The Homeland Security Advanced Research Projects Agency (HSARPA) recently awarded the grant to a group of bioinformatics researchers at UH to study DNA probes for detecting emerging or engineered pathogens. The project, titled "Tools for Ultraspecific Probe/Primer Design," started in April as part of the Bioinformatics and Assays Development Program and is headed by Yuriy Fofanov, assistant professor of computer science and of biology and biochemistry.
"We anticipate that our research results will bring us closer to rapid detection and identification of microorganisms and viruses that might be used in a terrorist attack," Fofanov said.
As principal investigator, Fofanov, director of the UH Bioinformatics Lab, is joined by co-investigators George Fox, a professor of biology and biochemistry and adjunct professor of chemical engineering, and Richard C. Willson, a professor of chemical engineering and professor of biology and biochemistry. For Phase I of the project, anticipated to last 10 months, HSARPA awarded nearly $300,000 to UH, with approximately $500,000 to be awarded for Phase II, depending upon results and how the agency's program and budget evolves over the next year.
At the core of this research is bioinformatics, the use of computer science in biological research to analyze the composition of molecules, especially in understanding genomic data. HSARPA chose to fund the UH bioinformatics project based on preliminary results made possible through financial assistance from the university's Texas Learning and Computation Center that gave $225,000 in funding for the UH program's initial research.
"The project uses the most advanced genomic computations to develop biological threat agent detection reagents that do not react to background clutter and cannot easily be evaded," Willson said. "These reagents should also have direct application to clinical diagnostics."
Along with polymerase chain reaction (PCR) primers, the new approach will deliver DNA probes that bind to organisms of interest and carry a highly detectable "label" to signal the presence of the organism. The PCR primers can amplify a specific sequence of DNA by as many as one billion times to reduce the amount of false positives, as well as resist evasion by threat agent engineering. The project focuses on choosing primers that detect, but don't mistakenly PCR-amplify, human or background-bacterial DNA. This advanced technology is a reality because of the UH team's insight into the statistical properties of useful probes, primer pairs and targets.
The ultimate goals of the research project are to improve future detection systems, efficiently detect engineered threats and to reduce the frequency of false positives. While false positives do not occur often, the UH research team agrees that taking precautions are necessary to avoid the chaos, mass anxiety and economic disruption that come with this type of misinformation.
"You don't want to have a test that says you might have anthrax in a sample, such as the air in a building or train station, when you don't," Fox said. "And since it's theoretically possible to use genetic engineering to disguise a threat from traditional detection methods that are based on single probes or primers, our approach realizes this and won't be fooled by it."
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