SEQUENCE #7: Looking to genomics for hope and solutions

“There is hope”.

This is how Dr. Martin Alda summed up the promise of genomics as a potential game-changer for diagnosing and treating bipolar disorder (BD). Clinicians have known for some time that BD tends to run in families, and Dr. Alda and his colleague Dr. Rudolf Uher are at the forefront of new research that is using genetics to diagnose BD more quickly in high-risk individuals and to predict which treatment will work best for which people.

Drs. Alda and Uher, psychiatrists and researchers with Dalhousie University and the Nova Scotia Health Authority, were speaking at a recent panel discussion on genomics and bipolar disorder co-hosted by Genome Atlantic and Genome Canada. The event opened up with some exciting news: Genome Atlantic and Genome Canada were joined by the Nova Scotia Health Authority, Dalhousie Medical Research Foundation, Research Nova Scotia Trust, and the Dalhousie Department of Psychiatry in announcing $975,000 in funding for a new research project co-led by Drs. Alda and Uher, which aims to develop new clinical screening tools to better diagnose and treat BD. Also read our interview with Dr. Alda.

It was a big week. A few days earlier, Genome Atlantic celebrated the announcement of a $1.4 million project co-led by Dr. Rob Beiko of Dalhousie University, that will develop new genomic tools to fight superbugs. These tools, consisting of bioinformatics algorithms and software, will track genes that contribute to antimicrobial resistance (AMR) – a huge problem for the agri-food industry and the health of Canadians.

The mental health and superbugs projects are on the cutting edge of health innovation. The work led by Drs. Alda and Uher has the potential to improve lives through speedier, personalized medicine-based treatments. Dr. Beiko and his team are leading the charge in developing tools that will allow us for the first time ever, to track AMR as a dynamic phenomenon involving the transfer of genes among AMR-resistant bacteria.

Genomics is the impact driver in the innovation toolkit. But not just in health. In November, we launched a $1.1 million New Brunswick-based project to advance cannabis research and increase productivity – and we’ll soon have some exciting project news on the aquaculture and environment fronts too. All the above projects are supported by Genome Atlantic, with funding from Genome Canada and other public and private partners.

Recently, Genome Atlantic took part in an important announcement for the Maritime apple industry: the launch of the National Apple Breeding Consortium which brings together Canadian researchers, breeders and marketers with the aim to streamline apple development and boost returns to the industry. Genome Atlantic and Dalhousie University apple researcher Dr. Sean Myles were instrumental in getting the Consortium off the ground, and we hope to pursue future research through the Consortium, using genomics to improve and accelerate the development of successful new Maritime apple varieties.

The ability to recruit and keep top talent is critical for Atlantic Canada. And so, we’re pleased to share with you the stories of three talented scientists working in Prince Edward Island, Nova Scotia and New Brunswick, and a doctoral student at Memorial University in Newfoundland – all living and working here in part because of Genome Atlantic projects.

Finally, a big thanks to Invest Nova Scotia who recently announced funding of $325,000 over three years to support Genome Atlantic’s business development activities in Nova Scotia. Genome Atlantic’s strategy is driven by the needs of end-users, and this investment will help us to meet the rapidly-growing demands for genomic solutions across health and resource sectors.

Sequence #11: A path to economic recovery

As this unforgettable year nears its close, we have upbeat news to report in this issue from the health care and oceans sectors.

Despite the COVID-19 pandemic, Genome Atlantic has never been busier. Our current portfolio has 23 active, funded projects worth nearly $50 million, encompassing 25 companies and 15 university partners.

These projects span all four Atlantic provinces and represent a broad range of sectors including human health, oceans (aquaculture and energy), environment, agriculture, forestry and mining.

Significantly, our portfolio includes an ever-increasing amount of private sector investment, which has grown from eight per cent in 2008 to between 20-30% in recent years.

As we track the beneficial, unfolding effects of the projects on our list, we continue to pilot new opportunities through our business development pipeline.

Based on our activity, genomics is poised to be a driving force in our region’s economic recovery.

