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Genome Québec, Sainte-Justine Hospital Evaluating Tech for New Clinical Pediatric Sequencing Center


Ahead of opening a new clinical pediatric sequencing center next year, Genome Québec and The Sainte-Justine Mother and Child University Hospital Centre are evaluating technology to provide clinical exome sequencing to children with suspected genetic diseases throughout Quebec.

The two organizations this week announced the creation of the center, which will be located at Saint-Justine UHC in Montreal, but will rely on Genome Québec to lead sequencing and bioinformatics analysis.

Marc LePage, president and CEO of Genome Québec and Jacques Michaud, a doctor and geneticist at Sainte-Justine UHC spoke with Clinical Sequencing News this week about preparations to get the center up and running, which the group expects to happen next spring.

LePage said the partners are still deciding what sequencing technology will support the center's activities and exactly how many machines the new effort will rely on, although he noted it will most likely start with around four systems. He said Genome Québec has 15 Illumina machines at its McGill University core facility, as well as at least one PacBio platform, and is overall platform agnostic.

According to Michaud, the primary goal of the center will be to serve the population of Québec province. Based on the overall population, and frequency of non-sequencing-based tests for things like neurological disease and birth defects, he said the new center anticipates sequencing "at least a few hundred samples a year."

He said the center will focus on whole-exome sequencing, at least for the first year or so of the project, but the group expects to eventually move to whole-genome sequencing as the field of clinical sequencing shifts that way in the future.

Michaud said that the team is currently completing a pilot project on 100 patients that has allowed them to crystallize a sequencing and analysis pipeline for the new clinical center. "We have resolved a number of issues, [and] agreed on a pipeline and the filters we are applying to remove common variants and restrict the list to the most likely candidates," he said. "We also have strategies to annotate variants that we are still working to improve."

"The first year may be more experimental," LePage added. "We can produce lots of whole genomes, but that then has to go to a clinical team for interpretation, so [we will look at] what is the capability and what are the requirements of that … and learn by doing."

Québec has universal healthcare, Michaud said, so the center's sequencing will be free to local patients, as long as they fit eligibility criteria for the service. "If a patient wants a test, it has to be ordered by a physician. But then it would be free to them," Michaud explained. "Because we are working in an integrated healthcare system, this is really an opportunity to decide what the indications for exome sequencing should be that would result in higher diagnostic yield."

"There will be a filter, as there is for all specialized medical services as to when and how to provide this," LePage added. "And there will be some experimentation, at least in the first year, as we come to understand the interplay of all these dynamics."

Based on evaluations of the bare-bones costs of sequencing, Michaud said that the per-patient cost for exome sequencing the center plans to perform would probably be somewhere around $3,000 or $4,000.

"We are a not-for-profit," LePage said, "so when we are sequencing, we are not trying to make money, we are just trying to do this without losing any money."

As the center eases into its activities, Michaud and LePage said the eventual plan would be to also offer sequencing both across Canada, and potentially internationally.

"We are thinking, if we offer this at a lower cost, it may be attractive to doctors outside of Canada, in the US, for example," LePage said. "That three to four thousand per exome — it's the baseline of what it costs once we have the infrastructure in place, not counting paying for the machines."

"Production of sequences is a relatively small thing. Clinical interpretation [and] genetic counseling is also a significant part of cost, so in the end, offering this internationally it might be a higher price," he said.