Next generation sequencing: Chemistry, technology and applications

Topics in Current Chemistry

Volumn 336, Issue , 2014, Pages 1-18

  Hui, Pei ^a  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Genomic medicine; Next generation sequencing

Indexed keywords

ARTICLE; HIGH THROUGHPUT SEQUENCING; HUMAN; METHODOLOGY;

HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS;

EID: 84890963215     PISSN: 03401022     EISSN: None     Source Type: Book Series    
DOI: 10.1007/128-2012-329     Document Type: Article

References (77)

1. International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431(7011):931-945
2. Cancer Genome Atlas Research Network (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455(7216):1061-1068
3. Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, Chen K, Dooling D, Dunford-Shore BH, McGrath S, Hickenbotham M et al (2008) DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 456(7218):66-72
4. Pao W, Miller V, Zakowski M, Doherty J, Politi K, Sarkaria I, Singh B, Heelan R, Rusch V, Fulton L et al (2004) EGF receptor gene mutations are common in lung cancers from "never smokers" and are associated with sensitivity of tumors to gefitinib and erlotinib. Proc Natl Acad Sci U S A 101(36):13306-13311
5. Dietz HC (2010) New therapeutic approaches to mendelian disorders. N Engl J Med 363(9):852-863
6. Green ED, Guyer MS (2011) Charting a course for genomic medicine from base pairs to bedside. Nature 470(7333):204-213
7. Hawkins RD, Hon GC, Ren B (2010) Next-generation genomics: An integrative approach. Nat Rev Genet 11(7):476-486
8. Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26(10):1135-1145
9. Martinez DA, Nelson MA (2010) The next generation becomes the now generation. PLoS Genet 6(4):e1000906
10. Voelkerding KV, Dames SA, Durtschi JD (2009) Next-generation sequencing: From basic research to diagnostics. Clin Chem 55(4):641-658
11. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT et al (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature 452(7189):872-876
12. Niedringhaus TP, Milanova D, Kerby MB, Snyder MP, Barron AE (2011) Landscape of nextgeneration sequencing technologies. Anal Chem 83(12):4327-4341
13. Fuller CW, Middendorf LR, Benner SA, Church GM, Harris T, Huang X, Jovanovich SB, Nelson JR, Schloss JA, Schwartz DC et al (2009) The challenges of sequencing by synthesis. Nat Biotechnol 27(11):1013-1023
14. Ekblom R, Galindo J (2011) Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity 107(1):1-15
15. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74(12):5463-5467
16. Maxam AM, GilbertW(1977) A new method for sequencing DNA. Proc Natl Acad Sci U S A 74(2):560-564
17. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G et al (2007) The diploid genome sequence of an individual human. PLoS Biol 5(10):e254
18. Metzker ML (2010) Sequencing technologies - The next generation. Nat Rev Genet 11 (1):31-46
19. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437(7057):376-380
20. Schuster SC (2008) Next-generation sequencing transforms today's biology. Nat Methods 5(1):16-18
21. Ronaghi M, Uhlen M, Nyren P (1998) A sequencing method based on real-time pyrophosphate. Science 281(5375):363-365
22. Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387-402
23. Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K et al (2008) A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 18(7):1051-1063
24. Wu H, Irizarry RA, Bravo HC (2010) Intensity normalization improves color calling in SOLiD sequencing. Nat Methods 7(5):336-337
25. Efcavitch JW, Thompson JF (2010) Single-molecule DNA analysis. Annu Rev Anal Chem (Palo Alto Calif) 3:109-128
26. Thompson JF, Milos PM (2011) The properties and applications of single-molecule DNA sequencing. Genome Biol 12(2):217
27. Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, Dimeo J, Efcavitch JW et al (2008) Single-molecule DNA sequencing of a viral genome. Science 320(5872):106-109
28. 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 (5910):133-138
29. Lundquist PM, Zhong CF, Zhao P, Tomaney AB, Peluso PS, Dixon J, Bettman B, Lacroix Y, Kwo DP, McCullough E et al (2008) Parallel confocal detection of single molecules in real time. Opt Lett 33(9):1026-1028
