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.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Relman, D.A. Science 284, 1308–1310 (1999).
Relman, D.A., Loutit, J.S., Schmidt, T.M., Falkow, S. & Tompkins, L.S. N. Engl. J. Med. 323, 1573–1580 (1990).
Relman, D.A., Schmidt, T.M., MacDermott, R.P. & Falkow, S. N. Engl. J. Med. 327, 293–301 (1992).
Lisitsyn, N. & Wigler, M. Science 259, 946–951 (1993).
Chang, Y. et al. Science 266, 1865–1869 (1994).
Lander, E.S. et al. Nature 409, 860–892 (2001).
Venter, J.C. et al. Science 291, 1304–1305 (2001).
Adams, M.D. et al. Science 252, 1651–1656 (1991).
Boguski, M.S., Lowe, T.M. & Tolstoshev, C.M. Nature Genet. 4, 332–333 (1993).
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. J. Mol. Biol. 215, 403–410 (1990).
Zhang, Z., Schwartz, S., Wagner, L. & Miller, W. J. Comput. Biol. 7, 203–214 (2000).
Befeler, A.S. & Di Bisceglie, A.M. Infect. Dis. Clin. North Am. 14, 617–632 (2000).
Boshart, M. et al. EMBO J. 3, 1151–1157 (1984).
Burger, R.A. et al. J. Natl Cancer Inst. 88, 1360–1368 (1996).
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
Authors and Affiliations
Corresponding author
Rights 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
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/ng818
This article is cited by
-
Tissue-associated microbial detection in cancer using human sequencing data
BMC Bioinformatics (2020)
-
Dual RNA-seq of the plant pathogen Phytophthora ramorum and its tanoak host
Tree Genetics & Genomes (2014)
-
Viral expression associated with gastrointestinal adenocarcinomas in TCGA high-throughput sequencing data
Human Genomics (2013)
-
CaPSID: A bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes
BMC Bioinformatics (2012)
-
PathSeq: software to identify or discover microbes by deep sequencing of human tissue
Nature Biotechnology (2011)