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New Horizons in Next-Generation Sequencing

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Book cover Next Generation Sequencing Technologies and Challenges in Sequence Assembly

Part of the book series: SpringerBriefs in Systems Biology ((BRIEFSBIOSYS,volume 7))

Abstract

In the previous chapters, we described the most common and well-established next-generation sequencing technologies and platforms. However, several methodologies and sequencers with outstanding features have also been released in the last few years. Furthermore, additional technologies demonstrating great promise are currently in development. In this chapter, we will briefly describe these recent and ongoing developments that may have a profound impact on the future of sequencing.

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References

  1. Rusk N (2009) Cheap third-generation sequencing. Nature Methods 6 (4):244-245. doi:10.1038/nmeth0409-244a

    Article  CAS  Google Scholar 

  2. Pushkarev D, Neff NF, Quake SR (2009) Single-molecule sequencing of an individual human genome. Nature Biotechnology 27 (9):847-850. doi:10.1038/Nbt.1561

    Article  CAS  PubMed  Google Scholar 

  3. Thompson JF, Steinmann KE (2010) Single molecule sequencing with a HeliScope genetic analysis system. Curr Protoc Mol Biol Chapter 7:Unit7 10. doi:10.1002/0471142727.mb0710s92

  4. Harris TD, Buzby PR, Babcock H, Beer E, Bowers J et al. (2008) Single-molecule DNA sequencing of a viral genome. Science 320 (5872):106-109. doi:10.1126/science.1150427

    Article  CAS  PubMed  Google Scholar 

  5. Levene MJ, Korlach J, Turner SW, Foquet M, Craighead HG et al. (2003) Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299 (5607):682-686. doi:10.1126/science.1079700

    Article  CAS  PubMed  Google Scholar 

  6. Eid J, Fehr A, Gray J, Luong K, Lyle J et al. (2009) Real-time DNA sequencing from single polymerase molecules. Science 323 (5910):133-138. doi:10.1126/science.1162986

    Article  CAS  PubMed  Google Scholar 

  7. Kasianowicz JJ, Brandin E, Branton D, Deamer DW (1996) Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci U S A 93 (24):13770-13773

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  8. Schadt EE, Turner S, Kasarskis A (2010) A window into third-generation sequencing. Hum Mol Genet 19 (R2):R227-240. doi:10.1093/hmg/ddq416

    Article  CAS  PubMed  Google Scholar 

  9. McNally B, Singer A, Yu Z, Sun Y, Weng Z et al. (2010) Optical recognition of converted DNA nucleotides for single-molecule DNA sequencing using nanopore arrays. Nano Lett 10 (6):2237-2244. doi:10.1021/nl1012147

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  10. Stoddart D, Heron AJ, Mikhailova E, Maglia G, Bayley H (2009) Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore. Proc Natl Acad Sci U S A 106 (19):7702-7707. doi:10.1073/pnas.0901054106

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  11. Purnell RF, Mehta KK, Schmidt JJ (2008) Nucleotide identification and orientation discrimination of DNA homopolymers immobilized in a protein nanopore. Nano Lett 8 (9):3029-3034. doi:10.1021/nl802312f

    Article  CAS  PubMed  Google Scholar 

  12. Stoddart D, Maglia G, Mikhailova E, Heron AJ, Bayley H (2010) Multiple base-recognition sites in a biological nanopore: two heads are better than one. Angew Chem Int Ed Engl 49 (3):556-559. doi:10.1002/anie.200905483

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  13. Glenn TC (2011) Field guide to next-generation DNA sequencers. Mol Ecol Resour 11 (5):759-769. doi:10.1111/j.1755-0998.2011.03024.x

    Article  CAS  PubMed  Google Scholar 

  14. Glenn TC (2013) Field guide to next-generation DNA sequencers-Update. http://www.molecularecologist.com/next-gen-fieldguide-2013/. Accessed 10-01-2014

  15. Oxford Nanopore Technologies Ltd. (2014) The GridION System. https://www.nanoporetech.com/technology/the-gridion-system/the-gridion-system. Accessed 10-01-2014

  16. Collins FS, Hamburg MA (2013) First FDA authorization for next-generation sequencer. N Engl J Med 369 (25):2369-2371. doi:10.1056/NEJMp1314561

    Article  CAS  PubMed  Google Scholar 

  17. Hanna GJ, Johnson VA, Kuritzkes DR, Richman DD, Martinez-Picado J et al. (2000) Comparison of sequencing by hybridization and cycle sequencing for genotyping of human immunodeficiency virus type 1 reverse transcriptase. J Clin Microbiol 38 (7):2715-2721

