Next generation sequencing technology: Advances and applications

Biochimica et Biophysica Acta - Molecular Basis of Disease

Volumn 1842, Issue 10, 2014, Pages 1932-1941

  Buermans, H P J ^a   den Dunnen, J T ^a  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

Applications; Basic technology; Nanopore; Next generation sequencing; Sequence by synthesis; Single molecule sequencing

Indexed keywords

DNA; DNA FRAGMENT; ION; RNA;

DRUG MIXTURE; GENE IDENTIFICATION; GENE SEQUENCE; GENOME; HEALTH; HUMAN; MEDICAL RESEARCH; METHYLATION; MICROSCOPE; MOLECULAR BIOLOGY; MOLECULAR WEIGHT; NANOPORE; PRENATAL DIAGNOSIS; PYROSEQUENCING; REVIEW; SAMPLE; TECHNOLOGY;

EID: 84908513108     PISSN: 09254439     EISSN: 1879260X     Source Type: Journal    
DOI: 10.1016/j.bbadis.2014.06.015     Document Type: Review

References (66)

1. Dabney J., Meyer M. Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. Biotechniques 2012, 52:87-94.
2. Hafner M., Renwick N., Brown M., Mihailović A., Holoch D., Lin C., Pena J.T., Nusbaum J.D., Morozov P., Ludwig J., et al. RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries. RNA 2011, 17:1697-1712.
3. Mitra R.D., Church G.M. In situ localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Res. 1999, 27:e34-e39.
4. Bentley D.R., Balasubramanian S., Swerdlow H.P., Smith G.P., Milton J., Brown C.G., Hall K.P., Evers D.J., Barnes C.L., Bignell H.R., et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456:53-59.
5. Nakano M., Komatsu J., Matsuura S.-i., Takashima K., Katsura S., Mizuno A. Single-molecule pcr using water-in-oil emulsion. J. Biotechnol. 2003, 102:117-124.
6. Dressman D., Yan H., Traverso G., Kinzler K.W., Vogelstein B. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc. Natl. Acad. Sci. 2003, 100:8817-8822.
7. Golan D., Medvedev P. Using state machines to model the ion torrent sequencing process and to improve read error rates. Bioinformatics 2013, 29:i344-i351.
8. Merriman B., IonTorrentR&D-team, Rothberg J.M. Progress in ion torrent semiconductor chip based sequencing. Electrophoresis 2012, 33:3397-3417.
9. Ma Z., Lee R.W., Li B., Kenney P., Wang Y., Erikson J., Goyal S., Lao K. Isothermal amplification method for next-generation sequencing. Proc. Natl. Acad. Sci. 2013, 110(35):14320-14323.
10. Coupland P., Chandra T., Quail M., Reik W., Swerdlow H. Direct sequencing of small genomes on the pacific biosciences RS without library preparation. Biotechniques 2012, 53:365-372.
11. Levene M.J., Korlach J., Turner S.W., Foquet M., Craighead H.G., Webb W.W. Zero-mode waveguides for single-molecule analysis at high concentrations. Science 2003, 299:682-686.
12. Korlach J., Marks P.J., Cicero R.L., Gray J.J., Murphy D.L., Roitman D.B., Pham T.T., Otto G.A., Foquet M., Turner S.W. Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures. Proc. Natl. Acad. Sci. 2008, 105:1176-1181.
13. Lundquist P.M., Zhong C.F., Zhao P., Tomaney A.B., Peluso P.S., Dixon J., Bettman B., Lacroix Y., Kwo D.P., McCullough E., et al. Parallel confocal detection of single molecules in real time. Opt. Lett. 2008, 33:1026-1028.
14. de Vega M., Lazaro J.M., Salas M., Blanco L. Primer-terminus stabilization at the 3'-5'exonuclease active site of phi29 DNA polymerase. Involvement of two amino acid residues highly conserved in proofreading DNA polymerases. EMBO J. 1996, 15:1182.
