genome Bc: open for Business

genome BC:

open For BuSineSS

Secrets uncovered

What does a mighty red cedar in Vancouver Island’s Cathedral Grove have in common with a miniscule microbiota fl oating in the drainage water of a Cape Breton mine? It is simple: they both have a genome. Genomes have no secrets - they are an open book but until recently they have been written in an alien language.

Today, with the help of advanced tools and technologies, we are decoding genomes and more importantly, using this information to address challenges facing the agri-food, aquaculture and fi sheries, energy and mining, forestry, and healthcare sectors. Within these sectors there are challenges associated with complex biological systems. A better understanding of these systems at a molecular level will provide the groundwork for developing effective solutions.

Meeting unmet needs

Genome BC integrates its program design with feedback from industry to ensure that the research it funds is addressing genuine problems within realistic timelines. While some issues such as climate change will require more time to integrate genomics strategies into solutions, other problems like wait times for cancer screening need to see real-time results. The recently launched User Partnership Program (UPP) is designed to directly address the challenges defi ned by users and the imbalances between academic research ‘push’ and needs of industry ‘pull.’ By engaging industry, government regulators, health authorities, not-for-profi t organizations and other users early in the implementation process, Genome BC is proactively managing the translation of research innovations to products, services and policies.

partnerships and Outcomes: Hitting all the Targets

Nothing Fishy Here

An example of UPP is the Strategic Salmon Health Initiative (SSHI) that addresses concerns outlined in the fi nal report of the Cohen Commission Inquiry into the Decline of Fraser River Sockeye Salmon. This report noted that a deeper examination is needed to make accurate assessments about the range of possible impacts on wild fi sh stocks. The SSHI project, which was already underway when the report came out, is concentrating on the specifi c recommendations related to fi sh pathogens and diseases.

Our current knowledge about salmon comes primarily from observations of cultured fi sh (both in hatcheries and in aquaculture). Consequently, there is a fair understanding of pathogens and diseases that impact salmon in freshwater hatcheries and sea-water net pens. However, we know less about pathogens affecting wild Pacifi c salmon. Genome BC and the Pacifi c Salmon Foundation are spearheading a fi ve-year project that is utilizing more than a decade of research and $37.5 million worth of past investments to be the largest ever evaluation of the distribution and impact of potential disease agents conducted on BC salmon (wild and hatchery). While identifi cation of a specifi c microbe won’t necessarily indicate the presence of disease, it will provide a critical baseline for future monitoring activities. And rigorous analysis and categorization could determine which microbes have the potential to cause disease in salmon. A public interest panel comprised of key government, aquaculture industry, sport fi shery, salmon gillnetters and environmental experts also plays an important role in determining disease agent information that is important to them and other end-users. Ongoing engagement with these vested groups will assist in the development of an effective strategy for commuHealth Initiative (SSHI) that addresses concerns nicating research outcomes and help identify applications that may assist in the management of wild and cultured salmon resources.

may assist in the management of wild and cultured salmon resources.

Clean Water

Just over a decade ago, a small Ontario town was the epicentre of a drinking water-related disaster. Close to half of Walkerton’s 5,000 residents fell ill and seven people lost their lives due

The journey leading to scientifi c discovery is never direct or easy to navigate. It’s fi lled with leaps of intuition, false starts, happy accidents and unexpected results. But, however it zigs or zags; the path to discovery and innovation is propelled by the need to make an impact.

to the highly dangerous strain of E. coli bacteria found in their drinking water.

A team at the BC Centre for Disease Control (BCCDC) is working to prevent another such disaster. Genome BC is enabling their research that aims to develop a better way to identify the presence of fecal pollutants in watersheds and provide new tools to track sources of water contamination.

Current drinking water testing collects samples from the tap, rather than the watershed source and testing for bacteria contaminants, such as E. coli, often takes more than two days to complete. Additionally, these tests do not always refl ect contamination of water by non-bacterial pathogens such as parasites or viruses. By applying metagenomics, a much more robust method that can identify many pollutants at once, future analysis methods will become much faster as testing can occur at the watershed level. This simplifi ed process will reduce testing time from days to hours and provide profi les of all microbes present in a water sample.

The BCCDC, responsible in BC for investigative water analysis around microbiological threats, will be an early adopter of this testing method and the research project is partnering with the Canadian Water Network in the near future to pilot the watertesting prototype in watersheds across Canada.

Forest Health

Invasive species pose a signifi cant threat to Canadian forests. The evidence is all around us— blighted leaves, spotted needles, bare branches, cankered stems—all proof that increasing numbers of trees are succumbing to invasive pests. Traditional techniques used to isolate and identify pathogens take weeks to perform, requiring precious time that forest professionals just don’t have when dangerous pathogens like sudden oak death are detected in a foreign shipment. And, by looking only for known pathogens, unknown ones can slip through. Genome BC-funded research in this area has morphed to application and is now providing tools to detect known and novel pathogens in real time, preventing an imported, infectious sapling from fi nding its way into a Canadian nursery or forest. Research outcomes are making inroads in the forest sector and anticipate generating signifi cant economic benefi ts from a reduction in losses due to forest diseases.

For example, one research project ran approximately 10,000 tests on samples for several end-users, including the BC Ministry of Forests Lands and Natural Resource Operations (MFL), the Québec Ministry of Natural Resources, and the cities of Victoria and West Vancouver. These tests detect and map pathogens, and provide risk assessments. Based on the results generated by this project, the MFL is considering options of how the exotic poplar canker pathogen could be eradicated to protect planted and natural poplars on the West Coast.

Cancer Screening

If a woman inherits a mutation in the BRCA1 or BRCA2 gene, her lifetime risk to develop both breast and ovarian cancer is greatly increased over that of other women in the general population. The Centre for Clinical Diagnostic Genomics (CDG) at the Provincial Health Services Authority (PHSA), in partnership with the PHSA Cancer Genetics Laboratory, is the fi rst clinical laboratory in Canada to develop and use a revolutionary “NextGen” DNA sequencing process for routine clinical testing. With funding from Genome BC, the new technology has reduced the time to detect BRCA1 and BRCA2 mutations from six months to two months, which means therapy decisions are made more quickly.

An additional benefi t of the work done by the CDG is the potential for growth of the service. With the capacity of the CDG for inherited cancer testing being four times that of current provincial demand within BC, the province is well-poised to expand services across Canada and provide testing for other provinces to become a national centre for inherited cancer sequencing. The CDG will continue to expand its services to include new tests for both cancer and other chronic diseases.

Beyond the scope

The journey leading to scientifi c discovery is never direct or easy to navigate. It’s fi lled with leaps of intuition, false starts, happy accidents and unexpected results. But, however it zigs or zags; the path to discovery and innovation is propelled by the need to make an impact. And impact cannot be made without support from our funders and partners. Investment in Genome BC is something of a self-fulfi lling prophecy: dollars from the provincial government allow BC researchers to compete for federal and international funds which in turn draw new investments into the province.

Genome BC is an essential cog in Canada’s Science & Technology Strategy, and our unique co-funding model attracts millions in international funding and valuable collaborations. With help from our funding partners we invest in the very best people, the very best genomics research programs, and the most advanced technologies because we are propelled by a single desire: to pave the way for research to have a direct impact on our lives and our future, and to deliver critical benefi ts to people in British Columbia, Canada, and beyond.

To see this story online visit http://biotechnologyfocus.ca/?p=8701