The founder population of Newfoundland and Labrador make it an ideal place to conduct studies linking certain genetic markers with diseases prevalent in the province.  Sequence Bio, a private St. John’s-based biotech company, recently cleared a provincial regulatory hurdle to allow it to launch the NL Genome Project this summer to study the unique genetic makeup of Newfoundland and Labrador. The company’s hope is that the data will lead to improved treatments and health outcomes. We caught up with Sequence Bio CEO and co-founder Chris Gardner recently to talk about his vision for the company, the project, and what gets him excited to go to work every morning. 

What inspired you to co-found Sequence Bio in 2013? What was your vision for the company?

I have always been excited by the biggest and most important challenges. And healthcare is up there – it has such a wide, and significant, impact on all of our lives, but innovation has traditionally been slow. Now we are at this exciting crossroad because of rapid advances in genomics, personalized medicine and sequencing technologies. And for me, this presented an incredible opportunity to accelerate innovation and help deepen our understanding of disease and improve patient outcomes.

But what makes this opportunity truly special and inspired me to start Sequence Bio is that we believe the right place to make change happen is Newfoundland and Labrador. And even better, we can do it in a way that ensures that communities, families and participants in Newfoundland and Labrador benefit for generations to come. Innovation that brings everyone along and leaves no one behind is my vision for Sequence Bio.

What makes Newfoundland a good place to study genetics sequencing?

Modern drug discovery relies on the right kind of information. This information isn’t found everywhere, but it is found in Newfoundland and Labrador. And it all starts with our unique history. As a founder population, it’s estimated that over 90% of our province’s residents are descendants of approximately 25,000 English and Irish settlers from the 1700’s. Founder populations like ours are rare, and can identify genetic changes from tens or hundreds of people instead of thousands or millions in other admixed populations. Coupled with our province’s high disease rates and comprehensive longitudinal health records, we believe Newfoundland and Labrador is the best unexplored cohort for human data to discover novel variants and potential drug targets.

Sequence Bio’s main focus has been to lead a large-scale genetic research project in Newfoundland and Labrador.  Now that the company has cleared the provincial regulator hurdle, where does that project stand? What are the short-term and long-term goals?

We’re incredibly excited to share that the pilot phase of the NL Genome Project is launching this summer! This pilot phase will recruit 2,500 Newfoundlanders and Labradorians through participating physician’s offices. We’ll combine genetic information from a simple saliva sample, with medical records, to deeply characterize the population and help design a larger research project in Newfoundland and Labrador with tens of thousands of individuals. All with the long-term goal to produce novel, validated drug targets no one else can find.

How do you access the patients in these studies? And what is done with the data you collect?

Sequence Bio is working with local, dedicated family physicians who see the value of integrating genomics into their own practice and the ability to positively influence the care of their patients. For the NL Genome Project, participating physicians will introduce the study to interested participants, who can then enroll with a research nurse at the clinic.

There is no greater priority to Sequence Bio than protecting participant data. Sequence Bio’s security program is built to align with ISO 27001/2 standards. All data is handled with extreme care and is immediately encrypted using AES 256 bit encryption and protected with the latest military-grade security measures. We know that if we want to be trusted with people’s most personal information, we have to earn that trust.

You are a recognized innovation leader. You’ve been named a Change Agent by Canadian Business and you’ve been asked to sit on the federal government’s Health/Bio-Science Economic Strategy Table.  You’ve said that Canada is sometimes slow to embrace change. What’s slowing us down and how can we as a country and a society do more to nurture innovation?

Canada’s regulatory processes present significant hurdles for the rapid adoption of innovation – reducing patient access to leading-edge therapeutic products and harming the international competitiveness of Canadian health and biosciences firms. This is why modernizing Canada’s regulatory processes is something I am so passionate about.

An effective regulatory environment ensures patient safety and well-being while encouraging the development and adoption of innovative products and services. Innovation and improved patient care are not mutually exclusive – in fact, it’s quite the opposite, they go hand in hand! A high performing regulatory system should be predictable, efficient, consistent and transparent, while ensuring patient safety and encouraging innovation. It’s been done in other jurisdictions and it’s time for Canada to do the same.

Things move quickly in the biotech world.  But six years after you launched your company, and even after a number of setbacks, Sequence Bio remains proudly Newfoundland.  What does this province mean to you, and what do you hope to accomplish that will benefit the people of this province?

