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.
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References
Mardis, E.R. Next-generation sequencing platforms. Annu. Rev. Anal. Chem. (Palo Alto Calif) 6, 287–303 (2013).
Picelli, S. et al. Tn5 transposase and tagmentation procedures for massively scaled sequencing projects. Genome Res. 24, 2033–2040 (2014).
Head, S.R. et al. Library construction for next-generation sequencing: overviews and challenges. Biotechniques 56, 61–64, 66, 68 passim (2014).
Metzker, M.L. Sequencing technologies: the next generation. Nat. Rev. Genet. 11, 31–46 (2010).
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).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Bainbridge, M.N. et al. Whole exome capture in solution with 3 Gbp of data. Genome Biol. 11, R62 (2010).
Gnirke, A. et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 27, 182–189 (2009).
Hodges, E. et al. Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing. Nat. Protoc. 4, 960–974 (2009).
Altshuler, D. et al. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407, 513–516 (2000).
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).
Baetens, M. et al. Applying massive parallel sequencing to molecular diagnosis of Marfan and Loeys-Dietz syndromes. Hum. Mutat. 32, 1053–1062 (2011).
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).
International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431, 931–945 (2004).
Mardis, E.R. Sequencing the AML genome, transcriptome, and epigenome. Semin. Hematol. 51, 250–258 (2014).
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).
Alkan, C., Sajjadian, S. & Eichler, E.E. Limitations of next-generation genome sequence assembly. Nat. Methods 8, 61–65 (2011).
Huddleston, J. & Eichler, E.E. An incomplete understanding of human genetic variation. Genetics 202, 1251–1254 (2016).
Sudmant, P.H. et al. An integrated map of structural variation in 2,504 human genomes. Nature 526, 75–81 (2015).
Huddleston, J. et al. Reconstructing complex regions of genomes using long-read sequencing technology. Genome Res. 24, 688–696 (2014).
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).
Berlin, K. et al. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat. Biotechnol. 33, 623–630 (2015).
Goodwin, S. et al. Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Res. 25, 1750–1756 (2015).
Pirola, Y. et al. HapCol: accurate and memory-efficient haplotype assembly from long reads. Bioinformatics 32, 1610–1617 (2016).
Pendleton, M. et al. Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat. Methods 12, 780–786 (2015).
Madoui, M.A. et al. Genome assembly using Nanopore-guided long and error-free DNA reads. BMC Genomics 16, 327 (2015).
The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 526, 68–74 (2015).
Chaisson, M.J. et al. Resolving the complexity of the human genome using single-molecule sequencing. Nature 517, 608–611 (2015).
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).
Robertson, G. et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 4, 651–657 (2007).
Zhao, J. et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol. Cell 40, 939–953 (2010).
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).
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).
Tarailo-Graovac, M. et al. Exome sequencing and the management of neurometabolic disorders. N. Engl. J. Med. 374, 2246–2255 (2016).
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).
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).
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).
Le, D.T. et al. PD-1 blockade in tumors with mismatch-repair deficiency. N. Engl. J. Med. 372, 2509–2520 (2015).
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).
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).
Fritsch, E.F., Hacohen, N. & Wu, C.J. Personal neoantigen cancer vaccines: the momentum builds. OncoImmunology 3, e29311 (2014).
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).
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.
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E.R.M. conceptualized, wrote and edited the manuscript in its entirety.
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E.R.M. is a member of the Supervisory Board of Qiagen N.V.
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Mardis, E. DNA sequencing technologies: 2006–2016. Nat Protoc 12, 213–218 (2017). https://doi.org/10.1038/nprot.2016.182
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DOI: https://doi.org/10.1038/nprot.2016.182
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