30. Korlach J, Marks PJ, Cicero RL, Gray JJ, Murphy DL, Roitman DB, Pham TT, Otto GA, Foquet M, Turner SW (2008) Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures. Proc Natl Acad Sci U S A 105(4):1176-1181
31. Korlach J, Bjornson KP, Chaudhuri BP, Cicero RL, Flusberg BA, Gray JJ, Holden D, Saxena R, Wegener J, Turner SW (2010) Real-time DNA sequencing from single polymerase molecules. Methods Enzymol 472:431-455
32. Munroe DJ, Harris TJ (2010) Third-generation sequencing fireworks at Marco Island. Nat Biotechnol 28(5):426-428
33. Flusberg BA, Webster DR, Lee JH, Travers KJ, Olivares EC, Clark TA, Korlach J, Turner SW (2010) Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods 7(6):461-465
34. Uemura S, Aitken CE, Korlach J, Flusberg BA, Turner SW, Puglisi JD (2010) Real-time tRNA transit on single translating ribosomes at codon resolution. Nature 464(7291):1012-1017
35. Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, Carnevali P, Nazarenko I, Nilsen GB, Yeung G et al (2010) Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 327(5961):78-81
36. Porreca GJ (2010) Genome sequencing on nanoballs. Nat Biotechnol 28(1):43-44
37. Roach JC, Glusman G, Smit AF, Huff CD, Hubley R, Shannon PT, Rowen L, Pant KP, Goodman N, Bamshad M et al (2010) Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328(5978):636-639
38. Lee W, Jiang Z, Liu J, Haverty PM, Guan Y, Stinson J, Yue P, Zhang Y, Pant KP, Bhatt D et al (2010) The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature 465(7297):473-477
39. Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M et al (2011) An integrated semiconductor device enabling nonoptical genome sequencing. Nature 475(7356):348-352
40. Clarke J, Wu HC, Jayasinghe L, Patel A, Reid S, Bayley H (2009) Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol 4(4):265-270
41. 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
42. Branton D, Deamer DW, Marziali A, Bayley H, Benner SA, Butler T, Di Ventra M, Garaj S, Hibbs A, Huang X et al (2008) The potential and challenges of nanopore sequencing. Nat Biotechnol 26(10):1146-1153
43. Bayley H (2006) Sequencing single molecules of DNA. Curr Opin Chem Biol 10(6):628-637
44. Astier Y, Braha O, Bayley H (2006) Toward single molecule DNA sequencing: Direct identification of ribonucleoside and deoxyribonucleoside 5'-monophosphates by using an engineered protein nanopore equipped with a molecular adapter. J Am Chem Soc 128(5):1705-1710
45. Manolio TA (2010) Genomewide association studies and assessment of the risk of disease. N Engl J Med 363(2):166-176
46. Rioux JD, Xavier RJ, Taylor KD, Silverberg MS, Goyette P, Huett A, Green T, Kuballa P, Barmada MM, Datta LW et al (2007) Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nat Genet 39(5):596-604
47. Van Limbergen J, Wilson DC, Satsangi J (2009) The genetics of Crohns disease. Annu Rev Genomics Hum Genet 10:89-116
48. Hoffmann TJ, Kvale MN, Hesselson SE, Zhan Y, Aquino C, Cao Y, Cawley S, Chung E, Connell S, Eshragh J et al (2011) Next generation genome-wide association tool: Design and coverage of a high-throughput European-optimized SNP array. Genomics 98(2):79-89
49. Need AC, Goldstein DB (2009) Next generation disparities in human genomics: Concerns and remedies. Trends Genet 25(11):489-494
50. Miller W, Hayes VM, Ratan A, Petersen DC, Wittekindt NE, Miller J, Walenz B, Knight J, Qi J, Zhao F et al (2011) Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). Proc Natl Acad Sci U S A 108(30):12348-12353
51. Zalapa JE, Cuevas H, Zhu H, Steffan S, Senalik D, Zeldin E, McCown B, Harbut R, Simon P (2012) Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am J Bot 99:193-208
52. Mohandas N, Gallagher PG (2008) Red cell membrane: Past, present, and future. Blood 112 (10):3939-3948
53. Hershberger RE, Siegfried JD (2011) Update 2011: Clinical and genetic issues in familial dilated cardiomyopathy. J Am Coll Cardiol 57(16):1641-1649
54. Kingsmore SF, Dinwiddie DL, Miller NA, Soden SE, Saunders CJ (2011) Adopting orphans: Comprehensive genetic testing of Mendelian diseases of childhood by next-generation sequencing. Expert Rev Mol Diagn 11(8):855-868
55. Tsurusaki Y, Okamoto N, Suzuki Y, Doi H, Saitsu H, Miyake N, Matsumoto N (2011) Exome sequencing of two patients in a family with atypical X-linked leukodystrophy. Clin Genet 80(2):161-166
