Investment in Genomics-led Precision Health Initiative Delivers Rare Disease Diagnosis in Ontario

This study mining cancer genetics for targeted treatment options is an integral part of the All for One Canada-wide initiative geared towards providing equitable access to genome-wide sequencing for diagnosis and treatment of genetic disease.

Ontario Genomics is pleased to play an integral role in the All for One precision health initiative to advance a new standard of health care for Canadians, expanding access to genome-wide sequencing for diagnosis and treatment of life-threatening genetic diseases.

The $39 million All for One initiative includes $13 million in federal investment through Genome Canada and $26 million in co-funding from industry, health care organizations, provincial and other partners brought in through six regional Genome Centres, including Ontario Genomics.

As part of this initiative, CHEO and the Hospital for Sick Children (SickKids), in collaboration with the Ontario Ministry of Health are piloting an optimized clinical genome-wide sequencing service for patients with rare diseases in Ontario. This project is receiving $950,000 from Genome Canada, through Ontario Genomics.

Currently, more than one-third of the estimated 930,000 Ontarians with a rare disease lack a genetic diagnosis, despite lengthy and costly investigations. Advances in precision health—which harnesses the power of genome sequencing to diagnose and inform treatment of genetic conditions—are revolutionizing health care, but access to clinical genomic testing across Canada remains inconsistent, which was the case for most of Anna\’s life.

Genome-wide sequencing pilot project helps Ontario families get answers

Anna had a childhood filled with regular injuries as a result of persistent muscle weakness, with hundreds of doctor’s visits. Her clinical team at CHEO completed dozens of tests, including muscle biopsies, metabolic testing and at least five different genetic tests, but no conclusive diagnosis was reached.

Conventional genetic testing involves testing subsets of genes, often leading to multiple tests and investigations, which can present a complicated and time-consuming process for clinicians, patients and families. In contrast, Genome-Wide Sequencing can search all known genes for variants that could be disease-causing, providing a much more comprehensive look at a patient’s genetic data.

Isla had severe jaundice, skin rashes, extremely low energy, difficulty feeding and problems with growth associated with high levels of inflammation markers in her blood at just one week of age. She spent over a year in and out of SickKids with high fevers, infections, breathing issues and extreme acid reflux. Her clinical team addressed the symptoms while they searched to find the underlying cause, but tests to check her blood, bone marrow, immune system, DNA and more yielded nothing.

A diagnosis can often be the first step to accessing targeted care and for families, it can provide emotional relief and improved access to support and resources.

Isla was started on a biologic drug to reduce her inflammation levels with the hopes it would help address her other health issues. Still, her clinical team and her family wanted an explanation for all of Isla’s health concerns to help optimize treatment and prevent complications. Isla had exome sequencing as one of the last diagnostic options, which found a new DNA change in a gene called CDC42, which is known to cause severe inflammation. Armed with this knowledge, Isla’s family and clinical team were confident that their treatment plan was the right one.

Anna had genome sequencing as part of GSO’s quality improvement study to evaluate the benefit of interrogating the entire genome. GSO reported that she has a rare genetic condition because of two variants affecting a gene called SELENON. She inherited one variant from her mother and one from her father. Genome sequencing was critical to the identification of these variants in Anna as they were not detectable via the previous testing technologies and would not have been identified using exome sequencing. Although she is small for her age and her bone development is delayed, she takes swimming lessons, does her best to keep up with friends at recess, gets good grades and is an avid reader. Like any 12-year-old, she loves spending time on her tablet playing games. “More than I probably should,” Anna says.

“It took 12 years to finally put a name to what Anna was experiencing every day since she was an infant. When we got the genome sequencing results and diagnosis, it was the first time in 12 years that we were able to read something with a name on it and say, ‘That’s it! That’s what we’ve been dealing with,’” said Mallory Boileau, Anna’s mother. “It would be great for families to get this type of answer at the beginning of their journey. Twelve years is a long road not to have answers.”

Now, Anna’s family and care team can keep an eye out for potential complications that are associated with her diagnosis. Mallory says, “The not knowing is sometimes more terrifying than anything. We’re no longer guessing all the time and can address things before they become an issue. It’s such a relief.”

Isla’s family is thankful, too. “After Isla started her treatment, you could tell how much better she was feeling. Isla started to have more energy and began smiling and even laughing,” says Miki Simmons, Isla’s mother. “At four years old, Isla’s keeping up with all her older siblings and I’m not sure where we would be if we didn’t have the treatment plan and diagnostic answers that we did when she was a baby.”

“Early diagnosis of rare diseases at the molecular level is vital to shorten the diagnostic journey of rare disease patients, like Anna and Isla, and make sure they can access appropriate care as soon as possible. This partnership uses genomics tools to inform provincial and cross-provincial policies that improve rare disease diagnosis and quality of life.” – Dr. Bettina Hamelin, President and CEO, Ontario Genomics

This project advances a new standard of health care for Ontarians and Canadians, expanding access to genome-wide sequencing for diagnosis and treatment of life-threatening genetic diseases.

“Our government is proud to support this pilot with CHEO and SickKids, which is already helping Ontario families just one year into implementation. This promising project will improve patient outcomes by providing timely access to genetic diagnoses, which is another way Ontario is building a better-connected health-care system, centred on the needs of patients.” – Christine Elliott, Ontario’s Deputy Premier and Minister of Health

With pan-Canadian reach and strong partnership from provincial and regional health services authorities, All for One will be a core building block of a coordinated human health genomics ecosystem in Canada, bridging clinical care and cutting-edge research.

Partner Quotes

“Quick access to comprehensive genetic testing, like exome or genome sequencing, must be a cornerstone of health care for children and youth who have suspected, but undiagnosed, genetic conditions. With GSO, not only are we able to provide this testing, but we’re also preparing for the future when genome sequencing may become the new standard-of-care clinical test for these patients. This pilot is another step in the path to achieve SickKids’ vision of Precision Child Health, where every patient and family receives individualized care.” – Dr. Martin Somerville, Division Head of Genome Diagnostics, SickKids

“For parents like Anna’s, there is an unbelievable and largely unseen stress that goes with not knowing what is causing their child’s condition. Along with this stress is a desperate desire to find answers and do the best thing for them. And having that uncertainty linger for years and years is such a burden. As clinicians, we want to provide more certainty to these families as soon as possible. We hope the findings from our project will bring that possibility closer to a reality.” – Dr. Kym Boycott, Chair, Department of Genetics, CHEO

About Ontario Genomics

Established in 2000, Ontario Genomics (OG) is a not-for-profit organization leading the application of genomics-based solutions to drive economic growth, improved quality of life and global leadership for Ontario. Ontario Genomics plays a vital role in advancing projects and programs like wastewater surveillance by supporting the development of their proposals, helping them access diverse funding sources, and finding the right industry partners to take this research out of the lab to apply it to the world’s most pressing challenges. Since its inception in 2000, Ontario Genomics has raised more than $1.27 billion for genomics applied research in Ontario and directly supported more than 9,100 trainees and jobs. We have 110+ active projects, 500+ impactful partnerships and have secured $1.34 billion in follow-on investments.

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