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Genomics data to be shared via the National Genomics Platform

This following the signing of agreements between Genomic Medicine Sweden’s (GMS) fourteen partnering regions and universities.

Thus far, this is being done within research projects pending an update in legislation.

“The ability to share health data, such as genomics data, is a prerequisite for precision medicine. Not only to be able to provide the right care and treatment, but also for research and development,” says Clara Hellner, Research Director at Region Stockholm.

The National Genomics Platform

Today, there is a fragmented IT infrastructure at the university hospitals in Sweden, where information is stored in several systems that are not interconnected. In order to enable data sharing nationally between GMS partners, i.e. the healthcare regions and universities, GMS has established a national infrastructure, the National Genomics Platform (NGP).

The NGP is creating new opportunities for the coordination and standardisation of genomic data, which in turn enables data to be shared and compared in new ways. In the long run, this will result in better diagnosis and a greater understanding of the biology of diseases.

“We in the GMS Steering Group applaud the fact that the NGP is now in operation. This is something we have been working on for a long time and which is anchored at a high level in our respective regions and universities,” says Mats Ulfendahl, Chairman of GMS Steering Group and Research Director at Region Östergötland.

Agreements have been signed between the Västra Götaland Region (VGR), which operates the NGP, and the seven regions with university healthcare as well as with the seven universities with a medical faculty. This means that the NGP can be used to share personal data, such as genomics data. At present, however, data can only be shared for research, as Swedish legislation still prevents the sharing of personal data from many individuals for the care and treatment of another patient. The next important step will be the results from the ongoing inquiry on secondary use of health data and the changes in legislation that this will hopefully lead to.

“We now have an IT infrastructure in place that can be used to share genomics data on a national basis. The platform is the only one in Sweden that enables real-time data sharing between the seven healthcare regions, thereby providing a unique opportunity in the future for national variant databases and interpretation tools,” says Jan Kilhamn, Research Director at Region Västra Götaland.

Three primary functions

The NGP has three primary functions; to store, index, and process data. All seven Genomic Medicine Centres (GMCs) within GMS are linked to the NGP via the SjuNet hospital network. Thus, data and metadata can be retrieved from local laboratory information systems and storage systems and be uploaded to the central platform. In addition to genomics data, quality data is also stored, such as information from analytical instruments and bioinformatic pipelines, as well as the interpreted data created during the diagnostic process. Within the platform, data is logically separated by a tenant system where each GMC has full control over their own data, including access and user control.

“Each region will own its own piece of the cake. This means that the region itself can control who gets access to the data in the platform. A precise agreement has subsequently been reached on what data should be shared and with whom,” says Per Sikora, co-chair for GMS Informatics. “GMS’s goal for a knowledge database for better diagnostics and equality of care for all patients presupposes that data is collected in the National Genomics Platform. So, we are now starting the work of entering data from our national projects within GMS, where we have started the implementation of a whole genome sequencing of cancer.”

Photo: iStock