    CAS  PubMed Central  PubMed  Google Scholar 

  18. Morey M, Fernandez-Marmiesse A, Castineiras D, Fraga JM, Couce ML et al. (2013) A glimpse into past, present, and future DNA sequencing. Mol Genet Metab 110 (1-2):3-24. doi:10.1016/j.ymgme.2013.04.024

    Article  CAS  PubMed  Google Scholar 

  19. Qin Y, Schneider TM, Brenner MP (2012) Sequencing by hybridization of long targets. PLoS One 7 (5):e35819. doi:10.1371/journal.pone.0035819

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  20. Di Ventra M (2013) Fast DNA sequencing by electrical means inches closer. Nanotechnology 24 (34):342501. doi:10.1088/0957-4484/24/34/342501

    Article  PubMed  Google Scholar 

  21. Ohshiro T, Matsubara K, Tsutsui M, Furuhashi M, Taniguchi M et al. (2012) Single-molecule electrical random resequencing of DNA and RNA. Sci Rep 2:501. doi:10.1038/srep00501

    Article  PubMed Central  PubMed  Google Scholar 

  22. Bell DC, Thomas WK, Murtagh KM, Dionne CA, Graham AC et al. (2012) DNA base identification by electron microscopy. Microsc Microanal 18 (5):1049-1053. doi:10.1017/S1431927612012615

    Article  CAS  PubMed  Google Scholar 

  23. Helmy M, Tomita M, Ishihama Y (2012) Peptide identification by searching large-scale tandem mass spectra against large databases: bioinformatics methods in proteogenomics. Genes Genome Genomics 6:76-85

    Google Scholar 

  24. Ishii N, Nakahigashi K, Baba T, Robert M, Soga T et al. (2007) Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science 316 (5824):593-597. doi:10.1126/science.1132067

    Article  CAS  PubMed  Google Scholar 

  25. Edwards JR, Ruparel H, Ju J (2005) Mass-spectrometry DNA sequencing. Mutat Res 573 (1-2):3-12. doi:S0027-5107(05)00023-0

    Google Scholar 

  26. Beres SB, Carroll RK, Shea PR, Sitkiewicz I, Martinez-Gutierrez JC et al. (2010) Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics. Proc Natl Acad Sci U S A 107 (9):4371-4376. doi:10.1073/pnas.0911295107

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  27. Monforte JA, Becker CH (1997) High-throughput DNA analysis by time-of-flight mass spectrometry. Nat Med 3 (3):360-362

    Article  CAS  PubMed  Google Scholar 

  28. Howard R, Encheva V, Thomson J, Bache K, Chan YT et al. (2013) Comparative analysis of human mitochondrial DNA from World War I bone samples by DNA sequencing and ESI-TOF mass spectrometry. Forensic Sci Int Genet 7 (1):1-9. doi:10.1016/j.fsigen.2011.05.009

    Article  CAS  PubMed  Google Scholar 

  29. Greenleaf WJ, Block SM (2006) Single-molecule, motion-based DNA sequencing using RNA polymerase. Science 313 (5788):801. doi:313/5788/801

    Google Scholar 

  30. Pareek CS, Smoczynski R, Tretyn A (2011) Sequencing technologies and genome sequencing. J Appl Genet 52 (4):413-435. doi:10.1007/s13353-011-0057-x

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  31. Fujimori S, Hirai N, Ohashi H, Masuoka K, Nishikimi A et al. (2012) Next-generation sequencing coupled with a cell-free display technology for high-throughput production of reliable interactome data. Sci Rep 2:691. doi:10.1038/srep00691

    Article  PubMed Central  PubMed  Google Scholar 

  32. Chen YJ, Roller EE, Huang X (2010) DNA sequencing by denaturation: experimental proof of concept with an integrated fluidic device. Lab Chip 10 (9):1153-1159. doi:10.1039/b921417h

    Article  PubMed Central  PubMed  Google Scholar 

  33. Gurevich A, Saveliev V, Vyahhi N, Tesler G (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics 29 (8):1072-1075. doi:10.1093/bioinformatics/btt086

    Article  CAS  PubMed Central  PubMed  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Computer Science, Mansoura University, Mansoura, Egypt

    Sara El-Metwally & Osama M. Ouda

  2. Department of Information Technology, Michigan State University (MSU), East Lansing, MI, USA

    Osama M. Ouda

  3. Botany Department and Biotechnology Department, Al-Azhar University, Cairo, Egypt

    Mohamed Helmy

  4. The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto (UofT), Toronto, Canada

    Mohamed Helmy

Authors
  1. Sara El-Metwally
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  2. Osama M. Ouda
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  3. Mohamed Helmy
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El-Metwally, S., Ouda, O.M., Helmy, M. (2014). New Horizons in Next-Generation Sequencing. In: Next Generation Sequencing Technologies and Challenges in Sequence Assembly. SpringerBriefs in Systems Biology, vol 7. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-0715-1_6

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