New tools to improve disease management, analysis

April 25, 2013

Simon Fraser University researchers will use new grants from Genome Canada to develop improved analytical tools leading to better management of communicable diseases and more accurate analysis of DNA in cancer patients.

The grants are part of $2.7 million in funding going to local researchers from a recent national funding competition covering a total of $6.2 million in bioinformatics related research.

A research team led by SFU computing scientist Cenk Sahinalp aims to use a mathematical approach called compressed sensing/sparse recovery to discover all possible RNA products of genes and estimate their abundance through the analysis of transcript sequence data.

“A gene can have multiple RNA products and thus multiple proteins, due to a process called alternative splicing,” explains Sahinalp. His team will develop new algorithms and computational tools to investigate the role of alternative splicing in cancer.

The tools will also help Sahinalp and collaborators from the Vancouver Prostate Centre to study differences between commonly observed ”adenocarcinoma” type prostate cancer (which is typically treated by androgen depletion) and “neuroendocrine,” a rare but highly aggressive and lethal form of prostate cancer.

The latter can emerge after an adenocarcinoma patient is androgen depleted during treatment. Researchers will investigate how this transition occurs.

In another project, SFU researcher Fiona Brinkman’s team, working with the Public Health Agency of Canada and BC Public Health Microbiology & Reference Lab, will develop new tools to help public health investigators more effectively use and share genomics information.

Despite advances in medical, sanitary and public health practices, bacterial diseases continue to be a serious threat.

“While whole genome sequencing of disease-causing bacteria can provide detailed data to identify and track these organisms, the tools used to investigate and share information are difficult to use,” says Brinkman, a professor of molecular biology and biochemistry.

The funding is from Genome Canada’s 2012 Bioinformatics and Computational Biology Competition, in partnership with the Canadian Institutes of Health Research (CIHR). In all, 17 projects across the country received funding.

Simon Fraser University is Canada's top-ranked comprehensive university and one of the top 50 universities in the world under 50 years old. With campuses in Vancouver, Burnaby and Surrey, B.C., SFU engages actively with the community in its research and teaching, delivers almost 150 programs to more than 30,000 students, and has more than 120,000 alumni in 130 countries.

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Contact:
Cenk Sahinalp, 778.782.5415; cenk@cs.sfu.ca
Fiona Brinkman, 778.782.5646; brinkman@sfu.ca
Marianne Meadahl, Public Affairs, 778.782.9017; Marianne_Meadahl@sfu.ca