Overview of DNA Sequencing Strategies

Jay A. Shendure1, Gregory J. Porreca2, George M. Church3, Andrew F. Gardner4, Cynthia L. Hendrickson5, Jan Kieleczawa6, Barton E. Slatko4

1 Department of Genome Sciences, University of Washington, Seattle, Washington, 2 Good Start Genetics, Inc., Cambridge, Massachusetts, 3 Department of Genetics, Harvard Medical School, Boston, Massachusetts, 4 New England Biolabs, Ipswich, Massachusetts, 5 HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, 6 Wyzer Biosciences, Cambridge, Massachusetts
Publication Name:  Current Protocols in Molecular Biology
Unit Number:  Unit 7.1
DOI:  10.1002/0471142727.mb0701s96
Online Posting Date:  October, 2011
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Efficient and cost‐effective DNA sequencing technologies are critical to the progress of molecular biology. This overview of DNA sequencing strategies provides a high‐level review of seven distinct approaches to DNA sequencing: (a) dideoxy sequencing; (b) solid phase sequencing; (c) sequencing‐by‐hybridization; (d) mass spectrometry; (e) cyclic array sequencing; (f) microelectrophoresis; and (g) nanopore sequencing. Other platforms currently in development are also briefly described. The primary focus here is on Sanger dideoxy sequencing, which has been the dominant technology since 1977, and on cyclic array strategies, for which several competitive implementations have been developed since 2005. Because the field of DNA sequencing is changing rapidly, this unit represents a snapshot as of September, 2011. Curr. Protoc. Mol. Biol. 96:7.1.1‐7.1.23. © 2011 by John Wiley & Sons, Inc.

Keywords: DNA sequencing; next‐generation sequencing; polony; cyclic array sequencing; genomics; sequencing by ligation; nanopore sequencing

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Table of Contents

  • Introduction
  • DNA Sequencing Strategies
  • Choosing a Sequencing Strategy
  • Platforms
  • Handling NextGen Sequence Data
  • Additional Technologies on the Horizon
  • Literature Cited
  • Figures
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Literature Cited

Literature Cited
   Adams, S. and Blakesley, R. 1991. Linear amplification sequencing. Focus (BRL) 13:56‐57.
   Albert, T.J., Dailidiene, D., Dailide, G., Norton, J.E., Kalia, A., Richmond, T.A., Molla, M., Singh, J., Green, R.D., and Berg, D.E. 2005. Mutation discovery in bacterial genomes: Metronidazole resistance in Helicobacter pylori. Nat. Methods 2:951‐953.
   Andries, K., Verhasselt, P., Guillemont, J., Gohlmann, H.W., Neefs, J.M., Winkler, H., Van Gestel, J., Timmerman, P., Zhu, M., Lee, E., Williams, P., de Chaffoy, D., Huitric, E., Hoffner, S., Cambau, E., Truffot‐Pernot, C., Lounis, N., and Jarlier, V. 2005. A diarylquinoline drug active on the ATP synthase of Mycobacterium tuberculosis. Science 307:223‐227.
   Applied, Biosystems. 1989. Model 370 and 370A Automated Sequencer User Bulletin. Applied Biosystems, Foster City, Calif.
   Astier, Y., Braha, O., and 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. 128:1705‐1710.
   Baker, M. 2010. Next‐generation sequencing: Adjusting to data overload. Nat. Methods 7:495‐499.
   Beck, S., O'Keefe, T.O., Coull, J.M., and Koster, H. 1989. Chemiluminescent detection of DNA: Application for DNA sequencing and hybridization. Nucleic Acids Res. 17:5115‐5123.
   Berezikov, E., Thuemmler, F., van Laake, L.W., Kondova, I., Bontrop, R., Cuppen, E., and Plasterk, R.H. 2006. Diversity of microRNAs in human and chimpanzee brain. Nat. Genet. 38:1375‐1377.
   Blazej, R.G., Kumaresan, P., and Mathies, R.A. 2006. Microfabricated bioprocessor for integrated nanoliter‐scale Sanger DNA sequencing. Proc. Natl. Acad. Sci. U.S.A. 103:7240‐7245.
