Abstract
DNA referred to as blueprint of life codes for the diversity and function of all the living organisms. Determining DNA sequences of the living organisms not only gives an overview of their genetic makeup, but also provides information about their function. Nonetheless it was not easy to determine the genome sequencing of all the diversity around us especially with the technologies available before 2010. Therefore, determining the sequence of humans and some other organisms only was prioritized. Pioneering methods for DNA sequencing given discovered by Maxam and Gilbert, and Sanger although were very powerful and popular but were not high throughput and economic. Therefore, it was necessary to develop new economic and high-throughput methods that can sequence the biodiversity consequently providing better insights of their possible function. New methods were developed and commercialized by Roche Life Sciences, Thermo Fisher Scientific, Illumina, and Applied Biosystems. These methods generally referred to as next-generation sequencing methods have revolutionized the DNA sequencing. Many sequencing platforms employing NGS have been developed including pyrosequencing, Ion Torrent technology, Illumina/Solexa platform, and SOLiD (Sequencing by Oligonucleotide Ligation and Detection). Further optimization has led to innovative third and fourth-generation platforms as single molecule real-time (SMRT) sequencing by PacBio, nanopore sequencing, etc. As a consequence there is a sharp increase in the number of genomes being published and other genome-based studies since 2012. This has made it easy even to imagine of sequencing the genomes of individuals. Furthermore, scientists are now looking for third-generation sequencers that may be significantly different from the sequencers that are currently available.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Abernathy J, Overturf K (2016) Comparison of ribosomal RNA removal methods for transcriptome sequencing workflows in teleost fish. Anim Biotechnol 27(1):60–65. https://doi.org/10.1080/10495398.2015.1086365
Adelson ME, Feola M, Trama J, Tilton RC, Mordechai E (2005) Simultaneous detection of herpes simplex virus types 1 and 2 by real-time PCR and pyrosequencing. J Clin Virol 33(1):25–34
Adessi C, Matton G, Ayala G, Turcatti G, Mermod J-J, Mayer P, Kawashima E (2000) Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms. Nucleic Acids Res 28(20):e87
Ahmadian A, Gharizadeh B, Gustafsson AC, Sterky F, Nyrén P, Uhlén M, Lundeberg J (2000) Single-nucleotide polymorphism analysis by pyrosequencing. Anal Biochem 280(1):103–110
Alic AS, Ruzafa D, Dopazo J, Blanquer I (2016) Objective review of de novo stand-alone error correction methods for NGS data. Wiley Interdisc Rev Comput Mol Sci 6(2):111–146
Allie F, Pierce EJ, Okoniewski MJ, Rey C (2014) Transcriptional analysis of South African cassava mosaic virus-infected susceptible and tolerant landraces of cassava highlights differences in resistance, basal defense and cell wall associated genes during infection. BMC Genomics 15:1006. https://doi.org/10.1186/1471-2164-15-1006
AppliedBiosystems (2008) The SOLID generation delivers. Retrieved from http://www.columbia.edu/cu/biology/courses/w3034/Dan/readings/SOLiD_System_Brochure.pdf
Ari S, Arıkan M (2016) Next-generation sequencing: advantages, disadvantages, and future. In: Plant omics: trends and applications. Springer, Cham, pp 109–135. https://doi.org/10.1007/978-3-319-31703-8_5
Avery OT, Macleod CM, McCarty M (1944) Studies on the chemical nature of the substance inducing transformation of pneumococcal types: induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type iii. J Exp Med 79(2):137–158
Balasubramanian S (2015) Solexa sequencing: decoding genomes on a population scale. Clin Chem 61(1):21–24
