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Pan-European Initiative to Build Infrastructure, Tools for Sharing Genomic Health Data


NEW YORK – Twenty-three European countries and counting have signed a declaration to make data from a million genomes accessible to researchers across the region by 2022. Realizing the aims of the 1+ Million Genomes Initiative however will require legal guidance, best practices and recommendations, and new infrastructure and tools to manage such a vast trove of genomic data.

To support the 1+ Million Genomes Initiative, the EC has funded a new project called Beyond 1 Million Genomes with €4 million ($4.7 million) over the next three years. Serena Scollen, head of human genomics and translational data at ELIXIR, the European life sciences infrastructure for biological information initiative, is the principal investigator on the project, dubbed B1MG.

"Accessing genomic data across borders at a scale that will have socio-economic impact is hampered by lack of interoperable infrastructure and agreed-upon guidelines to ensure full consideration of the ethical, legal, and social issues," said Scollen via email. "B1MG brings together research infrastructures, academics, and other key stakeholders to create legal guidance, best practices and recommendations to create this infrastructure and the toolkits required," she said. She noted that the B1MG project will also benefit from the support and commitment of the 23 countries that have signed the declaration to make a million genomes available.

"Using genomics in healthcare holds great promise," said Scollen. "This project outlines how each relevant domain needs to develop to make this a reality."

'Providing the glue'

The 1+ Million Genomes Initiative emerged after years of discussions led in part by a Brussels-based nonprofit called the European Alliance for Personalized Medicine. In April 2018, 17 countries signed a declaration to have a million genomes sequenced and shareable by 2022. Since then, the number of countries has risen to 23.

Currently, Austria, Belgium, Bulgaria, Croatia, Cyprus, the Czech Republic, Estonia, Finland, Germany, Greece, Hungary, Italy, Latvia, Lithuania, Luxembourg, Malta, the Netherlands, Norway, Portugal, Slovenia, Spain, Sweden, and the UK have signed the declaration. Denmark, France, Ireland, and Switzerland currently have observer status within the initiative. Germany and Belgium were the latest to join earliest this year.

In February, the initiative laid out a roadmap for achieving its main aims. These include engaging various stakeholders to define the requirements for making genomic and personalized medicine data accessible across borders; creating technical specifications and implementation guidelines to represent European best practice; and sharing, sustaining, and scaling the effort. The initiative also includes a variety of use cases to pilot future data sharing efforts, specifically in rare diseases, cancer, common and complex diseases, and infectious disease. The latter use case was added in part due to the ongoing COVID-19 pandemic.

"It's coming together nicely, it is getting a lot of structure," said Ivo Gut, director of the National Center for Genomic Analysis (CNAG) in Barcelona. "Obviously, the goal is to get to a level of organization that will allow us to safely and securely share genome data together with clinical and phenotype data," said Gut. "That is the objective of the entire exercise."

The role of the B1MG project is to do the detailed work alongside the 1+ Million Genomes Initiative. The European Commission-backed effort commenced in June and will run through May 2023. B1MG involves 28 partners from across 25 countries, one of which is Gut's own CNAG. Its core concept is to set the framework to not only achieve the sharing of a million genomes by 2022, but to be able to continuously share more and more data beyond that milestone.

"B1MG is essentially the glue," said Gut. "It provides the glue so that all of us can seriously work with each other," he said. "This will provide a platform for everyone to standardize their sequencing and their reporting and recording of phenotyping and clinical information, so that we can through a federated system exploit this information for the benefit of the patients."

Accomplishing that is not an easy task, he acknowledged. "As you can imagine, it's a huge leap," said Gut. "You have to worry about the legal and ethical aspects, the technical aspects of sequencing patients," he said. "There are also the 27-plus languages contained in electronic health records and how to make them interoperable." And all of this new infrastructure has to be set up in a way that does not violate local guidelines covering data protection, which can vary from country to country.

B1MG contains six work packages: stakeholder engagement; ethical, legal, and social issues; standards and quality guidelines; federating secure cross-border infrastructure; delivering personalized medicine across borders; and a coordination office. Gut is co-leader of the standards and quality guidelines work package. He said that while coordinating such an effort might seem daunting at first, frameworks do exist that cover other kinds of tests, including International Standards Organization guidelines and various accreditation systems.

"A lot of these mechanisms already exist, but no one has really dialed it up to genome sequencing yet," said Gut. "It's complicated, but you can do it."

A 'wonderful use case'

Those involved in B1MG see the ongoing 1+ Million Genomes Initiative as a departure point for remaking the way European researchers share both genomic as well as clinical and phenotypic data. A thoroughly integrated Europe could also eventually join with projects around the world, making much more data more immediately accessible to researchers everywhere for studying rare conditions.

"A million genomes is a wonderful use case to drive the establishment of infrastructure and approaches to be able to access personal data across borders," said Ruben Kok, director of the Dutch Techcenter for Life Sciences, based in Utrecht, the Netherlands, which is taking part in B1MG. "Of course if we can do that in Europe, we can be interoperable with global initiatives," he said.

Yet first, there is the challenge of Europe. The idea is not to consolidate all data within one centralized database, but to create a secure environment for data sharing. Ideally a user in the Netherlands would be able to access resources in, say, neighboring Belgium, or in Finland or Estonia, giving far more power to their studies.

"My dream is to have this grow into a fully federated system in which we can get access to local, clinical information," he said. "Data will by default not leave countries."

B1MG was needed, commented Kok, because creating such a system needs dedicated resources. "It was needed to have a more substantial organization structure with some capacity of people to put time into this," he said. "The role of B1MG is to boost the level of coordination at the level of the workstreams carved out in the road map."

Currently, the project is working toward recruiting stakeholders to support its different work packages, noted Kok. This will involve liaising with existing clinical health projects in Europe that can align their efforts to the aims of the 1+ Million Genomes Initiative, ongoing projects that are "doing part of this but not the full picture." Via these projects, participants can test out the feasibility of making data available throughout the region. "We are going to set up tangible examples now of how … a number of countries can already start exchanging information," said Kok.

But the longer-term goal is, as Kok noted, to have the framework in place to share genomic data far beyond 2022, a vision that CNAG's Gut agreed with.

"The objective is not one million and then we stop," said Gut. "The idea is to build a system that each member state works with and to continue sharing their data so that when there are 300 million Europeans sequenced, we will have all 300 million European genomes to share," he said. "That would be the dream."

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