The US Department of Homeland Security’s Advanced Research Project Agency (HSARPA) has launched a $4 million program called Bioinformatics and Assays Development (BIAD), and expects to grant around 10 awards through the initiative before the end of the year. The program seeks bids to develop bioinformatics tools to support detection and forensics assays for biodefense applications.
Bioinformatics is “a key enabling technology for environmental surveillance for pathogens,” said Steve Buchsbaum, a program manager for HSARPA. “It’s really that informatics construct that defines what is and is not a pathogen.”
The BIAD program builds upon an earlier HSARPA solicitation (RA03-01, Detection Systems for Biological and Chemical Countermeasures) that awarded $48 million to more than a dozen teams earlier this year for new sensor technologies as part of the DHS BioWatch biosurveillance initiative. One particular program under that initiative, called Bioagent Autonomous Network Detector (BAND), has “a very important bioinformatics component,” Buchsbaum said, but the focus of that program was more on the sensors than on the informatics. BIAD, by contrast, was designed to be an informatics “building-block” initiative for future detection programs, he said. “We have a detection program today, and there were [proposals] that came in on that that were too high risk for us. So what we’re trying to do is build up the infrastructure so that they may not be so high risk in the future,” he said.
The BIAD solicitation (at http://www.hsarpabaa.com/Solicitations/BAA04-03_Assays_PIP_FINALe.pdf) calls for new assays and bioinformatics tools to support HSARPA’s future biodetection goals. Specific bioinformatics tools of interest include “fully integrated microbial pathogen database systems that provide high levels of data organization and enhanced data-mining capabilities,” and software and computational analysis tools that are “tightly coupled” with high-throughput laboratory instrumentation methods. The solicitation notes that HSARPA is particularly interested in data analysis tools that “maximize both sensitivity and specificity of detection assays,” as well as computational modeling tools able to predict “system response in the presence of confounding analytes, background levels of non-pathogenic organisms, potential inhibitors of assay reactions, and temperature and other environmental extremes.”
Buchsbaum said that one particular challenge for DHS is gaining a better understanding of the natural background environment for airborne biological particles. “There’s lots of work that’s been done in that area, but not at the specificity and sensitivity that we need to be able to build sensors,” Buchsbaum said, “So we’d certainly leverage the Department of Defense’s work, which is somewhat similar, but we’d be really asking more specific questions — how do our sensors work today, what might they see, what might they get fooled by, and what informatics would help us to make them more robust?”
Another requirement for DHS projects, Buchsbaum added, is low cost. Although HSARPA was built upon the model of DARPA, its counterpart under the Department of Defense, Buchsbaum said that HSARPA is more focused on short-term applicability, as opposed to basic research. It is also much more cost sensitive. “The Department of Defense deploys far fewer, high-intensity operations. Whereas when we think of a Homeland Security deployment, we’re thinking of committing to a much broader deployment, and doing it all the time, and doing it in state and local communities where they’re much more cost sensitive to these sorts of things,” Buchsbaum said.
Buchsbaum said that much of what the program funds will likely leverage related efforts currently funded by DARPA, DOE, NSF, NIH, or other sources. The DOE’s Los Alamos National Laboratory, for example, is engaged in a project to computationally identify DNA and protein signatures that can be used for RT-PCR pathogen detection tools as part of the BioWatch initiative [BioInform 10-13-03].
In the commercial sector, Ibis Therapeutics, a division of Isis Pharmaceuticals, has pocketed around $55 million in funding from DARPA, the US Army Medical Research Institute of Infectious Diseases, the US Centers for Disease Control and Prevention, and other government agencies to develop a biosensor system called TIGER (Triangulation Identification Genetic Evaluation of Risks) to identify emerging or genetically altered infectious organisms. A key component of the TIGER system is a database called the Microbial Rosetta Stone that Ibis created to help make sense of the Babel of publicly available data on microbial genomes.
Kumar Hari, senior bioinformatics scientist at Ibis, said that the primary challenge in compiling the database involved reconciling the terminology — and taxonomy locations — for the same organisms from different resources. The database contains threat agent names and physical properties, disease and epidemiology data, DNA sequences, taxonomic lineages, and laboratory protocols. The FBI is currently using the database for a new microbial forensics program, Hari said, and has contributed additional funding for its continued development.
Hari commended HSARPA for being “forward thinking” in its bioinformatics approach. “They recognize that there’s a ton of data out there ... but it’s all coming from different platforms so they have to be able to compare apples to apples,” he said. The prospects are actually “pretty broad” for companies looking for funding in this area, he added. “There are a lot of opportunities coming from biodefense that many of the standard software groups haven’t even thought about, so it’s nice to see that HSARPA is so forward-looking in the types of tools that they’re trying to bring in.”
Final proposals for the BIAD program are due by August 2. Although the May 14 deadline for initial submissions for white papers has passed, Buchsbaum said that white papers aren’t necessary for a full proposal, but are “strongly encouraged.” So far, he said, 213 white papers have been submitted.
Buchsbaum said that HSARPA plans to reopen the proposal next summer, “to take a next tier of performers against the same topics where we see that there are gaps, and potentially adding new topics.”
A pilot-stage website for information on HSARPA’s funding opportunities is available at http://www.hsarpabaa.com/index.asp. In addition, DHS is hosting a conference July 12-15 in San Diego to discuss its science and technology activities and funding opportunities (Further information is available at http://www.dhstech.com/).