Next Generation Sequencing: an Emerging Bioinformatics Field
DOI:
https://doi.org/10.26438/ijcse/v5i12.130134Keywords:
Next generation sequencing, Roche, Illumina, SOLiD, SangerAbstract
DNA sequences are the store house of all the biological information. DNA sequencing focuses on determining the exact order of the nucleotides in a DNA sequence. Many research efforts have been put to the development of cheaper and increasingly higher-throughput sequencing techniques. This lead to development of a massively parallel and efficient method called as Next Generation Sequencing (NGS). The massively parallel NGS technologies have a high throughput with reduced cost. This paper gives a brief working principle of sequencer such as Roche 454 (GS FLX Titanium/GS Junior), Illumina (Genome Analyzer/HiSeq 2000/MiSeq) and Life Technologies (SOLiD/Ion Torrent PGM) along with a their comparison.
References
[1] A. Jiwan and S. Singh, “A review on RNA pseudoknot structure prediction techniques,” in 2012 International Conference on Computing, Electronics and Electrical Technologies (ICCEET). IEEE, 2012, pp. 975–978.
[2] R. Garc´ıa, “Prediction of RNA pseudoknotted secondary structure using Stochastic Context Free Grammars (SCFG),” CLEI Electronic Journal, vol. 9, no. 2, 2006.
[3] Y. Tateno, T. Imanishi, S. Miyazaki, K. Fukami-Kobayashi, N. Saitou,
H. Sugawara, and T. Gojobori, “DNA Data Bank of Japan (DDBJ) for genome scale research in life science,” Nucleic Acids Res, vol. 30, no. 1, pp. 27–30, 2002.
[4] G. H. Hamm and G. N. Cameron, “The EMBL data library,” Nucleic Acids Res, vol. 14, no. 1, pp. 5–9, 1986.
[5] C. Kanz, P. Aldebert, N. Althorpe, W. Baker, A. Baldwin, K. Bates,
P. Browne, A. van den Broek, M. Castro, G. Cochrane et al., “The EMBL nucleotide sequence database,” Nucleic Acids Res, vol. 33, no. suppl 1, pp. D29–D33, 2005.
[6] D. A. Benson, M. Cavanaugh, K. Clark, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and E. W. Sayers, “Genbank,” Nucleic Acids Res, vol. 41, no. D1, pp. D36–D42, 2013.
[7] P. D. Stenson, E. V. Ball, M. Mort, A. D. Phillips, J. A. Shiel, N. S. Thomas, S. Abeysinghe, M. Krawczak, and D. N. Cooper, “Human gene mutation database (HGMD R ): 2003 update,” Hum Mutat, vol. 21, no. 6, pp. 577–581, 2003.
[8] M. Cariaso and G. Lennon, “SNPedia: a wiki supporting personal genome annotation, interpretation and analysis,” Nucleic Acids Res, vol. 40, no. D1, pp. D1308–D1312, 2012.
[9] U. Consortium et al., “Reorganizing the protein space at the Universal Protein Resource (UniProt),” Nucleic Acids Res, p. gkr981, 2011.
[10] C. H. Wu, L.-S. L. Yeh, H. Huang, L. Arminski, J. Castro-Alvear,
Y. Chen, Z. Hu, P. Kourtesis, R. S. Ledley, B. E. Suzek et al., “The protein information resource,” Nucleic Acids Res, vol. 31, no. 1, pp. 345–347, 2003.
[11] H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat,
H. Weissig, I. N. Shindyalov, and P. E. Bourne, “The protein data bank,” Nucleic Acids Res, vol. 28, no. 1, pp. 235–242, 2000.
[12] A. Andreeva, D. Howorth, S. E. Brenner, T. J. Hubbard, C. Chothia, and
A. G. Murzin, “SCOP database in 2004: refinements integrate structure and sequence family data,” Nucleic Acids Res, vol. 32, no. suppl 1, pp. D226–D229, 2004.
[13] S. Griffiths-Jones, A. Bateman, M. Marshall, A. Khanna, and S. R. Eddy, “Rfam: an RNA family database,” Nucleic Acids Res, vol. 31, no. 1, pp. 439–441, 2003.
[14] T. Weirick, D. John, S. Dimmeler, and S. Uchida, “C-It-Loci: a knowl-edge database for tissue-enriched loci,” Bioinformatics, p. btv410, 2015.
[14] G. D. Bader, D. Betel, and C. W. Hogue, “BIND: the biomolecular interaction network database,” Nucleic Acids Res, vol. 31, no. 1, pp. 248–250, 2003.
[15] C. Stark, B.-J. Breitkreutz, T. Reguly, L. Boucher, A. Breitkreutz, and
M. Tyers, “BioGRID: a general repository for interaction datasets,” Nucleic Acids Res, vol. 34, no. suppl 1, pp. D535–D539, 2006.
