Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

DNA sequencing at 40: past, present and future

A Publisher Correction to this article was published on 04 April 2019

Abstract

This review commemorates the 40th anniversary of DNA sequencing, a period in which we have already witnessed multiple technological revolutions and a growth in scale from a few kilobases to the first human genome, and now to millions of human and a myriad of other genomes. DNA sequencing has been extensively and creatively repurposed, including as a ‘counter’ for a vast range of molecular phenomena. We predict that in the long view of history, the impact of DNA sequencing will be on a par with that of the microscope.

Your institute does not have access to this article

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: DNA sequencing technologies.
Figure 2: DNA sequencing applications.

References

  1. Sanger, F. Sequences, sequences, and sequences. Annu. Rev. Biochem. 57, 1–28 (1988)

    CAS  PubMed  Article  Google Scholar 

  2. Sanger, F. Nobel lecture: the chemistry of insulin. https://www.nobelprize.org/nobel_prizes/chemistry/laureates/1958/sanger-lecture.html (2017)

  3. Edman, P. Method for determination of the amino acid sequence in peptides. Acta Chem. Scand. 4, 283–293 (1950)

    CAS  Article  Google Scholar 

  4. Holley, R. W. et al. Structure of a ribonucleic acid. Science 147, 1462–1465 (1965)

    ADS  CAS  PubMed  Article  Google Scholar 

  5. Sanger, F., Brownlee, G. G. & Barrell, B. G. A two-dimensional fractionation procedure for radioactive nucleotides. J. Mol. Biol. 13, 373–398 (1965)

    CAS  PubMed  Article  Google Scholar 

  6. Wu, R. & Kaiser, A. D. Structure and base sequence in the cohesive ends of bacteriophage lambda DNA. J. Mol. Biol. 35, 523–537 (1968)

    CAS  PubMed  Article  Google Scholar 

  7. Gilbert, W. & Maxam, A. The nucleotide sequence of the lac operator. Proc. Natl Acad. Sci. USA 70, 3581–3584 (1973)

    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

  8. Sanger, F., Nicklen, S. & Coulson, A. R. DNA sequencing with chain-terminating inhibitors. Proc. Natl Acad. Sci. USA 74, 5463–5467 (1977). Refs 8, 9 : The seminal papers by Sanger, Nicklen & Coulson and Maxam & Gilbert describing the first widely adopted methods for DNA sequencing.

    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

  9. Maxam, A. M. & Gilbert, W. A new method for sequencing DNA. Proc. Natl Acad. Sci. USA 74, 560–564 (1977)

    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

  10. Maniatis, T., Jeffrey, A. & van deSande, H. Chain length determination of small double- and single-stranded DNA molecules by polyacrylamide gel electrophoresis. Biochemistry 14, 3787–3794 (1975)

    CAS  PubMed  Article  Google Scholar 

  11. Staden, R. A strategy of DNA sequencing employing computer programs. Nucleic Acids Res. 6, 2601–2610 (1979)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  12. Messing, J., Crea, R. & Seeburg, P. H. A system for shotgun DNA sequencing. Nucleic Acids Res. 9, 309–321 (1981)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  13. Sanger, F., Coulson, A. R., Hong, G. F., Hill, D. F. & Petersen, G. B. Nucleotide sequence of bacteriophage lambda DNA. J. Mol. Biol. 162, 729–773 (1982)

    CAS  PubMed  Article  Google Scholar 

  14. Smith, L. M. et al. Fluorescence detection in automated DNA sequence analysis. Nature 321, 674–679 (1986)

    ADS  CAS  PubMed  Article  Google Scholar 

  15. Connell, C. et al. Automated DNA sequence analysis. Biotechniques 5, 342–348 (1987)

    CAS  Google Scholar 

  16. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990)

    CAS  PubMed  Article  Google Scholar 

  17. Prober, J. M. et al. A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. Science 238, 336–341 (1987)

    ADS  CAS  PubMed  Article  Google Scholar 

  18. Tabor, S. & Richardson, C. C. DNA sequence analysis with a modified bacteriophage T7 DNA polymerase. Proc. Natl Acad. Sci. USA 84, 4767–4771 (1987)