Bao S, Jiang R, Kwan W, Wang B, Ma X, Song Y-Q (2011) Evaluation of next-generation sequencing software in mapping and assembly. J Hum Genet 56(6):406
Barozzi I, Termanini A, Minucci S, Natoli G (2011) Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data. Biol Direct 6:51. https://doi.org/10.1186/1745-6150-6-51
Bennett S (2004) Solexa ltd. Pharmacogenomics 5(4):433–438
Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG et al (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456(7218):53–59. https://doi.org/10.1038/nature07517
Bhan B, Koul A, Sharma D, Manzoor MM, Kaul S, Gupta S, Dhar MK (2019) Identification and expression profiling of miRNAs in two color variants of carrot (Daucus carota L.) using deep sequencing. PLoS One 14(3):e0212746. https://doi.org/10.1371/journal.pone.0212746
Braukmann TWA, Ivanova NV, Prosser SWJ, Elbrecht V, Steinke D, Ratnasingham S et al (2019) Metabarcoding a diverse arthropod mock community. Mol Ecol Resour. https://doi.org/10.1111/1755-0998.13008
Buermans HPJ, Den Dunnen JT (2014) Next generation sequencing technology: advances and applications. Biochim Biophys Acta 1842(10):1932–1941
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
Chi AS, Batchelor TT, Dias-Santagata D, Borger D, Stiles CD, Wang DL et al (2012) Prospective, high-throughput molecular profiling of human gliomas. J Neuro-Oncol 110(1):89–98. https://doi.org/10.1007/s11060-012-0938-9
Choudhuri S (2014) Bioinformatics for beginners: genes, genomes, molecular evolution, databases and analytical tools. Elsevier
Cross I, Merlo MA, Rodriguez ME, Portela-Bens S, Rebordinos L (2014) Adaptation to abiotic stress in the oyster Crassostrea angulata relays on genetic polymorphisms. Fish Shellfish Immunol 41(2):618–624. https://doi.org/10.1016/j.fsi.2014.10.011
Cui L, Rui C, Yang D, Wang Z, Yuan H (2017) De novo transcriptome and expression profile analyses of the Asian corn borer (Ostrinia furnacalis) reveals relevant flubendiamide response genes. BMC Genomics 18(1):20. https://doi.org/10.1186/s12864-016-3431-6
Dohm JC, Lottaz C, Borodina T, Himmelbauer H (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 36(16):e105
Elahi E, Pourmand N, Chaung R, Rofoogaran A, Boisver J, Samimi-Rad K et al (2003) Determination of hepatitis C virus genotype by pyrosequencing. J Virol Methods 109(2):171–176
Elert-Dobkowska E, Stepniak I, Krysa W, Ziora-Jakutowicz K, Rakowicz M, Sobanska A et al (2019) Next-generation sequencing study reveals the broader variant spectrum of hereditary spastic paraplegia and related phenotypes. Neurogenetics. https://doi.org/10.1007/s10048-019-00565-6
Fakruddin M, Chowdhury A, Hossain MN, Mannan KS, Mazumda RM (2012) Pyrosequencing-principles and applications. Int J Life Sci Pharma Res 2:65–76
Forin-Wiart M-A, Poulle M-L, Piry S, Cosson J-F, Larose C, Galan M (2018) Evaluating metabarcoding to analyse diet composition of species foraging in anthropogenic landscapes using ion torrent and Illumina sequencing. Sci Rep 8(1):17091. https://doi.org/10.1038/s41598-018-34430-7
Fujimoto M, Moyerbrailean GA, Noman S, Gizicki JP, Ram ML, Green PA, Ram JL (2014) Application of ion torrent sequencing to the assessment of the effect of alkali ballast water treatment on microbial community diversity. PLoS One 9(9):1–9. https://doi.org/10.1371/journal.pone.0107534
Fujita S, Masago K, Okuda C, Hata A, Kaji R, Katakami N, Hirata Y (2017) Single nucleotide variant sequencing errors in whole exome sequencing using the ion proton system. Biomedical Reports 7(1):17–20. https://doi.org/10.3892/br.2017.911
Gharizadeh B (2003) Method development and applications of Pyrosequencing technology. Bioteknologi
Gharizadeh B, Kalantari M, Garcia CA, Johansson B, Nyrén P (2001) Typing of human papillomavirus by pyrosequencing. Lab Investig 81(5):673
