NEW YORK (GenomeWeb) – Denmark has established a new national genome center to support the development of its personalized medicine program. The Scandinavian country set aside DKK 100 million ($14.2 million) last year to support the initiative, dubbed Per Med, through 2020.
The center, set to open next year, will serve as a national sequencing infrastructure, manage a national genome database, and make the data available for research. Gert Sørensen, the former CEO of Aarhus University Hospital, has been tapped to lead the Danish National Genome Center, given his background in healthcare administration.
"My job is to head this new center and establish the framework within which this center can operate," Sørensen said.
A country of about 5.8 million people spread across a peninsula and many islands, Denmark has a healthcare system that is managed at the regional level, and there are five healthcare regions across the country. To date, most clinical exome or whole-genome sequencing data generated has been held in regional databases. The purpose of the national genome center is to consolidate that data in one database going forward, while expanding access to clinical next-generation sequencing within the country.
While the national genome center has been envisioned for years, the Danish parliament in May passed a bill outlining its responsibilities, which was signed into law in June. The law provides the legal framework for the creation and use of the data stored in the database. According to the law, patients must consent to have their whole-genome sequencing data made available in the database before it can be added.
"Security is a very high priority for the center," Sørensen noted. "If you consent to having whole-genome sequencing performed, you also have the possibility to opt out," he added. "You can decide that the data produced is only to be used for your own treatment, excluding any purpose of research."
According to the law, the genome center is administered by Denmark's Ministry of Health. The center's prerogative is to "support the development of personalized medicine in collaboration with the Danish healthcare [system], research institutions, and patient associations." The law also stipulates that data managed by the center may be made accessible so long as it is relevant to healthcare management or for "scientific studies of social significance."
The new center is based in two locations: in Copenhagen, its capital city and at Risø, outside the university city of Roskilde. Sørensen said that it currently employs 15 staffers and plans to fill around 10 more positions throughout the country in all five healthcare regions. The center is currently involved in setting up high-performance computing resources, as well as several sequencing facilities.
Data generated by these new facilities will be stored in the database, but no archival data from the Danish healthcare regions will be imported. "The law states clearly that the national genome database starts from day one and builds up from there," said Sørensen.
The center has not yet selected instruments and tools to serve its computational and sequencing needs, Sørensen noted. "We want to use existing competencies in the Danish healthcare system," he said.
Financial support for the center is drawn from the initial investment of DKK 100 million but Sørensen said this was "put in place to get the project and center started." In the future, additional public funding will be made available through an annual budget. Per Med as a whole is expected to be co-financed by public research resources, regional healthcare resources, and private funding, he added.
The national genome center will offer its sequencing and computational infrastructure throughout Denmark. In addition, centers within the five Danish health regions will be able to upload new data they generate to the new database. "The system will operate so that any sequencing facility in Denmark will be able to report to the database," said Sørensen.
The center will also be responsible for standardizing the sequencing data, he noted.
Denmark's choice to store new patient data in a database and make it available for research differs somewhat from other ongoing genomics efforts in Northern Europe. Multiple countries in the region, including Iceland, Finland, and Estonia, have opted for cohort genotyping, based on population reference panels developed from whole-genome sequencing, and then filtering discoveries back into the healthcare system for use in personalized medicine. Finland, for instance, last year announced plans to genotype 500,000 people by 2023, while the Estonian government has budgeted €5 million ($5.7million) to support the genotyping of 100,000 people this year.
"The Danish point of departure is the patient situation," Sørensen said. "The need for sequencing takes place in the context of the need for patient care. That is different."
"This will not be cohort sequencing, this will be patient sequencing in the healthcare system," added Søren Brunak, a professor and bioinformatician at the University of Copenhagen who played a role in the creation of Per Med. "However, this type of infrastructure will be well suited for addressing research project needs as well."
Supporting such research and development projects is a core goal of Per Med. By studying sequencing data together with the country's extensive electronic medical records — Danes have had their health records linked to their social security numbers since 1968 — Danish researchers hope to make discoveries that will improve care.
To achieve that, though, will require the consolidation of resources through the national genome center, as well as more funding.
Denmark is not "going from no precision medicine to precision medicine," said Brunak. Efforts in the country to date have been driven by "early pioneers who developed their own infrastructures, without the ability to scale to the national needs," he added.
The new law now makes it clear that the country will rely on a national genome database going forward. It also stipulates that if a person is sequenced in the healthcare system and gives consent, that person's data will go into the new database. "You can opt out of making data available for research, but you cannot opt out of having your data in the database," Brunak noted, "because the healthcare system wants to keep the evidence that was used to make treatment decisions."
Another issue that the genome center should address is access to sequencing within the Danish healthcare system. Brunak said that hospitals differ in how much exome sequencing they have done, and some have more experience than others. "The most frequent use has been exome sequencing in oncology and in the rare disease domain, where the latter also includes non-inherited rare diseases," said Brunak.
The new center should "expand sequencing capacity drastically" in the country, he said.
Private and public foundations have indicated that they are prepared to support the Per Med initiative in Denmark, Brunak said, and organizers hope the amount of funding for Per Med will be "significantly higher" than the DKK100 million that the state has invested so far.
"The 100 million kroner was just to get this thing off the ground," he said.
Sørenson noted that researchers could opt to store data from their own projects in the database, too, so long as it is approved by the country's ethics committee. Still, he stressed that subjects must agree to have their data held in the national genome database.
"Whether it is patient data or research data, there will have to be written consent by the people whose data is in the center," he said.