    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

  19. Craxton, M. Linear amplification sequencing, a powerful method for sequencing DNA. Methods 3, 20–26 (1991)

    CAS  Article  Google Scholar 

  20. DeAngelis, M. M., Wang, D. G. & Hawkins, T. L. Solid-phase reversible immobilization for the isolation of PCR products. Nucleic Acids Res. 23, 4742–4743 (1995)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  21. Zhang, J. et al. Use of non-cross-linked polyacrylamide for four-color DNA sequencing by capillary electrophoresis separation of fragments up to 640 bases in length in two hours. Anal. Chem. 67, 4589–4593 (1995)

    CAS  PubMed  Article  Google Scholar 

  22. Green, P. phred, phrap, consed. http://www.phrap.org/phredphrapconsed.html (2017). phred introduced quantitative, reliable metrics for base quality, substituting human judgement with computers, a process that occurred repeatedly over the course of the HGP.

  23. Edwards, A. et al. Automated DNA sequencing of the human HPRT locus. Genomics 6, 593–608 (1990)

    CAS  PubMed  Article  Google Scholar 

  24. Sutton, G. G., White, O., Adams, M. D. & Kerlavage, A. R. TIGR assembler: a new tool for assembling large shotgun sequencing projects. Genome Sci. Technol. 1, 9–19 (1995)

    CAS  Article  Google Scholar 

  25. Myers, E. W. et al. A whole-genome assembly of Drosophila. Science 287, 2196–2204 (2000). The Celera assembler introduced an overlap–layout–consensus approach to deal with the problems posed by repeats and the millions of reads needed to produce a reliable assembly.

    ADS  CAS  PubMed  Article  Google Scholar 

  26. Fleischmann, R. D. et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496–512 (1995)

    ADS  CAS  PubMed  Article  Google Scholar 

  27. Goffeau, A. et al. Life with 6000 genes. Science 274, 546–567 (1996)

    ADS  CAS  PubMed  Article  Google Scholar 

  28. The C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012–2018 (1998)

  29. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001). Refs 29 : The HGP and Celera produced draft sequences of the human genome with the HGP later publishing a more complete, relatively error-free reference.

  30. International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431, 931–945 (2004)

  31. Venter, J. C. et al. The sequence of the human genome. Science 291, 1304–1351 (2001)

    ADS  CAS  PubMed  Article  Google Scholar 

  32. Adams, M. D. et al. The genome sequence of Drosophila melanogaster. Science 287, 2185–2195 (2000)

    PubMed  Article  Google Scholar 

  33. Balasubramanian, S., Klenerman, D. & Barnes, C. Arrayed polynucleotides and their use in genome analysis. Patent US20030022207 (2003)

  34. Braslavsky, I., Hebert, B., Kartalov, E. & Quake, S. R. Sequence information can be obtained from single DNA molecules. Proc. Natl Acad. Sci. USA 100, 3960–3964 (2003)

    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

  35. Harris, T. D. et al. Single-molecule DNA sequencing of a viral genome. Science 320, 106–109 (2008)

    ADS  CAS  PubMed  Article  Google Scholar 

  36. Adams, C. P. & Kron, S. J. Method for performing amplification of nucleic acid with two primers bound to a single solid support. Patent US5641658 (1997)

  37. Chetverina, H. V. & Chetverin, A. B. Cloning of RNA molecules in vitro. Nucleic Acids Res. 21, 2349–2353 (1993)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  38. Mitra, R. D. & Church, G. M. In situ localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Res. 27, e34–e39 (1999)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  39. Adessi, C. et al. Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms. Nucleic Acids Res. 28, e87 (2000)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  40. Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380 (2005). Refs 40, 41 : These papers described the first integrated systems for next-generation DNA sequencing.