15. Esteban J., Salas M., Blanco L. Fidelity of phi 29 DNA polymerase. Comparison between protein-primed initiation and DNA polymerization. J. Biol. Chem. 1993, 268:2719-2726.
16. Blanco L., Bernad A., Lázaro J.M., Martin G., Garmendia C., Salas M. Highly efficient DNA synthesis by the phage phi 29 DNA polymerase. Symmetrical mode of DNA replication. J. Biol. Chem. 1989, 264:8935-8940.
17. Chin C.-S., Alexander D.H., Marks P., Klammer A.A., Drake J., Heiner C., Clum A., Copeland A., Huddleston J., Eichler E.E., et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 2013, 10(6):563-569.
18. Ashkenasy N., Snchez-Quesada J., Bayley H., Ghadiri M.R. Recognizing a single base in an individual DNA strand: a step toward DNA sequencing in nanopores. Angew. Chem. Int. Ed. 2005, 44:1401-1404.
19. Clarke J., Wu H.-C., Jayasinghe L., Patel A., Reid S., Bayley H. Continuous base identification for single-molecule nanopore DNA sequencing. Nat. Nanotechnol. 2009, 4:265-270.
20. Li J., Gershow M., Stein D., Brandin E., Golovchenko J.A. DNA molecules and configurations in a solid-state nanopore microscope. Nat. Mater. 2003, 2:611-615.
21. Fologea D., Gershow M., Ledden B., McNabb D.S., Golovchenko J.A., Li J. Detecting single stranded DNA with a solid state nanopore. Nano Lett. 2005, 5:1905-1909.
22. A.'t Hoen P., Ariyurek Y., Thygesen H.H., Vreugdenhil E., Vossen R.H., de Menezes R.X., Boer J.M., van Ommen G.-J.B., den Dunnen J.T. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res. 2008, 36:e141.
23. Lappalainen T., Sammeth M., Friedlander M.R., 't Hoen P.A.C., Monlong J., Rivas M.A., Gonzalez-Porta M., Kurbatova N., Griebel T., Ferreira P.G., Barann M., Wieland T., Greger L., van Iterson M., Almlof J., Ribeca P., Pulyakhina I., Esser D., Giger T., Tikhonov A., Sultan M., Bertier G., MacArthur D.G., Lek M., Lizano E., Buermans H.P.J., Padioleau I., Schwarzmayr T., Karlberg O., Ongen H., Kilpinen H., Beltran S., Gut M., Kahlem K., Amstislavskiy V., Stegle O., Pirinen M., Montgomery S.B., Donnelly P., McCarthy M.I., Flicek P., Strom T.M., Consortium T.G., Lehrach H., Schreiber S., Sudbrak R., Carracedo A., Antonarakis S.E., Hasler R., Syvanen A.-C., van Ommen G.-J., Brazma A., Meitinger T., Rosenstiel P., Guigo R., Gut I.G., Estivill X., Dermitzakis E.T. Transcriptome and genome sequencing uncovers functional variation in humans. Nature 2013, 501:506-511.
24. Westra H.J., Peters M.J., Esko T., Yaghootkar H., Schurmann C., Kettunen J., Christiansen M.W., Fairfax B.P., Schramm K., Powell J.E., Zhernakova A., Zhernakova D.V., Veldink J.H., Van den Berg L.H., Karjalainen J., Withoff S., Uitterlinden A.G., Hofman A., Rivadeneira F., 't Hoen P.A.C., Reinmaa E., Fischer K., Nelis M., Milani L., Melzer D., Ferrucci L., Singleton A.B., Hernandez D.G., Nalls M.A., Homuth G., Nauck M., Radke D., Volker U., Perola M., Salomaa V., Brody J., Suchy-Dicey A., Gharib S.A., Enquobahrie D.A., Lumley T., Montgomery G.W., Makino S., Prokisch H., Herder C., Roden M., Grallert H., Meitinger T., Strauch K., Li Y., Jansen R.C., Visscher P.M., Knight J.C., Psaty B.M., Ripatti S., Teumer A., Frayling T.M., Metspalu A., van Meurs J.B.J., Franke L. Systematic identification of trans eQTLs as putative drivers of known disease associations. Nat. Genet. 2013, 45:1238-1243.
