Genome Atlantic project offers hope for faster diagnosis of rare diseases

Dr. Karen Bedard, a Dalhousie molecular geneticist and academic co-leader of a new $4.8 million project to speed up the diagnosis of rare diseases in children. The project is supported by Genome Atlantic and funded through Genome Canada’s All for One precision health initiative.

New Atlantic Canada-based genomic research, announced for Dalhousie University and IWK Health, Oct. 26, and supported by Genome Atlantic, hopes to cut wait times for anxious families and pare the cost of diagnosing rare diseases in Canadian children.

Dr. Karen Bedard, a Dalhousie molecular geneticist and academic co-leader for the Dalhousie-IWK collaborative venture, predicts “this project will provide a bedrock for future medical advances as genomic medicine becomes an increasingly broadly used tool across all fields of medicine.”

The team is set to examine whole exome sequencing – the process of identifying and analyzing individuals’ gene sets, to see if the technology makes financial and clinical sense for standard diagnostic use in Atlantic Canada and across the country. The aim is to use the sequencing data to achieve faster, cost-effective diagnosis of suspected rare disease in children at the embryonic, fetal and postnatal stages of development. As well, the project will examine broader potential implications of the potential transition to this new diagnostic approach, such as the effect on health care resources.

The three-year, $4.8 million project, Implementation of Clinical Exomes in a Pre-and Peri-Natal Setting, is managed by Genome Atlantic and funded through Genome Canada’s All For One precision health initiative. Six related projects across the country were chosen to be part of the initiative and Dr. Bedard says, “the leads from each of these groups are meeting regularly – virtually of course – to ensure that the benefits of increased genome-wide testing are achieved across Canada.”

The biggest challenge in genetic diagnosis, explained Dr. Bedard, is not in detecting genetic variations, but in sorting out whether they are harmful or harmless. This is one issue for which she hopes other research teams in the All For One precision health initiative will help supply answers.

Rare genetic disorders affect roughly one in every 15 Canadian children and make up 30 per cent of the pediatric inpatient population. IWK Health President and CEO Krista Jangaard pointed out, “these conditions affect children and families across the Maritimes.” Speaking about the Dalhousie-IWK research project, she said, “We are excited about this opportunity, giving patients and their families earlier and more complete information about their diagnosis and treatment options.”

Currently a series of tests can be required to uncover suspected rare disease in the pediatric population. Sometimes the disease is quickly identified, but in other cases it can be a lengthy process. Even after many tests the disorder can remain elusive. These circumstances bring added cost to the health care system, increase parental anxiety, and in some cases, risk the possibility of reduced options to respond to, or manage, the condition if diagnosis is delayed too long.

Dr. Anthony Vandersteen, a medical geneticist and a co-leader on the project, said, in cases where “there are a clear set of clinical features, suggestive of a specific disorder, a specific test can often be the fastest and most efficient route to a diagnosis.” However, he said, “in the prenatal or newborn setting, some aspects of a given disease that might give a clue to the diagnosis may not yet have appeared.” In these circumstances, a broader initial sequencing strategy might be the better option. It has the added benefit of being able to answer several diagnostic questions at once.

Genome-wide sequencing is known to be helpful in providing a diagnosis in 30-40 per cent of cases with undiagnosed genetic disorders. Of the two commonly used methods to achieve it, exome sequencing is faster and cheaper, requiring less data collection than its whole genome sequencing counterpart. On the other hand, whole genome sequencing yields more data because it processes an individual’s entire DNA, making it easier to spot duplications and deletions in the genome.

Both types of sequencing produce massive amounts of data from across the entire genome, but Dr. Bedard says clinical analysis for this project will actually be restricted to “genes known to be clinically relevant for the indicated reason for testing.”

Making clinical use of genome wide sequencing, she said, will require “a step change in infrastructure, laboratory systems and clinical care.” Currently this kind of testing is done in commercial labs outside Canada, she said, and “the major change here is that we will begin to perform these tests locally.”

Dr. Vandersteen noted, “this state-of-the-art technology can provide a diagnosis where even a few years ago, none was possible. This can provide immense comfort to families, can guide care, and in some cases can direct treatment. In addition, a broad-based testing strategy, even when an answer is not identified, can provide reassurance that nothing has been overlooked.”

He said “finding the genetic cause of disease is an important step in the quest for treatments. Our medical geneticists have seen their practice transformed in under a decade by this technology, with far higher diagnostic rates, new treatments, and new understandings of the mechanisms of disease.”

Co-leading this project with Drs. Bedard and Vandersteen are Dr. Jo-Ann Brock, a molecular geneticist and Head of the Division of Pathology and Lab Medicine, IWK Health and Associate Professor of Pathology, Dalhousie University, and Dr. Sarah Dyack, a medical geneticist, Head of the Division of Medical Genetics, Department of Pediatrics, IWK Health, and Associate Professor of Pediatrics and Medicine, Dalhousie University.

Dr. Bedard is a molecular geneticist with the Department of Pathology and Laboratory Medicine and Associate Professor, Department of Pathology, Dalhousie University, while Dr. Vandersteen is a medical geneticist, Department of Pediatrics, IWK Health and Associate Professor of Pediatrics and Medicine, Dalhousie University.

The project is funded by Genome Canada, IWK Health, Research Nova Scotia, and Dalhousie Medical Research Foundation, and is supported by various industry partners.

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.

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