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New Swiss Initiative to Mine Genomics Data for Personalized Health Network


NEW YORK (GenomeWeb) – The Swiss government has launched an initiative that will create a new national infrastructure for sharing clinical data, including genomics data, among university hospitals, institutes, and others involved in personalized healthcare research in Switzerland.

Called the Swiss Personalized Health Network (SPHN), the effort is expected to commence in January 2017 and run through 2020. The Swiss government has budgeted CHF 40 million ($41 million) alone to support IT and clinical data interoperability, with an additional CHF 40 million set aside for biobanking and research projects.

"The SPHN initiative is unique worldwide as it brings together all university hospitals and associated academic research institutions in the country in a joint effort to transform the way biomedical information is used for research to benefit personalized healthcare," said Torsten Schwede, an investigator at Biozentrum, the Center for Molecular Life Sciences at the University of Basel.

Schwede, who is involved with the project, told GenomeWeb that the inclusion of genomic data in SPHN will provide a "crucial framework" for mapping clinical and phenotypic information. Swiss investigators will then be able to use that genomic data as part of their research projects.

SPHN does face a number of challenges, Schwede noted, including establishing data interoperability between diverse health systems in the country's three national languages — German, French, and Italian. He also acknowledged that Switzerland, with a population of 8 million, can "hardly generate large volumes of big data."

At the same time, Schwede and others involved with SPHN believe the project could demonstrate how to implement high standards of data generation and phenotypic characterization at hospitals and universities in a federal setting. It's an effort no doubt welcome at a time when similar initiatives are underway across the continent, be it at the national level — such as the UK Biobank — or in a European context. In recent months, the European Commission announced the allocation of $7.6 billion for a European Open Science Cloud, while the idea of a Million European Genomes Alliance, linking genomic data repositories across the continent, has been mooted by the European Alliance for Personalized Medicine.

The Swiss State Secretariat for Education, Research, and Innovation (SERI) initiated the SPHN and commissioned the Swiss Academy of Medical Sciences (SAMS) to draw up a concept for its development, structure, and implementation, which it delivered in a report in November 2015. In its report, SAMS called for the creation of a network that would both enable the harmonization of different data and information systems as well as smooth the exchange of data for research.

Schwede said that SAMS is managing the SPHN, while the Swiss Institute of Bioinformatics in Lausanne will operate the program's data coordination center. SIB, Schwede noted, already oversees bioinformatics research groups, service facilities, and service providers in Switzerland. Because of this, it is in a "unique position" to implement data interoperability standards and computational infrastructure for data sharing across the country, he said.

In the first phase of the project, SPHN will address data generated in university hospitals as part of patient care, said Schwede. This will not only include clinical data and electronic health records, but also genomics and other omics data as they have been collected during patient management, such as the molecular characterization of tumors, profiling of bacterial and viral infections, or rare disease diagnostics.

A second source of genomic data for SPHN will be clinical research projects focused on phenotypic and molecular characterization. This will include all data generated in the course of disease management, such as genomic sequences, molecular tumor profiles, gene expression profiles, proteomics, metabolomics, and microbiomes.

Peter Meier-Abt, president of SAMS and a professor of biomedicine at the University Hospital of Basel, told GenomeWeb that in the initial stages of SPHN, all genomics and other omics data will be drawn from patients, while data from healthy citizens will be added at a later date as a reference.

"We are in the process to define the exact type of data to be included and the data semantics, but with respect to genomics data, we will take all data that are analyzed in the course of disease management, such as molecular profiles of tumors, DNA sequences, siRNA, proteomics, metabolomics, microbiomes, et cetera," Meier-Abt said.

"Whatever is needed for individualized disease prevention, management, and therapy will be included, following the provisions of precision medicine and personalized health," he added.

Schwede said that SPHN will store its data in regional clinical bioinformatics competence centers associated with participating research hospitals and universities. The SPHN data coordination center will support and coordinate these competence centers to form a federated research infrastructure, he said. This will serve as a framework for research projects at the national level.

All of this data will eventually be made available to investigator-initiated research projects, subject to review board approval, according to Schwede. Potential themes for projects could include individualized disease prevention, predictive and prognostic digital biomarkers, and personalized therapy management, he suggested. Researchers may also request to access the data to "elucidate disease etiology" or better understand the molecular mechanisms of diseases, allowing for the development of more targeted treatments, he said.

SPHN intends to implement data interoperability over the course of 2017 and 2018, while coordinators expect to shift toward funding research projects in 2019 and 2020. Future projects could be funded if the Swiss government agrees to a second phase of the project after 2020.

While Schwede, Meier-Abt, and others are laying the ground to create the new network over the next few years, they noted that it is still subject to government approval. The Swiss parliament must sign off on the funding for SPHN by the end of this year prior to its official start in January.