   Branton, D., Deamer, D.W., Marziali, A., Bayley, H., Benner, S.A., Butler, T., Di Ventra, M., Garaj, S., Hibbs, A., Huang, X., Jovanovich, S.B., Krstic, P.S., Lindsay, S., Ling, X.S., Mastrangelo, C.H., Meller, A., Oliver, J.S., Pershin, Y.V., Ramsey, J.M., Riehn, R., Soni, G.V., Tabard‐Cossa, V., Wanunu, M., Wiggin, M., and Schloss, J.A. 2008. The potential and challenges of nanopore sequencing. Nat. Biotechnol. 26:1146‐1153.
   Braslavsky, I., Hebert, B., Kartalov, E., and Quake, S.R. 2003. Sequence information can be obtained from single DNA molecules. Proc. Natl. Acad. Sci. U.S.A. 100:3960‐3964.
   Carothers, A.M., Urlab, G., Mucha, J., Grunburger, D., and Chasin, L.A. 1989. Point mutation analysis in a mammalian gene: Rapid preparation of total RNA, PCR amplification of cDNA and Taq sequencing by a novel method. BioTechniques 7:494‐499.
   Chen, E.Y. and Seeburg, P.H. 1985. Supercoil sequencing: A fast and simple method for sequencing plasmid DNA. DNA (N.Y.) 4:165‐170.
   Chin, C.S., Sorenson, J., Harris, J.B., Robins, W.P., Charles, R.C., Jean‐Charles, R.R., Bullard, J., Webster, D.R., Kasarskis, A., Peluso, P., Paxinos, E.E., Yamaichi, Y., Calderwood, S.B., Mekalanos, J.J., Schadt, E.E., and Waldor, M.K. 2011. The origin of the Haitian cholera outbreak strain. N. Engl. J. Med. 364:33‐42.
   Church, G. and Gilbert, W. 1984. Genomic sequencing. Proc. Natl. Acad. Sci. U.S.A. 81:1991‐1995.
   Church, G. and Kiefer‐Higgins, S. 1988. Multiplex DNA sequencing. Science 240:185‐188.
   Craxton, M. 1993. Cosmid sequencing. Methods Mol. Biol. 23:149‐167.
   Creasey, A., D'Angio, L.M., Dunne, T., Kissinger, C., O'Keefe, T., Perry‐O'Keefe, H., Moran, L., Roskey, M., Shildkraut, I., Sears, L., and Slatko, B. 1991. Application of a novel chemiluminescent‐based DNA detection method to single‐vector and multiplex DNA sequencing. BioTechniques 11:102‐109.
   Deamer, D.W. and Akeson, M. 2000. Nanopores and nucleic acids: Prospects for ultrarapid sequencing. Trends Biotechnol. 18:147‐151.
   Derrington, I.M., Butler, T.Z., Collins, M.D., Manrao, E., Pavlenok, M., Niederweis, M., and Gundlach, J.H. 2010. Nanopore DNA sequencing with MspA. Proc. Natl. Acad. Sci. U.S.A. 107:16060‐16065.
   Diehl, F., Li, M., Dressman, D., He, Y., Shen, D., Szabo, S., Diaz, L.A. Jr., Goodman, S.N., David, K.A., Juhl, H., Kinzler, K.W., and Vogelstein, B. 2005. Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proc. Natl. Acad. Sci. U.S.A. 102:16368‐16373.
   Diehl, F., Li, M., He, Y., Kinzler, K.W., Vogelstein, B., and Dressman, D. 2006. BEAMing: Single molecule PCR on microparticles in water‐in‐oil emulsions. Nat. Methods 3:551‐559.
   Dressman, D., Yan, H., Traverso, G., Kinzler, K.W., and Vogelstein, B. 2003. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc. Natl. Acad. Sci. U.S.A. 100:8817‐8822.