We believe that to be successful we have to build a company that makes the entire province proud. That’s why the model for our population genetics project ensures that the people who contribute to research also benefit from that research. We’ll share discoveries with local researchers, policy makers, and doctors across the province. Plus, all participants can choose to receive findings about their genetic makeup, including information on medically actionable genes and carrier status information.

Our genetic founder population has the opportunity to meaningfully contribute to health research, and we can ensure research participants benefit at the same time we build a great company.  We have the chance, right here in Newfoundland and Labrador, to change lives by coming together and being part of ground-breaking research.

What role does Government play in projects like yours?

Initiatives like ours have the potential to reap social, economic and health benefits, but there are still incredible associated costs and risks – from sequencing to storage to infrastructure. Through job grants, SRED credits, subsidies, or non-dilutive funding, Government plays a critical role in helping with the underlying costs and risk management for those willing to innovate. And the return on investment benefits us all as we create the next generation of companies that will drive economic and regional growth. Our country has the opportunity to be leaders in genomics, but the only way we can do this is if we continue to support public and private research and work together along the way.

Finally, can you tell me a little bit about Sequence Bio? What about the company culture & philosophy gets you and your team excited to go to work every morning?  

We have a committed team in Newfoundland and Labrador and with teammates across Canada. We all come to work for our own reasons, but I can say with confidence that it all comes back to a shared desire to make this province a better place for us all – through improved healthcare, growing the biotech sector, and tackling the diseases that impact this province the most. We know what we’re trying to do is ambitious. But whether it’s our leaders in science, technology or research, we all believe it is possible. And I think in the end, it’s that drive, passion and commitment to the province that makes this such an incredible company.

Environmental DNA (eDNA) is a promising new tool for environmentally monitoring living organisms in water and on land. It works by analyzing DNA found in expelled skin samples, feces, etc. collected from environmental samples (e.g. of seawater, soil and even air) to determine what species are present. eDNA is non-invasive and can be done at considerably lower sampling effort and cost and has been shown to be an effective monitoring tool in many environments.

But how effective is eDNA for monitoring marine species at risk in turbulent marine conditions like the Minas Passage in the Bay of Fundy where more than 160 billion tons of seawater flow through twice a day driven by the world’s highest tides? In partnership with Genome Atlantic, the Offshore Energy Research Association of Nova Scotia (OERA), the University of Guelph, and Dalhousie University, Stantec’s Dr. Marc Skinner is trying to answer this question.

The Minas Basin is home to several marine species at risk such as striped bass, Bay of Fundy salmon and Atlantic sturgeon that are important to First Nations and inshore fisherman. It’s also the site of planned tidal power development. Maintaining the health of marine species and monitoring the environmental effects of tidal development sites on these species will require a science-based approach and the best tools of the trade. Dr. Skinner, Stantec’s Marine Ecology Technical Leader for Canada, believes that eDNA could be a promising option in this regard.

“Traditional sonar and fisheries methods weren’t able to adequately capture the diversity and richness of species, including species at risk, in the Minas Basin, so we were asked by OERA if eDNA had a role to play in helping do that, in a more objective fashion.”

To find out, Dr. Skinner is carrying out a laboratory-based study conducted at Dalhousie University’s Aquatron facility in Halifax, which can simulate multiple marine conditions. The project, which is supported by a Genome Atlantic Genomics Opportunity Review Program grant, is using striped bass as the sample species. Dr. Skinner and his team hope to develop a ‘proof of concept’ for eDNA’s effectiveness and reliability as an environmental monitoring tool in high flow marine conditions – ultimately, providing reliable data for monitoring the environmental impact of developments such as tidal turbine projects on marine species.

The study has answered several critical questions. The first is whether the technology can detect the striped bass DNA at different levels of the water column – the answer being a resounding yes. (The Aquatron marine simulation tanks are as deep as a two-storey building is tall.) Secondly, Dr. Skinner wanted to determine how long the DNA signal is detectable after the fish leave an area. He discovered that DNA is readable for up to 24 to 48 hours, after which it starts to break down. Thirdly, he was able to demonstrate that eDNA can be used to measure relative abundance of certain species in an area, such as how many striped bass were present in an area over a two-week period.

Having tested the technology in both benign and turbulent simulations in the Aquatron, Dr. Skinner will soon take the equipment into the field, testing it in the Minas Basin. Given the results so far, he is hopeful that eDNA will prove to be a useful environmental monitoring tool in challenging marine conditions.