At this time, we want to acknowledge the tremendous support of our many partners in government, academia, and industry throughout this unprecedented period. They have been a pleasure to work with.

To you, our subscribers, we extend our seasonal best wishes and the hope that you’ll find inspiration for the year ahead in the people and applied genomics projects highlighted in this issue.

We all know recovery won’t be instant or easy, and that it will be more important than ever for Atlantic Canada to back innovations with a proven track record of impact. Genomics is one of these technologies, delivering impressive ROI across a range of sectors strategic to Atlantic Canada’s health and prosperity and attracting high levels of private sector investment.

Our sleeves are rolled up and the path to our region’s greater prosperity lies ahead.

Steve Armstrong


In This Issue….

Climate proofing P.E.I.’s blue mussels
Early diagnosis of rare genetic disorders in children
Initial findings on track in offshore energy project
One to watch: Dr. Stephanie Colombo
One genomic discovery leads to many more
Cleaner fish for salmon farming

Sequence Past Issues

Sequence #10: Pandemic response & economic renewal go hand in hand

The last few months have been unprecedented as we have all struggled to respond to a global pandemic. We hope that through it all, you and your families have stayed healthy. Even as restrictions ease and the economy re-opens, we are mindful of the need for continuing vigilance to ensure that we can all move forward, propelled by cautious optimism and a shared commitment to renewal.

Despite the challenges, this has been an especially productive time for Genome Atlantic as we have actively advanced an array of initiatives on two independent tracks: those focused on COVID-19 surveillance and the genetic determinants of disease severity, in parallel with ongoing efforts to continue to strengthen the bioeconomy of Atlantic Canada. Both are necessary for our region’s economic recovery and well-being. In this issue of Sequence, we share some exciting examples of each, including some great new video content.

We recently announced funding to Dalhousie University researchers to support important COVID-19 genomics projects. One, led by Drs. David and Alyson Kelvin, aims to find COVID-19 biomarkers that will help doctors triage patients and inform patient care protocols in settings like long-term care facilities, emergency rooms, hospitals, and ICUs. The second project, led by Drs. Nikhil Thomas, John Archibald and Morgan Langille, is piloting a surveillance tool to quickly identify early trends in transmission in high-risk settings like long-term care facilities, food processing plants or fishing vessels.

Genomics is a vital tool in our battle against COVID-19. Watch our short, animated videos “On the Trail of Covid-19” and “The Race for a Vaccine” to find out why.

On the economic development front, find out how forestry giant JD Irving Ltd. is using genomic selection to significantly improve forestry tree breeding practices and increase production. Take a deeper dive into the headline-making New Brunswick oyster breeding project through an engaging project video and a Q/A (Scroll down) with L’Étang Ruisseau Bar’s Dr. Martin Mallet and Laval University’s Dr. Louis Bernatchez. And hear from Dr. Kurt Gamperl at Memorial University and Dr. Mark Fast at UPEI for an update on their work addressing the adverse effects of climate change on farmed Atlantic salmon.

To round out this issue, medical research innovator Dr. Janessa Laskin of the BC Cancer Agency tells us why genomics could be the future of cancer treatment. And we profile our long-time industry collaborator Dr. Richard Taylor, recently retired from a long career with EWOS and Cargill, who shares some tips on forging successful industry-academic partnerships.


Sequence Past Issues

SEQUENCE # 9: De-risking investments through genomics R&D

Recently we visited the Research and Productivity Council (RPC) in New Brunswick to film how they use genomics in testing, developing and improving products and processes.  RPC is a global leader in material and environmental testing, work that puts them in daily contact with innovation at every stage of technology and market readiness. For many years, Genome Atlantic has collaborated with RPC – for example, working with RPC scientists like extractive metallurgist Neri Botha to improve the efficiency of bioleaching for mining clients. (See link to our story and video below.) 

