High Throughput Sequencing: An Overview of Sequencing Chemistry

Indian Journal of Microbiology

Volumn 56, Issue 4, 2016, Pages 394-404

  Ambardar, Sheetal ^a,c,d   Gupta, Rikita ^a   Trakroo, Deepika ^a   Lal, Rup ^b   Vakhlu, Jyoti ^a  

^a UNIVERSITY OF JAMMU   (India)

^b UNIVERSITY OF DELHI   (India)

^c TATA INSTITUTE OF FUNDAMENTAL RESEARCH   (India)

^d Trans Disciplinary University   (India)

Author keywords

High throughput sequencing; NGS; Second generation sequencing; Sequencing platforms; Third generation sequencing

Indexed keywords

EID: 84978117026     PISSN: 00468991     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12088-016-0606-4     Document Type: Review

References (46)

1. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. PNAS 74:5463–5467. doi:10.1073/pnas.74.12.5463
2. Maxam AM, Gilbert W (1977) A new method for sequencing DNA. PNAS 74:560–564. doi:10.1073/pnas.74.2.560
3. 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 IlluminaMiSeq sequencers. BMC Genom 13:13. doi:10.1186/1471-2164-13-341
4. Metzker ML (2005) Emerging technologies in DNA sequencing. Genome Res 15:1767–1776. doi:10.1101/gr.3770505
5. Metzker ML (2009) Sequencing technologies: the next generation. Nat Rev Genet 11:31–46. doi:10.1038/nrg2626
6. Scholz MB, Lo CC, Chain PSG (2012) Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr Opin Biotechnol 23:9–15. doi:10.1016/j.copbio.2011.11.013
7. Marzorati M, Maignien L, Verhelst A, Luta G, Sinnott R, Kerckhof FM, Possemiers S (2013) Barcoded pyrosequencing analysis of the microbial community in a simulator of the human gastrointestinal tract showed a colon region-specific microbiota modulation for two plant-derived polysaccharide blends. Antonie Van Leeuwenhoek 103:409–420. doi:10.1007/s10482-012-9821-0
8. Patel RK, Jain M (2012) NGS QC toolkit: a toolkit for quality control of next generation sequencing data. PLoS ONE 7:e30619. doi:10.1371/journal.pone.0030619
9. Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, Knight R (2012) Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J 6:1007–1017. doi:10.1038/ismej.2011.159
10. Caruccio N (2011) Preparation of next-generation sequencing libraries using Nextera™ technology: simultaneous DNA fragmentation and adaptor tagging by in vitro transposition. Method Mol Biol 733:241–255. doi:10.1007/978-1-61779-089-8_17
11. Knierim E, Lucke B, Schwarz JM, Schuelke M, Seelow D (2011) Systematic comparison of three methods for fragmentation of long-range PCR products for next generation sequencing. PLoS ONE 6:e28240. doi:10.1371/journal.pone.0028240
12. Parkinson NJ, Maslau S, Ferneyhough B, Zhang G, Gregory L, Buck D, Ragoussis J, Ponting CP, Fischer MD (2012) Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA. Genome Res 22:125–133. doi:10.1101/gr.124016.111
13. Hingamp P, Grimsley N, Acinas SG, Clerissi C, Subirana L et al (2013) Exploring nucleo-cytoplasmic large DNA viruses inTara Oceans microbial metagenomes. ISME Journal 7:1678–1695. doi:10.1038/ismej.2013.59
14. Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, Chisholm SW et al (2008) Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci USA 105:3805–3810. doi:10.1073/pnas.0708897105
15. Shi Y, Tyson GW, Eppley JM, DeLong EF (2011) Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. ISME J 5:999–1013. doi:10.1038/ismej.2010.189
16. Lesniewski RA, Jain S, Anantharaman K, Schloss PD, Dick GJ (2012) The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs. ISME J 6:2257–2268. doi:10.1038/ismej.2012.63
17. Shao K, Ding W, Wang F, Li H, Ma D, Wang H (2011) Emulsion PCR: a High Efficient Way of PCR Amplification of Random DNA Libraries in Aptamer Selection. PLoS ONE 6:e24910. doi:10.1371/journal.pone.0024910
18. Kawashima Eric H, Laurent Farinelli; Pascal Mayer (2005-05-12). ”Patent: Method of nucleic acid amplification”. Retrieved 2012-12-22
19. Fakruddin M, Chowdhury A, Hossain M, Mannan KSB, Mazumdar RM (2012) Pyrosequencing-principles and applications. Life 50:65
20. Berglund EC, Kiialainen A, Syvänen AC (2011) Next-generation sequencing technologies and applications for human genetic history and forensics. Investig Genet 2:23. doi:10.1186/2041-2223-2-23
21. Chen Y, Sonnaert M, Roberts SJ, Luyten FP, Schrooten J (2012) Tissue engineering part C. Methods 18:444–452. doi:10.1089/ten.tec.2011.0304
