May 5, 2020 | Alumni

Software tool built by U of T alum startup shares genetic data with COVID-19 researchers around the world

By Paul Fraumeni

Marc Fiume smiles as he looks away from an array of computer monitors displaying the logo of his company DNAstack.

Co-founded by U of T alumnus Marc Fiume (BSc 2009 SMC, MSc 2011, PhD 2015), DNAstack launched a search engine aimed at the global research community that scans and indexes genomic information about the novel coronavirus (photo by Jeff Beardall)

One of the most puzzling things about the novel coronavirus is how it affects people in such different ways. 

Among a single group of very similar people of the same age, some who contract COVID-19 will be asymptomatic, others mildly ill, while still others will be seriously sick and some will die.

Marc Fiume (BSc 2009 SMC, MSc 2011, PhD 2015) doesn’t know why this is the case. The University of Toronto alumnus is a computer scientist, not a medical researcher. But he does know what the scientists studying the virus and developing treatments need: a near-constant flow of information. 

So he and his colleagues at DNAstack are adapting their health-oriented search engine technology to a new tool that offers shared genetic data about COVID-19

“What we know about the virus is changing hourly as researchers and clinicians accumulate and analyze data,” says Fiume, who earned his PhD, master’s and bachelor’s degrees from U of T. “So we are deploying our technologies at DNAstack to support researchers investigating the virus.”

“potential to improve knowledge of COVID-19 at a speed and scale that isn’t otherwise possible”

Dubbed COVID-19 Beacon, DNAstack launched their new tool in late March. It’s a search engine that scans and indexes genomic information about the virus shared by scientists from around the world, making it possible for users to share and discover knowledge about the genetics of the virus in real time.

Researchers can then use the information – a mix of the virus’s genome (a complete set of genes) and other biological data – to see how the virus is changing as it moves through the global population.

“By sharing this genomic information over a cloud-based global network, there is the potential to improve knowledge of COVID-19 at a speed and scale that isn’t otherwise possible,” Fiume says. 

“That will contribute to new ways to fight the virus, such as the development of a vaccine.”

“If you talk to anyone, within one or two degrees of separation they have someone close to them who’s affected by a genetic disease”

Fiume launched DNAstack with partner Ryan Cook in 2014. The startup received support and guidance from U of T Entrepreneurship.  As Fiume told MaRS Magazine two years ago, the inspiration to start the company came from his best friend, Dan, who has cystic fibrosis. Genetic disease is “…actually a very common problem. If you talk to anyone, within one or two degrees of separation they have someone in their family, or someone close to them, who’s affected by a genetic disease.” But given the complexity of individuals’ genetic make-up, Fiume said he quickly realized that his field – computer science – would play an important role in the search for treatments for genetic ailments. 

Since then, the startup has built software to facilitate collaborative biomedical research and has partnered with leaders in cloud computing, sequencing, software and security to form the Canadian Genomics Cloud to further research discovery. DNAstack has also embarked on a partnership with Autism Speaks to enhance the agency’s research portal. Through the collaboration, DNAstack organized one of the largest collections of autism genomes in the world and made them more easily accessible and able to be analyzed by researchers. 

“DNAstack has demonstrated remarkable leadership in its innovative and collaborative approach towards finding a solution for COVID-19,” says Sue Paish, CEO of Canada’s Digital Technology Supercluster, a cross-industry collaboration of diverse organizations, including DNAstack, that aims to position Canada as a global leader in digital technologies. 

“The global opportunity to aggregate, track and share real-time data across medical communities has enormous potential to unlock a cure for the virus.”

DNAstack is getting noticed

DNAstack is getting noticed – and supported, too.  Prime Minister Justin Trudeau recently mentioned the company in his April 21 announcement about the bold ideas being put forth by groups working with Canada’s Digital Technology Supercluster. And the company’s COVID-19 tool was one of the winning submissions in Roche Canada’s Open Innovation Challenge, which called for solutions to the challenges of the pandemic.

COVID-19 Beacon is a first step in DNAstack’s efforts to support the research community with cloud-based tools for conducting research on the novel coronavirus.

“This service is intended to help share data on COVID-19 as broadly as possible and connect a global ecosystem of data generators and researchers,” says Fiume. “We’re urging researchers who are interested in making data available through this service, or using it for analysis, to get in touch with us.”

“so much better than it was even five years ago”

Fiume notes that scientists developing drugs and vaccines for COVID-19 are in a much stronger position today because of the increasing sophistication of technology. 

“The technology is so much better than it was even five years ago. We now have better tools for cloud computing, more mature standards for data sharing and better frameworks for machine learning – and the technology keeps improving. We also have a better ability to understand genetics and translate that into precision medicines.”

While the world waits for a vaccine to be developed, Fiume says DNAstack will do what it can to help researchers in their quest. “We’re trying to do our part to minimize the impact of COVID-19,” he says.

“There is so much that scientists don’t understand about this virus. Our job is to get people the information they need, so we can find solutions and get people back to normal.”

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