25. Valen E., Pascarella G., Chalk A., Maeda N., Kojima M., Kawazu C., Murata M., Nishiyori H., Lazarevic D., Motti D., et al. Genome-wide detection and analysis of hippocampus core promoters using deepcage. Genome Res. 2009, 19:255-265.
26. de Klerk E., Venema A., Anvar S.Y., Goeman J.J., Hu O., Trollet C., Dickson G., den Dunnen J.T., van der Maarel S.M., Raz V., et al. Poly (a) binding protein nuclear 1 levels affect alternative polyadenylation. Nucleic Acids Res. 2012, 40:9089-9101.
27. Berezikov E., Thuemmler F., van Laake L.W., Kondova I., Bontrop R., Cuppen E., Plasterk R.H.A. Diversity of microRNAs in human and chimpanzee brain. Nat. Genet. 2006, 38:1375-1377.
28. Nolte-'t Hoen E.N.M., Buermans H.P.J., Waasdorp M., Stoorvogel W., Wauben M.H.M., t Hoen P.A.C. Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions. Nucleic Acids Res. 2012, 40:9272-9285.
29. Andersson R., Gebhard C., Miguel-Escalada I., Hoof I., Bornholdt J., Boyd M., Chen Y., Zhao X., Schmidl C., Suzuki T., Ntini E., Arner E., Valen E., Li K., Schwarzfischer L., Glatz D., Raithel J., Lilje B., Rapin N., Bagger F.O., Jorgensen M., Andersen P.R., Bertin N., Rackham O., Burroughs A.M., Baillie J.K., Ishizu Y., Shimizu Y., Furuhata E., Maeda S., Negishi Y., Mungall C.J., Meehan T.F., Lassmann T., Itoh M., Kawaji H., Kondo N., Kawai J., Lennartsson A., Daub C.O., Heutink P., Hume D.A., Jensen T.H., Suzuki H., Hayashizaki Y., Muller F., Consortium T.F., Forrest A.R.R., Carninci P., Rehli M., Sandelin A. An atlas of active enhancers across human cell types and tissues. Nature 2014, 507:455-461.
30. Ingolia N.T., Ghaemmaghami S., Newman J.R., Weissman J.S. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 2009, 324:218-223.
31. Blat Y., Kleckner N. Cohesins bind to preferential sites along yeast chromosome III, with differential regulation along arms versus the centric region. Cell 1999, 98:249-259.
32. Consortium E.P., et al. The encode (encyclopedia of DNA elements) project. Science 2004, 306:636-640.
33. Laird P.W. Principles and challenges of genome-wide DNA methylation analysis. Nat. Rev. Genet. 2010, 11:191-203.
34. Herb B.R., Wolschin F., Hansen K.D., Aryee M.J., Langmead B., Irizarry R., Amdam G.V., Feinberg A.P. Reversible switching between epigenetic states in honeybee behavioral subcastes. Nat. Neurosci. 2012, 15:1371-1373.
35. Li R., Fan W., Tian G., Zhu H., He L., Cai J., Huang Q., Cai Q., Li B., Bai Y., et al. The sequence and de novo assembly of the giant panda genome. Nature 2009, 463:311-317.
36. Rohland N., Reich D., Mallick S., Meyer M., Green R.E., Georgiadis N.J., Roca A.L., Hofreiter M. Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation of forest and savanna elephants. PLoS Biol. 2010, 8:e1000564.
37. Reich D., Green R.E., Kircher M., Krause J., Patterson N., Durand E.Y., Viola B., Briggs A.W., Stenzel U., Johnson P.L., et al. Genetic history of an archaic hominin group from denisova cave in Siberia. Nature 2010, 468:1053-1060.
38. Cox-Foster D.L., Conlan S., Holmes E.C., Palacios G., Evans J.D., Moran N.A., Quan P.-L., Briese T., Hornig M., Geiser D.M., et al. A metagenomic survey of microbes in honey bee colony collapse disorder. Science 2007, 318:283-287.