   Drmanac, R., Sparks, A.B., Callow, M.J., Halpern, A.L., Burns, N.L., Kermani, B.G., Carnevali, P., Nazarenko, I., Nilsen, G.B., Yeung, G., Dahl, F., Fernandez, A., Staker, B., Pant, K.P., Baccash, J., Borcherding, A.P., Brownley, A., Cedeno, R., Chen, L., Chernikoff, D., Cheung, A., Chirita, R., Curson, B., Ebert, J.C., Hacker, C.R., Hartlage, R., Hauser, B., Huang, S., Jiang, Y., Karpinchyk, V., Koenig, M., Kong, C., Landers, T., Le, C., Liu, J., McBride, C.E., Morenzoni, M., Morey, R.E., Mutch, K., Perazich, H., Perry, K., Peters, B.A., Peterson, J., Pethiyagoda, C.L., Pothuraju, K., Richter, C., Rosenbaum, A.M., Roy, S., Shafto, J., Sharanhovich, U., Shannon, K.W., Sheppy, C.G., Sun, M., Thakuria, J.V., Tran, A., Vu, D., Zaranek, A.W., Wu, X., Drmanac, S., Oliphant, A.R., Banyai, W.C., Martin, B., Ballinger, D.G., Church, G.M., and Reid, C.A. 2010. Complete genomics: Human genome sequencing using unchained base reads on self‐assembling DNA nanoarrays. Science 327:78‐81.
   Du, L. and Egholm, M. 2008. The next generation genome sequencing: 454/Roche GS FLX. In Next‐generation Genome Sequencing and Analysis: Towards Personalized Medicine ( M. Janitz, ed). pp. 43‐56. Wiley‐Blackwell, Malden, Massachusetts.
   Edwards, J. 2008. Polony sequencing: history, technology and applications. In Next‐generation Genome Sequencing and Analysis: Towards Personalized Medicine ( M. Janitz, ed). pp. 57‐76. Wiley‐Blackwell, Malden, Massachusetts.
   Edwards, J.R., Ruparel, H., and Ju, J. 2005. Mass spectrometry DNA sequencing. Mutat. Res. 573:3‐12.
   Edwards, R.A., Rodriguez‐Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D.M., Saar, M.O., Alexander, S., Alexander, E.C. Jr., and Rohwer, F. 2006. Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 7:57.
   Emrich, C.A., Tian, H., Medintz, I.L., and Mathies, R.A. 2002. Microfabricated 384‐lane capillary array electrophoresis bioanalyzer for ultra high‐throughput genetic analysis. Anal. Chem. 74:5076‐5083.
   Evans, S. 1991. Millipore's system speeds up DNA sequencing and eliminates radioactivity. Genet. Eng. News 14:29‐41.
   Fedurco, M., Romieu, A., Williams, S., Lawrence, I., and Turcatti, G. 2006. BTA, a novel reagent for DNA attachment on glass and efficient generation of solid‐phase amplified DNA colonies. Nucleic Acids Res. 34:e22.
   Flicek, P. and Birney, E. 2009. Sense from sequence reads: Methods for alignment and assembly. Nat. Methods 6:S6‐S12.
   Fologea, D., Gershow, M., Ledden, B., McNabb, D.S., Golovchenko, J.A., and Li, J. 2005. Detecting single stranded DNA with a solid state nanopore. Nano. Lett. 5:1905‐1909.
   Forster, R., Fredlake, C. and Barron, A. 2008. Microchip‐based Sanger sequencing of DNA. In Next‐generation Genome Sequencing and Analysis: Towards Personalized Medicine ( M. Janitz, ed). pp. 153‐163. Wiley‐Blackwell, Malden, Massachusetts.
   Goldberg, S.M., Johnson, J., Busam, D., Feldblyum, T., Ferriera, S., Friedman, R., Halpern, A., Khouri, H., Kravitz, S.A., Lauro, F.M., Li, K., Rogers, Y.H., Strausberg, R., Sutton, G., Tallon, L., Thomas, T., Venter, E., Frazier, M., and Venter, J.C. 2006. A Sanger/pyrosequencing hybrid approach for the generation of high‐quality draft assemblies of marine microbial genomes. Proc. Natl. Acad. Sci. U.S.A. 103:11240‐11245.
   Grabherr, M.G., Haas, B.J., Yassour, M., Levin, J.Z., Thompson, D.A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., Chen, Z., Mauceli, E., Hacohen, N., Gnirke, A., Rhind, N., di Palma, F., Birren, B.W., Nusbaum, C., Lindblad‐Toh, K., Friedman, N., and Regev, A. 2011. Full‐length transcriptome assembly from RNA‐Seq data without a reference genome. Nat. Biotechnol. 29:644‐652.
   Gresham, D., Ruderfer, D.M., Pratt, S.C., Schacherer, J., Dunham, M.J., Botstein, D., and Kruglyak, L. 2006. Genome‐wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science 311:1932‐1936.