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  41. Shendure, J. et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309, 1728–1732 (2005)

    ADS  CAS  PubMed  Article  Google Scholar 

  42. 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. USA 100, 8817–8822 (2003)

    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

  43. Drmanac, R. et al. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 327, 78–81 (2010)

    ADS  CAS  PubMed  Article  Google Scholar 

  44. Ronaghi, M., Karamohamed, S., Pettersson, B., Uhlén, M. & Nyrén, P. Real-time DNA sequencing using detection of pyrophosphate release. Anal. Biochem. 242, 84–89 (1996)

    CAS  PubMed  Article  Google Scholar 

  45. Toumazou, C. & Purushothaman, S. Sensing apparatus and method. Patent US7686929 (2004)

  46. Rothberg, J. M., Hinz, W., Johnson, K. L. & Bustillo, J. Apparatus for measuring analytes using large scale FET arrays. Patent EP2639579 (2016)

  47. Brenner, S. et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol. 18, 630–634 (2000)

    ADS  CAS  PubMed  Article  Google Scholar 

  48. McKernan, K. J. et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res. 19, 1527–1541 (2009)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  49. Mitra, R. D., Shendure, J., Olejnik, J., Edyta-Krzymanska-Olejnik, & Church, G. M. Fluorescent in situ sequencing on polymerase colonies. Anal. Biochem. 320, 55–65 (2003)

    CAS  PubMed  Article  Google Scholar 

  50. Ost, T. B. et al. Improved polymerases. Patent WO2006120433 (2006)

  51. Ruparel, H. et al. Design and synthesis of a 3′-O-allyl photocleavable fluorescent nucleotide as a reversible terminator for DNA sequencing by synthesis. Proc. Natl Acad. Sci. USA 102, 5932–5937 (2005)

    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

  52. Seo, T. S. et al. Four-color DNA sequencing by synthesis on a chip using photocleavable fluorescent nucleotides. Proc. Natl Acad. Sci. USA 102, 5926–5931 (2005)

    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

  53. Barnes, C., Balasubramanian, S., Liu, X., Swerdlow, H. & Milton, J. Labelled nucleotides. Patent US7057026 (2006)

  54. Smith, T. J. Cloned single molecule sequencing with reversible terminator chemistry.Genome Sequencing and Analysis Conference (2015).

  55. Bentley, D. R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53–59 (2008). Advances in sequencing-by-synthesis culminated in the Solexa, later Illumina, platform, which quickly became, and remains today, the most widely used sequencing instrument.

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  56. Wetterstrand, K. DNA sequencing costs: data from the NHGRI Genome Sequencing Program (GSP). http://www.genome.gov/sequencingcostsdata (2017)

  57. Levene, M. J . et al. Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299, 682–686 (2003). One of earliest real time observations of DNA synthesis in single molecules, using fluorescently labelled nucleotides and a DNA polymerase anchored in zero-mode waveguides, which with further development led to the PacBio platform.

    ADS  CAS  PubMed  Article  Google Scholar 

  58. Eid, J. et al. Real-time DNA sequencing from single polymerase molecules. Science 323, 133–138 (2009)

    ADS  CAS  Article  PubMed  Google Scholar 

  59. Deamer, D., Akeson, M. & Branton, D. Three decades of nanopore sequencing. Nat. Biotechnol. 34, 518–524 (2016)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  60. Bayley, H. Nanopore sequencing: from imagination to reality. Clin. Chem. 61, 25–31 (2015)

    CAS  PubMed  Article  Google Scholar 

  61. Church, G., Deamer, D. W., Branton, D., Baldarelli, R. & Kasianowicz, J. Characterization of individual polymer molecules based on monomer-interface interactions. Patent US5795782 (1998). The concept of ssDNA modulating an electronic signal while moving through a membrane pore led eventually to practical nanopore sequencing.

  62. Branton, D. et al. The potential and challenges of nanopore sequencing. Nat. Biotechnol. 26, 1146–1153 (2008)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  63. Laszlo, A. H. et al. Decoding long nanopore sequencing reads of natural DNA. Nat. Biotechnol. 32, 829–833 (2014)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  64. Jain, M. et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Preprint at https://www.biorxiv.org/content/early/2017/04/20/128835 (2017)

  65. Flusberg, B. A. et al. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat. Methods 7, 461–465 (2010)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  66. Smith, A. M., Jain, M., Mulroney, L., Garalde, D. R. & Akeson, M. Reading canonical and modified nucleotides in 16S ribosomal RNA using nanopore direct RNA sequencing. Preprint at https://www.biorxiv.org/content/early/2017/04/29/132274 (2017)

