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A large genome center's improvements to the Illumina sequencing system

Nature Methods volume 5, pages 10051010 (2008) | Download Citation

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Abstract

The Wellcome Trust Sanger Institute is one of the world's largest genome centers, and a substantial amount of our sequencing is performed with 'next-generation' massively parallel sequencing technologies: in June 2008 the quantity of purity-filtered sequence data generated by our Genome Analyzer (Illumina) platforms reached 1 terabase, and our average weekly Illumina production output is currently 64 gigabases. Here we describe a set of improvements we have made to the standard Illumina protocols to make the library preparation more reliable in a high-throughput environment, to reduce bias, tighten insert size distribution and reliably obtain high yields of data.

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References

  1. 1.

    Whole-genome re-sequencing. Curr. Opin. Genet. Dev. 16, 545–552 (2006).

  2. 2.

    The impact of next-generation sequencing technology on genetics. Trends Genet. 24, 133–141 (2008).

  3. 3.

    et al. Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res. 18, 1638–1642 (2008).

  4. 4.

    DNA sequencing. in Basic Techniques in Molecular Biology 377–380 (Springer-Verlag, Berlin, 2000).

  5. 5.

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

  6. 6.

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

  7. 7.

    , & Molecular Cloning: A Laboratory Manual, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1989).

  8. 8.

    & Asymmetrical adapters and uses thereof. US patent 0172839 (2007).

  9. 9.

    et al. A novel, rapid method for the isolation of terminal sequences from yeast artificial chromosome (YAC) clones. Nucleic Acids Res. 18, 2887–2890 (1990).

  10. 10.

    , , & DNA purification and isolation using a solid-phase. Nucleic Acids Res. 22, 4543–4544 (1994).

  11. 11.

    et al. From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing. Nucleic Acids Res. 36, e5 (2008).

  12. 12.

    The denaturation of DNA. Gene 135, 77–79 (1993).

  13. 13.

    & Use of ultraviolet absorbance-temperature profile for determining the guanine plus cytosine content of DNA. Methods Enzymol. 12, 195–206 (1968).

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Acknowledgements

We thank all the staff at Illumina for their support, particularly T. Ost, M. Gibbs, J. Smith, N. Gormley, V. Smith and K. Hall. We also thank C. Brown, A. Brown, R. Pettett, T. Skelly, N. Whiteford, L. Mamanova, E. Sheridan and E. Huckle for helpful discussions and assistance.

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Affiliations

  1. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.

    • Michael A Quail
    • , Iwanka Kozarewa
    • , Frances Smith
    • , Aylwyn Scally
    • , Philip J Stephens
    • , Richard Durbin
    • , Harold Swerdlow
    •  & Daniel J Turner

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Competing interests

H.S. is an Illumina shareholder and share option holder.

Corresponding author

Correspondence to Daniel J Turner.

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    Supplementary Text and Figures

    Supplementary Table 1 , Supplementary Protocols 1–13

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DOI

https://doi.org/10.1038/nmeth.1270

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