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.

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

Nature Methods volume 5, pages 1005–1010 (2008)Cite this article

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.

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

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Learn more

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

Figure 1: Illumina sequencing workflow.
Figure 2: Sample fragmentation.
Figure 3: A-tailing, ligation and size selection.
Figure 4: PCR.
Figure 5: Quantification.
Figure 6: Denaturation.

References

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Chapter  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  7. Sambrook, J., Fritsch, E. & Maniatis, T. Molecular Cloning: A Laboratory Manual, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1989).

    Google Scholar 

  8. Smith, D. & Malek, J. Asymmetrical adapters and uses thereof. US patent 0172839 (2007).

  9. Riley, J. 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).

    Article  CAS  Google Scholar 

  10. Hawkins, T.L., O'Connor-Morin, T., Roy, A. & Santillan, C. DNA purification and isolation using a solid-phase. Nucleic Acids Res. 22, 4543–4544 (1994).

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

Download references

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.

Author information

Authors and Affiliations

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

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

Authors
  1. Michael A Quail
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Iwanka Kozarewa
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Frances Smith
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Aylwyn Scally
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Philip J Stephens
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Richard Durbin
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Harold Swerdlow
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Daniel J Turner
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Daniel J Turner.

Ethics declarations

Competing interests

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

Supplementary information

Supplementary Text and Figures

Supplementary Table 1 , Supplementary Protocols 1–13 (PDF 110 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Quail, M., Kozarewa, I., Smith, F. et al. A large genome center's improvements to the Illumina sequencing system. Nat Methods 5, 1005–1010 (2008). https://doi.org/10.1038/nmeth.1270

Download citation

  • Published:

  • Issue Date:

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

This article is cited by

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