   Haltiner, M., Kempe, T., and Tjian, R. 1985. A novel strategy for constructing clustered point mutations. Nucleic Acids Res. 13:1015‐1025.
   Hardin, S. 2008. Real‐time DNA sequencing. In Next‐generation Genome Sequencing and Analysis: Towards Personalized Medicine ( M. Janitz, ed). pp. 97‐101. Wiley‐Blackwell, Malden, Massachusetts.
   Hattori, M. and Sakaki, Y. 1986. Dideoxy DNA sequencing method using denatured plasmid templates. Anal. Biochem. 152:232‐238.
   Heiner, C.R., Hunkapiller, K.L., Chen, S.M., Glass, J.I., and Chen, E.Y. 1998. Sequencing multimegabase‐template DNA with BigDye terminator chemistry. Genome Res. 8:557‐561.
   Herring, C.D., Raghunathan, A., Honisch, C., Patel, T., Applebee, M.K., Joyce, A.R., Albert, T.J., Blattner, F.R., van den Boom, D., Cantor, C.R., and Palsson, B.Ø. 2006. Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat. Genet. 38:1406‐1412.
   Hoffman, L. and Jendrisak, J. 1999. Transposon‐based strategies for efficient DNA sequencing and functional Genomics. Epicentre Forum 6:1‐4.
   Hornblower, B., Coombs, A., Whitaker, R.D., Kolomeisky, A., Picone, S.J., Meller, A., and Akeson, M. 2007. Single‐molecule analysis of DNA‐protein complexes using nanopores. Nat. Methods 4:315‐317.
   Hultman, T., Stahl, S., Hornes, E., and Uhlen, M. 1989. Direct solid phase sequencing of genomic and plasmid DNA using magnetic beads as solid support. Nucleic Acids Res. 17:4937‐4946.
   Hultman, T., Bergh, S., Moks, T., and Uhlen, M. 1991. Bidirectional solid phase sequencing of in vitro amplified plasmid DNA. BioTechniques 10:84‐93.
   Hyman, E.D. 1988. A new method of sequencing DNA. Anal. Biochem. 174:423‐436.
   Igartua, C., Turner, E.H., Ng, S.B., Hodges, E., Hannon, G.J., Bhattacharjee, A., Rieder, M.J., Nickerson, D.A., and Shendure, J. 2010. Targeted enrichment of specific regions in the human genome by array hybridization. Curr. Protoc. Hum. Genet. 66:18.3.1‐18.3.14.
   Jones, D.S., Schofield, J.P., and Vaudin, M. 1991. Fluorescent and radioactive solid phase dideoxy sequencing of PCR products in microtitre plates. J. DNA Seq. Map. 1:279‐283.
   Ju, J. 1999. Nucleic acid sequencing with solid phase capturable terminators. U.S. Patent number. 5,876,936.
   Ju, J., Ruan, C., Fuller, C.W., Glazer, A.N., and Mathies, R.A. 1995. Energy transfer fluorescent dye‐labeled primers for DNA sequencing and analysis. Proc. Natl. Acad. Sci. U.S.A. 92:4347‐4351.
   Ju, J., Glazer, A.N., and Mathies, R.A. 1996. Energy transfer primers: A new fluorescence labeling paradigm for DNA sequencing and analysis. Nature Med. 2:246‐249.
   Ju, J., Zaro, M., Doctorelo, M., Goralski, T., Konrad, K., Lachenmeier, E., and Cathcart, R. 1997. DNA sequencing with solid phase capturable terminators. Microb. Comp. Genomics 2:223.
   Ju, J., Kim, D., Bi, L., Meng, Q., Bai, X, Li, Z., Li, X., marma, M., Shi, S., Wu, J., Edwards, J., Romu, A., and Turro, N. 2006. Four‐color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators. Proc. Natl. Acad Sci. U.S.A. 103:19635‐19640.
   Kaneoka, H., Lee, D.R., Hsu, K.‐C., Sharp, G.C., and Hoffman, R.W. 1991. Solid phase DNA sequencing of allele specific polymerase chain reaction amplified HLA‐DR genes. BioTechniques 10:30‐40.
   Kasianowicz, J.J., Brandin, E., Branton, D., and Deamer, D.W. 1996. Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl. Acad. Sci. U.S.A. 93:13770‐13773.