[16] H. Parkinson, M. Kapushesky, M. Shojatalab, N. Abeygunawardena,
R. Coulson, A. Farne, E. Holloway, N. Kolesnykov, P. Lilja, M. Lukk et al., “ArrayExpressa public database of microarray experiments and gene expression profiles,” Nucleic Acids Res, vol. 35, no. suppl 1, pp. D747–D750, 2007.
[18] T. Barrett, D. B. Troup, S. E. Wilhite, P. Ledoux, D. Rudnev, C. Evan-gelista, I. F. Kim, A. Soboleva, M. Tomashevsky, and R. Edgar, “NCBI GEO: mining tens of millions of expression profilesdatabase and tools update,” Nucleic Acids Res, vol. 35, no. suppl 1, pp. D760–D765, 2007.
[19] R. Backofen and D. Gilbert, “Bioinformatics and constraints,” CSTR, vol. 6, no. 2-3, pp. 141–156, 2001.
[20] N. M. Luscombe, D. Greenbaum, and M. Gerstein, “What is bioinfor-matics? an introduction and overview,” Yearb Med Inform, vol. 1, pp. 83–99, 2001.
[21] M. V. Schneider, J. Watson, T. Attwood, K. Rother, A. Budd, J. Mc-Dowall, A. Via, P. Fernandes, T. Nyronen, T. Blicher et al., “Bioin-formatics training: a review of challenges, actions and support require-ments,” Briefings in bioinformatics, p. bbq021, 2010.
[22] M. J. Munoz and D. L. Riddle, “Positive selection of caenorhabditis el-egans mutants with increased stress resistance and longevity,” Genetics, vol. 163, no. 1, pp. 171–180, 2003.
[23] M. P. Sawicki, G. Samara, M. Hurwitz, and E. Passaro, “Human genome project,” Am J Surg, vol. 165, no. 2, pp. 258–264, 1993.
[24] M. Fedurco, A. Romieu, S. Williams, I. Lawrence, and G. Turcatti, “BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies,” Nucleic Acids Res, vol. 34, no. 3, p. e22, 2006.
[25] KA Wetterstrand, “DNA Sequencing Costs: Data from the NHGRI Genome Sequencing Program (GSP)” National Human Genome Research Institute the cost of sequencing a human genome, 2016.
[26] M. Ronaghi, S. Karamohamed, B. Pettersson, M. Uhlen,´ and P. Nyren,´ “Real-time DNA sequencing using detection of pyrophosphate release,” Anal. Biochem., vol. 242, no. 1, pp. 84–89, 1996.
[27] J. M. Heather, and B. Chain, “The sequence of sequencers: the history of sequencing DNA,” Genomics, vol. 107.1, pp. 1-8, 2016.
[28] G. Turcatti, A. Romieu, M. Fedurco, and A.-P. Tairi, “A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis,” Nucleic Acids Res, vol. 36, no. 4, p. e25, 2008.
[29] C. Adessi, G. Matton, G. Ayala, G. Turcatti, J.-J. Mermod, P. Mayer, and E. Kawashima, “Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms,” Nucleic Acids Res, vol. 28, no. 20, p. e87, 2000.
[30] J. Shendure, G. J. Porreca, N. B. Reppas, X. Lin, J. P. McCutcheon,
A. M. Rosenbaum, M. D. Wang, K. Zhang, R. D. Mitra, and G. M. Church, “Accurate multiplex polony sequencing of an evolved bacterial genome,” Science, vol. 309, no. 5741, pp. 1728–1732, 2005.
[31] K. McKernan, A. Blanchard, L. Kotler, and G. Costa, “Reagents, methods, and libraries for bead-based sequencing,” Feb. 1 2006.
[32] S. Myllykangas , J. Buenrostro , and H. P. Ji “Bioinformatics for High Throughput Sequencing”, Springer, pp 255, 2012 .
[33] S. Pabinger, A. Dander, M. Fischer, R. Snajder, M. Sperk, M. Efremova,
B. Krabichler, M. R. Speicher, J. Zschocke, and Z. Trajanoski, “A survey of tools for variant analysis of next-generation genome sequencing data,” Briefings Bioinf., vol. 15, no. 2, pp. 256–278, 2014.
[34] R. Bao, L. Huang, J. Andrade, W. Tan, W. A. Kibbe, H. Jiang, and
G. Feng, “Review of current methods, applications, and data man-agement for the bioinformatics analysis of whole exome sequencing,” Cancer Inform, pp. 67–83, 2014.
Downloads
Published
How to Cite
Issue
Section
License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Authors contributing to this journal agree to publish their articles under the Creative Commons Attribution 4.0 International License, allowing third parties to share their work (copy, distribute, transmit) and to adapt it, under the condition that the authors are given credit and that in the event of reuse or distribution, the terms of this license are made clear.
