Abstract
It has been more than 35 years since the development of the groundbreaking method for DNA sequencing by Frederick Sanger and colleagues. This revolutionary study triggered the improvement of new methods that have provided great opportunities for low-cost and fast DNA sequencing. Strikingly after the Human Genome Project, the time interval between each sequencing technology started decreasing while amount of scientific knowledge has continued growing exponentially. Considering Sanger sequencing as the first generation, new generations of DNA sequencing have been introduced consequently. The development of the next-generation sequencing (NGS) technologies has contributed to this trend substantially by reducing costs and producing massive sequencing data. Hitherto, four sequencing generations have been defined. Second-generation sequencing that is currently the most commonly used NGS technology consists of library preparation, amplification, and sequencing steps while in third-generation sequencing, individual nucleic acids are sequenced directly in order to avoid biases and have higher throughput. Recently described fourth-generation sequencing aims conducting genomic analysis directly in the cell. Classified to different generations, NGS has led to overcome the limitations of conventional DNA sequencing methods and has found usage in a wide range of molecular biology applications. On the other hand, plenty of technical challenges, which need to be deeply analyzed and solved, emerged with these technologies. Every sequencing generation and platform, by reason of its methodological approach, carries characteristic advantages and disadvantages which determine the fitness for certain applications. Thus, assessment of these features, limitations, and potential applications help shaping the studies that will determine the route of omic technologies.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Adessi C, Matton G, Ayala G, Turcatti G, Mermod JJ, Mayer P, Kawashima E (2000) Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms. Nucleic Acids Res 28(20):e87
Bahassi EM, Stambrook PJ (2014) Next-generation sequencing technologies: breaking the sound barrier of human genetics. Mutagenesis 29(5):303–310
Bao S, Jiang R, Kwan W, Wang B, Ma X, Song YQ (2011) Evaluation of next-generation sequencing software in mapping and assembly. J Hum Genet 56:406–414
Beck S, O’Keeffe T, Coull JM, Köster H (1989) Chemiluminescent detection of DNA: application for DNA sequencing and hybridization. Nucleic Acids Res 17(13):5115–5123
Bennett S (2004) Solexa Ltd. Pharmacogenomics 5:433–438
Bennett ST, Barnes C, Cox A, Davies L, Brown C (2005) Toward the 1,000 dollars human genome. Pharmacogenomics 6:373–382
Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E, Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O’Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59
Biggin MD, Gibson TJ, Hong GF (1983) Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination. Proc Natl Acad Sci U S A 80(13):3963–3965
Bowers J, Mitchell J, Beer E, Buzby PR, Causey M, Efcavitch JW, Jarosz M, Krzymanska-Olejnik E, Kung L, Lipson D, Lowman GM, Marappan S, McInerney P, Platt A, Roy A, Siddiqi SM, Steinmann K, Thompson JF (2009) Virtual terminator nucleotides for next-generation DNA sequencing. Nat Methods 6(8):593–595
Buermans HPJ, den Dunnen JT (2014) Next generation sequencing technology: advances and applications. Biochim Biophys Acta 1842(10):1932–1941
Chen EY (1994) The efficiency of automated DNA sequencing. In: Adams MD, Fields C, Venter JC (eds) Automated DNA sequencing and analysis. Academic, San Diego, pp 3–9
Chen CY (2014) DNA polymerases drive DNA sequencing-by-synthesis technologies: both past and present. Front Microbiol 5:305
