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.

  • Perspective
  • Published:

DNA sequencing technologies: 2006–2016

Nature Protocols volume 12, pages 213–218 (2017)Cite this article

Subjects

Abstract

Recent advances in the field of genomics have largely been due to the ability to sequence DNA at increasing throughput and decreasing cost. DNA sequencing was first introduced in 1977, and next-generation sequencing technologies have been available only during the past decade, but the diverse experiments and corresponding analyses facilitated by these techniques have transformed biological and biomedical research. Here, I review developments in DNA sequencing technologies over the past 10 years and look to the future for further applications.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: NGS instruments introduced over the past decade.

Similar content being viewed by others

References

  1. Mardis, E.R. Next-generation sequencing platforms. Annu. Rev. Anal. Chem. (Palo Alto Calif) 6, 287–303 (2013).

    Article  CAS  Google Scholar 

  2. Picelli, S. et al. Tn5 transposase and tagmentation procedures for massively scaled sequencing projects. Genome Res. 24, 2033–2040 (2014).

    Article  CAS  Google Scholar 

  3. Head, S.R. et al. Library construction for next-generation sequencing: overviews and challenges. Biotechniques 56, 61–64, 66, 68 passim (2014).

    Article  CAS  Google Scholar 

  4. Metzker, M.L. Sequencing technologies: the next generation. Nat. Rev. Genet. 11, 31–46 (2010).

    Article  CAS  Google Scholar 

  5. Goodwin, S., McPherson, J.D. & McCombie, W.R. Coming of age: ten years of next-generation sequencing technologies. Nat. Rev. Genet. 17, 333–351 (2016).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  7. Bainbridge, M.N. et al. Whole exome capture in solution with 3 Gbp of data. Genome Biol. 11, R62 (2010).

    Article  Google Scholar 

  8. Gnirke, A. et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 27, 182–189 (2009).

    Article  CAS  Google Scholar 

  9. Hodges, E. et al. Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing. Nat. Protoc. 4, 960–974 (2009).

    Article  CAS  Google Scholar 

  10. Altshuler, D. et al. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407, 513–516 (2000).

    Article  CAS  Google Scholar 

  11. Springer, N.M., Xu, X. & Barbazuk, W.B. Utility of different gene enrichment approaches toward identifying and sequencing the maize gene space. Plant Physiol. 136, 3023–3033 (2004).

    Article  CAS  Google Scholar 

  12. Baetens, M. et al. Applying massive parallel sequencing to molecular diagnosis of Marfan and Loeys-Dietz syndromes. Hum. Mutat. 32, 1053–1062 (2011).

    Article  CAS  Google Scholar 

  13. Hollants, S., Redeker, E.J. & Matthijs, G. Microfluidic amplification as a tool for massive parallel sequencing of the familial hypercholesterolemia genes. Clin. Chem. 58, 717–724 (2012).

    Article  CAS  Google Scholar 

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

  15. Mardis, E.R. Sequencing the AML genome, transcriptome, and epigenome. Semin. Hematol. 51, 250–258 (2014).

    Article  CAS  Google Scholar 

  16. Wong, K., Keane, T.M., Stalker, J. & Adams, D.J. Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly. Genome Biol. 11, R128 (2010).

    Article  Google Scholar 

  17. Alkan, C., Sajjadian, S. & Eichler, E.E. Limitations of next-generation genome sequence assembly. Nat. Methods 8, 61–65 (2011).

    Article  CAS  Google Scholar 

  18. Huddleston, J. & Eichler, E.E. An incomplete understanding of human genetic variation. Genetics 202, 1251–1254 (2016).

    Article  CAS  Google Scholar 

  19. Sudmant, P.H. et al. An integrated map of structural variation in 2,504 human genomes. Nature 526, 75–81 (2015).

    Article  CAS  Google Scholar 

  20. Huddleston, J. et al. Reconstructing complex regions of genomes using long-read sequencing technology. Genome Res. 24, 688–696 (2014).

    Article  CAS  Google Scholar 

  21. Chaisson, M.J., Wilson, R.K. & Eichler, E.E. Genetic variation and the de novo assembly of human genomes. Nat. Rev. Genet. 16, 627–640 (2015).

    Article  CAS  Google Scholar 

  22. Berlin, K. et al. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat. Biotechnol. 33, 623–630 (2015).

    Article  CAS  Google Scholar 

  23. Goodwin, S. et al. Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Res. 25, 1750–1756 (2015).

    Article  CAS  Google Scholar 

  24. Pirola, Y. et al. HapCol: accurate and memory-efficient haplotype assembly from long reads. Bioinformatics 32, 1610–1617 (2016).

    Article  CAS  Google Scholar 

  25. Pendleton, M. et al. Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat. Methods 12, 780–786 (2015).

    Article  CAS  Google Scholar 

  26. Madoui, M.A. et al. Genome assembly using Nanopore-guided long and error-free DNA reads. BMC Genomics 16, 327 (2015).

    Article  Google Scholar 

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

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

    Article  CAS  Google Scholar 

  29. Akeson, M., Branton, D., Kasianowicz, J.J., Brandin, E. & Deamer, D.W. Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules. Biophys. J. 77, 3227–3233 (1999).

    Article  CAS  Google Scholar 

  30. Robertson, G. et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 4, 651–657 (2007).

    Article  CAS  Google Scholar 

  31. Zhao, J. et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol. Cell 40, 939–953 (2010).

    Article  CAS  Google Scholar 

  32. Buenrostro, J.D., Giresi, P.G., Zaba, L.C., Chang, H.Y. & Greenleaf, W.J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213–1218 (2013).

    Article  CAS  Google Scholar 

  33. Harris, R.A. et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat. Biotechnol. 28, 1097–1105 (2010).

    Article  CAS  Google Scholar 

  34. Tarailo-Graovac, M. et al. Exome sequencing and the management of neurometabolic disorders. N. Engl. J. Med. 374, 2246–2255 (2016).

    Article  CAS  Google Scholar 

  35. Tsimberidou, A.M. et al. Personalized medicine in a phase I clinical trials program: the MD Anderson Cancer Center initiative. Clin. Cancer Res. 18, 6373–6383 (2012).

    Article  CAS  Google Scholar 

  36. Wagle, N. et al. High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. Cancer Discov. 2, 82–93 (2012).

    Article  CAS  Google Scholar 

  37. Susswein, L.R. et al. Pathogenic and likely pathogenic variant prevalence among the first 10,000 patients referred for next-generation cancer panel testing. Genet. Med. 18, 823–832 (2016).

    Article  CAS  Google Scholar 

  38. Le, D.T. et al. PD-1 blockade in tumors with mismatch-repair deficiency. N. Engl. J. Med. 372, 2509–2520 (2015).

    Article  CAS  Google Scholar 

  39. Rizvi, N.A. et al. Cancer immunology: mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science 348, 124–128 (2015).

    Article  CAS  Google Scholar 

  40. Carreno, B.M. et al. Cancer immunotherapy: a dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells. Science 348, 803–808 (2015).

    Article  CAS  Google Scholar 

  41. Fritsch, E.F., Hacohen, N. & Wu, C.J. Personal neoantigen cancer vaccines: the momentum builds. OncoImmunology 3, e29311 (2014).

    Article  Google Scholar 

  42. Stadler, Z.K. et al. Reliable detection of mismatch repair deficiency in colorectal cancers using mutational load in next-generation sequencing panels. J. Clin. Oncol. 34, 2141–2147 (2016).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The author wishes to acknowledge her PhD mentor, B.A. Roe, whose encouragement and enthusiasm for technology and its applications to biology have inspired her career.

Author information

Authors and Affiliations

  1. McDonnell Genome Institute, Washington University, St. Louis, Missouri, USA

    Elaine R Mardis

Authors
  1. Elaine R Mardis
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

E.R.M. conceptualized, wrote and edited the manuscript in its entirety.

Corresponding author

Correspondence to Elaine R Mardis.

Ethics declarations

Competing interests

E.R.M. is a member of the Supervisory Board of Qiagen N.V.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Mardis, E. DNA sequencing technologies: 2006–2016. Nat Protoc 12, 213–218 (2017). https://doi.org/10.1038/nprot.2016.182

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nprot.2016.182

This article is cited by

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

Advanced 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