. BMC Genomics 14:425.[PubMed]
98. Willner D, Hugenholtz P. 2013. From deep sequencing to viral tagging: recent advances in viral metagenomics. BioEssays 35:436442.[PubMed]
99. Budowle B, Connell ND, Bielecka-Oder A, Colwell RR, Corbett CR, Fletcher J, Forsman M, Kadavy DR, Markotic A, Morse SA, Murch RS, Sajantila A, Schmedes SE, Ternus KL, Turner SD, Minot S. 2014. Validation of high throughput sequencing and microbial forensics applications. Investig Genet 5:9.[PubMed]
100. Wandelt S, Rheinländer A, Bux M, Thalheim L, Haldemann B, Leser U. 2012. Data Management challenges in next generation sequencing. Datenbank-Spektrum 12:161171.
101. Mariette J, Escudié F, Allias N, Salin G, Noirot C, Thomas S, Klopp C. 2012. NG6: integrated next generation sequencing storage and processing environment. BMC Genomics 13:462.[PubMed]
102. Leinonen R, Sugawara H, Shumway M International Nucleotide Sequence Database Collaboration. 2011. The sequence read archive. Nucleic Acids Res 39(Database):D19D21.[PubMed]
103. Yang X, Chockalingam SP, Aluru S. 2013. A survey of error-correction methods for next-generation sequencing. Brief Bioinform 14:5666.[PubMed]
104. Li H, Ruan J, Durbin R. 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18:18511858.[PubMed]
105. Ruffalo M, Koyutürk M, Ray S, LaFramboise T. 2012. Accurate estimation of short read mapping quality for next-generation genome sequencing. Bioinformatics 28:i349i355.[PubMed]
106. Haiminen N, Kuhn DN, Parida L, Rigoutsos I. 2011. Evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results. PLoS One 6:e24182.[PubMed]
107. Li H. 2014. Toward better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics 30:28432851.[PubMed]
108. Oyola SO, Otto TD, Gu Y, Maslen G, Manske M, Campino S, Turner DJ, Macinnis B, Kwiatkowski DP, Swerdlow HP, Quail MA. 2012. Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC Genomics 13:1.[PubMed]
109. Jabara CB, Jones CD, Roach J, Anderson JA, Swanstrom R. 2011. Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID. Proc Natl Acad Sci USA 108:2016620171.[PubMed]
110. Sheward DJ, Murrell B, Williamson C. 2012. Degenerate Primer IDs and the birthday problem. Proc Natl Acad Sci USA 109:21.E1330; author reply E1331.
111. Brodin J, Hedskog C, Heddini A, Benard E, Neher RA, Mild M, Albert J. 2015. Challenges with using primer IDs to improve accuracy of next generation sequencing. PLoS One 10:e0119123.[PubMed]
112. McElroy K, Thomas T, Luciani F. 2014. Deep sequencing of evolving pathogen populations: applications, errors, and bioinformatic solutions. Microb Inform Exp 4:1.[PubMed]
113. Ahmad-Nejad P, Dorn-Beineke A, Pfeiffer U, Brade J, Geilenkeuser W-J, Ramsden S, Pazzagli M, Neumaier M. 2006. Methodologic European external quality assurance for DNA sequencing: the EQUALseq program. Clin Chem 52:716727.[PubMed]
114. Patton SJ, Wallace AJ, Elles R. 2006. Benchmark for evaluating the quality of DNA sequencing: proposal from an international external quality assessment scheme. Clin Chem 52:728736.[PubMed]
115. Yang GS, Stott JM, Smailus D, Barber SA, Balasundaram M, Marra MA, Holt RA. 2005. High-throughput sequencing: a failure mode analysis. BMC Genomics 6:2.[PubMed]