   Kothiyal, P., Cox, S., Ebert, J., Aronow, B., Greinwald, J., and Rehm, H. 2009. An overview of custom array sequencing. Curr. Protoc. Hum. Genet. 61:7.17.1‐7.17.11.
   Krishnan, B.R., Blakesley, R.W., and Berg, D.E. 1991. Linear amplification DNA sequencing directly from single phage plaques and bacterial colonies. Nucleic Acids. Res. 19:1153.
   Lakdawalla, A. and VanSternhouse, H. 2008. Illumina genome analyzer II system. In Next‐generation Genome Sequencing and Analysis: Towards Personalized Medicine ( M. Janitz, ed). pp. 13‐28. Wiley‐Blackwell, Malden, Massachusetts.
   Lee, L.G., Spurgeon, S.L., Heiner, C.R., Benson, S.C., Rosenblum, B.B., Menchen, S.M., Graham, R.J., Constantinescu, A., Upadhya, K.G., and Cassel, J.M. 1997. New energy transfer dyes for DNA sequencing. Nucleic Acids Res. 25:2816‐2822.
   Levene, M.J., Korlach, J., Turner, S.W., Foquet, M., Craighead, H.G., and Webb, W.W. 2003. Zeromode waveguides for single‐molecule analysis at high concentrations. Science 299:682‐686.
   Li, M., Diehl, F., Dressman, D., Vogelstein, B., and Kinzler, K.W. 2006. BEAMing up for detection and quantification of rare sequence variants. Nat. Methods 3:95‐97.
   Lieberman, K., Cherf, G., Doody, M., Olasagasti, F., Kolodji, Y., and Akeson, M. 2010. Processive replication of single DNA molecules in a nanopore catalyzed by phi29 DNA polymerase. J. Am. Chem. Soc. 132:17961‐17972.
   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., Dewell, S.B., Du, L., Fierro, J.M., Gomes, X.V., Godwin, B.C., He, W., Helgesen, S., Ho, C.H., Irzyk, G.P., Jando, S.C., Alenquer, M.L., Jarvie, T.P., Jirage, K.B., Kim, J.B., Knight, J.R., Lanza, J.R., Leamon, J.H., Lefkowitz, S.M., Lei, M., Li, J., Lohman, K.L., Lu, H., Makhijani, V.B., McDade, K.E., McKenna, M.P., Myers, E.W., Nickerson, E., Nobile, J.R., Plant, R., Puc, B.P., Ronan, M.T., Roth, G.T., Sarkis, G.J., Simons, J.F., Simpson, J.W., Srinivasan, M., Tartaro, K.R., Tomasz, A., Vogt, K.A., Volkmer, G.A., Wang, S.H., Wang, Y., Weiner, M.P., Yu, P., Begley, R.F., and Rothberg, J.M. 2005. Genome sequencing in microfabricated high‐density picolitre reactors. Nature 437:376‐380.
   Marra, M., Weinstock, L.A., and Mardis, E.R. 1996. End sequence determination from large insert clones using energy transfer fluorescent primers. Genome Res. 6:1118‐1122.
   Martin, C., Bresnick, L., Juo, R.‐R., Voyta, J.C., and Bronstein, I. 1991. Improved chemiluminescence DNA sequencing. BioTechniques 11:110‐113.
   McPherson, J. 2009. Next‐generation gap. Nat Methods 6:S2‐S5.
   Medvedev, P., Stanciu, M., and Brudno, M. 2009. Computational methods for discovering structural variation with next‐generation sequencing. Nat. Methods 6:S13‐S20.
   Metzker, M.L. 2010. Sequencing technologies: The next generation. Nat. Rev. Genet. 11:31‐46.
   Mitra, R.D. and Church, G.M. 1999. In situ localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Res. 27:e34.
   Mitra, R.D., Shendure, J., Olejnik, J., Edyta, K.O., and Church, G.M. 2003. Fluorescent in situ sequencing on polymerase colonies. Anal. Biochem. 320:55‐65.
   Moore, G.E. 1965. Cramming more components onto integrated circuits. Electronics 38:4‐7.
   Morrissy, S., Zhao, Y., Delaney, A., Asano, J., Dhalla, N., Li, I., McDonald, H., Pandoh, P., Prabhu, A‐L., Tam, A., and Hirst, M.M. 2010. Digital gene expression by Tag sequencing on the Illumina Genome Analyzer. Curr. Protoc. Hum. Genet. 65:11.11.1‐11.11.36.
