Rise of the double FELIX

What made the corn go bad?

Advances in genetic manipulation have raised the possibility of a new kind of attack on our food supply. 

"Right now, we'd have no easy way to know if a pathogen that attacked our corn, or any crop, was natural or engineered with malicious intent," says Nic Roehner, Ph.D. and a principal investigator for Raytheon Technologies on the Finding Engineering-Linked Indicators, or FELIX, program.

The Intelligence Advanced Research Projects Activity is sponsoring the FELIX program to develop a set of tools that would help us tell the difference between a naturally occurring pathogen and one that was engineered to cause harm. Raytheon Technologies is applying its cyber skills to the challenge of spotting human manipulation in genetic codes.

"If we could distinguish between engineered bio-threats and naturally occurring diseases, we'd be in a much better position to respond quickly and appropriately," Roehner explained. 

Raytheon Technologies' approach to detecting engineered organisms is twofold, combining single-cell DNA sequencing for rapid response and the company’s cybersecurity techniques for comprehensive threat detection. By using a platform called Tapestri developed by the biotech firm Mission Bio, engineers can screen for several hundred target engineered sequences. It's the same single-cell sequencing tech that top cancer centers use to profile cancer cells.

Tapestri "bar codes" cells so engineers can detect when two target sequences appear together in a single cell. If multiple suspicious genetic sequences are detected in a single cell, then a sample is sent for more costly whole-genome sequencing. That’s where Raytheon Technologies applies software inspired by malware detection to find a much wider range of signatures of DNA engineering. 

"DNA screening and cybersecurity have more in common than you might think," said Roehner. "In both cases, parts can be reused to create new designs, and both engineered DNA sequences and malware can have small footprints that are difficult to detect."

The approach seems to be working. Using Raytheon Technologies software, engineers have successfully detected 99 percent of all engineered regions in samples tested so far. They have also achieved a false-discovery rate of less than 1 percent.

FELIX is one of several projects the U.S. government is sponsoring in the emerging field of synthetic biology. Synthetic biology combines advances in chemistry, biology, computer science and engineering to design and construct new biological entities or redesign existing biological systems to meet specific needs.

"Synthetic biology technologies have great potential benefits, ranging from more effective medicines to renewable energy sources,” Roehner said. “We need to be prepared, however, for the possibility of their accidental or deliberate misuse."