Berlin joins national genome data network

Last year, the German Federal Ministry of Health launched a National Strategy for Genomic Medicine: The “genomDE model project” aims to establish genomic medicine as standard care for patients with rare diseases or cancer; the ability to quickly diagnose genetic diseases or identify specific mutations responsible for a person’s cancer will enable personalized and more effective treatment for all patients. 

This year, the Max Delbrück Center and the Berlin Institute of Health at Charité (BIH) started operations as one of six Genome Data Centers, or Genomerechenzentren (GRZs) – high-performance computing and data storage facilities. “We take the pseudonymized data from clinical partners including Charité – Universitätsmedizin Berlin, check for quality, and archive it for future research projects,” explains Professor Dieter Beule, Head of the Translational Bioinformatics group and who is responsible for the GRZ and Data Hub at BIH. So far, data from more than 6,000 patients have been processed by the six GRZs combined.

Rare diseases often cause vague symptoms that overlap with many common diseases, sending patients on long and frustrating “diagnostic odysseys.” Quick and easy access to genome sequencing can significantly shorten this path, explains Beule. In oncology, genomic insights can help match patient’s cancers to specific therapies, and thus improve outcomes, he adds. “We provide a secure and cost-effective digital infrastructure for handling large amounts of data. This is an essential prerequisite for scientific projects that will lead to further improvements in genome diagnostics, while ensuring the necessary data privacy.”

Data storage for future research

Storing and processing such massive amounts of data requires an equally massive amount of computing power, adds Karsten Häcker, Head of IT at the Max Delbrück Center. “A single human genome dataset can take up around hundred gigabytes of storage. This kind of research needs a high-performance technical infrastructure.” The Berlin hub, jointly operated by the Max Delbrück Center and BIH has an initial capacity of about 3,000 terabytes. 

The entire genomeDE model project infrastructure, which consists of clinical data nodes in addition to the GRZs, is being operated by the Federal Institute for Drugs and Medical Devices (BfArM). Health insurance companies have thus far committed to providing participating university hospitals with a budget of €700 million over the next few years, with more funding expected. The funds are intended to reimburse hospitals for the costs of sequencing patient samples and data analysis. 

Providing data for research purposes

The six data hubs are part of the German Human Genome-Phenome Archive (GHGA).  Since 2024, GHGA has been collecting, archiving, and making available existing datasets for research. The GHGA operates under strict ethical and data privacy safeguards. Its mission: to make genetic and clinical data FAIR – Findable, Accessible, Interoperable, and Reusable – so that insights gained from one study can power discoveries in many others. The GHGA is part of Germany’s National Research Data Infrastructure (NFDI) and currently includes 28 participating institutions – it already contains genomics data from many study participants and healthy volunteers.

Data collected by the GRZs is also being made accessible to the GHGA for research purposes, but only from those patients who have expressly consented. Security is a top priority, says Häcker. “The already pseudonymized data is also encrypted,” he emphasizes. Even if someone were to carry the hard drives out of our secure data center, they would have to break into two other locations at the same time to get the de-cryption keys.” If a research group wants access to genomeDE model project data, it must submit an application to the BfArM and adhere to strict ethical and legal regulation. A committee decides whether the project is scientifically sound before granting access.

“Our participation would not have been possible without excellent cooperation among all partners, says Häcker. “The project clearly contributes to our goals: quickly translating knowledge into benefits for society.”

Further information

• The German Human Genome-Phenome Archive
• Model Project Genome Sequencing
• Data Science und AI at the Max Delbrück Center
• Beule lab