   Murray, V. 1989. Improved double‐stranded DNA sequencing using the linear polymerase chain reaction. Nucleic Acids Res. 17:88‐89.
   Nyrén, P. and Lundin, A. 1985. Enzymatic method for continuous monitoring of inorganic pyrophosphate synthesis. Anal. Biochem. 151:504‐509.
   Ozsolak, F. and Milos, P.M. 2011a. RNA sequencing: Advances, challenges and opportunities. Nat. Rev. Genet. 12:87‐98.
   Ozsolak, F. and Milos, P.M. 2011b. Transcriptome profiling using single‐molecule direct RNA sequencing. Methods Mol. Biol. 733:51‐61.
   Paegel, B.M., Blazej, R.G., and Mathies, R.A. 2003. Microfluidic devices for DNA sequencing: Sample preparation and electrophoretic analysis. Curr. Opin. Biotechnol. 14:42‐50.
   Pandey, V., Nutter, R., and Prediger, E. 2008. Applied biosystems SOLiD™ system: Ligation‐based sequencing. In Next‐generation Genome Sequencing and Analysis: Towards Personalized Medicine ( M. Janitz, ed). pp. 20‐42. Wiley‐Blackwell Press, Malden, Massachusetts.
   Patil, N., Berno, A.J., Hinds, D.A., Barrett, W.A., Doshi, J.M., Hacker, C.R., Kautzer, C.R., Lee, D.H., Marjoribanks, C., McDonough, D.P., Nguyen, B.T., Norris, M.C., Sheehan, J.B., Shen, N., Stern, D., Stokowski, R.P., Thomas, D.J., Trulson, M.O., Vyas, K.R., Frazer, K.A., Fodor, S.P., and Cox, D.R. 2001. Blocks of limited haplotype diversity revealed by high resolution scanning of human chromosome 21. Science 294:1719‐1723.
   Pepke, S., Wold, B., and Mortazavi, A. 2009. Computation for ChIP‐seq and RNA‐seq studies. Nat. Methods. 6:S22‐S32.
   Porter, S., Olson, N.E., and Smith, T. 2009. Analyzing gene expression data from microarray and next‐generation DNA sequencing transcriptome profiling assays using GeneSifter Analysis Edition. Curr. Protoc. Bioinformatics 27:7.14.1‐7.14.35.
   Pushkarev, D., Neff, N.F., and Quake, S.R. 2009. Single‐molecule sequencing of an individual human genome. Nat. Biotechnol. 27:847‐850.
   Quail, M., Swerdlow, H., and Turner, D. 2009. Improved protocols for the Illumina Genome Analyzer sequencing system. Curr. Protoc. Hum. Genet. 62:18.2.1‐18.2.27.
   Ragoussis, J., Elvidge, G.P., Kaur, K., and Colella, S. 2006. Matrix‐assisted laser desorption/ionisation, time‐of‐flight mass spectrometry in genomics research. PLoS Genet. 2:e100.
   Raz, T., Causey, M., Jones, D.R., Kieu, A., Letovsky, S., Lipson, D., Thayer, E., Thompson, J.F., Milos, P.M. 2011. RNA sequencing and quantitation using the Helicos Genetic Analysis System. Methods Mol. Biol. 733:37‐49.
   Ronaghi, M., Karamohamed, S., Pettersson, B., Uhlén, M., and Nyrén, P. 1996. Real‐time DNA sequencing using detection of pyrophosphate release. Anal. Biochem. 242:84‐89.
   Rothberg, J.M., Hinz, W., Rearick, T.M., Schultz, J., Mileski, W., Davey, M., Leamon, J.H., Johnson, K., Milgrew, M.J., Edwards, M., Hoon, J., Simons, J.F., Marran, D., Myers, J.W., Davidson, J.F., Branting, A., Nobile, J.R., Puc, B.P., Light, D., Clark, T.A., Huber, M., Branciforte, J.T., Stoner, I.B., Cawley, S.E., 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, J.A., Namsaraev, E., McKernan, K.J., Williams, A., Roth, G.T., and Bustillo, J. 2011. An integrated semiconductor device enabling non‐optical genome sequencing. Nature 47:348‐352
   Ruby, J.G., Jan, C., Player, C., Axtell, M.J., Lee, W., Nusbaum, C., Ge, H., and Bartel, D.P. 2006. Large‐scale sequencing reveals 21U‐RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127:1193‐1207.