39. Bos K.I., Schuenemann V.J., Golding G.B., Burbano H.A., Waglechner N., Coombes B.K., McPhee J.B., DeWitte S.N., Meyer M., Schmedes S., et al. A draft genome of Yersinia pestis from victims of the black death. Nature 2011, 478:506-510.
40. Somboonna N., Wilantho A., Jankaew K., Assawamakin A., Sangsrakru D., Tangphatsornruang S., Tongsima S. Microbial ecology of Thailand tsunami and non-tsunami affected terrestrials. PLoS One 2014, 9:e94236.
41. Kraaijeveld K., de Weger L.A., Ventayol Garcã-a M., Buermans H., Frank J., Hiemstra P.S., den Dunnen J.T. Efficient and sensitive identification and quantification of airborne pollen using next-generation DNA sequencing. Mol. Ecol. Resour. 2014, (http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12288/abstract). 10.1111/1755-0998.12288.
42. Venter J.C., Remington K., Heidelberg J.F., Halpern A.L., Rusch D., Eisen J.A., Wu D., Paulsen I., Nelson K.E., Nelson W., et al. Environmental genome shotgun sequencing of the Sargasso sea. Science 2004, 304:66-74.
43. Ercolini D., De Filippis F., La Storia A., Iacono M. Remake by high-throughput sequencing of the microbiota involved in the production of water buffalo mozzarella cheese. Appl. Environ. Microbiol. 2012, 78:8142-8145.
44. Wang Z., Gerstein M., Snyder M. RNA-seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009, 10:57-63.
45. Arumugam M., Raes J., Pelletier E., Le Paslier D., Yamada T., Mende D.R., Fernandes G.R., Tap J., Bruls T., Batto J.-M., et al. Enterotypes of the human gut microbiome. Nature 2011, 473:174-180.
46. Turnbaugh P.J., Bäckhed F., Fulton L., Gordon J.I. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 2008, 3:213-223.
47. Norton M.E., Brar H., Weiss J., Karimi A., Laurent L.C., Caughey A.B., Rodriguez M.H., J.W., Mitchell M.E., Adair C.D., Lee H., Jacobsson B., Tomlinson M.W., Oepkes D., Hollemon D., Sparks A.B., Oliphant A., Song K. Non-invasive chromosomal evaluation (nice) study: results of a multicenter prospective cohort study for detection of fetal trisomy 21 and trisomy 18. Am. J. Obstet. Gynecol. 2012, 207:137.e1-137.e8.
48. Kitzman J.O., Snyder M.W., Ventura M., Lewis A.P., Qiu R., Simmons L.E., Gammill H.S., Rubens C.E., Santillan D.A., Murray J.C., Tabor H.K., Bamshad M.J., Eichler E.E., Shendure J. Noninvasive whole-genome sequencing of a human fetus. Sci. Transl. Med. 2012, 4:137ra76.
49. Hoischen A., van Bon B.W.M., Gilissen C., Arts P., van Lier B., Steehouwer M., de Vries P., de Reuver R., Wieskamp N., Mortier G., Devriendt K., Amorim M.Z., Revencu N., Kidd A., Barbosa M., Turner A., Smith J., Oley C., Henderson A., Hayes I.M., Thompson E.M., Brunner H.G., de Vries B.B.A., Veltman J.A. De novo mutations of SETBP1 cause Schinzel-Giedion syndrome. Nat. Genet. 2010, 42:483-485.
50. Vissers L.E.L.M., de Ligt J., Gilissen C., Janssen I., Steehouwer M., de Vries P., van Lier B., Arts P., Wieskamp N., del Rosario M., van Bon B.W.M., Hoischen A., de Vries B.B.A., Brunner H.G., Veltman J.A. A de novo paradigm for mental retardation. Nat. Genet. 2010, 42:1109-1112.
51. Ng S.B., Buckingham K.J., Lee C., Bigham A.W., Tabor H.K., Dent K.M., Huff C.D., Shannon P.T., Jabs E.W., Nickerson D.A., Shendure J., Bamshad M.J. Exome sequencing identifies the cause of a Mendelian disorder. Nat. Genet. 2010, 42:30-35.