56. Tsurusaki Y, Osaka H, Hamanoue H, Shimbo H, Tsuji M, Doi H, Saitsu H, Matsumoto N, Miyake N (2011) Rapid detection of a mutation causing X-linked leucoencephalopathy by exome sequencing. J Med Genet 48(9):606-609
57. Schraders M, Haas SA, Weegerink NJ, Oostrik J, Hu H, Hoefsloot LH, Kannan S, Huygen PL, Pennings RJ, Admiraal RJ et al (2011) Next-generation sequencing identifies mutations of SMPX, which encodes the small muscle protein, X-linked, as a cause of progressive hearing impairment. Am J Hum Genet 88(5):628-634
58. Hu H, Wrogemann K, Kalscheuer V, Tzschach A, Richard H, Haas SA, Menzel C, Bienek M, Froyen G, Raynaud M et al (2009) Mutation screening in 86 known X-linked mental retardation genes by droplet-based multiplex PCR and massive parallel sequencing. Hugo J 3 (1-4):41-49
59. Jones MA, Bhide S, Chin E, Ng BG, Rhodenizer D, Zhang VW, Sun JJ, Tanner A, Freeze HH, Hegde MR (2011) Targeted polymerase chain reaction-based enrichment and next generation sequencing for diagnostic testing of congenital disorders of glycosylation. Genet Med 13 (11):921-932
60. Doi H, Yoshida K, Yasuda T, Fukuda M, Fukuda Y, Morita H, Ikeda S, Kato R, Tsurusaki Y, Miyake N et al (2011) Exome sequencing reveals a homozygous SYT14 mutation in adultonset, autosomal-recessive spinocerebellar ataxia with psychomotor retardation. Am J Hum Genet 89(2):320-327
61. Artuso R, Fallerini C, Dosa L, Scionti F, Clementi M, Garosi G, Massella L, Epistolato MC, Mancini R, Mari F et al (2012) Advances in Alport syndrome diagnosis using next-generation sequencing. Eur J Hum Genet 20(1):50-57
62. Bowne SJ, Sullivan LS, Koboldt DC, Ding L, Fulton R, Abbott RM, Sodergren EJ, Birch DG, Wheaton DH, Heckenlively JR et al (2011) Identification of disease-causing mutations in autosomal dominant retinitis pigmentosa (adRP) using next-generation DNA sequencing. Invest Ophthalmol Vis Sci 52(1):494-503
63. Choi M, Scholl UI, Ji W, Liu T, Tikhonova IR, Zumbo P, Nayir A, Bakkaloglu A, Ozen S, Sanjad S et al (2009) Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci U S A 106(45):19096-19101
64. Choi M, Scholl UI, Yue P, Bjorklund P, Zhao B, Nelson-Williams C, Ji W, Cho Y, Patel A, Men CJ et al (2011) K+ channel mutations in adrenal aldosterone-producing adenomas and hereditary hypertension. Science 331(6018):768-772
65. Bell CJ, Dinwiddie DL, Miller NA, Hateley SL, Ganusova EE, Mudge J, Langley RJ, Zhang L, Lee CC, Schilkey FD et al (2011) Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci Transl Med 3(65):65ra4
66. Park PJ (2009) ChIP-seq: Advantages and challenges of a maturing technology. Nat Rev Genet 10(10):669-680
67. Fouse SD, Nagarajan RP, Costello JF (2010) Genome-scale DNA methylation analysis. Epigenomics 2(1):105-117
68. Meaburn E, Schulz R (2011) Next generation sequencing in epigenetics: Insights and challenges. Semin Cell Dev Biol 23:192-199
69. Ku CS, Naidoo N, Wu M, Soong R (2011) Studying the epigenome using next generation sequencing. J Med Genet 48(11):721-730
70. Gibbons JG, Janson EM, Hittinger CT, Johnston M, Abbot P, Rokas A (2009) Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. Mol Biol Evol 26(12):2731-2744
71. Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nat Rev Genet 12 (10):671-682
72. Levin JZ, Berger MF, Adiconis X, Rogov P, Melnikov A, Fennell T, Nusbaum C, Garraway LA, Gnirke A (2009) Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts. Genome Biol 10(10):R115
73. Tripathy S, Jiang RH (2012) Massively parallel sequencing technology in pathogenic microbes. Methods Mol Biol 835:271-294
74. Mellmann A, Harmsen D, Cummings CA, Zentz EB, Leopold SR, Rico A, Prior K, Szczepanowski R, Ji Y, Zhang W et al (2011) Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS One 6(7):e22751
75. Hu B, Xie G, Lo CC, Starkenburg SR, Chain PS (2011) Pathogen comparative genomics in the next-generation sequencing era: Genome alignments, pangenomics and metagenomics. Brief Funct Genomics 10(6):322-333
76. Barzon L, Lavezzo E, Militello V, Toppo S, Palu G (2011) Applications of next-generation sequencing technologies to diagnostic virology. Int J Mol Sci 12(11):7861-7884
77. Barzon L, Militello V, Lavezzo E, Franchin E, Peta E, Squarzon L, Trevisan M, Pagni S, Dal Bello F, Toppo S et al (2011) Human papillomavirus genotyping by 454 next generation sequencing technology. J Clin Virol 52(2):93-97