Gharizadeh B, Käller M, Nyrén P, Andersson A, Uhlén M, Lundeberg J, Ahmadian A (2003) Viral and microbial genotyping by a combination of multiplex competitive hybridization and specific extension followed by hybridization to generic tag arrays. Nucleic Acids Res 31(22):e146
Gharizadeh B, Oggionni M, Zheng B, Akom E, Pourmand N, Ahmadian A et al (2005) Type-specific multiple sequencing primers: a novel strategy for reliable and rapid genotyping of human papillomaviruses by pyrosequencing technology. J Mol Diagn 7(2):198–205
Gharizadeh B, Ghaderi M, Nyrén P (2007) Pyrosequencing technology for short DNA sequencing and whole genome sequencing. Seibutsu Butsuri 47:129. https://doi.org/10.2142/biophys.47.129
Goodwin S, McPherson JD, McCombie WR (2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17(6):333
Gooneratne SL, Alinejad-Rokny H, Ebrahimi D, Bohn PS, Wiseman RW, O’Connor DH et al (2014) Linking pig-tailed macaque major histocompatibility complex class I haplotypes and cytotoxic T lymphocyte escape mutations in simian immunodeficiency virus infection. J Virol 88(24):14310–14325
Gorski MM, Lecchi A, Femia EA, La Marca S, Cairo A, Pappalardo E et al (2019) Complications of whole-exome sequencing for causal gene discovery in primary platelet secretion defects. Haematologica. https://doi.org/10.3324/haematol.2018.204990
Grahn N, Olofsson M, Ellnebo-Svedlund K, Monstein H-J, Jonasson J (2003) Identification of mixed bacterial DNA contamination in broad-range PCR amplification of 16S rDNA V1 and V3 variable regions by pyrosequencing of cloned amplicons. FEMS Microbiol Lett 219(1):87–91
Gu S, Lin S, Ye D, Qian S, Jiang D, Zhang X et al (2019) Genome-wide methylation profiling identified novel differentially hypermethylated biomarker MPPED2 in colorectal cancer. Clin Epigenetics 11(1):41. https://doi.org/10.1186/s13148-019-0628-y
Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, Beeson KY et al (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol 10(3):R32. https://doi.org/10.1186/gb-2009-10-3-r32
Harlid S, Xu Z, Kirk E, Wilson LE, Troester MA, Taylor JA (2019) Hormone therapy use and breast tissue DNA methylation: analysis of epigenome wide data from the normal breast study. Epigenetics:1–12. https://doi.org/10.1080/15592294.2019.1580111
Hearn NL, Coleman AS, Ho V, Chiu CL, Lind JM (2019) Comparing DNA methylation profiles in saliva and intestinal mucosa. BMC Genomics 20(1):163. https://doi.org/10.1186/s12864-019-5553-0
Hedges DJ, Guettouche T, Yang S, Bademci G, Diaz A, Andersen A et al (2011) Comparison of three targeted enrichment strategies on the SOLiD sequencing platform. PLoS One 6(4):e18595. https://doi.org/10.1371/journal.pone.0018595
Heo Y (2015) Improving quality of high-throughput sequencing reads. University of Illinois at Urbana-Champaign
Ho A, Murphy M, Wilson S, Atlas SR, Edwards JS (2011) Sequencing by ligation variation with endonuclease V digestion and deoxyinosine-containing query oligonucleotides. BMC Genomics 12(1):598
Hodzic J, Gurbeta L, Omanovic-Miklicanin E, Badnjevic A (2017) Overview of next-generation sequencing platforms used in published draft plant genomes in light of Genotypization of immortelle plant (Helichrysium Arenarium). Med Arch (Sarajevo, Bosnia and Herzegovina) 71(4):288–292. https://doi.org/10.5455/medarh.2017.71.288-292
Hsiao Y-P, Lu C-T, Chang-Chien J, Chao W-R, Yang J-J (2016) Advances and applications of ion torrent personal genome machine in cutaneous squamous cell carcinoma reveal novel gene mutations. Materials (Basel) 9(6):464. https://doi.org/10.3390/ma9060464
Hu Y, Lan W, Miller D (2017) Next-generation sequencing for MicroRNA expression profile. Methods Mol Biol (Clifton, N.J.) 1617:169–177. https://doi.org/10.1007/978-1-4939-7046-9_12