  67. Garalde, D. R. et al. Highly parallel direct RNA sequencing on an array of nanopores. Preprint at https://www.biorxiv.org/content/early/2016/08/12/068809 (2016)

  68. Nivala, J., Marks, D. B. & Akeson, M. Unfoldase-mediated protein translocation through an α-hemolysin nanopore. Nat. Biotechnol. 31, 247–250 (2013)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  69. Zhao, Y. et al. Single-molecule spectroscopy of amino acids and peptides by recognition tunnelling. Nat. Nanotechnol. 9, 466–473 (2014)

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  70. Wilson, J., Sloman, L., He, Z. & Aksimentiev, A. Graphene nanopores for protein sequencing. Adv. Funct. Mater. 26, 4830–4838 (2016)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  71. Di Ventra, M. & Taniguchi, M. Decoding DNA, RNA and peptides with quantum tunnelling. Nat. Nanotechnol. 11, 117–126 (2016)

    ADS  CAS  PubMed  Article  Google Scholar 

  72. Sanger, F. et al. Nucleotide sequence of bacteriophage phi X174 DNA. Nature 265, 687–695 (1977)

    ADS  CAS  PubMed  Article  Google Scholar 

  73. Schneider, V. A. et al. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Res. 27, 849–864 (2017)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  74. Pevzner, P. A., Tang, H. & Waterman, M. S. An Eulerian path approach to DNA fragment assembly. Proc. Natl Acad. Sci. USA 98, 9748–9753 (2001)

    ADS  MathSciNet  CAS  PubMed  MATH  Article  PubMed Central  Google Scholar 

  75. Zerbino, D. R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821–829 (2008)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  76. Adey, A. et al. In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Res. 24, 2041–2049 (2014)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  77. Mostovoy, Y. et al. A hybrid approach for de novo human genome sequence assembly and phasing. Nat. Methods 13, 587–590 (2016)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  78. Burton, J. N. et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat. Biotechnol. 31, 1119–1125 (2013)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  79. Kaplan, N. & Dekker, J. High-throughput genome scaffolding from in vivo DNA interaction frequency. Nat. Biotechnol. 31, 1143–1147 (2013)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  80. Bickhart, D. M. et al. Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nat. Genet. 49, 643–650 (2017)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  81. Koren, S. et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27, 722–736 (2017)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  82. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  83. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009)

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  84. Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009)

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  85. McKenna, A. et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  86. Chaisson, M. J. et al. Resolving the complexity of the human genome using single-molecule sequencing. Nature 517, 608–611 (2015)

    ADS  CAS  PubMed  Article  Google Scholar 

  87. Snyder, M. W., Adey, A., Kitzman, J. O. & Shendure, J. Haplotype-resolved genome sequencing: experimental methods and applications. Nat. Rev. Genet. 16, 344–358 (2015)

    CAS  PubMed  Article  Google Scholar 

  88. Green, R. E. et al. A draft sequence of the Neandertal genome. Science 328, 710–722 (2010)

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  89. Levy, S. et al. The diploid genome sequence of an individual human. PLoS Biol. 5, e254 (2007)

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  90. Wheeler, D. A. et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 452, 872–876 (2008)

    ADS  CAS  PubMed  Article  Google Scholar 

  91. Wang, J. et al. The diploid genome sequence of an Asian individual. Nature 456, 60–65 (2008)

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  92. Ley, T. J. et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 456, 66–72 (2008)

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  93. Albert, T. J. et al. Direct selection of human genomic loci by microarray hybridization. Nat. Methods 4, 903–905 (2007)

    CAS  PubMed  Article  Google Scholar 

  94. Okou, D. T. et al. Microarray-based genomic selection for high-throughput resequencing. Nat. Methods 4, 907–909 (2007)

    CAS  PubMed  Article  Google Scholar 

  95. Porreca, G. J. et al. Multiplex amplification of large sets of human exons. Nat. Methods 4, 931–936 (2007)

    CAS  PubMed  Article  Google Scholar 

  96. Hodges, E. et al. Genome-wide in situ exon capture for selective resequencing. Nat. Genet. 39, 1522–1527 (2007)

    CAS  PubMed  Article  Google Scholar 

  97. Ng, S. B. et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461, 272–276 (2009). Refs 97, 103, 106 : Targeting all coding sequences or the exome, by PCR and later by exome capture, facilitated the direct discovery of cancer driver genes and Mendelian disease genes.

