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Canadian Precision Health Infrastructure Emphasizes Secure Data Sharing, Privacy, Consent


NEW YORK – Discussions about secure data sharing across regional boundaries as well as ensuring public comfort with clinical and genomic data use are at the forefront of an initiative to develop infrastructure for precision health in Canada.

The Secure Health & Genomics Data Platform (SGHP) initiative is one of seven projects selected by Canada's Digital Technology Supercluster, a federally funded consortium focused on advancing the country's efforts to develop and apply digital technologies to challenges in the natural resources, healthcare, and industry. The consortium has received over C$150 million (about $113 million) from the Canadian government to invest in developing competitive and innovative digital technologies for use in this context, with the first cohort receiving a total of C$40 million (about $30 million) in investment over three years.

THe SGHP project partners include DNAstack, Deloitte, Genome BC, LifeLabs, Microsoft, Molecular You, Provincial Health Services Authority, and the University of British Columbia. This group has been tasked with developing an initial proof of concept to aggregate and integrate health and genomic data with an eye towards building a pan-Canadian digital health platform.

The team will build on infrastructure previously developed by DNAstack for sharing and accessing genomic data. In addition to new features, the partners are also exploring patient consent models and monitoring policy changes that will allow for data sharing on a national scale. The first phase of the SGHP will focus on planning, designing, and building a prototype solution that will include two avenues for researchers to share data and resources — a data library and an application marketplace.

The current project grew out of a need for collaboration and data sharing on a national scale. It's part of Canada's efforts to build infrastructure that can support national scale health initiatives comparable to other countries, Marc Fiume, CEO of DNAstack, said in an interview. His company's software, which will be used for the project, is designed to simplify the task of finding, accessing, and computing on genomics and clinical data.

For example, DNAstack was previously tapped by Autism Speaks to restructure the research portal for its MSSNG project, an open repository of whole-genome sequence, phenotype, and clinical information from more than 10,000 individuals and families with autism. DNAstack was also chosen to develop a web-accessible service aimed at making it possible to share sensitive genotype and associated information between doctors and researchers.

The proposed Secure Health & Genomics Platform, which will run on the Microsoft Azure platform, builds on DNAstack's Canadian Genomics Cloud, which is the first public cloud platform for genomics with data sovereignty within Canada's boundaries, according to Fiume. Launched in 2018, the Canadian Genomics Cloud is designed to support research into the genetic causes of autism, adult and pediatric cancers, heart disease, mental health, cystic fibrosis, and other rare diseases.

Around the world, "data sovereignty is a big issue … and you need to be careful about where data resides to comply with regional regulatory conditions," Fiume said. His company's solution helps "tick a lot more boxes in terms of what organizations were willing to use cloud computing for," he said.

For the current project, DNAstack and its partners will add new features and capabilities to the company's platform that leverage standards developed by the Global Alliance for Genomics and Health. The list of features includes a new biomedical search engine that will enable researchers to identify new biomarkers as well as recruit patients for research studies based on the genomic, clinical, and phenotypic information.

"One of the problems with complex disorders like cancer and autism is that you really can't consider the genome independent of the clinical and phenotypic information," Fiume explained. The integrated solution will support "basically any inquiry that you can imagine across phenotypic and clinical data as well as with genomics."

Other features include a rule-based authentication and authorization system designed to streamline the current process of requesting access to data. Currently, researchers access controlled datasets by applying to data access committees which conduct background checks to verify scientists' credentials including institutional affiliations, research interests, and so on.

DNAstack is integrating mechanisms to codify this information about researchers into an identity — a kind of "digital passport" that can be used to streamline access to multiple controlled access datasets at once. In the future, when the researcher applies for access to a new dataset, these credentials will be provided to the new committee, or an algorithm that can instantly broker access to the data based on use restrictions.

The partners that GenomeWeb spoke to for this story said they were motivated to join the project because of the promise of combining genomic and clinical information for more personalized health, and cited the importance of sharing and combining information for achieving that goal. In addition to infrastructure, partners are also providing expertise around matters of consent and data privacy.

