Article thumbnail

The Sensitivity of Massively Parallel Sequencing for Detecting Candidate Infectious Agents Associated with Human Tissue

By Richard A. Moore, René L. Warren, J. Douglas Freeman, Julia A. Gustavsen, Caroline Chénard, Jan M. Friedman, Curtis A. Suttle, Yongjun Zhao and Robert A. Holt


Massively parallel sequencing technology now provides the opportunity to sample the transcriptome of a given tissue comprehensively. Transcripts at only a few copies per cell are readily detectable, allowing the discovery of low abundance viral and bacterial transcripts in human tissue samples. Here we describe an approach for mining large sequence data sets for the presence of microbial sequences. Further, we demonstrate the sensitivity of this approach by sequencing human RNA-seq libraries spiked with decreasing amounts of an RNA-virus. At a modest depth of sequencing, viral transcripts can be detected at frequencies less than 1 in 1,000,000. With current sequencing platforms approaching outputs of one billion reads per run, this is a highly sensitive method for detecting putative infectious agents associated with human tissues

Topics: Research Article
Publisher: Public Library of Science
OAI identifier:
Provided by: PubMed Central

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.

Suggested articles


  1. (2007). A metagenomic survey of microbes in honey bee colony collapse disorder.
  2. (2008). A new arenavirus in a cluster of fatal transplant-associated diseases.
  3. (1998). Base-calling of automated sequencer traces using phred. I. Accuracy assessment.
  4. (1998). Base-calling of automated sequencer traces using phred. II. Error probabilities.
  5. (2003). Characterization of HaRNAV, a single-stranded RNA virus causing lysis of Heterosigma akashiwo (Raphidophyceae).
  6. (2009). Circos: an information aesthetic for comparative genomics.
  7. (2008). Clonal integration of a polyomavirus in human Merkel cell carcinoma.
  8. (2009). Fast and accurate short read alignment with BurrowsWheeler transform.
  9. (2004). Genome sequence and characterization of a virus (HaRNAV) related to picorna-like viruses that infects the marine toxic bloom-forming alga Heterosigma akashiwo.
  10. (2004). Infectious agents and cancer: criteria for a causal relation.
  11. (1993). Marine cyanophages infecting oceanic and coastal strains of Synechococcus: Abundance, morphology, cross-infectivity and growth characteristics.
  12. (2009). Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution.
  13. (2008). Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing.
  14. (1998). The Effect of Cyanophages on the Mortality of Synechococcus spp. and Selection for UV Resistant Viral Communities.
  15. (2006). The global health burden of infection-associated cancers in the year