Improving treatment & diagnosis of rare diseases in Atlantic Canada

Q&A with Dr. Victor Martinez, Clinical Genomics Specialist, IWK Health Centre; Assistant Professor, Department of Pathology, Dalhousie University

The Genome Canada-led All for One initiative is advancing precision health across the country, increasing equitable and timely access to accurate, genomics-enabled clinical diagnosis for Canadians with serious genetic diseases.

At the heart of the initiative are six implementation projects located across Canada. We asked Dr. Victor Martinez from the project team in Atlantic Canada about how All for One will have an impact in his region.

“Currently, if a patient needs to have their whole exome or genome analyzed, those tests are being sent out mainly to private US companies. Our objective is to bring all those tests in-house and increase the diagnostic rate and speed of results, which will have significant benefit for patients.”

– Dr. Victor Martinez

Can you tell us a bit about the work you’re engaged in?

My role is focused on interpreting and trying to find the biological consequences of genetic variants in patients affected by rare diseases or other hereditary conditions. This work is also linked with the research side of things, as we create the systems necessary to analyze genetic data and develop solutions to the challenges associated with new sequencing technologies.

The All for One initiative was launched to provide a new, and more consistent, standard of care for Canadians by increasing clinical genomic testing capacity across Canada. How would you describe the availability of this testing in Halifax and Atlantic Canada?

In Atlantic Canada, and specifically Halifax, it’s a little bit different than other provinces in Canada. The IWK Health Center is a publicly funded Women’s and Children’s Hospital, and it’s also a Health Authority that serves all the Maritimes provinces. This situation put us in an excellent position to take this specific All for One project and have a big impact on the diagnosis of rare diseases in the region.

Currently, we offer sequencing analysis for some patients, and this is funded by the province. Each case is reviewed, and if the patient might benefit from genetic analysis, we offer that to the patient. However, this analysis looks at a limited number of genes compared to what will be available with All for One. We currently analyze around 300 genes and look for a limited number of diseases. With expanded genomic sequencing capacity through All for One, we expect to be able to sequence whole genomes, or whole exomes [the collection of pieces of an individual’s DNA that provide instructions for making proteins], for patients. This will generate a lot more information, allowing us to increase the number of diseases we can look for.

Currently, if a patient needs to have their whole exome or genome analyzed, those tests are being sent out mainly to private US companies. That information remains outside Canada and cannot be used to improve future diagnoses locally. Our objective is to bring all those tests in-house and increase the diagnostic rate and speed of results, which will have significant benefit for patients.

How long does it typically take to diagnose a child with a rare disease? How can these wait times be reduced?

It is very difficult to estimate, but it could take seven to eight years to diagnose a rare case without sequencing. One of the milestones for our project is improving the time it takes to make a diagnosis. One of the most significant benefits of increasing sequencing capacity in Canada is being able to share that data across Canada. With rare diseases, we might have only one patient in our area with the condition.  If we can identify additional patients in other provinces, we will be able to share genetic and  clinical information about our patients and thus, significantly improve the diagnosis of these cases.

All for One is being deployed through six related projects across Canada. What is the focus of your research team in Halifax?

Our main aim is to develop and implement clinical and laboratory systems for whole exome and whole genome sequencing for pediatric patients in Atlantic Canada. We are implementing the systems needed to analyze the whole genome of a patient, which is new for us. But there is a lot of experience across Canada, so we are also harnessing that existing experience to ensure our work is compatible with other centres across Canada.

We are also working to assess the clinical utility and cost of sequencing. For example, we are looking to identify whether using exomes or whole genomes can reduce the time to diagnosis or improve other key aspects of patient care and healthcare services.

Could the work you are doing also help bring down the cost of diagnosing and treating rare diseases in children?

Cost savings should come if we can diagnose patients faster. I don’t want to overpromise, but if we can reduce the number of years it takes for a patient to be diagnosed using more sequencing-based tests, it can significantly reduce the costs associated with treatment and monitoring of patients. Whole genome sequencing technologies can also replace other tests that we offer now in the lab, such as microarrays. For example, instead doing two tests for the same patient, we could do one test via sequencing that produces a lot more information.

As we envision a future where precision health is a standard of care available to people across the country, can you describe the major barriers Canada needs to address?

The sharing of genetic data is a completely new challenge for regulatory agencies in each of Canada’s provinces and territories, which means there will always be concerns about data privacy and security. We are committed to ensuring proper privacy protocols are followed and that we have the cybersecurity mechanisms in place to protect patient data. Communicating effectively to hospitals, patients and regulators about how we are protecting patient data will be a key component of our success.

Learn more about the All for One rare diseases project Dr. Martinez is working on.

Climate Action Genomics Initiative: Climate-Smart Agriculture and Food Systems

Climate change poses a significant risk to our agriculture, aquaculture, and food production systems and will increasingly impact availability of food and other vital resources.   Innovative new technologies, products and approaches are required to reduce emissions, maintain productivity and competitiveness, and ensure food security at home and abroad. 

In response to this major challenge, Genome Canada is launching the Climate-Smart Agriculture and Food Systems genomics initiative which is investing $30M in interdisciplinary, collaborative, and cutting-edge genomic research and innovation to reduce the carbon footprint of Canada’s food production systems.

This large-scale initiative will fund a portfolio of interdisciplinary genomics research and innovation projects while connecting these efforts with cross-cutting programs to support knowledge mobilization, data coordination and solution implementation across Canada.  This portfolio approach allows benefits from one solution to translate into other production systems or supply chains and cascade impact throughout the broader national food system. 

The Interdisciplinary Challenge Team Funding Opportunity ($24M) is the first of the programs to be launched under the Climate-Smart Agriculture and Food Systems Initiative.   Projects should involve multidisciplinary teams including GE3LS* researchers, must focus on the use of genomic approaches to develop tools and technologies, and demonstrate significant potential to achieve impact in reduction the footprint of Canada’s food systems.  The funding process will involve three stages: Registration, Letter of Intent, and Full Application.   Co-funding will be required.    

Eligible research themes include, but are not limited to:

  • Increasing production efficiencies to existing food systems while reducing environmental footprints
  • Carbon sequestration (cultivars, soil microbial communities etc.)
  • Sustainability in food production systems e.g., with decreased use of water, fertilizers, and pesticides; improving fish feed
  • Cellular agriculture (e.g., tissue engineering, precision fermentation techniques, etc.)
  • Controlled environment agriculture

Please see for more information on this funding opportunity. 

Interested researchers should contact Genome Atlantic as soon as possible for more information on deadlines and proposal development support.  

For more information or to apply, please contact Kristin Tweel ( and/or Andrew Yoshioka (  

*The acronym GE3LS stands for genomics and its ethical, environmental, economic, legal and social aspects. However, it should be understood broadly as research into the implications of genomics in society from the perspective of the social sciences and humanities. Therefore, it is not strictly limited to the disciplines that comprise the acronym, but rather encompasses all those that rely on quantitative and qualitative methodologies to investigate the implications of genomics in society and to inform applications, practices and policies.