“EDNA can certainly be an effective tool for species detections and quantifications like we’re using in this project for species at risk,” he said. “But overall, the potential application of eDNA and genomics in the ocean space is virtually unlimited – for example, for biodiversity assessments, tracking pathogens and invasive species, ocean exploration for resource development, prospecting for oil and gas seeps, asset integrity, infrastructure development….the list goes on.”

Genome Atlantic will provide an update on this and other eDNA projects in the near future. Stay tuned for some exciting innovations in the ocean space!

FAQ With Dr. Marc Skinner

Using EDNA in Marine Conservation

In June 2019, Genome Atlantic is hosting the world’s leading conference on microbiology and molecular biology in the oil and gas industry. Join us for ISMOS-7 (the International Symposium on Applied Microbiology and Molecular Biology in Oil Systems), June 18-21 in Halifax, Nova Scotia.

ISMOS brings together professionals in the oil & gas industry and in academia to explore how emerging microbial and molecular tools can help solve key challenges facing the industry – including biocorrosion, souring, and conducting energy extraction in a sustainable manner.

Register today.

With its fertile soil and mild temperatures, Nova Scotia’s Annapolis Valley has long been famous for its apple harvest. Now, thanks to a recently-announced National Apple Breeding Consortium that  Genome Atlantic helped co-found, apple researchers, growers and marketers will share data that will allow them to bring new varieties to market more quickly – including varieties that grow best in local conditions.

It’s all about genomics. Genomics is a key technology for breeding apples with commercially desirable traits – increasing the likelihood of success in breeding better apple varieties. Genomics reduces the time it takes to develop a new apple variety by allowing breeders to predict what apples will taste like before the trees are fully mature. 

The National Apple Breeding Consortium grew, in part, out of a vision of Dalhousie apple researcher Dr. Sean Myles and a project he led supported by Genome Atlantic. Myles’ vision was simple:  One day, every novel apple tree developed by a breeder will be screened at the seedling stage to determine whether it is a potential winner in one of Canada’s growing regions.  In this manner, apple growers across Canada will end up planting only new varieties anticipated (or predicted) to thrive in their unique growing conditions.  

Over the years, Dr. Myles has collected an enormous amount of genomic data and planted more than 1,000 varieties of apples together with collaborators at Agriculture and Agri-Food Canada’s Kentville Research and Development Centre.  It is no small task to manage, analyze and interpret all the information necessary to determine desirable genetic profiles of new varieties. So, Dr. Myles’ team received support from Genome Atlantic and Genome Canada to develop new user-friendly software, now licensed, to enable desirable DNA profiles to be easily identified, removing the guesswork and increasing productivity of apple breeding. 

Imagine if apple researchers across Canada pooled their information and innovations. Enter the National Apple Breeding Consortium, which brings together Canadian researchers, breeders and marketers.  Genome Atlantic and Dr. Myles were instrumental in getting the Consortium off the ground.  (The Consortium co-founders include Genome Atlantic, Genome BC, Ontario Genomics and Agriculture and Agri-Food Canada.)

“How do we measure what the consumer really wants and then rapidly breed it using genomics? The National Apple Breeding Consortium is particularly well-equipped to tackle this, and it is precisely in this area of “fruit quality genomics” where we feel Nova Scotia and Canada can lead internationally,” says Dr. Myles.

The Consortium aims to streamline apple development in Canada and boost returns to the industry, while increasing consumer satisfaction.  It will also help growers by providing them with  new apple varieties uniquely suited to their growing regions.  

Developing new varieties is important. Witness the success of the Honeycrisp apple which grows well in Nova Scotia.  The big, crisp variety can bring in five times more money for Nova Scotia growers than more traditional varieties grown here and as a result, it has helped to reinvigorate the province’s once-dwindling apple industry.

Continued success for Nova Scotia growers depends on being able to develop the next big apple variety and get it to market quickly.

Scotian Gold Cooperative Ltd., a member of the National Apple Breeding Consortium, believes that finding the right variety for the local growing environment is key.  “It is about finding a variety that is best suited for our unique climate that will allow Nova Scotia growers to produce a superior product,” says Joan Hebb, Tree Fruit Coordinator for Scotian Gold.

Genome Atlantic, in partnership with the National Apple Breeding Consortium, wants to help Maritime apple growers get a head start developing the next generation of successful signature varieties.  Currently, Genome Atlantic is helping the Consortium seek funding for a project led by Dr. Myles, using genomics to improve variety development.