116. Holm-Hansen C, Vainio K. 2009. Sequencing of viral genes. Methods Mol Biol 551:203215.
117. Gargis AS, Kalman L, Berry MW, Bick DP, Dimmock DP, Hambuch T, Lu F, Lyon E, Voelkerding KV, Zehnbauer BA, Agarwala R, Bennett SF, Chen B, Chin ELH, Compton JG, Das S, Farkas DH, Ferber MJ, Funke BH, Furtado MR, Ganova-Raeva LM, Geigenmüller U, Gunselman SJ, Hegde MR, Johnson PLF, Kasarskis A, Kulkarni S, Lenk T, Liu CSJ, Manion M, Manolio TA, Mardis ER, Merker JD, Rajeevan MS, Reese MG, Rehm HL, Simen BB, Yeakley JM, Zook JM, Lubin IM. 2012. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat Biotechnol 30:10331036.[PubMed]
118. Ladner JT, Beitzel B, Chain PSG, Davenport MG, Donaldson EF, Frieman M, Kugelman JR, Kuhn JH, O'Rear J, Sabeti PC, Wentworth DE, Wiley MR, Yu G-Y, Sozhamannan S, Bradburne C, Palacios G Threat Characterization Consortium. 2014. Standards for sequencing viral genomes in the era of high-throughput sequencing. MBio 5:e0136014.[PubMed]
119. US Food and Drug Administration (FDA). Ultra High Throughput Sequencing for Clinical Diagnostic Applications—Approaches to Assess Analytical Validity, June 23, 2011 http://www.fda.gov/MedicalDevices/NewsEvents/WorkshopsConferences/ucm255327.htm
120. Collins FS, Hamburg MA. 2013. First FDA authorization for next-generation sequencer. N Engl J Med 369:23692371.[PubMed]
121. Barzon L, Lavezzo E, Militello V, Toppo S, Palù G. 2011. Applications of next-generation sequencing technologies to diagnostic virology. Int J Mol Sci 12:78617884.[PubMed]
122. Barzon L, Lavezzo E, Costanzi G, Franchin E, Toppo S, Palù G. 2013. Next-generation sequencing technologies in diagnostic virology. J Clin Virol 58:346350.[PubMed]
123. Capobianchi MR, Giombini E, Rozera G. 2013. Next-generation sequencing technology in clinical virology. Clin Microbiol Infect 19:1522.[PubMed]
124. Li L, Delwart E. 2011. From orphan virus to pathogen: the path to the clinical lab. Curr Opin Virol 1:282288.[PubMed]
125. Radford AD, Chapman D, Dixon L, Chantrey J, Darby AC, Hall N. 2012. Application of next-generation sequencing technologies in virology. J Gen Virol 93:18531868.[PubMed]
126. Köser CU, Ellington MJ, Cartwright EJP, Gillespie SH, Brown NM, Farrington M, Holden MTG, Dougan G, Bentley SD, Parkhill J, Peacock SJ. 2012. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog 8:e1002824.[PubMed]
127. Marston HD, Folkers GK, Morens DM, Fauci AS. 2014. Emerging viral diseases: confronting threats with new technologies. Sci Transl Med 6(253):253ps10. [PubMed]
128. Holmes KV, Dominguez SR. 2013. The new age of virus discovery: genomic analysis of a novel human betacoronavirus isolated from a fatal case of pneumonia. MBio 4:e0054812.[PubMed]
129. Pallen MJ. 2014. Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections. Parasitology 141:18561862.[PubMed]
130. Quan P-L, Briese T, Palacios G, Ian Lipkin W. 2008. Rapid sequence-based diagnosis of viral infection. Antiviral Res 79:15.[PubMed]
131. Bexfield N, Kellam P. 2011. Metagenomics and the molecular identification of novel viruses. Vet J 190:191198.[PubMed]
132. Chiu CY. 2013. Viral pathogen discovery. Curr Opin Microbiol 16:468478.[PubMed]
133. Ambrose HE, Clewley JP. 2006. Virus discovery by sequence-independent genome amplification. Rev Med Virol 16:365383.[PubMed]
134. Delwart EL. 2007. Viral metagenomics. Rev Med Virol 17:115131.[PubMed]
135. Bibby K. 2013. Metagenomic identification of viral pathogens. Trends Biotechnol 31:275279.[PubMed]
136. Fuller C, Cebelinski E, Bartkus J, Juni B, Smith K, Besser J. 2008. Enhanced laboratory testing of enteric disease outbreaks of unknown etiology in Minnesota. Abstr Int Conf Emerg Infect Dis.
137. Jones MS, Lukashov VV, Ganac RD, Schnurr DP. 2007. Discovery of a novel human picornavirus in a stool sample from a pediatric patient presenting with fever of unknown origin. J Clin Microbiol 45:21442150.[PubMed]
138. Svraka S, Rosario K, Duizer E, van der Avoort H, Breitbart M, Koopmans M. 2010. Metagenomic sequencing for virus identification in a public-health setting. J Gen Virol 91:28462856.[PubMed]
139. Shaukat S, Angez M, Alam MM, Jebbink MF, Deijs M, Canuti M, Sharif S, de Vries M, Khurshid A, Mahmood T, van der Hoek L, Zaidi SSZ. 2014. Identification and characterization of unrecognized viruses in stool samples of non-polio acute flaccid paralysis children by simplified VIDISCA. Virol J 11:146.
140. de Vries M, Deijs M, Canuti M, van Schaik BDC, Faria NR, van de Garde MDB, Jachimowski LCM, Jebbink MF, Jakobs M, Luyf ACM, Coenjaerts FEJ, Claas ECJ, Molenkamp R, Koekkoek SM, Lammens C, Leus F, Goossens H, Ieven M, Baas F, van der Hoek L. 2011. A sensitive assay for virus discovery in respiratory clinical samples. PLoS One 6:e16118.[PubMed]
141. Finkbeiner SR, Li Y, Ruone S, Conrardy C, Gregoricus N, Toney D, Virgin HW, Anderson LJ, Vinjé J, Wang D, Tong S. 2009. Identification of a novel astrovirus (astrovirus VA1) associated with an outbreak of acute gastroenteritis. J Virol 83:1083610839.[PubMed]
142. Yang J, Yang F, Ren L, Xiong Z, Wu Z, Dong J, Sun L, Zhang T, Hu Y, Du J, Wang J, Jin Q. 2011. Unbiased parallel detection of viral pathogens in clinical samples by use of a metagenomic approach. J Clin Microbiol 49:34633469.[PubMed]
143. McMullan LK, Frace M, Sammons SA, Shoemaker T, Balinandi S, Wamala JF, Lutwama JJ, Downing RG, Stroeher U, MacNeil A, Nichol ST. 2012. Using next generation sequencing to identify yellow fever virus in Uganda. Virology 422:15.[PubMed]
144. Feng H, Taylor JL, Benos PV, Newton R, Waddell K, Lucas SB, Chang Y, Moore PS. 2007. Human transcriptome subtraction by using short sequence tags to search for tumor viruses in conjunctival carcinoma. J Virol 81:1133211340.[PubMed]