RPC’s Executive Director Eric Cook believes that genomics is a critical biotechnology for driving innovation and he credits Genome Atlantic for helping to de-risk business investment in genomics projects.  Genome Atlantic does this by providing advice and guidance at every step – from assessing the feasibility of a genomic solution, to helping with proposal development, to securing funding, to project management – to ensure that projects deliver maximum benefit to our business and public-sector clients.  And because all our projects are industry-led, we’re committed to finding practical solutions and delivering maximum benefit for our business and public-sector clients – whether we’re using genomics to help de-risk offshore oil and gas exploration decisions, develop novel clinical aquaculture feeds, or find new treatments for Atlantic Canadians with genetic diseases. 

The fact that private sector investment makes up almost 30% of our portfolio speaks to the high level of confidence Atlantic Canadian businesses have in genomic technologies and in Genome Atlantic’s ability to maximize and de-risk their investment. 

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 In this issue of Sequence we zero in on three innovative examples of genomics applications relevant to Atlantic Canada. Three years ago, Genome Canada and Genome Atlantic launched a large-scale R&D project aimed at tackling Microbiologically Influenced Corrosion (MIC), which is a multi-million-dollar problem for our oil and gas energy sector.  We caught up with project co-lead Dr. Lisa Gieg to find out what she and her team have learned so far and how this information could be used to help predict and manage MIC.  At RPC, we met up with Neri Botha to see how using naturally occurring bacteria to extract metal could be a viable and environmentally friendly solution for the mining industry.  And we talk with two plant geneticists who are passionate about helping the region’s apple industry shine – Dr. Sean Myles dishes on apple breeding (and cannabis traceability) and Dr. Zoë Migicovsky tells us why her love of apples drew her to Nova Scotia (watch our video profile and story on Zoë.). 

SEQUENCE # 8: New technologies, real solutions

There’s no denying genomics is cool. The study of genes and their functions is adding to our understanding of every living thing. But there’s more to genomics than the wow factor. Genomic technologies are driving solutions for our resource industries, human health, and the environment.

One of the most promising new genomic technologies is eDNA, an environmental monitoring tool that identifies species’ DNA from their genetic material (scales, fur, feces, etc.) collected in water or land samples. It’s non-invasive, accurate and relatively inexpensive. In Atlantic Canada, Parks Canada is using eDNA to track invasive chain pickerel in Nova Scotia’s Kejimkujik National Park. EDNA led scientists at New Brunswick’s Canadian Rivers Institute to a unique population of Saint John River striped bass thought to be lost forever. And in St. John’s, NL, The Centre for Environmental Applications (CEGA) is using eDNA to conduct environmental monitoring around the province’s offshore oil and gas platforms.

But how effective is eDNA in extreme turbulent marine conditions? Could it, for example, be used to monitor marine species-at-risk in a place like the Bay of Fundy’s Minas Passage where 160 billion tons of seawater flow through twice a day driven by the world’s highest tides? That’s what Stantec’s Dr. Marc Skinner wanted to find out when we partnered with him, the Offshore Energy Research Association of NS (OERA), the University of Guelph and Dalhousie University on a unique eDNA test using Dalhousie’s Aquatron. The results so far are promising. Check out the article and our two new videos with Marc! (Scroll down the article for the second video.)

Another environmental use for genomics is in remediating contaminated industrial sites like abandoned mines. Saint Mary’s University’s Dr. Linda Campbell, world-renowned researcher in the field of environmental contamination, is partnering with Genome Atlantic (with support from the NS Department of Energy and Mines) to explore biological solutions to the age-old problem of remediating toxic arsenic and mercury in tailings from legacy gold mining sites.

In human health, genomics contributes to improved diagnosis and treatment of cancers and inherited and infectious diseases. Sequence Bio, a biotechnology company based in St. John’s, NL, is launching its NL Genome Project this summer to study the unique genetic makeup of Newfoundland and Labrador – with the ultimate aim of improving treatments and health outcomes. Genome Atlantic recently caught up with Sequence Bio CEO and co-founder Chris Gardner for an update on the company’s ambitious plans and goals.

