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Brendan Frey says the predictive power of algorithms are key to how Deep Genomics will serve its clients. (Matthew Sherwood For The Globe and Mail)
Brendan Frey says the predictive power of algorithms are key to how Deep Genomics will serve its clients. (Matthew Sherwood For The Globe and Mail)

Toronto startup aims to shake up genome sequencing market Add to ...

A University of Toronto computer scientist known for combining artificial intelligence with big data genomics is launching a company that could create a roadmap for DNA-based therapy.

The company, called Deep Genomics, is set to launch on Wednesday.

It will be wading in to the growing market for diagnostics and personalized medicine based on whole genome squencing.

While it has become common for researchers to identify genetic mutations that appear to correlate with various diseases – thousands of mutations have been linked to cancer, for example – the technology behind Deep Genomics involves the use of computer algorithms that can tease out cause and effect relationships.

It’s a method that was developed by Brendan Frey, a professor in the university’s department of computer and electrical engineering.

“My approach was let’s train a neural network to figure out why a mutation leads to a disease,” said Prof. Frey, who is the company’s president and CEO. “That’s what makes our technology unique.”

The method draws on a rapidly growing discipline in computer science known as deep learning, which has lately been making inroads in a range of tough computational problems – including visual identification and speech recognition – where context plays an important role in arriving at the right answer. The field has a long history as a branch of artificial intelligence in which a computer program can adjust itself to become better and better at a complex task. In deep learning, the software is one step further removed from human guidance and can learn to make associations beyond what a human expert might discern.

In recent years, Prof. Frey has taken the same principles to create a set of computer algorithms that can look at the pattern of mutations in an individual’s DNA and make inferences about how those mutations collectively affect the operation of different types of cells in the body.

It’s the predictive power of the algorithms that are key to how Deep Genomics will serve its clients, including other companies that offer diagnostic services to hospitals and health care providers. By linking the DNA sequence to cellular function, the objective is to help determine not only what may be the source of a health problem but what treatment may be more likely to succeed.

Prof. Frey said that when he and his colleagues first published work on the approach in 2010, he expected it would quickly be taken up by entrepreneurs in the biomedical sector and was surprised when that didn’t happen. He concluded that there were too few research groups with the combined expertise in genomics and artificial intelligence to turn the approach into something that would be of use to clinicians and patients.

He decided to launch the company last fall, he said. Angel investors have provided the initial capital to launch the eight-person Toronto-based company, which Prof. Frey hopes will double by the end of the year and quickly find a niche in genetic diagnostics.

Yann LeCun, the New York-based director of artificial intelligence at Facebook and an adviser to the new company, said that while the importance of deep learning is now well established in many areas of data analysis, its impact on medicine is just beginning to be felt.

“The potential applications are really huge,” he said.

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