Decoding a deluge of data

Two University of Toronto research projects have won $1 million each in funding from the Government of Canada through Genome Canada and the Ontario Genomics Institute.

The Genome Canada 2012 Bioinformatics and Computational Biology competition, a partnership with the Canadian Institutes of Health Research, supports the development of the next generation of tools to deal with the large influx of data produced by today’s genomics technologies

“Bioinformatics becomes increasingly important as researchers are able to generate more and more data,” said Judith Chadwick, U of T’s assistant vice-president, Research Services.

“Tools that help us make sense of these data are the keys to better health and quality of life," Chadwick said. "On behalf of the University of Toronto, thanks to Genome Canada for these awards—and to the Ontario Genomics Institute for facilitating them. And congratulations to the researchers on these richly-deserved awards.”

Professors Michael Brudno and Gary Bader received $998,546 to develop software that will help doctors use a patient’s genome to search for information about his or her risk of developing a disease.

“Genome sequencing is evolving from being a research project to a routine medical test,” says Brudno. He and Bader want to help clinicians interpret these tests to better target medical treatment.

The data generated when a human genome is sequenced are in the terabyte range—much more than any human could make sense of. (A terabyte of paper stacked would make a 66,000-mile tower.) The team’s software will help distil the data down to a few megabytes of information that is actually useful. (A megabyte is roughly equivalent to 500 pages of text.)

“Often it is hard to figure out the exact type of disorder a patient has,” says Brudno. “Two disorders that look the same may have different genetic causes—and need different courses of treatment.” Sequencing a patient’s genome allows for precisely targeted treatment.

The software can also be used to help healthy patients understand their risk of developing genetic diseases such as cancer, diabetes and Alzheimer’s.

The funding, half of which comes from Genome Canada, and half from the Hospital for Sick Children (SickKids), will allow the researchers to test and refine their software in collaboration doctors treating patients at SickKids. Brudno notes that a previous grant from the Ontario Genomics Institute was instrumental in getting the project started.

Brudno is affiliated with U of T's Department of  Computer Science, the Donnelly Centre for Cellular and Bimolecular Research, the Banting and Best Department of Medical Research and SickKids, where he is the director of the Centre for Computational Medicine. Bader is affiliated with the Banting and Best Department of Medical Research, the Donnelly Centre for Cellular and Bimolecular Research, the Department of Computer Science, the Department of Molecular Genetics and the Samuel Lunenfeld Research Institute at Mount Sinai Hospital.

Professors Nicholas Provart of the Department of Cell & Systems Biology and the Centre for the Analysis of Genome Evolution and Function and Stephen Wright of the Department of Ecology & Evolutionary Biology and the Centre for the Analysis of Genome Evolution and Function received $1 million to develop visualization tools and applications to accelerate advances in plant biology, which are important for feeding, housing, clothing and providing energy to the world’s growing population.

Recent advances in DNA sequencing and other high throughput technologies have generated a deluge of information about Arabidopsis thaliana, an organism that biologists use as a model plant species—“the fruit fly of plants,” says Provart.

Interpreting and visualizing the data, Provart says, “can be overwhelming for biologists, who aren’t necessarily skilled in the art of writing computer code.”

Currently, plant biologists in search of genetic data have to visit multiple sources and the result is fragmentation and inefficiency—and useful data often ends up languishing.

He and Wright will participate in the development of international portal that will make existing data available to scientists in a desktop interface where they can pick and choose the data they want with the click of a mouse. The portal will help plant biologists advance a variety of research questions, many of which will be essential to supporting the world’s population, which is expected to reach nine billion by 2050.

Half the funding for Provart and Wright’s project will come from Genome Canada, the other half from the Moore Foundation and other sources.