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Gene42, Care4Rare Launch Cloud-Based Platform for Rare Disease Research

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CHICAGO (GenomeWeb) – The first national omics-based software and analytics system for rare disease research in Canada went online late last month to coincide with the annual global commemoration of Rare Disease Day.

The cloud-based data repository and analytics platform, called Genomics4RD, is built on top of PhenoTips, software from Toronto-based Gene42 that helps clinicians capture, standardize, and analyze phenotypic information at the point of care for patients with genetic disorders. Gene42 licensed the technology to the Care4Rare Canada consortium, which has received C$12.9 million ($9.7 million) from three provincial governments to support a program called Care4Rare-Solve that seeks to apply multi-omics research to diagnose rare genetic diseases.

Care4Rare-Solve researchers are studying transcriptomics, metabolomics, lipidomics, and deep whole-exome data to detect mosaicism, according to principal investigator Kym Boycott, a senior scientist at the Children's Hospital of Eastern Ontario's Research Institute and co-chair of the International Rare Disease Research Consortium's diagnostics committee. They are in search of new disease and mutational mechanisms.

Care4Rare was one of the first partners in the original development of PhenoTips, starting even before the University of Toronto spun out Gene42 as a separate company in 2014. "The open-source core [in PhenoTips] makes it pretty accessible to researchers, and so we've had the pleasure and honor of working with Care4Rare for a really long time and on a variety of different projects," said Gene42 CEO Orion Buske.

Buske did some of his PhD work on the PhenomeCentral matchmaking portal for rare diseases that was a collaboration between the University of Toronto and the Ottawa-based Children's Hospital of Eastern Ontario. That technology eventually was built on top of PhenoTips.

"This Genomics4RD platform is another flavor," Buske said. "It's a data-sharing platform with the core of it being built on top of PhenoTips, but here the focus is really around collaboration and data harmonization across Canada."

Notably, Genomics4RD supports data types that PhenoTips has not historically captured, including diagnostic outcomes, health outcomes, healthcare utilization, and patient-reported information, according to Buske. It also incorporates computable consent codes to "try to streamline the process of allowing researchers to access everything they should have access to," he said.

"We've been using PhenoTips itself since 2012, but we needed some place where we could actually then find the phenotypic information that we've collected via PhenoTips with their [Human Phenotype Ontology] terms with genomic variants," Boycott explained. "We needed to bring it all under one system in the cloud."

The result was a database that Care4Rare has amassed from 14 different rare-disease research projects across Canada, but Genomics4RD now will have to harmonize those disparate, siloed sources to make the records more accessible. "Bringing that all into one place under a unified consent model so that researchers can actually get access to those is really what we're pushing for," said Buske. "It's a really hard problem, but it's really critical to address."

To harmonize the data, Gene42 and Care4Rare are relying on work the Global Alliance for Genomics and Health (GA4GH) has done to standardize consent codes, just like the recently launched Common Infrastructure for National Cohorts in Europe, Canada, and Africa (CINECA).

So far, the Genomics4RD platform has rolled out functionality for health utilization and diagnostic outcomes. Since PhenoTips is able to create structure around phenotypic data, a short-term priority for the Genomics4RD effort is to facilitate genome analysis in the context of a patient's clinical presentation, a function expected to be added in the next couple of months, according to Buske.

Boycott noted that the Ontario Ministry of Health — one of the funders of Care4Rare-Solve — already is relying on PhenoTips to help researchers understand outcomes related to whole-genome sequencing and the impact such tests have on individuals and small populations. "That was all custom work that Gene42 had to do to build out PhenoTips to be able to collect that kind of information," she said.

The new collaboration is different in that it is dealing with larger cohorts of individuals, but the Genomics4RD partners anticipate that their work eventually will branch out beyond research into clinical practice.

"I do actually see clinical utility to this platform because as more and more genome-wide sequencing becomes available at individual institutions within our country, we don't want to see that data become siloed in that context," Boycott said.

"On the Gene42 side, we're very interested in taking the lessons and the technology that we develop from this and transferring that over into a clinical setting," Buske said.

He noted that his company has invested substantial effort into integrating Gene42 with electronic health records at its other clients' sites to bring genomic and phenotypic data together within physician workflows.

"It adds an additional functionality to the medical records system that they have to really support the genomics workflow there," Buske said. "We've been working hard to make sure that that can feed into this sort of ecosystem like Genomics4RD for cases [of undiagnosed rare diseases] that are seen clinically."

All members of Care4Rare feed into that database, and there are now "several hundred" participating clinicians and scientists across Canada, Boycott said.

By following GA4GH protocols, Genomics4RD feeds into the Matchmaker Exchange and other international data-sharing initiatives. For now, though, the Genomics4RD partners are focusing on the core job of harmonizing and freeing the data they have collected within Canada.

"By the end of the year, we would like to have most of the available Canadian data centralized in Genomics4RD and made available for discovery and research," Boycott said.

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