Huang Y-F, Chen S-C, Chiang Y-S, Chen T-H, Chiu K-P (2012) Palindromic sequence impedes sequencing-by-ligation mechanism. BMC systems biology 6:S10. BioMed Central
Huang J-X, Li Y-L, Xu N, Yin C-X, Zhou X, Pan C-Y et al (2017) Establishing the ion torrent PGM sequencing methods for the clinical diagnosis of MPN patients. Zhongguo Shi Yan Xue Ye Xue Za Zhi 25(6):1744–1750. https://doi.org/10.7534/j.issn.1009-2137.2017.06.030
Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8(7):R143. https://doi.org/10.1186/gb-2007-8-7-r143
Hutchison CA III (2007) DNA sequencing: bench to bedside and beyond. Nucleic Acids Res 35(18):6227–6237
Ichida H, Abe T (2019) An improved and robust method to efficiently deplete repetitive elements from complex plant genomes. Plant Sci 280:455–460. https://doi.org/10.1016/j.plantsci.2018.10.021
Illumina (2014) Nextera DNA Library Preparation Kits data sheet. 2014
Illumina (2017) No Title Data calculations on _le. Illumina, Inc., 2017
Johansen SD, Karlsen BO, Furmanek T, Andreassen M, Jorgensen TE, Bizuayehu TT et al (2011) RNA deep sequencing of the Atlantic cod transcriptome. Comp Biochem Physiol Part D Genomics Proteomics 6(1):18–22. https://doi.org/10.1016/j.cbd.2010.04.005
Jonasson J, Olofsson M, Monstein H (2002) Classification, identification and subtyping of bacteria based on pyrosequencing and signature matching of 16S rDNA fragments. APMIS 110(3):263–272
Kanda K, Pflug JM, Sproul JS, Dasenko MA, Maddison DR (2015) Successful recovery of nuclear protein-coding genes from small insects in museums using Illumina sequencing. PLoS One 10(12):e0143929. https://doi.org/10.1371/journal.pone.0143929
Li S-C, Chan W-C, Ho M-R, Tsai K-W, Hu L-Y, Lai C-H et al (2010) Discovery and characterization of medaka miRNA genes by next generation sequencing platform. BMC Genomics 11(Suppl 4):S8. https://doi.org/10.1186/1471-2164-11-S4-S8
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(5):434–439. https://doi.org/10.1038/nbt.2198
Mangul S, Caciula A, Al Seesi S, Brinza D, Mndoiu I, Zelikovsky A (2014) Transcriptome assembly and quantification from Ion Torrent RNA-Seq data. BMC Genomics 15(Suppl 5):S7. https://doi.org/10.1186/1471-2164-15-S5-S7
Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9(1):387–402. https://doi.org/10.1146/annurev.genom.9.081307.164359
Mardis ER (2013) Next-generation sequencing platforms. Annu Rev Anal Chem 6:287–303
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376
Marklund S, Carlborg O (2010) SNP detection and prediction of variability between chicken lines using genome resequencing of DNA pools. BMC Genomics 11:665. https://doi.org/10.1186/1471-2164-11-665
Marmontel O, Charriere S, Simonet T, Bonnet V, Dumont S, Mahl M et al (2018) Single, short in-del, and copy number variations detection in monogenic dyslipidemia using a next-generation sequencing strategy. Clin Genet 94(1):132–140. https://doi.org/10.1111/cge.13250
Merriman B, Rothberg JM (2012) Progress in ion torrent semiconductor chip based sequencing. Electrophoresis 33(23):3397–3417. https://doi.org/10.1002/elps.201200424
Metzker ML (2010) Sequencing technologies — the next generation. Nat Rev Genet 11(1):31–46
Milan D, Jeon J-T, Looft C, Amarger V, Robic A, Thelander M et al (2000) A mutation in PRKAG3 associated with excess glycogen content in pig skeletal muscle. Science 288(5469):1248–1251
Minei R, Hoshina R, Ogura A (2018) De novo assembly of middle-sized genome using MinION and Illumina sequencers. BMC Genomics 19(1):700. https://doi.org/10.1186/s12864-018-5067-1
Morey M, Fernandez-Marmiesse A, Castineiras 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. https://doi.org/10.1016/j.ymgme.2013.04.024
Morozova O, Marra MA (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics 92(5):255–264. https://doi.org/10.1016/j.ygeno.2008.07.001