   Sanger, F. 1988. Sequences, sequences, and sequences. Annu. Rev. Biochem. 57:1‐28.
   Sanger, F., Nicklen, S., and Coulson, A.R. 1977a. DNA sequencing with chain‐terminating inhibitors. Proc. Natl. Acad. Sci. U.S.A. 74:5463‐5467.
   Sanger, F., Air, G.M., Barrell, B.G., Brown, N.L., Coulson, A.R., Fiddes, C.A., Hutchison, C.A., Slocombe, P.M., and Smith, M. 1977b. Nucleotide sequence of bacteriophage phi X174 DNA. Nature 265:687‐695.
   Schatz, M.C., Langmead, B., and Salzberg, S.L. 2010. Cloud computing and the DNA data race. Nat. Biotechnol. 28:691‐693.
   Sears, L., Moran, L., Kissinger, C., Creasey, T., Perry‐O'Keefe, H., Roskey, M., Sutherland, E., and Slatko, B. 1992. CircumVent™ thermal cycle sequencing and alternative manual and automated DNA sequencing protocols using the highly thermostable VentR (exo−) DNA polym‐ erase. BioTechniques 13:626‐633.
   Shendure, J. and Ji, H. 2008. Next‐generation DNA sequencing. Nat. Biotechnol. 10:1135‐1145.
   Shendure, J., Mitra, R.D., Varma, C., and Church, G.M. 2004. Advanced sequencing technologies: Methods and goals. Nat. Rev. Genet. 5:335‐344.
   Shendure, J., Porreca, G.J., Reppas, N.B., Lin, X., McCutcheon, J.P., Rosenbaum, A.M., Wang, M.D., Zhang, K., Mitra, R.D., and Church, G.M. 2005. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309:1728‐1732.
   Slatko, B. 1996. Thermal cycle dideoxy DNA sequencing. Mol. Biotechnol. 6:311‐322.
   Smith, M.G., Gianoulis, T.A., Pukatzki, S., Mekalanos, J.J., Ornston, L.N., Gerstein, M., and Snyder, M. 2007. New insights into Acinetobacter baumannii pathogenesis revealed by high density pyrosequencing and transposon mutagenesis. Genes. Dev. 21:601‐614.
   Stein, LD. 2010. The case for cloud computing in genome informatics. Genome Biol. 11:207.
   Steinmann, K.E., Hart, C.E., Thompson, J.F., and Milos, P.M. 2011. Helicos single‐molecule sequencing of bacterial genomes. Methods Mol. Biol. 733:3‐24.
   Strathmann, M., Hamilton, B., Mayeda, C., Simon, M., Meyerowitz, E., and Palazzolo, M. 1991. Transposon‐facilitated DNA sequencing. Proc. National Acad. Sci. U.S.A. 88:1247‐1250.
   Tabor, S. and Richardson, C.C. 1987a. Selective oxidation of the exonuclease domain of bacteriophage T7 DNA polymerase. J. Biol. Chem. 262:15330‐15333.
   Tabor, S. and Richardson, C.C. 1987b. DNA sequence analysis with a modified bacteriophage T7 DNA polymerase. Proc. Natl. Acad. Sci. U.S.A. 84:4767‐4771.
   Tabor, S. and Richardson, C.C. 1989a. Selective inactivation of the exonuclease activity of bacteriophage T7 DNA polymerase by in vitro mutagenesis. J. Biol. Chem. 264:6447‐6458.
   Tabor, S. and Richardson, C.C. 1989b. Effect of manganese ions on the incorporation of dideoxynucleotides by bacteriophage T7 DNA polymerase and Escherichia coli DNA polymerase I. Proc. Natl. Acad. Sci. U.S.A. 86:4076‐4080.
   Tabor, S. and Richardson, C.C. 1990. DNA sequence analysis with a modified bacteriophage T7 DNA polymerase: Effect of pyrophosphorolysis and metal ions. J. Biol. Chem. 265:8322‐8328.
   Tabor, S., Huber, H., and Richardson, C.C. 1987. Escherichia coli thioredoxin confers processivity of the DNA polymerase activity of the gene 5 protein of bacteriophage T7. J. Biol. Chem. 262:16212‐16223.
