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. 2011 Aug 1;27(15):2027-30.
doi: 10.1093/bioinformatics/btr349. Epub 2011 Jun 11.

Pathogen detection using short-RNA deep sequencing subtraction and assembly

Ofer Isakov  1 , Shira Modai, Noam Shomron
Affiliations

Pathogen detection using short-RNA deep sequencing subtraction and assembly

Ofer Isakov et al. Bioinformatics. .

Abstract

Early and accurate detection of human pathogen infection is critical for treatment and therapeutics. Here we describe pathogen identification using short RNA subtraction and assembly (SRSA), a detection method that overcomes the requirement of prior knowledge and culturing of pathogens, by using degraded small RNA and deep sequencing technology. We prove our approach's efficiency through identification of a combined viral and bacterial infection in human cells.

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Figures

Fig. 1.
Fig. 1.
PCR products visualized in 1.5% agarose gel, a single band for both SupT1 + HIV-1 sample (lane 4) and the positive control (c) from the mycoplasma detection kit (lane 2) observed within the predicted marker (m) size range (270 bp). Lane 3 is the uninfected cells.
See this image and copyright information in PMC

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