BIOTHREATSNatural or Not? Identifying Genetically Engineered Organisms
Ever since gene editing became feasible, researchers and health officials have sought tools that can quickly and reliably distinguish genetically modified organisms from those that are naturally occurring. Following the emergence of SARS-CoV-2, the world at large became aware of this need. Now, such tools are being built. The development of new tools to detect modified bacteria, viruses, and cells has bolstered national security against biological threats.
Ever since gene editing became feasible, researchers and health officials have sought tools that can quickly and reliably distinguish genetically modified organisms from those that are naturally occurring. Though scientists can make these determinations after careful genetic analysis, the research and national security communities have shared a longstanding unmet need for a streamlined screening tool. Following the emergence of SARS-CoV-2, the world at large became aware of this need.
Now, such tools are being built.
A suite of techniques – one lab-based platform and four computational DNA sequence analysis models – was developed and refined over the course of a six-year program funded by the United States Intelligence Advanced Research Projects Activity (IARPA). These approaches have the potential to dramatically shift current screening capabilities for detecting engineered organisms.
Susan Celniker’s team at Lawrence Berkeley National Laboratory (Berkeley Lab) was chosen to lead the testing and evaluation phase of the program, called Finding Engineering-Linked Indicators, or FELIX. She and her colleagues designed and produced increasingly challenging biological samples and assessed how well the tools made by participating academic and industry groups performed.
“What the FELIX program revealed in its initial months was that the capability to efficiently identify modified organisms in the environment does not exist. And so, the program really started at the foundations to developing first-in-class capabilities to identify modified organisms,” said Ben Brown, a staff scientist computational biologist in Berkeley Lab’s Biosciences Area, who co-led the project design with Celniker. “It’s a very important program in that it created the tools to fill an important segment of our national security space.”
Testing the Testers
To evaluate the work accomplished by its research teams, IARPA leveraged national laboratories to perform Test and Evaluation. This process ensures capabilities and tools that are developed under programs like FELIX can achieve the same results as reported by the researchers and are meeting program metrics, enabling evaluation of progress within the program. To ensure the tests would be as useful as possible for national security applications, the teams evaluated their performance with samples based on current and potential real-world scenarios.