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  98. The 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061–1073 (2010)

  99. The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 526, 68–74 (2015)

  100. Fu, W. et al. Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature 493, 216–220 (2013)

    ADS  CAS  PubMed  Article  Google Scholar 

  101. Chiu, R. W. et al. Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proc. Natl Acad. Sci. USA 105, 20458–20463 (2008)

    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

  102. Fan, H. C., Blumenfeld, Y. J., Chitkara, U., Hudgins, L. & Quake, S. R. Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proc. Natl Acad. Sci. USA 105, 16266–16271 (2008)

    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

  103. Choi, M. et al. Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc. Natl Acad. Sci. USA 106, 19096–19101 (2009)

    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

  104. Vissers, L. E. L. M., Gilissen, C. & Veltman, J. A. Genetic studies in intellectual disability and related disorders. Nat. Rev. Genet. 17, 9–18 (2016)

    CAS  PubMed  Article  Google Scholar 

  105. Yang, Y. et al. Molecular findings among patients referred for clinical whole-exome sequencing. J. Am. Med. Assoc. 312, 1870–1879 (2014)

    CAS  Article  Google Scholar 

  106. Wood, L. D. et al. The genomic landscapes of human breast and colorectal cancers. Science 318, 1108–1113 (2007)

    ADS  CAS  Article  PubMed  Google Scholar 

  107. Adams, M. D. et al. Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252, 1651–1656 (1991)

    ADS  CAS  PubMed  Article  Google Scholar 

  108. Putney, S. D., Herlihy, W. C. & Schimmel, P. A new troponin T and cDNA clones for 13 different muscle proteins, found by shotgun sequencing. Nature 302, 718–721 (1983)

    ADS  CAS  PubMed  Article  Google Scholar 

  109. Velculescu, V. E., Zhang, L., Vogelstein, B. & Kinzler, K. W. Serial analysis of gene expression. Science 270, 484–487 (1995). The SAGE method captures 3′ tags from mRNAs, therefore introducing the idea of using a DNA sequencer to count molecules, an idea that has exploded with the later introduction of RNA-seq, chromatin immunoprecipitation followed by sequencing (ChIP–seq) and so on.

    ADS  CAS  PubMed  Article  Google Scholar 

  110. Cloonan, N. et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat. Methods 5, 613–619 (2008)

    CAS  PubMed  Article  Google Scholar 

  111. Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523–536 (2008)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  112. Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat. Methods 5, 621–628 (2008)

    CAS  Article  PubMed  Google Scholar 

  113. Nagalakshmi, U. et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344–1349 (2008)

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  114. Wilhelm, B. T. et al. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453, 1239–1243 (2008)

    ADS  CAS  PubMed  Article  Google Scholar 

  115. Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-seq. Bioinformatics 25, 1105–1111 (2009)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  116. Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  117. Johnson, D. S., Mortazavi, A., Myers, R. M. & Wold, B. Genome-wide mapping of in vivo protein–DNA interactions. Science 316, 1497–1502 (2007)

    ADS  CAS  PubMed  Article  Google Scholar 

  118. Boyle, A. P. et al. High-resolution mapping and characterization of open chromatin across the genome. Cell 132, 311–322 (2008)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  119. 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 324, 218–223 (2009)

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  120. Shendure, J. & Lieberman Aiden, E. The expanding scope of DNA sequencing. Nat. Biotechnol. 30, 1084–1094 (2012)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  121. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214 (2012)

  122. Tyson, G. W. et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37–43 (2004)

    ADS  CAS  PubMed  Article  Google Scholar 

  123. Venter, J. C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66–74 (2004)

    ADS  CAS  PubMed  Article  Google Scholar 

  124. Blaser, M., Bork, P., Fraser, C., Knight, R. & Wang, J. The microbiome explored: recent insights and future challenges. Nat. Rev. Microbiol. 11, 213–217 (2013)