"Our engagement with the supercluster is based on our mandate as an ecosystem builder," Pascal Spothelfer, Genome BC's president and CEO, said in an interview. "We wanted to engage because we want to be part of that amalgamation of different stakeholders that quite often don't have an opportunity of working together." His organization is contributing subject matter expertise to the project and helping to connect the project with additional partners as needed. "We have worked with many different partners on many aspects of the data challenge so we'll be contributing some of that expertise."

In addition to Genome BC, the list of project partners includes medical testing laboratory LifeLabs, which provides testing services for patients across Canada. Its portfolio of services includes tests for endocrinology, gastrointestinal health, and cardiovascular health. The company also provides genetic testing services including non-invasive prenatal testing and pharmacogenomics testing. Both Genome BC and LifeLabs are also listed as partners on a second supercluster project focused on building a pharmacogenetics ecosystem that will connect testing labs and medication decision support software with primary care and pharmacy management systems.

Other partners on the Secure Health and Genomics platform initiative are Molecular You, which seeks ways to integrate its data with information from other organizations in a way that preserves customer privacy. The digital health company uses an artificial intelligence-driven system to help individuals proactively take control of their health. It does so by providing multidimensional analysis of different kinds of patient data including results from microbiome testing, data from metabolomics, proteomics, and environmental exposure testing, and clinical data.

Molecular You uses its rich dataset to provide customers with "a clear understanding of where they are currently with their health and what sort of risks they face," CEO Robert Fraser explained in an interview. The company also provides its customers with action plans that are intended to keep them healthy including details such as which exercise regimens, diets, and supplements are best suited for them.

"One of our big projects in the [supercluster] partnership is the consenting model to ensure that people are in control of their data," he said. Given its experiences working with different kinds of health information, Molecular You is providing expertise in the design of infrastructure intended for ensuring patient privacy as part of its role in the initiative. "We've been doing a lot of work in our own organization on what's the best way for an individual to control the data," he explained. "We do have a lot of background around consent in the way we operate so we'll bring that to the group."

For its part, Deloitte as "ecosystem integrator" will work on integrating different aspects of the project infrastructure and ecosystem stakeholders, according to Joyce Drohan, a partner and British Columbia leader for Omnia AI, Deloitte Canada's Artificial Intelligence and Advanced Analysis Practice. Drohan is leading Deloitte's work on the precision health and genomics platform.

In addition, the company will work on commercial and governance models for the infrastructure, support DNAstacks' efforts to build out its bioinformatics tools, and help build out the Azure platform that the bioinformatics tools will sit on. "We have the BC Ministry of Health as part of our steering committee and they will be supporting us to understand what government needs are," she said. "We want to make sure that the work that we are doing transparently helps the organizations that would potentially be using this when we are done."

Most of the challenges the partners expect to face as they move forward in this project will be largely on the policy and governance front. In Canada, "all the provinces have different data management regimes from a privacy, data exchange, and data ownership point of view," Genome BC's Spothelfer explained. This has resulted in the formation of data silos both across and within provinces. There have been several initiatives in Canada that have called for data sharing across provinces but none have focused specifically on genomic data. "Dealing with that diversity will certainly be one of the challenges," he said. "There has to be a solution to getting access to data without that data leaving the province."

"[We're] hoping that this project could be a first step in gaining the public trust on the value of sharing health information," she said. Also needed are "better consent models which give the patients the ability to determine what is done and gives them full ability to not only consent to have their data shared but also retract that consent when they are uncomfortable with that."

Partners like Molecular You will be keeping an eye on shifts in policies and regulations that could support more cross-organizational data sharing. "I think most people are willing to share their data but we do hear more and more concerns about how their data is used," Fraser said. He expects another matter for the group to address will be finding a way to be interoperable across platforms. "I think that's going to be one of the next challenges that we all face."

Deloitte's Drohan noted that "there are policy questions right now with the government and ministries that haven't been answered around genomics data yet." Given the sensitivity of genomic data, addressing those questions "will help escalate and prioritize the things that [we] need to work with," she said.