NEW YORK (GenomeWeb) — A multi-institution research collaborative led by scientists at Arizona State University's Biodesign Institute has entered into the second phase of a government-funded project to develop a qPCR-based multi-gene expression assay to rapidly assess an individual's exposure to radiation in the event of a nuclear incident.
As part of this next step, the team has been awarded approximately $9 million from the Biomedical Advanced Research and Development Authority, which follows a roughly $9.3 million contract option it received last year for phase one of the project. Overall, the team could potentially reel in a total of $31.2 million from BARDA, a federal agency within the Office of the Assistant Secretary for Preparedness and Response of the US Department of Health and Human Services.
The assay, which is being developed on high-throughput qPCR platforms from Thermo Fisher brand Life Technologies, currently assesses 29 genes that the team previously identified as being associated with radiation response, Joshua LaBaer, director of the Biodesign Institute's Virginia G. Piper Center for Personalized Medicine and principal investigator on the project, told PCR Insider in an email.
"The work done last year focused on building a biodosimeter in non-human primates," LaBaer said. "Obviously, for this program we have to rely on animal models because there is no way to do this experiment in humans. We used a combination of DNA microarrays and next-generation RNA sequence analysis to identify radiation-responsive genes."
LaBaer added that the team has developed an automated pipeline to assay candidate genes using one of the Life Tech high-throughput qPCR platforms, the ABI 7500 Fast Dx and the QuantStudio Dx.
"Using the qPCR platform we further refined our mathematical gene model to develop a biodosimeter that predicts the absorbed radiation dose in non-human primates during the first seven days after a radiation dose ranging from 0 to 10 Gy. The next steps of the program are to refine this dosimeter, lock down the final model, and then validate it."
When the Biodesign Institute-led team began the project in early 2013, it noted that assay throughput was a key BARDA requirement, with the agency seeking a test that could analyze approximately 2,000 samples per day.
Life Tech's 7500 Fast Dx platform is a five-color real-time PCR system that is compatible with 96-well plates and eight-tube strips. Although it received US Food and Drug Administration clearance a few years ago — a key attribute for the Biodesign team, since it eventually hopes to produce an FDA-approved test — it may not have the throughput necessary for the BARDA requirements.
Meantime, the QuantStudio Dx accommodates 96- or 384-well plates, as well as qPCR microfluidic cards, which can perform 48 tests on eight samples simultaneously. That platform was not FDA-cleared when the Biodesign-led team began its project, but it has since received regulatory approval.
The 7500 Fast Dx has a much larger installed base, making it an attractive platform as the team begins to envision an FDA-cleared test. Still, LaBaer said that the group is working with both platforms.
"The 7500 has the advantage of wide placement already and FDA approval on several applications," he noted. "The QuantStudio is the future direction of the company, and we plan to stay current with that."
The Biodesign team has also upped the number of genes in its test, though that number may still fluctuate. Last year the group noted that its test would likely contain between 10 and 20 genes, with each well of an assay plate containing a single gene probe set, and the assays for the multiple targets being run in parallel.
"Our gene panel increased somewhat when we migrated to non-human primates," LaBaer said this week. "Currently, it is 29 genes. We are doing some refinement of this list and it may adjust pending some experiments."
Currently, no high-throughput, rapid, FDA-cleared assay platform exists to measure the radiation dose absorbed by individuals within a large population. Of 11 project teams launched in 2010 under the BARDA initiative, the Biodesign group is one of six continuing development of a medical device to address this application.
Other collaborators on the project include Columbia University Medical Center's Sally Amundson, who has extensive experience in researching radiation responsive genes, and Mayo Clinic's William Wong, who is providing access to patient clinical samples needed for biomarker development, the Biodesign Institute said.