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.

  • Brief Communication
  • Published:

Identification of foreign gene sequences by transcript filtering against the human genome

Nature Genetics volume 30, pages 141–142 (2002)Cite this article

Abstract

We have developed a computational subtraction approach to detect microbial causes for putative infectious diseases by filtering a set of human tissue–derived sequences against the human genome. We demonstrate the potential of this method by identifying sequences from known pathogens in established expressed–sequence tag libraries.

Access through your institution
Buy or subscribe

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

Access options

Access through your institution

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

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

Figure 1: Computational subtraction of the human transcriptome.

Similar content being viewed by others

References

  1. Relman, D.A. Science 284, 1308–1310 (1999).

    Article  CAS  Google Scholar 

  2. Relman, D.A., Loutit, J.S., Schmidt, T.M., Falkow, S. & Tompkins, L.S. N. Engl. J. Med. 323, 1573–1580 (1990).

    Article  CAS  Google Scholar 

  3. Relman, D.A., Schmidt, T.M., MacDermott, R.P. & Falkow, S. N. Engl. J. Med. 327, 293–301 (1992).

    Article  CAS  Google Scholar 

  4. Lisitsyn, N. & Wigler, M. Science 259, 946–951 (1993).

    Article  CAS  Google Scholar 

  5. Chang, Y. et al. Science 266, 1865–1869 (1994).

    Article  CAS  Google Scholar 

  6. Lander, E.S. et al. Nature 409, 860–892 (2001).

    Article  CAS  Google Scholar 

  7. Venter, J.C. et al. Science 291, 1304–1305 (2001).

    Article  CAS  Google Scholar 

  8. Adams, M.D. et al. Science 252, 1651–1656 (1991).

    Article  CAS  Google Scholar 

  9. Boguski, M.S., Lowe, T.M. & Tolstoshev, C.M. Nature Genet. 4, 332–333 (1993).

    Article  CAS  Google Scholar 

  10. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. J. Mol. Biol. 215, 403–410 (1990).

    Article  CAS  Google Scholar 

  11. Zhang, Z., Schwartz, S., Wagner, L. & Miller, W. J. Comput. Biol. 7, 203–214 (2000).

    Article  CAS  Google Scholar 

  12. Befeler, A.S. & Di Bisceglie, A.M. Infect. Dis. Clin. North Am. 14, 617–632 (2000).

    Article  CAS  Google Scholar 

  13. Boshart, M. et al. EMBO J. 3, 1151–1157 (1984).

    Article  CAS  Google Scholar 

  14. Burger, R.A. et al. J. Natl Cancer Inst. 88, 1360–1368 (1996).

    Article  Google Scholar 

Download references

Acknowledgements

We thank P. Vaglio, M. Vidal and W. Wong for assistance with computational platforms; R. DePinho, W. Kaelin, K. Polyak and M. Vidal for discussion and the National Cancer Institute (D.T.) and the Pew Scholars in the Biomedical Sciences (M.M.) for support. M.M. is a Claudia Adams Barr investigator.

Author information

Author notes

  1. Griffin Weber and Jay Shendure: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Adult Oncology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, 02115, Massachusetts, USA

    Griffin Weber, David M. Tanenbaum & Matthew Meyerson

  2. Department of Pathology, Harvard Medical School, Boston, 02115, Massachusetts, USA

    Griffin Weber, David M. Tanenbaum & Matthew Meyerson

  3. Decision Systems Group, Brigham and Women's Hospital, 75 Francis Street, Boston, 02115, Massachusetts, USA

    Griffin Weber

  4. Department of Genetics, Harvard Medical School, Boston, 02115, Massachusetts, USA

    Jay Shendure & George M. Church

Authors
  1. Griffin Weber
    View author publications

    You can also search for this author inPubMed Google Scholar

  2. Jay Shendure
    View author publications

    You can also search for this author inPubMed Google Scholar

  3. David M. Tanenbaum
    View author publications

    You can also search for this author inPubMed Google Scholar

  4. George M. Church
    View author publications

    You can also search for this author inPubMed Google Scholar

  5. Matthew Meyerson
    View author publications

    You can also search for this author inPubMed Google Scholar

Corresponding author

Correspondence to Matthew Meyerson.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Cite this article

Weber, G., Shendure, J., Tanenbaum, D. et al. Identification of foreign gene sequences by transcript filtering against the human genome. Nat Genet 30, 141–142 (2002). https://doi.org/10.1038/ng818

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng818

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