52. Bernards R. Finding effective cancer therapies through loss of function genetic screens. Curr. Opin. Genet. Dev. 2014, 24:23-29.
53. Macaulay I.C., Voet T. Single cell genomics: advances and future perspectives. PLoS Genet. 2014, 10:e1004126.
54. Zhang J., Baran J., Cros A., Guberman J.M., Haider S., Hsu J., Liang Y., Rivkin E., Wang J., Whitty B., Wong-Erasmus M., Yao L., Kasprzyk A. International cancer genome consortium data portal: a one-stop shop for cancer genomics data. Database 2011, 2011. bar026 http://dx.doi.org/10.1093/database/bar026.
55. Chen R., Mias G., Li-Pook-Than J., Jiang L., Lam H., Chen R., Miriami E., Karczewski K., Hariharan M., Dewey F., Cheng Y., Clark M., Im H., Habegger L., Balasubramanian S., O'Huallachain M., Dudley J., Hillenmeyer S., Haraksingh R., Sharon D., Euskirchen G., Lacroute P., Bettinger K., Boyle A., Kasowski M., Grubert F., Seki S., Garcia M., Whirl-Carrillo M., Gallardo M., Blasco M., Greenberg P., Snyder P., Klein T., Altman R., Butte A.J., Ashley E., Gerstein M., Nadeau K., Tang H., Snyder M. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell 2012, 148:1293-1307.
56. English A.C., Richards S., Han Y., Wang M., Vee V., Qu J., Qin X., Muzny D.M., Reid J.G., Worley K.C., et al. Mind the gap: upgrading genomes with pacific biosciences RS long-read sequencing technology. PLoS One 2012, 7:e47768.
57. Loomis E.W., Eid J.S., Peluso P., Yin J., Hickey L., Rank D., McCalmon S., Hagerman R.J., Tassone F., Hagerman P.J. Sequencing the unsequenceable: expanded CGG-repeat alleles of the fragile X gene. Genome Res. 2013, 23:121-128.
58. Flusberg B.A., Webster D.R., Lee J.H., Travers K.J., Olivares E.C., Clark T.A., Korlach J., Turner S.W. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat. Methods 2010, 7:461-465.
59. Clark T.A., Spittle K.E., Turner S.W., Korlach J., et al. Direct detection and sequencing of damaged DNA bases. Genome Biol. 2011, 2.
60. Murray I.A., Clark T.A., Morgan R.D., Boitano M., Anton B.P., Luong K., Fomenkov A., Turner S.W., Korlach J., Roberts R.J. The methylomes of six bacteria. Nucleic Acids Res. 2012, 40:11450-11462.
61. Fang G., Munera D., Friedman D.I., Mandlik A., Chao M.C., Banerjee O., Feng Z., Losic B., Mahajan M.C., Jabado O.J., et al. Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nat. Biotechnol. 2012, 30(12):1232-1239.
62. Clark T.A., Lu X., Luong K., Dai Q., Boitano M., Turner S.W., He C., Korlach J. Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tet1 oxidation. BMC Biol. 2013, 11:4.
63. Sharon D., Tilgner H., Grubert F., Snyder M. A single-molecule long-read survey of the human transcriptome. Natl. Biotechnol. Adv. Online Publ. 2013, 31(11):1009-1014.
64. Shendure J., Porreca G.J., Reppas N.B., Lin X., McCutcheon J.P., Rosenbaum A.M., Wang M.D., Zhang K., Mitra R.D., Church G.M. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 2005, 309:1728-1732.
65. Metzker M.L. Sequencing technologies-the next generation. Nat. Rev. Genet. 2009, 11:31-46.
66. Margulies M., Egholm M., Altman W.E., Attiya S., Bader J.S., Bemben L.A., Berka J., Braverman M.S., Chen Y.-J., Chen Z., et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-380.