Chen F, Dong M, Ge M, Zhu L, Ren L, Liu G, Mu R (2013) The history and advances of reversible terminators used in new generations of sequencing technology. Genomics Proteomics Bioinformatics 11(1):34–40
Crick FHC (1958) On protein synthesis. Symp Soc Exp Biol 7:138–163
Derrington IM, Butler TZ, Collins MD, Manrao E, Pavlenok M, Niederweis M, Gundlach JH (2010) Nanopore DNA sequencing with MspA. Proc Natl Acad Sci U S A 107(37):16060–16065
Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, Dewinter A, Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G, Kong X, Kuse R, Lacroix Y, Lin S, Lundquist P, Ma C, Marks P, Maxham M, Murphy D, Park I, Pham T, Phillips M, Roy J, Sebra R, Shen G, Sorenson J, Tomaney A, Travers K, Trulson M, Vieceli J, Wegener J, Wu D, Yang A, Zaccarin D, Zhao P, Zhong F, Korlach J, Turner S (2009) Real-time DNA sequencing from single polymerase molecules. Science 323(5910):133–138
Fischbein MD, Drndić M (2008) Electron beam nanosculpting of suspended graphene sheets. Appl Phys Lett 93(11):113107
Flanagan JH, Owens CV, Romero SE, Waddell E, Kahn SH, Hammer RP, Soper SA (1998) Near-infrared heavy-atom-modified fluorescent dyes for base-calling in DNA-sequencing applications using temporal discrimination. Anal Chem 70(13):2676–2684
França LT, Carrilho E, Kist TB (2002) A review of DNA sequencing techniques. Q Rev Biophys 35(02):169–200
Gardner AF, Wang J, Wu W, Karouby J, Li H, Stupi BP, Jack WE, Hersh MN, Metzker ML (2012) Rapid incorporation kinetics and improved fidelity of a novel class of 3′-OH unblocked reversible terminators. Nucleic Acids Res 40(15):7404–7415
Goodwin S, Gurtowski J, Ethe-Sayers S, Deshpande P, Schatz M, McCombie WR (2015) Oxford nanopore sequencing and de novo assembly of a eukaryotic genome. Genome Res 25(11):1750–1756
Heng JB, Ho C, Kim T, Timp R, Aksimentiev A, Grinkova YV, Sligar S, Schulten K, Timp G (2004) Sizing DNA using a nanometer-diameter pore. Biophys J 87(4):2905–2911
Huang YF, Chen SC, Chiang YS, Chen TH, Chiu KP (2012) Palindromic sequence impedes sequencing-by-ligation mechanism. BMC Syst Biol 6(Suppl 2):S10
Hui P (2014) Next generation sequencing: chemistry, technology and applications. Top Curr Chem 336:1–18
Hutchison CA (2007) DNA sequencing: bench to bedside and beyond. Nucleic Acids Res 35(18):6227–6237
Jain M, Fiddes IT, Miga KH, Olsen HE, Paten B, Akeson M (2015) Improved data analysis for the MinION nanopore sequencer. Nat Methods. doi:10.1038/nmeth.3290, Epub ahead of print
Kan CW, Fredlake CP, Doherty EA, Barron AE (2004) DNA sequencing and genotyping in miniaturized electrophoresis systems. Electrophoresis 25:3564–3588
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 93:13770–13773
Ke R, Mignardi M, Pacureanu A, Svedlund J, Botling J, Wählby C, Nilsson M (2013) In situ sequencing for RNA analysis in preserved tissue and cells. Nat Methods 10:857–860
Kircher M, Kelso J (2010) High‐throughput DNA sequencing-concepts and limitations. Bioessays 32(6):524–536
Korlach J, Bjornson KP, Chaudhuri BP, Cicero RL, Flusberg BA, Grey JJ, Holden D, Saxena R, Wegener J, Turner SW (2010) Real-time DNA sequencing from single polymerase molecules. Methods Enzymol 472:431–455
Kumar S, Sood A, Wegener J, Finn PJ, Nampalli S, Nelson JR, Sekher A, Mitsis P, Macklin J, Fuller CW (2005) Terminal phosphate labeled nucleotides: synthesis, applications, and linker effect on incorporation by DNA polymerases. Nucleosides Nucleotides Nucleic Acids 24(5–7):401–408
Larkin J, Henley R, Bell DC, Cohen-Karni T, Rosenstein JK, Wanunu M (2013) Slow DNA transport through nanopores in hafnium oxide membranes. ACS Nano 7(11):10121–10128
Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Yang JL, Ferrante TC, Terry R, Jeanty SS, Li C, Amamoto R, Peters DT, Turczyk BM, Marblestone AH, Inverso SA, Bernard A, Mali P, Rios X, Aach J, Church GM (2014) Highly multiplexed subcellular RNA sequencing in situ. Science 343:1360–1363
Li Z, Bai X, Ruparel H, Kim S, Turro NJ, Ju J (2003) A photocleavable fluorescent nucleotide for DNA sequencing and analysis. Proc Natl Acad Sci U S A 100(2):414–419
Li W, Bell NA, Hernandez-Ainsa S, Thacker VV, Thackray AM, Bujdoso R, Keyser UF (2013) Single protein molecule detection by glass nanopores. ACS Nano 7:4129–4134
Litosh VA, Wu W, Stupi BP, Wang J, Morris SE, Hersh MN, Metzker ML (2011) Improved nucleotide selectivity and termination of 30-OH unblocked reversible terminators by molecular tuning of 2-nitrobenzyl alkylated HOMedU triphosphates. Nucleic Acids Res 39:e39
Liu S, Lu B, Zhao Q, Li J, Gao T, Chen Y, Zhang Y, Liu Z, Fan Z, Yang F, You L, Yu D (2013a) Boron nitride nanopores: highly sensitive DNA single-molecule detectors. Adv Mater 25:4549–4554
Liu L, Yang C, Zhao K, Li J, Wu HC (2013b) Ultrashort single-walled carbon nanotubes in a lipid bilayer as a new nanopore sensor. Nat Commun 4:2989
Liu K, Feng J, Kis A, Radenoviç A (2014) Atomically thin molybdenum disulfide nanopores with high sensitivity for DNA translocation. ACS Nano 8:2504–2511
Loman NJ, Quick J, Simpson JT (2015) A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat Methods 12(8):733–735
Luckey JA, Drossman H, Kostichka AJ, Mead DA, D’Cunha J, Norris TB, Smith LM (1990) High speed DNA sequencing by capillary electrophoresis. Nucleic Acids Res 18(15):4417–4421
Mardis ER (2013) Next-generation sequencing platforms. Annu Rev Anal Chem 6:287–303
Metzker ML (2005) Emerging technologies in DNA sequencing. Genome Res 15(12):1767–1776
Metzker ML (2010) Sequencing technologies—the next generation. Nat Rev Genet 11(1):31–46
Mignardi M, Nilsson M (2014) Fourth-generation sequencing in the cell and the clinic. Genome Med 6(4):31
Morey M, Fernández-Marmiesse A, Castiñeiras D, Fraga JM, Couce ML, Cocho JA (2013) A glimpse into past, present, and future DNA sequencing. Mol Genet Metab 110(1–2):3–24
Müller R, Herten DP, Lieberwirth U, Neumann M, Sauer M, Schulz A, Siebert S, Drexhage KH, Wolfrum J (1997) Efficient DNA sequencing with a pulsed semiconductor laser and a new fluorescent dye set. Chem Phys Lett 279(5):282–288
Mullis KB, Faloona FA, Scharf SJ, Saiki RK, Horn GT, Erlich H (1986) Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb Symp Quant Biol 51:263–273
Novais RC, Thorstenson YR (2011) The evolution of Pyrosequencing® for microbiology: from genes to genomes. J Microbiol Methods 86(1):1–7
Nyrén P (2007) The history of pyrosequencing. Methods Mol Biol 373:1–14
Paegel BM, Blazej RG, Mathies RA (2003) Microfluidic devices for DNA sequencing: sample preparation and electrophoretic analysis. Curr Opin Biotechnol 14(1):42–50
Porreca GJ, Shendure J, Church GM (2006) Polony DNA sequencing. In: Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (eds) Current protocols in molecular biology. Greene and John Wiley, New York, pp 1–22, Unit 7.8
Prober JM, Trainor GL, Dam RJ, Hobbs FW, Robertson CW, Zagursky RJ, Cocuzza JA, Jensen MA, Baumeister K (1987) A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. Science 238(4825):336–341
Pushkarev D, Neff NF, Quake SR (2009) Single-molecule sequencing of an individual human genome. Nat Biotechnol 27:847–850
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(1):341
Roberts RJ, Carneiro MO, Schatz MC (2013) The advantages of SMRT sequencing. Genome Biol 14:405
Ronaghi M (2000) Improved performance of pyrosequencing using single stranded DNA-binding protein. Anal Biochem 286:282–288
Ronaghi M, Karamohamed S, Pettersson B, Uhlén M, Nyrén P (1996) Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem 242(1):84–89
