Detection of Genetic Engineering Signatures in Potential Pathogen Genomes

Hannah De Jong, Stanford University

The Livermore Metagenomics Analysis Toolkit (LMAT) can be used to monitor metropolitan areas for pathogens. DNA from environmental samples is sequenced and sequences matching known human pathogens are flagged for investigation. This system can facilitate the early detection of bioterrorism agents or exotic pathogens brought in by travelers.

Current or future bioterrorism agents, however, might include not just known pathogens but also other viruses, bacteria or fungi that have been genetically engineered to become pathogenic to humans. Furthermore, known pathogens might be engineered to become more virulent, infectious or deadly. Existing surveillance systems would not necessarily detect these agents.

For my DOE CGSF practicum, I am designing a tool to detect genetic engineering signatures in potential pathogen DNA sequences. I have conducted a review of genetic engineering methods currently in use or development and assembled a list of sequence artifacts likely to be left behind by these methods. I have translated these sequence artifacts into searchable motifs and am in the process of creating a tool to flag those motifs found in DNA sequences for further investigation.

Abstract Author(s): H. De Jong, T. Slezak