We also take a closer look at how genomics is being used to track genes that contribute to antimicrobial resistance (AMR), a big problem for the agri-food industry and the health of Canadians. Dalhousie University’s Dr. Rob Beiko is at the forefront of this new science, and he shares with us some of the cutting-edge tools that he’s developing to combat AMR.

In the last issue of Sequence, we told you how apple researchers across Canada are pooling their information and innovations to bring new apples to market more quickly. It’s all about developing new varieties that grow best in local conditions, says Dalhousie University’s Dr. Sean Myles. Find out how scientists like Myles are using genomic selection to develop varieties more quickly and how this could help Maritime apple producers.

Lastly, Genome Atlantic is hosting the 7th International Symposium on Applied Microbiology and Molecular Systems (ISMOS-7) from June 18-21 in Halifax. ISMOS is the world’s leading conference on microbiology and molecular biology in the oil and gas industry, and a forum where delegates from industry and academia come together to discuss how emerging microbial and molecular tools can help solve some of the industry’s biggest challenges like biocorrosion and sustainable oil extraction.

Registration is still open (editor’s note: registration is now closed) but it’s filling up fast so don’t miss out. Hope you can join us for a great program and a fun time!

Sequence #1: So What’s Up With The Microbiome?

The microbiome is a hot topic these days, embraced by research scientists and the media alike.  The microbiome refers to all the microorganisms and their collective genetic material that reside in human beings and other animals, plants, soil, and water.  These communities of ‘microbial flora’ have always been with us but we’re just beginning to understand the role they play in everything from human health to mining and agriculture. 

We know, for example, that not all microbes are equal.  Some are harmful, some benign and some essential for the health of their hosts.  Microbes can boost our immune systems and our natural resources – but maintaining a healthy microbiome is a balancing act that can be thrown out of whack by factors like diet(in humans) and chemicals (in soil and water). 

This issue of Sequence explores the new frontier of the microbiome. We’ll go behind the scenes with scientists on the cutting edge of human microbiome research, meet a hard-working sequencing facility that’s a hit with genetic researchers near and far, and see why microbes are the Midas touch for gold extraction, a better tool for cleaning oil spills, and the magic in making better wines. 

Sequence #5: Yes, Genomics Can Help With That

Genomics is proving to be a game changer for many resource industries critical to Atlantic Canada’s economic growth.

Nova Scotia’s Minister of Energy Geoff MacLellan recently announced details of his department’s $11.8-million commitment to Phase Two of Nova Scotia’s offshore growth strategy.

MacLellan acknowledged the important role of innovative technologies like genomics in helping to ‘de-risk’ offshore exploration and showed Genome Atlantic’s newly-produced video “Reducing the Risk”, about how genomics is contributing to a better picture of Nova Scotia’s offshore petroleum deposits.

Genomics is helping to tackle another big offshore challenge – microbiologically-influenced corrosion (MIC), which costs the oil and gas industry tens of millions of dollars a year.  Genome Atlantic joined international experts in St. John’s, NL recently for a workshop and research symposium dedicated to better understanding and managing MIC.  Check out Memorial University’s story on the event and the $7.8 million research project managed by Genome Atlantic and Genome Alberta aimed at improving pipeline integrity.  Click here for more information about the MIC research project.

Cannabis is an important emerging industry for Canada, and genomics plays an important role here too. Cultivars and breeders are using genomics to identify desired traits, accelerate breeding and unlock high-value opportunities for developing specialized strains. The Province of New Brunswick has identified cannabis as a major economic driver, and this spring, Genome Atlantic partnered with Opportunities New Brunswick and BioNB to host a panel discussion in Fredericton focused on maximizing cannabis opportunities along the entire value chain, including through genomics technologies.

In aquaculture, another important emerging industry for Atlantic Canada, genomics is driving growth by helping to boost breeding programs, reduce loss from disease and pests, and optimize feed formulas. Better feeds help keep farmed fish healthy, and Genome Atlantic spoke with two leading Ocean scientists at Memorial University who are working with researchers at Cargill Aqua Nutrition and UPEI to develop therapeutic feeds that optimize growth and disease resistance in farmed salmon.