Ronaghi M, Uhlén M, Nyrén P (1998) A sequencing method based on real-time pyrophosphate. Science 281(5375):363–365
Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, Hoon J, Simons JF, Marran D, Myers JW, Davidson JF, Branting A, Nobile JR, Puc BP, Light D, Clark TA, Huber M, Branciforte JT, Stoner IB, Cawley SE, Lyons M, Fu Y, Homer N, Sedova M, Miao X, Reed B, Sabina J, Feierstein E, Schorn M, Alanjary M, Dimalanta E, Dressman D, Kasinskas R, Sokolsky T, Fidanza JA, Namsaraev E, McKernan KJ, Williams A, Roth GT, Bustillo J (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475(7356):348–352
Rusk N (2014) Genomics: nanopores read long genomic DNA. Nat Methods 11(9):887
Sanger F (1988) Sequences, sequences, and sequences. Ann Rev Biochem 57:1–28
Sanger F, Coulson A (1975) A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol 94(3):441–448
Sanger F, Tuppy H (1951) The amino-acid sequence in the phenylalanyl chain of insulin. 1. The identification of lower peptides from partial hydrolysates. Biochem J 49(4):463–481
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74(12):5463–5467
Schadt EE, Turner S, Kasarskis A (2010) A window into third-generation sequencing. Hom Mol Genet 19(R2):R227–R240
Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26(10):1135–1145
Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309(5741):1728–1732
Siwy Z, Fuliñski A (2002) Fabrication of a synthetic nanopore ion pump. Phys Rev Lett 89:198103
Smith L, Sanders J, Kaiser R, Hughes P (1986) Fluorescence detection in automated DNA sequence analysis. Nature 321(6071):674–679
Song CX, Clark TA, Lu XY, Kislyuk A, Dai Q, Turner SW, He C, Korlach J (2012) Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine. Nat Methods 9(1):75–77
Soon WW, Hariharen M, Snyder MP (2013) High-throughput sequencing for biology and medicine. Mol Syst Biol 9(640):1–14
Srinivasan S, Batra J (2014) Four generations of sequencing—is it ready for the clinic yet? Next Generat Sequenc Applic 1:107
Stranneheim H, Lundeberg J (2012) Stepping stones in DNA sequencing. Biotechnol J 7(9):1063–1073
Thompson JF, Steinmann KE (2010) Single molecule sequencing with a HeliScope genetic analysis system. Curr Protoc Mol Biol. Chapter 7, Unit 7.10
Wang Y, Yang Q, Wang Z (2014) The evolution of nanopore sequencing. Frontiers Genet 5:449
Watson JD, Crick F (1953) A structure for deoxyribonucleic acid. Nature 171:737–738
Watts D, MacBeath J (2001) Automated fluorescent DNA sequencing on the ABI PRISM 310 genetic analyzer. Meth Mol Biol 167:153–170
Wetterstrand KA (2014) DNA sequencing costs: data from the NHGRI genome sequencing program (GSP).www.genome.gov/sequencingcosts. Accessed Dec 2014
Wiemann S, Schilke A, Rechmann S, Zimmermann J, Voss H, Ansorge W (1996) Reducing “double sequences” in automated DNA sequencing with T7 DNA polymerase and internal labeling. Biotechniques 20(5):791–792
Wu R, Kaiser AD (1968) Structure and base sequence in the cohesive ends of bacteriophage lambda DNA. J Mol Biol 35(3):523–537
Wu W, Stupi BP, Litosh VA, Mansouri D, Farley D, Morris S, Mtezker S, Metzker ML (2007) Termination of DNA synthesis by N6-alkylated, not 3′-O-alkylated, photocleavable 2′-deoxyadenosine triphosphates. Nucleic Acids Res 35:6339–6349
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Ari, Ş., Arikan, M. (2016). Next-Generation Sequencing: Advantages, Disadvantages, and Future. In: Hakeem, K., Tombuloğlu, H., Tombuloğlu, G. (eds) Plant Omics: Trends and Applications. Springer, Cham. https://doi.org/10.1007/978-3-319-31703-8_5
Download citation
DOI: https://doi.org/10.1007/978-3-319-31703-8_5
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-31701-4
Online ISBN: 978-3-319-31703-8
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)