Myllykangas S, Buenrostro J, Ji HP (2012) Overview of sequencing technology platforms. In: Bioinformatics for high throughput sequencing. Springer, New York, pp 11–25
National Human Genome Research Institute (NHGRI), NIH, D. of E. (DOE) (2003) International Consortium Completes Human Genome Project
Neve B, Froguel P, Corset L, Vaillant E, Vatin V, Boutin P (2002) Rapid SNP allele frequency determination in genomic DNA pools by PyrosequencingTM. BioTechniques 32(5):1138–1142
Nichols AC, Chan-Seng-Yue M, Yoo J, Xu W, Dhaliwal S, Basmaji J et al (2012) A pilot study comparing HPV-positive and HPV-negative head and neck squamous cell carcinomas by whole exome sequencing. ISRN Oncol 2012:809370. https://doi.org/10.5402/2012/809370
Niyomnaitham S, Parinyanitikul N, Roothumnong E, Jinda W, Samarnthai N, Atikankul T et al (2019) Tumor mutational profile of triple negative breast cancer patients in Thailand revealed distinctive genetic alteration in chromatin remodeling gene. PeerJ 7:e6501. https://doi.org/10.7717/peerj.6501
Nordström T, Ronaghi M, Forsberg L, De Faire U, Morgenstern R, Nyrén P (2000) Direct analysis of single-nucleotide polymorphism on double-stranded DNA by pyrosequencing. Biotechnol Appl Biochem 31(2):107–112
Nourizad N, Ehn M, Gharizadeh B, Hober S, Nyrén P (2003) Methylotrophic yeast Pichia pastoris as a host for production of ATP-diphosphohydrolase (apyrase) from potato tubers (Solanum tuberosum). Protein Expr Purif 27(2):229–237
Nowrousian M (2010) Next-generation sequencing techniques for eukaryotic microorganisms: sequencing-based solutions to biological problems. Eukaryot Cell 9(9):1300–1310. https://doi.org/10.1128/EC.00123-10
Nyren P, Skarpnack SE (2001) Method of sequencing DNA based on the detection of the release of pyrophosphate and enzymatic nucleotide degradation. Retrieved from http://ip.com/patent/US6258568
Orzinska A, Guz K, Mikula M, Kluska A, Balabas A, Ostrowski J et al (2019) Prediction of fetal blood group and platelet antigens from maternal plasma using next-generation sequencing. Transfusion 59(3):1102–1107. https://doi.org/10.1111/trf.15116
Petri K, Fronza R, Gabriel R, Käppel C, Nowrouzi A, Linden RM et al (2014) Comparative next-generation sequencing of adeno-associated virus inverted terminal repeats. BioTechniques 56(5):269–273
Petronella N, Ronholm J, Suresh M, Harlow J, Mykytczuk O, Corneau N et al (2018) Genetic characterization of norovirus GII.4 variants circulating in Canada using a metagenomic technique. BMC Infect Dis 18(1):521. https://doi.org/10.1186/s12879-018-3419-8
Pickrell WO, Rees MI, Chung S-K (2012) Chapter one – Next generation sequencing methodologies – an overview. In: M. I. B. T.-A. in P. C, Rees SB (eds) Challenges and opportunities of next-generation sequencing for biomedical research, vol 89. Academic, Cambridge, MA, pp 1–26. https://doi.org/10.1016/B978-0-12-394287-6.00001-X
Prins BP, Mead TJ, Brody JA, Sveinbjornsson G, Ntalla I, Bihlmeyer NA et al (2018) Exome-chip meta-analysis identifies novel loci associated with cardiac conduction, including ADAMTS6. Genome Biol 19(1):87. https://doi.org/10.1186/s13059-018-1457-6
Qiang-long Z, Shi L, Peng G, Fei-shi L (2014) High-throughput sequencing technology and its application. J Northeast Agric Univ (English Edition) 21(3):84–96. https://doi.org/10.1016/S1006-8104(14)60073-8
Rai TS, Adams PD (2016) ChIP-sequencing to map the epigenome of senescent cells using benzonase endonuclease. Methods Enzymol 574:355–364. https://doi.org/10.1016/bs.mie.2016.01.021
Reuter JA, Spacek DV, Snyder MP (2015) High-throughput sequencing technologies. Mol Cell 58(4):586–597. https://doi.org/10.1016/j.molcel.2015.05.004
Rickert AM, Premstaller A, Gebhardt C, Oefner PJ (2002) Genotyping of SNPs in a polyploid genome by pyrosequencing™. BioTechniques 32(3):592–603