   Tanaka, H. and Kawa, T. 2009. Partial sequencing of a single DNA molecule with a scanning tunnelling microscope. Nat. Nanotechnol. 4:518‐522.
   Tawfik, D.S. and Griffiths, A.D. 1998. Man‐made cell‐like compartments for molecular evolution. Nat. Biotechnol. 16:652‐656.
   Tehrani, R. 2000. As we may communicate. TMCNet, http://www.tmcnet.com/articles/comsol/0100/0100pubout.htm.
   Thomas, W. and Glover, W. 2008. Direct sequencing by TEM of z‐substituted DNA molecule. In Next‐generation Genome Sequencing and Analysis: Towards Personalized Medicine ( M. Janitz, ed.) pp. 103‐116. Wiley‐Blackwell, Malden, Massachusetts.
   Tizard, R., Cate, R.L., Ramachandran, K.L., Wysek, M., Voyta, J.C., Murphy, O.J., and Bronstein, I. 1990. Imaging of DNA sequences with chemiluminescence. Proc. Natl. Acad. Sci. U.S.A. 87:4514‐4518.
   Valdar, W., Solberg, L.C., Gauguier, D., Burnett, S., Klenerman, P., Cookson, W.O., Taylor, M.S., Rawlins, J.N., Mott, R., and Flint, J. 2006. Genome‐wide genetic association of complex traits in heterogeneous stock mice. Nat. Genet. 38:879‐887.
   Velicer, G.J., Raddatz, G., Keller, H., Deiss, S., Lanz, C., Dinkelacker, I., and Schuster, S.C. 2006. Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor. Proc. Natl. Acad. Sci. U.S.A. 103:8107‐8112.
   Vercoutere, W., Winters‐Hilt, S., Olsen, H., Deamer, D., Haussler, D., and Akeson, M. 2001. Rapid discrimination among individual DNA hairpin molecules at single‐nucleotide resolution using an ion channel. Nat. Biotechnol. 19:248‐252.
   Walter, C. 2005. Kryder's Law. Sci. Am. 293:32‐33.
   Wanunu, M., Cohen‐Karni, D., Johnson, R., Fields, F., Benner, J., Peterman, N., Zheng, Y., Klein, M., and Drndic, M. 2010. Discrimination of methylcytosine from hydroxymethylcytosine in individual DNA Molecule J. Am. Chem. Soc. 133:486‐492.
   Wiley, G., Macmil, S., Qu, C., Wang, P., Xing, Y., White, D., Li, J., White, J.D., Domingo, A., and Roe, B.A. 2009. Methods for generating shotgun and mixed shotgun/paired‐end libraries for the 454 DNA sequencer. Curr. Protoc. Hum. Genet. 61:18.1.1‐18.1.21.
   Winters‐Hilt, S., Vercoutere, W., DeGuzman, V.S., Deamer, D., Akeson, M., and Haussler, D. 2003. Highly accurate classification of Watson‐Crick basepairs on termini of single DNA molecules. Biophys. J. 84:967‐976.
   Xiao, M. and Kwok, P‐Y. 2008. A single DNA molecule barcoding method with applications in DNA mapping and molecular haplotyping. In: Next‐Generation Genome Sequencing and Analysis: Towards Personalized Medicine ( M. Janitz, ed.) pp. 117‐132. Wiley‐Blackwell, Malden, Massachusetts.
   Young, A. and Blakesley, R. 1991. Sequencing plasmids from single colonies with the dsDNA cycle sequencing system. Focus (BRL) 13:137.
   Zagursky, R., Baumeister, K., Lomax, N., and Berman, M. 1985. Rapid and easy sequencing of large double‐stranded DNA and supercoiled plasmid DNA. Gene Anal. Tech. 2:89‐94.
   Zagursky, R.J., Conway, P.S., and Kashdan, M.A. 1991. Use of 33P for Sanger DNA sequencing. BioTechniques 11:36‐38.
   Zimmerman, J., Dietrich, T., Voss, H., Erfle, H., Schwager, C., Stegemann, J., Hewitt, N., and Ansorge, W. 1992. Fully automated Sanger sequencing protocol for double‐stranded DNA. Methods Mol. Cell Biol. 3:39‐42.
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