    CAS  PubMed  Article  Google Scholar 

  125. Shokralla, S., Spall, J. L., Gibson, J. F. & Hajibabaei, M. Next-generation sequencing technologies for environmental DNA research. Mol. Ecol. 21, 1794–1805 (2012)

    CAS  PubMed  Article  Google Scholar 

  126. Nozaki, H. et al. A 100%-complete sequence reveals unusually simple genomic features in the hot-spring red alga Cyanidioschyzon merolae. BMC Biol. 5, 28 (2007)

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  127. Ovchinnikov, S. et al. Protein structure determination using metagenome sequence data. Science 355, 294–298 (2017)

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  128. Gymrek, M., McGuire, A. L., Golan, D., Halperin, E. & Erlich, Y. Identifying personal genomes by surname inference. Science 339, 321–324 (2013)

    ADS  CAS  PubMed  Article  Google Scholar 

  129. Larsson, C. et al. In situ genotyping individual DNA molecules by target-primed rolling-circle amplification of padlock probes. Nat. Methods 1, 227–232 (2004)

    CAS  PubMed  Article  Google Scholar 

  130. Lee, J. H. et al. Highly multiplexed subcellular RNA sequencing in situ. Science 343, 1360–1363 (2014)

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  131. McKenna, A. et al. Whole-organism lineage tracing by combinatorial and cumulative genome editing. Science 353, aaf7907 (2016)

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  132. Peikon, I. D. et al. Using high-throughput barcode sequencing to efficiently map connectomes. Nucleic Acids Res. 45, e115 (2017)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  133. Shipman, S. L., Nivala, J., Macklis, J. D. & Church, G. M. Molecular recordings by directed CRISPR spacer acquisition. Science 353, aaf1175 (2016)

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  134. Zamft, B. M. et al. Measuring cation dependent DNA polymerase fidelity landscapes by deep sequencing. PLoS ONE 7, e43876 (2012)

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  135. Organick, L. et al. Scaling up DNA data storage and random access retrieval. Preprint at https://www.biorxiv.org/content/early/2017/03/07/114553 (2017)

  136. Harrington, L., Alexander, L. T., Knapp, S. & Bayley, H. Pim kinase inhibitors evaluated with a single-molecule engineered nanopore sensor. Angew. Chem. Int. Edn Engl. 54, 8154–8159 (2015)

    CAS  Article  Google Scholar 

  137. Pulcu, G. S., Mikhailova, E., Choi, L. S. & Bayley, H. Continuous observation of the stochastic motion of an individual small-molecule walker. Nat. Nanotechnol. 10, 76–83 (2015)

    ADS  CAS  PubMed  Article  Google Scholar 

  138. Rodriguez-Larrea, D. & Bayley, H. Protein co-translocational unfolding depends on the direction of pulling. Nat. Commun. 5, 4841 (2014)

    ADS  CAS  PubMed  Article  Google Scholar 

  139. Hyman, E. D. A new method of sequencing DNA. Anal. Biochem. 174, 423–436 (1988)

    CAS  PubMed  Article  Google Scholar 

  140. Lee, L. G. et al. DNA sequencing with dye-labeled terminators and T7 DNA polymerase: effect of dyes and dNTPs on incorporation of dye-terminators and probability analysis of termination fragments. Nucleic Acids Res. 20, 2471–2483 (1992)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  141. Huang, S. et al. Identifying single bases in a DNA oligomer with electron tunnelling. Nat. Nanotechnol. 5, 868–873 (2010)

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  142. Rothberg, J. M. et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 475, 348–352 (2011)

    CAS  Article  PubMed  Google Scholar 

  143. Manrao, E. A. et al. Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat. Biotechnol. 30, 349–353 (2012)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  144. Cherf, G. M. et al. Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision. Nat. Biotechnol. 30, 344–348 (2012)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  145. Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222–226 (2012)

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  146. Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796–815 (2000)

  147. Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562 (2002)