22. Reuter JA, Spacek DV, Snyder MP (2015) High-Throughput Sequencing Technologies. Mol Cell 58:586–597. doi:10.1016/j.molcel.2015.05.004
23. http://www.illumina.com/technology/next-generation-sequencing/paired-end-sequencing_assay.html
24. Dijk EL, Auger H, Jaszczyszyn Y, Thermes C (2014) Ten years of next-generation sequencing technology. Trends Genetics 30:418–426. doi:10.1016/j.tig.2014.07.001
25. Eisenstein M (2015) Startups use short-read data to expand long-read sequencing market. Nat Biotechnol 33:433–435. doi:10.1038/nbt0515-433
26. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B et al (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133–138. doi:10.1126/science.1162986
27. Mascher M, Amand PS, Stein N, Poland J (2013) Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. PLoS ONE 8:e76925. doi:10.1371/journal.pone.0076925
28. Meldrum C, Doyle MR, Tothill RW (2011) Next-Generation Sequencing for Cancer Diagnostics: a Practical Perspective. Clin Biochem Rev 32:177–195. PMCID: PMC3219767
29. Veras AAO, de Sál PHCG, Pinheiro KC, das Graças DA, Baraúna RA, Schneider MPC, Azevedo V, Ramos RTJ, Silva A (2014) Efficiency of Corynebacterium pseudotuberculosis 31 Genome Assembly with the Hi-Q Enzyme on an Ion Torrent PGM Sequencing Platform. J Proteomics Bioinform 7:12. doi:10.4172/jpb.1000342
30. Liu L, Li Y, Li S et al (2012) Comparison of next-generation sequencing systems. J Biomed Biotechnol vol. 2012, Article ID 251364, 11 pages, 2012. doi:10.1155/2012/251364
31. Schadt EE, Turner S, Kasarskis Andrew (2010) A window into third-generation sequencing. Hum Mol Genet 2010:R227–R240. doi:10.1093/hmg/ddq416
32. Rusk N (2009) Cheap third-generation sequencing. Nat Methods 6:244. doi:10.1038/nmeth0409-244a
33. Mardis ER (2013) Next-generation sequencing platforms. Annu Rev Anal Chem 6:287–303. doi:10.1146/annurev-anchem-062012-092628
34. Harris TD, Buzby PR, Babcock H et al (2008) Single-molecule DNA sequencing of a viral genome. Science 320:106–109. doi:10.1126/science.1150427
35. Hart C, Lipson D, Ozsolak F, Raz T, Steinmann K, Thompson J, Milos PM (2010) Single molecule sequencing:sequence method to enable accurate quantitation. Methods Enzymol 472:407–430. doi:10.1016/S0076-6879(10)72002-4
36. Hayden EC (2012) Nanopore genome sequencer makes its debut. Nature. doi:10.1038/nature.2012.10051
37. Jain M, Fiddes IT, Miga KH, Olsen HE, Paten B, Akesen M (2015) Improved data analysis for the MinION nanopore sequencer. Nat Methods 12:351–356. doi:10.1038/nmeth.3290
38. Miles BN, Ivanov AP, Wilson KA, Doğan F, Japrung D, Edel JB (2013) Single molecule sensing with solid-state nanopores: novel materials, methods, and applications. Chem Soc Rev 42:15–28. doi:10.1039/c2cs35286a
39. Laver T, Harrison J, O’Neill PA, Moore K, Farbos A, Paszkiewicz K, Studholme DJ (2015) Assessing the performance of the Oxford Nanopore Technologies MinION. Biomol Detect Quantif 3:1–8. doi:10.1016/j.bdq.2015.02.001
40. http://nextgenseek.com/2012/07/complete-genomics-new-technology-to-produce-accurate-sequencing-with-small-amount-of-dna/
41. Basu A, Macosko E, Shalek A, McCarroll S, Regev A, and Weitz D (2014) Single-cell genomics using droplet-based microfuidics. Bull Am Phys Soc: APS March Meeting 2014 59:3–7, Denver, Colorado
42. Erlich Y (2015) A vision for ubiquitous sequencing. BioRxiv. doi:10.1101/019018
43. Rieber N, Zapatka M, Lasitschka B, Jones D, Northcott P, Hutter B et al (2013) Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies. PLoS ONE 8:e66621. doi:10.1371/journal.pone.0066621
44. Patnaik BB, Park SY, Kang SW, Hwang H-J, Wang TH, Park EB et al (2016) Transcriptome Profile of the Asian Giant Hornet (Vespa mandarinia) Using Illumina HiSeq 4000 Sequencing: De Novo Assembly, Functional Annotation, and Discovery of SSR Markers. Int J Genomics, 2016:4169587. http://doi.org/10.1155/2016/4169587
45. Rosenberg AZ, Armani MD, Fetsch PA, Xi L, Pham TT, Raffeld M et al (2016). High-Throughput Microdissection for Next-Generation Sequencing. PLoS ONE 11:e0151775. http://doi.org/10.1371/journal.pone.0151775
46. Yu P, Lin W (2016). Single-cell transcriptome study as big data. Genomics Proteomics Bioinf 14:21–30. http://doi.org/10.1016/j.gpb.2016.01.005