University of Maryland researchers are helping to create a tool that can assess the threat level of various DNA sequences.
With current technology, it is possible to create customized small DNA fragments for research or commercial reasons. Companies use automated machines to construct these genes and other long DNA strands, and while this can lead to huge scientific advances, these innovations are not always seen as positive.
“Scientists can actually go online and order a strand of DNA, which opens up the possibility that people might accidentally or purposefully order DNA that is harmful,” including smallpox, the plague and other viruses, said Mihai Pop, interim director of the University of Maryland Institute for Advanced Computer Studies and a computer science professor at this university.
He cited a recent case of a group of Canadian researchers who synthesized a variant of smallpox by ordering genetic pieces of the disease to be mailed to them.
“This software will hopefully prevent this,” he said.
This university partnered with the Fraunhofer Center for Experimental Software Engineering — which conducts research to support software-enabled innovations — and Signature Science LLC, a scientific and technical consulting firm, to create the software. It aims to screen custom DNA orders and tell companies in charge of synthesizing the requested strands if the sequence is safe, Pop said.
Researchers are developing algorithms for the prototype, as well as optimizing and testing the code. The Fraunhofer Center is providing software engineering expertise for validating and optimizing the project’s code, and Signature Science will manage the project while housing an internal testing evaluation team to test the prototype and determine its progress, said Todd Treangen, one of the project’s researchers.
The open-source project is funded by the federal government’s Intelligence Advanced Research Projects Activity through a $2.9 million contract that will last for 18 months. After this time is up, the project will be reevaluated to determine if they need more research or funding in order to make it usable to companies, Pop said.
Today, most global DNA synthesis activity is not screened for health or environmental risks, Treangen said.
“What these scientists are building is going to be applicable and will advance genomics in ways we haven’t seen in years,” said Brendan Joyce, a senior biology and computer science major. “While some future research might be halted because the machine will identify certain genes as harmful, that will be far and few between, in my opinion.”
No one has successfully created a similar tool that works at the speed and accuracy level the researchers are hoping to achieve, Pop said.
“It is rewarding to be a part of this program that is working on an important area of biodefense,” Treangen said. “It is a very complex and ambitious project, but I am reassured by having a wonderful team around me of everyone involved in the project to be able to push forward and make advances in this field.”