Rohit A, Kumar DS, Dhinakaran I, Joy J, Vijay Kumar D, Kumar Ballamoole K et al (2019) Whole-genome-based analysis reveals multiclone Serratia marcescens outbreaks in a non-neonatal intensive care unit setting in a tertiary care hospital in India. J Med Microbiol 68(4):616–621. https://doi.org/10.1099/jmm.0.000947
Ronaghi M, Karamohamed S, Pettersson B, Uhlen M, Nyren P (1996) Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem 242(1):84–89. https://doi.org/10.1006/abio.1996.0432
Ronaghi M, Nygren M, Lundeberg J, Nyrén P (1999) Analyses of secondary structures in DNA by pyrosequencing. Anal Biochem 267(1):65–71
Ross MG, Russ C, Costello M, Hollinger A, Lennon NJ, Hegarty R et al (2013) Characterizing and measuring bias in sequence data. Genome Biol 14(5):R51
Rosse IC, Assis JG, Oliveira FS, Leite LR, Araujo F, Zerlotini A et al (2017) Whole genome sequencing of Guzera cattle reveals genetic variants in candidate genes for production, disease resistance, and heat tolerance. Mamm Genome 28(1–2):66–80. https://doi.org/10.1007/s00335-016-9670-7
Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M et al (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348
Salipante SJ, Kawashima T, Rosenthal C, Hoogestraat DR, Cummings LA, Sengupta DJ et al (2014) Performance comparison of Illumina and ion torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling. Appl Environ Microbiol 80(24):7583–7591. https://doi.org/10.1128/AEM.02206-14
Sanger F, Coulson AR (1975) A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol 94(3):441–448. https://doi.org/10.1016/0022-2836(75)90213-2
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci 74(12):5463–5467. https://doi.org/10.1073/pnas.74.12.5463
Scaduto DI, Brown JM, Haaland WC, Zwickl DJ, Hillis DM, Metzker ML (2010) Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences. Proc Natl Acad Sci U S A 107(50):21242–21247. https://doi.org/10.1073/pnas.1015673107
Schatz MC, Witkowski J, McCombie WR (2012) Current challenges in de novo plant genome sequencing and assembly. Genome Biol 13(4):243. https://doi.org/10.1186/gb4015
Segawa H, Kukita Y, Kato K (2017) HLA genotyping by next-generation sequencing of complementary DNA. BMC Genomics 18(1):914. https://doi.org/10.1186/s12864-017-4300-7
Shen Y, Sarin S, Liu Y, Hobert O, Pe’er I (2008) Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing. PLoS One 3(12):e4012. https://doi.org/10.1371/journal.pone.0004012
Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26(10):1135–1145. https://doi.org/10.1038/nbt1486
Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM et al (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science (New York, NY) 309(5741):1728–1732. https://doi.org/10.1126/science.1117389
Shirasawa K, Fukuoka H, Matsunaga H, Kobayashi Y, Kobayashi I, Hirakawa H et al (2013) Genome-wide association studies using single nucleotide polymorphism markers developed by re-sequencing of the genomes of cultivated tomato. DNA Res 20(6):593–603. https://doi.org/10.1093/dnares/dst033
Sirichoat A, Buppasiri P, Engchanil C, Namwat W, Faksri K, Sankuntaw N et al (2018) Characterization of vaginal microbiota in Thai women. PeerJ 6:e5977. https://doi.org/10.7717/peerj.5977
Song Y, Milon B, Ott S, Zhao X, Sadzewicz L, Shetty A et al (2018) A comparative analysis of library prep approaches for sequencing low input translatome samples. BMC Genomics 19(1):696. https://doi.org/10.1186/s12864-018-5066-2
Stothard P, Choi J-W, Basu U, Sumner-Thomson JM, Meng Y, Liao X, Moore SS (2011) Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics 12:559. https://doi.org/10.1186/1471-2164-12-559
Strengman E, Barendrecht-Smouter FAS, de Voijs C, de Vree P, Nijman IJ, de Leng WWJ (2019) Amplicon-based targeted next-generation sequencing of formalin-fixed, paraffin-embedded tissue. Methods Mol Biol (Clifton, NJ) 1908:1–17. https://doi.org/10.1007/978-1-4939-9004-7_1
