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Sequence census methods for functional genomics

Nature Methods volume 5, pages 19–21 (2008)Cite this article

Next-generation sequencing technologies are beginning to facilitate genome sequencing. But in addition, new applications and new assay concepts have emerged that are vastly increasing our ability to understand genome function.

When Thomas Edison invented the phonograph, playing music was well down his list of possible uses. Something similar may now be happening in the genome world. A new generation of massively parallel DNA sequencing platforms is here (see Primer). They aim to replace the workhorse capillary sequencing systems that brought us—very beautifully—the human genome sequence. These machines, led by 454 and Illumina (formerly Solexa), and lately joined by ABI1, have emerged in DNA sequencing centers over the past two years, promising vastly more sequence (>1 gigabase of sequence per run) than standard capillary-based technology can produce. Still other new machines are on the way. Their development is driven by the US National Institutes of Health and National Human Genome Research Institute challenges for DNA sequencing at costs of $100,000 and then of less than $1,000 per human or human-size genome. 'If you build them, we will buy them' was implied, and other near-infinite sequencing appetites such as those of microbial metagenomics researchers have added fuel. As hoped, the new instruments are being explored in the world's genome centers for rapid and cheap genome sequencing. Read length limits, error rates and assembly algorithm issues, among other problems, mean that these new kids on the sequencing block have not fully reduced whole-genome sequencing to practice. Not yet, at least.

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Figure 1: Sequence census assays.

References

  1. Shendure, J. et al. Science 309, 1728–1732 (2005).

    CAS  Article  Google Scholar 

  2. Velculescu, V.E., Zhang, L., Vogelstein, B. & Kinzler, K.W. Science 270, 484–487 (1995).

    CAS  Article  Google Scholar 

  3. Brenner, S. et al. Nat. Biotechnol. 18, 630–634 (2000).

    CAS  Article  Google Scholar 

  4. Margulies, M. et al. Nature 437, 376–380 (2005).

    CAS  Article  Google Scholar 

  5. Barski, A. et al. Cell 129, 823–837 (2007).

    CAS  Article  Google Scholar 

  6. Johnson, D.S., Mortazavi, A., Myers, R.M. & Wold, B. Science 316, 1497–1502 (2007).

    CAS  Article  Google Scholar 

  7. Mikkelsen, T.S. et al. Nature 448, 553–560 (2007).

    CAS  Article  Google Scholar 

  8. Robertson, G. et al. Nat. Methods 4, 651–657 (2007).

    CAS  Article  Google Scholar 

  9. Lu, C. et al. Genome Res. 16, 1276–1288 (2006).

    CAS  Article  Google Scholar 

  10. Ruby, J.G. et al. Cell 127, 1193–1207 (2006).

    CAS  Article  Google Scholar 

Download references

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Authors and Affiliations

  1. Barbara Wold is in the Division of Biology, California Institute of Technology, Pasadena, California 91125, USA. bwold@caltech.edu,

    Barbara Wold

  2. Richard M. Myers is in the Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA. myers@shgc.stanford.edu,

    Richard M Myers

Authors
  1. Barbara Wold
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  2. Richard M Myers
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Wold, B., Myers, R. Sequence census methods for functional genomics. Nat Methods 5, 19–21 (2008). https://doi.org/10.1038/nmeth1157

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