Professor Fiona Brinkman is working to improve how health data is integrated and shared. SFU is co-leading a trio of big-data projects funded by Genome Canada.


SFU researchers develop new tools to combat infectious diseases

September 16, 2016

New funding from Genome Canada will help SFU scientists specializing in health informatics develop ways to more effectively analyse, interpret and apply big data to improve key health-related issues, from infectious disease outbreaks to managing the world’s food crops.

Three SFU co-led projects are among 16 to share $4 million in funding through the recent Genome Canada and Canadian Institutes of Health Research Bioinformatics and Computational Biology competition. Federal Minister of Science Kirsty Duncan announced the funding this week.

Professor Fiona Brinkman is co-leading development of the Genomic Epidemiology Application Ontology (GenEpiO), together with UBC, McMaster University and Genome BC. The project addresses the significant impact that infectious disease outbreaks have on human health, agri-food production and the economy.

“Ineffective tracking of infectious disease outbreaks, such as those involving food-borne illness, can have an enormous effect on the number of people—and countries—impacted,” says Brinkman. “DNA sequencing provides the complete ‘fingerprint’ of a microbe, enabling an unprecedented tracking of how infectious diseases spread.

“When outbreaks become global, however, it’s critical that data is shared across public health organizations securely and efficiently. Unfortunately data is often held in institution-specific formats, and sharing becomes difficult, time-consuming and costly.”

The researchers' goal is to improve data integration and how information on infectious disease and antimicrobial resistance is shared across public health agencies. Their platform will enable public health workers to share outbreak-related information faster and perform more powerful analyses, helping to reduce the negative health and economic impacts of disease outbreaks.

Brinkman is also working with colleagues at Dalhousie University and McMaster University to better identify antimicrobial resistance (AMR) occurring in a wide range of medical and agricultural conditions.

Currently, there is no software designed to specifically predict AMR profiles directly from metagenomic data (the sequence of all the DNA in a sample), which would enable more rapid AMR profiling, and aid in prioritizing candidate genes for further research. The team is developing new software and database tools capable of providing near-instantaneous pictures of AMR organisms in a sample. Not only will this aid AMR research but also AMR threats that impact both agri-food production and public health.

SFU researcher Cedric Chauve is co-leading a project to create PathOGIST, a computational framework. Working with SFU colleagues Leonid Chindelevitch and Brinkman, as well as William Hsiao, a former SFU student now based at UBC, their goal is to enable public health workers and others to quickly classify pathogens into epidemiologically related groups, based on sequencing data, and generate interpreted genomic reports to inform their actions.

Researchers hope that PathOGIST will revolutionize how disease outbreaks are managed, ensuring faster responses that will significantly reduce the impact of those outbreaks on both health and the economy.

All of these projects are associated with SFU’s Integrated Rapid Infectious Disease Analysis Project (IRIDA) led by Brinkman. The IRIDA is an initiative to build an open-end platform for infectious disease genomic epidemiology. Brinkman says there is growing interest in IRIDA, with countries from four continents installing the software for trial in their public health agencies.