Suzuki S, Ranade S, Osaki K, Ito S, Shigenari A, Ohnuki Y et al (2018) Reference grade characterization of polymorphisms in full-length HLA class I and II genes with short-read sequencing on the ION PGM system and long-reads generated by single molecule, real-time sequencing on the PacBio platform. Front Immunol 9:2294. https://doi.org/10.3389/fimmu.2018.02294
Szelinger S, Kurdoglu A, Craig DW (2011) Bar-coded, multiplexed sequencing of targeted DNA regions using the Illumina Genome Analyzer. Methods Mol Biol (Clifton, NJ) 700:89–104. https://doi.org/10.1007/978-1-61737-954-3_7
Tilak M-K, Botero-Castro F, Galtier N, Nabholz B (2018) Illumina library preparation for sequencing the GC-rich fraction of heterogeneous genomic DNA. Genome Biol Evol 10(2):616–622. https://doi.org/10.1093/gbe/evy022
Trama JP, Mordechai E, Adelson ME (2005a) Detection and identification of Candida species associated with Candida vaginitis by real-time PCR and pyrosequencing. Mol Cell Probes 19(2):145–152
Trama JP, Mordechai E, Adelson ME (2005b) Detection of Aspergillus fumigatus and a mutation that confers reduced susceptibility to itraconazole and posaconazole by real-time PCR and pyrosequencing. J Clin Microbiol 43(2):906–908
Tremblay ED, Kimoto T, Berube JA, Bilodeau GJ (2019) High-throughput sequencing to investigate phytopathogenic fungal propagules caught in baited insect traps. J Fungi (Basel) 5(1):15. https://doi.org/10.3390/jof5010015
Tumiotto C, Riviere L, Bellecave P, Recordon-Pinson P, Vilain-Parce A, Guidicelli G-L, Fleury H (2017) Sanger and next-generation sequencing data for characterization of CTL epitopes in archived HIV-1 proviral DNA. PLoS One 12(9):e0185211
Uhlmann K, Brinckmann A, Toliat MR, Ritter H, Nürnberg P (2002) Evaluation of a potential epigenetic biomarker by quantitative methyl-single nucleotide polymorphism analysis. Electrophoresis 23(24):4072–4079
Veeranagouda Y, Leonard J-F, Gautier J-C, Boitier E (2017) Next-generation sequencing to investigate urinary microRNAs from Macaca fascicularis (Cynomolgus monkey). Methods Mol Biol (Clifton, NJ) 1641:349–378. https://doi.org/10.1007/978-1-4939-7172-5_20
Xia F, Liu Y, Guo M-Y, Shen G-R, Lin J, Zhou X-W (2016) Pyrosequencing analysis revealed complex endogenetic microorganism community from natural DongChong XiaCao and its microhabitat. BMC Microbiol 16(1):196
Zhang H, Hall N, Goertzen LR, Bi B, Chen CY, Peatman E, Lowe EK, Patel J, McElroy JS (2019) Development of a goosegrass ( ) draft genome and application to weed science research. Pest Manag Sci
Zimmerman RS, Tao X, Marin D, Werner MD, Hong KH, Lonczak A et al (2018) Preclinical validation of a targeted next generation sequencing-based comprehensive chromosome screening methodology in human blastocysts. Mol Hum Reprod 24(1):37–45. https://doi.org/10.1093/molehr/gax060
Acknowledgments
Authors would like to acknowledge Zayed University office of research for providing financial support to avail NGS services for the ongoing Zayed University Research Cluster Project: Activity code R16092 awarded to the corresponding author (PI of the cluster research project). We thank Ms. Milred Sequeira for helping with the preparation of the figure used in this chapter.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Meera Krishna, B., Khan, M.A., Khan, S.T. (2019). Next-Generation Sequencing (NGS) Platforms: An Exciting Era of Genome Sequence Analysis. In: Tripathi, V., Kumar, P., Tripathi, P., Kishore, A., Kamle, M. (eds) Microbial Genomics in Sustainable Agroecosystems. Springer, Singapore. https://doi.org/10.1007/978-981-32-9860-6_6
Download citation
DOI: https://doi.org/10.1007/978-981-32-9860-6_6
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-32-9859-0
Online ISBN: 978-981-32-9860-6
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)