Genomics is also bearing fruit for agricultural researchers like Dalhousie University’s Dr. Sean Myles.  Myles wrote the book – literally – on grapevine breeding programs for the wine industry and was instrumental in leading the development of Canada’s National Apple Breeding Consortium. Check out our conversation with him about the role of genomics in value-added agricultural products, particularly here in Atlantic Canada.

Sequence Issue #4: 163 lives saved….and counting

Ten years ago, Newfoundland researchers cracked the genetic code of a cardiac disease that causes death in seemingly healthy young people. The disease, Type 5 ARVC, is particularly prevalent in Newfoundland and Labrador. Genome Atlantic recently caught up with researchers Drs. Terry-lynn Young and Kathy Hodgkinson to find out what’s happened since their genetic breakthrough – as it turns out, plenty.  More than 500 people have been tested and 163 people fitted with life-saving defibrillators. Watch one patient’s story in the brief, compelling video:

We also checked in with Drs. Chris McMaster and Johane Robitaille on their continuing work in orphan disease discovery and therapies. Seven years ago, McMaster launched a research project called IGNITE to improve our understanding, diagnosis and treatment of orphan diseases.  Multiple gene discoveries and therapies later, this remarkable research team continues to unlock the power of clinical genetics to improve the lives of people with orphan diseases.

Watch this brief video on how the Government of Canada’s recent announcement of $225 million for genomics and precision health research – including on orphan diseases – is bringing new hope for Canadian patients.

Genomics is a powerful tool for many sectors and is one of five pillars of the recently announced Atlantic Canada-based Ocean Supercluster. Genome Atlantic joined a recent Ocean Supercluster celebration in St. John’s, NL, hosted by Petroleum Research Newfoundland and Labrador.  Perhaps Hon. Seamus O’Regan summed it up best when he said, “We came here for the ocean’s riches. We have the expertise that can take on the world. So let’s take it on.”

Oil-eating microbes? They’re real and they may just help unlock the secret of Nova Scotia’s offshore petroleum reserves. We’ve commissioned a video to tell the story, and while it won’t wrap up for a bit, here’s a sneak peek.

Genome Atlantic is helping to “create great things from life” in Atlantic Canada’s bioscience sectors. Find out how in this Opinion Piece published in The Telegram (St. John’s, NL) and Guardian (Charlottetown, PE).

The role of genomics is expanding quickly – not just in traditional sectors but in emerging fields like synthetic biology. Ontario Genomics recently hosted Canada’s first national conference on synthetic biology which combines biology and engineering to design and construct new biological entities – or as one of the speakers put it, “Synthetic biology means engineering biology to make useful stuff.” The conference covered a lot of ground, from developing new therapeutics to reducing our climate footprint – all “useful stuff” indeed!

Sequence Issue #3: Clustering, Cannabis & Cleaning Up

Superclusters

Recently, Genome Atlantic attended an information session on Canada’s Ocean Supercluster, aimed at small and medium businesses who play a vital role in Atlantic Canada’s ocean economy. The session was well attended by business operators who came to find out more and how they can get involved. It’s exciting to see how the supercluster concept is bringing together ocean companies of every size across our region.

The Ocean Supercluster is one of nine potential superclusters shortlisted recently by the federal government which has committed to invest up to $950 million between 2017-2022 to support up to five business-led supercluster initiatives with the potential to super-charge the economy. Biotechnology and genomics are among the cross-cutting, enabling technologies identified as components of the ocean supercluster vision. (Our last issue of Sequence highlighted several large-scale genomics applications in ocean-related industries.)

This is an unprecedented opportunity for Atlantic Canada and for our ocean industries and businesses. You can find out more at the Canada’s Ocean Supercluster website.

Read more about all nine shortlisted supercluster projects.

Cannabis and public policy

The legalization of recreational cannabis is another huge public policy issue. This Fall, Genome Atlantic co-hosted a panel of experts that included the Honourable Anne McLellan, Chair of Canada’s Task Force on Cannabis Legalization and Regulation, to examine some key topics around the coming legislation, including health and genetics. Check out the full panel discussion video at the end of the article – worthwhile viewing for anyone interested in the issue.