  148. Gibbs, R. A. et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428, 493–521 (2004)

    ADS  CAS  PubMed  Article  Google Scholar 

  149. The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69–87 (2005)

  150. International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature 436, 793–800 (2005)

    Article  CAS  Google Scholar 

  151. Schnable, P. S. et al. The B73 maize genome: complexity, diversity, and dynamics. Science 326, 1112–1115 (2009)

    ADS  CAS  Article  PubMed  Google Scholar 

  152. Adey, A. et al. The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line. Nature 500, 207–211 (2013)

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  153. Landry, J. J. et al. The genomic and transcriptomic landscape of a HeLa cell line. G3 (Bethesda) 3, 1213–1224 (2013)

    Article  CAS  Google Scholar 

  154. Howe, K. et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature 496, 498–503 (2013)

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  155. Session, A. M. et al. Genome evolution in the allotetraploid frog Xenopus laevis. Nature 538, 336–343 (2016)

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  156. Smith, T. F. & Waterman, M. S. Identification of common molecular subsequences. J. Mol. Biol. 147, 195–197 (1981)

    CAS  PubMed  Article  Google Scholar 

  157. Burge, C. & Karlin, S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78–94 (1997)

    CAS  PubMed  Article  Google Scholar 

  158. Kent, W. J. BLAT—the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  159. Kent, W. J. et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  160. Hubbard, T. et al. The Ensembl genome database project. Nucleic Acids Res. 30, 38–41 (2002)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  161. Giardine, B. et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 15, 1451–1455 (2005)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  162. Butler, J. et al. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res. 18, 810–820 (2008)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  163. Chen, K. et al. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat. Methods 6, 677–681 (2009)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  164. Ye, K., Schulz, M. H., Long, Q., Apweiler, R. & Ning, Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25, 2865–2871 (2009)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  165. Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265–272 (2010)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  166. Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  167. Chin, C. S. et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563–569 (2013)

    CAS  PubMed  Article  Google Scholar 

  168. Wang, D. G. et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280, 1077–1082 (1998)

    ADS  CAS  PubMed  Article  Google Scholar 

  169. Li, R. et al. The sequence and de novo assembly of the giant panda genome. Nature 463, 311–317 (2010)

    ADS  CAS  PubMed  Article  Google Scholar 

  170. Kitzman, J. O. et al. Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nat. Biotechnol. 29, 59–63 (2011)

    CAS  PubMed  Article  Google Scholar 

  171. Fan, H. C., Wang, J., Potanina, A. & Quake, S. R. Whole-genome molecular haplotyping of single cells. Nat. Biotechnol. 29, 51–57 (2011)

    CAS  PubMed  Article  Google Scholar 

  172. Seo, J. S. et al. De novo assembly and phasing of a Korean human genome. Nature 538, 243–247 (2016). BLAST and GenBank (GenBank and WGS Statistics;https://www.ncbi.nlm.nih.gov/genbank/statistics/) were essential tools for sharing and searching sequencing data, vastly amplifying the value of each sequence to the field.

    ADS  CAS  PubMed  Article  Google Scholar 

Download references

Acknowledgements

This is a large topic to cover in a single review. We apologize to colleagues whose work we were unable to discuss or failed to cite owing to space constraints. We thank L. Starita, C. Trapnell and A. McKenna for suggestions, and T. Tolpa and M. Gillies for extensive assistance with preparing the manuscript.

Author information

Authors and Affiliations

Authors

Contributions

All authors contributed to the writing of this review.

Corresponding author

Correspondence to Jay Shendure.

Ethics declarations

Competing interests

J.S. is a compensated advisor of Bellwether Bio, Nanostring, Cambridge Epigenetix, Phase Genomics, GenePeeks, Adaptive Biotechnologies, Stratos Genomics. S.B. is a founder, advisor and shareholder of Cambridge Epigenetix Ltd. G.M.C. declares competing interests, see http://arep.med.harvard.edu/gmc/tech.html; W.G. is a director of Myriad Genetics and Amylyx. The other authors (J.R., J.A.S. and R.H.W.) declare no competing interests.

Additional information

Reviewer Information Nature thanks M. Gerstein, S. L. Salzberg and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Related audio

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Shendure, J., Balasubramanian, S., Church, G. et al. DNA sequencing at 40: past, present and future. Nature 550, 345–353 (2017). https://doi.org/10.1038/nature24286

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature24286

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing