A decade’s perspective on DNA sequencing technology

Elaine R. Mardis

doi:10.1038/nature09796

journal article Feb 01, 2011

A decade’s perspective on DNA sequencing technology

Elaine R. Mardis

Nature Vol. 470 No. 7333 pp. 198-203 · Springer Science and Business Media LLC

View at Publisher Save 10.1038/nature09796

Topics

No keywords indexed for this article. Browse by subject →

References

48

[1]

DNA sequencing with chain-terminating inhibitors

F. Sanger, S. Nicklen, A. R. Coulson

Proceedings of the National Academy of Sciences 1977 10.1073/pnas.74.12.5463

[2]

Initial sequencing and comparative analysis of the mouse genome

Nature 2002 10.1038/nature01262

[3]

Gibbs, R. A. et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428, 493–521 (2004) 10.1038/nature02426

[4]

International Chicken Genome Sequencing Consortium Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695–716 (2004) 10.1038/nature03154

[5]

Lindblad-Toh, K. et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438, 803–819 (2005) 10.1038/nature04338

[6]

The Chimpanzee Sequencing and Analysis Consortium Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69–87 (2005) 10.1038/nature04072

[7]

Gibbs, R. A. et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316, 222–234 (2007) 10.1126/science.1139247

[8]

Warren, W. C. et al. Genome analysis of the platypus reveals unique signatures of evolution. Nature 453, 175–183 (2008) 10.1038/nature06936

[9]

Elsik, C. G. et al. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324, 522–528 (2009) 10.1126/science.1169588

[10]

Mardis, E. R. New strategies and emerging technologies for massively parallel sequencing: applications in medical research. Genome Med 1, 40 (2009) 10.1186/gm40

[11]

Metzker, M. L. Sequencing technologies - the next generation. Nature Rev. Genet. 11, 31–46 (2010) 10.1038/nrg2626

[12]

Initial sequencing and analysis of the human genome

Eric S. Lander, Lauren M. Linton, Bruce Birren et al.

Nature 2001 10.1038/35057062

[13]

Finishing the euchromatic sequence of the human genome

Nature 2004 10.1038/nature03001

[14]

The International HapMap Project

Richard A. Gibbs, John W. Belmont, Paul Hardenbol et al.

Nature 2003 10.1038/nature02168

[15]

The International HapMap Consortium A haplotype map of the human genome. Nature 437, 1299–1320 (2005) 10.1038/nature04226

[16]

Frazer, K. A. et al. A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851–861 (2007) 10.1038/nature06258

[17]

Altshuler, D. M. et al. Integrating common and rare genetic variation in diverse human populations. Nature 467, 52–58 (2010) 10.1038/nature09298

[18]

Lander, E. S. Initial impact of the sequencing of the human genome. Nature doi:10.1038/nature09792 (this issue). 10.1038/nature09792

[19]

Harismendy, O. et al. Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level. Genome Biol. 11, R118 (2010)First demonstration that rare sequence variants could be identified using next-generation sequencing in well-phenotyped cases and controls, and that functional significance in the phenotype could be assigned to the suspect variants. 10.1186/gb-2010-11-11-r118

[20]

Kidd, J. M. et al. Mapping and sequencing of structural variation from eight human genomes. Nature 453, 56–64 (2008) 10.1038/nature06862

[21]

Tuzun, E. et al. Fine-scale structural variation of the human genome. Nature Genet. 37, 727–732 (2005) 10.1038/ng1562

[22]

Redon, R. et al. Global variation in copy number in the human genome. Nature 444, 444–454 (2006) 10.1038/nature05329

[23]

Conrad, D. F. et al. Origins and functional impact of copy number variation in the human genome. Nature 464, 704–712 (2010) 10.1038/nature08516

[24]

Korbel, J. O. et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 318, 420–426 (2007) 10.1126/science.1149504

[25]

Chen, K. et al. BreakDancer: an algorithm for high resolution mapping of genomic structural variation. Nature Methods 6, 677–681 (2009) 10.1038/nmeth.1363

[26]

Alkan, C. et al. Personalized copy number and segmental duplication maps using next-generation sequencing. Nature Genet. 41, 1061–1067 (2009) 10.1038/ng.437

[27]

Sudmant, P. H. et al. Diversity of human copy number variation and multicopy genes. Science 330, 641–646 (2010)Initial structural variation data analysis resulting from 1,000 Genomes Project data, demonstrating the yield of such information from a large-scale project using next-generation sequencing. 10.1126/science.1197005

[28]

Durbin, R. M. et al. A map of human genome variation from population-scale sequencing. Nature 467, 1061–1073 (2010) 10.1038/nature09534

[29]

Pao, W. et al. EGF receptor gene mutations are common in lung cancers from “never smokers” and are associated with sensitivity of tumors to gefitinib and erlotinib. Proc. Natl Acad. Sci. USA 101, 13306–13311 (2004) 10.1073/pnas.0405220101

[30]

The Consensus Coding Sequences of Human Breast and Colorectal Cancers

Tobias Sjöblom, Siân Jones, Laura D. Wood et al.

Science 2006 10.1126/science.1133427

[31]

Wood, L. D. et al. The genomic landscapes of human breast and colorectal cancers. Science 318, 1108–1113 (2007) 10.1126/science.1145720

[32]

Ley, T. J. et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 456, 66–72 (2008) 10.1038/nature07485

[33]

Mardis, E. R. Cancer genomics identifies determinants of tumor biology. Genome Biol. 11, 211 (2010) 10.1186/gb-2010-11-5-211

[34]

Mardis, E. R. The $1,000 genome, the $100,000 analysis? Genome Med 2, 84 (2010) 10.1186/gm205

[35]

Birney, E. et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816 (2007) 10.1038/nature05874

[36]

Green, E. D., Guyer, M. S. & National Human Genome Research Institute Charting a course for genomic medicine from base pairs to bedside. Nature doi:10.1038/nature09764 (this issue). 10.1038/nature09764

[37]

A Catalog of Reference Genomes from the Human Microbiome

Karen E. Nelson, George M. Weinstock, Sarah K. Highlander et al.

Science 2010 10.1126/science.1183605

[38]

Loh, J. et al. Detection of novel sequences related to African Swine Fever virus in human serum and sewage. J. Virol. 83, 13019–13025 (2009) 10.1128/jvi.00638-09

[39]

Presti, R. M. et al. Quaranfil, Johnston Atoll, and Lake Chad viruses are novel members of the family Orthomyxoviridae. J. Virol. 83, 11599–11606 (2009) 10.1128/jvi.00677-09

[40]

Finkbeiner, S. R. et al. Identification of a novel astrovirus (astrovirus VA1) associated with an outbreak of acute gastroenteritis. J. Virol. 83, 10836–10839 (2009) 10.1128/jvi.00998-09

[41]

Wheeler, D. A. et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 452, 872–876 (2008) 10.1038/nature06884

[42]

Lupski, J. R. et al. Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N. Engl. J. Med. 362, 1181–1191 (2010)Personal genome sequencing used to identify a rare allelic variant that causes Charcot-Marie-Tooth syndrome in the family of J. R. Lupski. 10.1056/nejmoa0908094

[43]

Roach, J. C. et al. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328, 636–639 (2010) 10.1126/science.1186802

[44]

Jones, S. J. et al. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biol. 11, R82 (2010) 10.1186/gb-2010-11-8-r82

[45]

Ng, S. B. et al. Exome sequencing identifies the cause of a mendelian disorder. Nature Genet. 42, 30–35 (2010) 10.1038/ng.499

[46]

Ng, S. B. et al. Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nature Genet. 42, 790–793 (2010)One of the first demonstrations of using exome sequencing to identify a major causative mutation in Kabuki syndrome, using genomic DNA from a small number of unrelated affected individuals. 10.1038/ng.646

[47]

Gilissen, C. et al. Exome sequencing identifies WDR35 variants involved in Sensenbrenner syndrome. Am. J. Hum. Genet. 87, 418–423 (2010) 10.1016/j.ajhg.2010.08.004

[48]

Chin, C. S. et al. The origin of the Haitian cholera outbreak strain. N. Engl. J. Med. 364, 33–42 (2011) 10.1056/nejmoa1012928

Cited By

698

Real-world clinical utility of tumor whole-genome sequencing in solid cancers

Jeffrey van Putten, Petur Snaebjornsson · 2026

Nature Medicine

Evolution of Vertebrate Hormones and Their Receptors: Insights from Non-Osteichthyan Genomes

Shigehiro Kuraku, Hiroyuki Kaiya · 2023

Annual Review of Animal Biosciences

Role of gene sequencing for the diagnosis, tracking and prevention of fungal infections

Rajendra Gudisa, Shivaprakash M Rudramurthy · 2022