The plunging cost of DNA sequencing has given rise to more genetic tests that help doctors identify best treatments for a range of conditions from genetic disorders to many kinds of cancers.  But genetic tests have a potentially thorny side too.  Recently, Canadian parliamentarians grappled with whether employers, insurance companies, and others could require an employee, client or customer to undergo genetic testing and divulge the results.  To get the inside story, we talked to the man behind Canada’s Genetic Non-Discrimination Act, Senator James Cowan.

Clean up and the power of microbes.

Offshore Technology magazine recently took a deep dive into the role of microorganisms in the offshore oil and gas industry while The Chemical Institute of Canada Magazine focused in on Microbiologically-Influenced Corrosion (MIC), a costly phenomenon that damages pipelines and offshore production and gathering lines. Another recent article, in Canadian Reclamation magazine, highlights three recent examples of how genomics is becoming an increasingly important part of environmental monitoring and cleanup. And speaking of cleanup, a team of Dalhousie University students are using a surprising substance – porcupine scat – to help transform the pulp and paper industry’s cellulose waste into a profitable biofuel on a commercial scale? Genome Atlantic is pleased to be a partner in much of the ground-breaking work highlighted.


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Sequence Issue #2: The Next Big Wave

Recently, Genome Atlantic’s Andy Stone and Stantec’s Marc Skinner teamed up at the monthly Ocean Connector in Halifax to talk about some of the latest genomics-based technologies making waves in ocean research.

Here in Atlantic Canada, we are seeing exciting applications of genomics technologies to solve problems in the offshore oil and gas industry.  One large-scale genomics project is studying microbiologically-influenced corrosion (MIC), a poorly understood phenomenon that accounts for 20% of structural corrosion in oil and gas pipelines.  Predicting how, where and why microbes cause corrosion would be a big win for the oil and gas industry and for the environment. This project has generated considerable attention from the industry and media alike – and this issue of Sequence takes a deeper dive into the project’s offshore component along with some insight from one of the world’s foremost MIC experts on how genomics just might provide the answer.

Genomics is also being used to de-risk offshore petroleum exploration in Nova Scotia’s offshore.   The Play Fairway Analysis completed in 2011 brought $2 billion in exploration activities to the province. Now, genomics is being combined with geology to paint an even clearer picture of petroleum deposits. We’ll have more to report on this exciting story in a future issue of Sequence.

Environmental DNA (eDNA) is another emerging genomics technology that is quickly becoming the Gold Standard for measuring and monitoring species and environmental samples.  eDNA works by collecting and analyzing biological material that organisms leave behind and matching them to specific species.

At the Ocean Connector, Marc Skinner talked about eDNA’s use as an environmental monitoring tool in aquaculture – you can read about it in his blog.  In New Brunswick, the Canadian Rivers Institute has been successfully using eDNA to study wetlands and fish populations in rivers.  Genome BC is leading a project using eDNA to monitor White Sturgeon, an endangered species in Canada.  And earlier this summer, Newfoundland launched the world’s first environmental genomics research centre that will employ eDNA to help industry and researchers monitor the marine environment.  (For a futuristic look at environmental sampling, check out this video Andy shared at the event on the Environmental Sample Processor from the Monterey Bay Aquarium Research Institute.)

*** PROJECT UPDATES ***  We want to share with you a couple of agriculture stories too.  One is about a unique genomics research project that could turn an oilseed wonder into a more sustainable feed ingredient for farmed fish – a potential win-win for both our regional aquaculture and agriculture sectors. We also sat down recently for a one-on-one with Kelci Miclaus, a leading genomics software developer with JMP Genomics/SAS. Kelci was the keynote speaker at an agriculture and genomics conference that Genome Atlantic hosted in New Brunswick in June. Her perspective on how genomics is transforming agriculture is fascinating. Enjoy!


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