Recently, the Government of Canada announced funding for 37 Genome Canada projects including $1.4 million for Antimicrobial Resistance: Emergence, Transmission, and Ecology (ARETE), a project co-led by Dalhousie University’s Dr. Robert Beiko and Dr. Fiona Brinkman of Simon Fraser University.  ARETE aims to develop new surveillance tools to help identify and track the genes that contribute to antimicrobial resistance (AMR), a huge problem for the agri-food industry and the health of Canadians.

Backed by his lab team at Dalhousie University, Dr. Beiko has earned a place on the front line of bioinformatics research, probing the mysteries of AMR in bacteria. It’s an area of pressing worldwide concern for human health, agriculture and the food industry, as the effectiveness of antibiotics declines and antimicrobial resistance grows.

A biologist and expert in computational biology, he applies the power of algorithms, machine-learning and biological data visualization to microbial research. His focus has been on gaining a better understanding of the genes that make bacteria resistant to antibiotics and how they spread.

Genomics has a central role in this research field.  Unfortunately, current analysis tools lack the needed software to predict antimicrobial resistance profiles in the huge datasets generated from genetic profiling of microbial communities (metagenomics). Software is needed to separate the wheat from the chaff. Dr. Beiko, alongside Drs. Andrew McArthur of McMaster University and Fiona Brinkman of Simon Fraser University, has been working on a software solution, enabled by Genome Canada’s Bioinformatics and Computational Biology funding program, with support from Genome Atlantic.  

Through ARETE, Drs. Beiko, Brinkman and their fellow researchers will take a closer look at lateral gene transfer (LGT), the process by which bacteria share genes with each other. Disease-resistant bacteria can move between habitats, such as soil and animals, but science has yet to learn the most important points of transmission – this information is vital for monitoring and regulating the process.

Dr. Beiko has led or been involved in numerous large-scale research projects funded by Genome Canada, Genome Atlantic and other regional Genome Centres, the Natural Sciences and Engineering Council of Canada, and other major national and international granting agencies.

How close are you to developing software that will open up microbe research for better genomics analysis?

It’s an ongoing process. You can draw a clear line from the tools developed in the 1980s, which were developed before genome sequencing really took off, to the ones we use today. Each technological revolution brings new challenges, and we were asking very different questions in 2000 when the first microbial genomes came out than we are now. Where once we had maybe one or two genomes of important species, we’re now looking at tens of thousands of genomes of E. coli or Salmonella alone. These rich datasets offer great opportunities for us to map out the fine points of the emergence and evolution of pathogens, and AMR in particular. But as you can probably guess, dealing with 100,000 genomes at a time opens up some new and very exciting challenges from a bioinformatics standpoint.

ARETE is built on a foundation of existing tools, including large databases of AMR genes and mutations, methods to identify regions of microbial genomes that pose a high risk for carrying and transmitting AMR, and software that can identify the transmission of genes between potentially very distantly-related bacteria. A key challenge in ARETE is getting these tools working together properly and to scale up the absurd number of genomes that are coming down the pipe. Consequently, and coming back to the original question, many pieces of the puzzle are in place, which makes us very optimistic about delivering a unified toolkit over the three years of the project.

What practical advantages do you envision for microbe research from this kind of software?

A key aspect of the ARETE project is the close involvement of researchers in the Public Health Agency of Canada. DNA sequencing has become the gold standard for mapping epidemics, which has resulted in a huge effort to sequence the genome of every pathogen that comes across our desk. But what are the benefits of having all this information? There are lots of practical outcomes of this research, but the key driver of ARETE and the wider umbrella of genomic epidemiology projects is the ability to study the transmission pathways of both AMR genes and the bacteria that contain them. If you see the exact same gene in chicken X and patient Y, in farm soil, sewage, or what have you, that can give you a pretty clear view of what is being transferred, where it is happening, and by whom. This knowledge can then drive efforts to contain the spread of AMR.

What intrigues you most about lateral gene transfer – the process of gene sharing among bacteria?  Why?

The realization that LGT is a defining aspect of microbial evolution broke most people’s preconceived notions about how bacteria evolve. When we think about inheritance, we almost invariably picture an unbroken line of transmission from parent to offspring. In a lot of cases this is not true of microorganisms. Although researchers always knew that some transmission was happening, the central role of LGT could only be appreciated when people started to sequence genomes en masse. We now know that when one microorganism has a good idea, evolutionarily speaking, it might not be long before its neighbours pick it up. While the life-or-death (for the bacterium) situation of AMR is a particularly acute driver, we see strong evidence for a central role of LGT in the evolution of everything from adaptation to extreme temperatures (in some cases, above the boiling point of water) to the breakdown of new compounds that humans have introduced into the environment.