GDI-NL
Genomic Data Infrastructure in The Netherlands
The GDI-NL infrastructure embodies the national node in the European Genomic Data Infrastructure and the other resulting infrastructure in the 1+MG initiative, making existing human genomics and genetics data, plus associated phenotypic health data, available for research, secondary use in health care, quality management and policy development. The infrastructure maintains a collection of high-quality data sets to which access in a federated infrastructure can be requested through a central portal. This is the infrastructure supporting the ambitions of the European one-million genomes initiative, the European Rare Disease Research Alliance (ERDERA) and is to become a seamless part of the European Health Data Space.
Infrastructure and User Services
GDI-NL facilitates access to human genomic data for use in research, secondary use in healthcare, quality management and policy development. Every year, many thousands of Whole Genome and Exome Sequencing datasets are generated at UMCs as part of routine diagnosis. An increasing fraction of these are whole genome sequencing data. Currently, these are mostly used to answer a single (diagnostic) question leaving a huge potential value to be unlocked. Access to genetic information collected by biobanks and cohorts with the aim of reusability (totaling a few 100k subjects) will also be facilitated. Work is ongoing in running projects on supporting federated querying of genetic and somatic variants, in addition development of DNA Large Language Models would also benefit from coherent and high computational performance infrastructure coupled to GDI-NL to pre-train the foundation model through federated learning. Multi-modal integration with other data, like transcriptomics, proteomics and metabolomics data, is ensured by strong alignment in architecture and (meta)data formats with the FAIR Data Cube, developed by LRSI X-omics.
Functionality includes the expertise and technology for including data into the infrastructure, storing it sustainably, allowing potential re-users to discover data using a catalogue and a subject-level data discovery system, requesting access to data, and giving access to the data in the secure processing environment. For each step, the infrastructure provides support including a helpdesk. To support compliance with GDPR, the infrastructure supports a subject information portal. The infrastructure will be compatible with and seamlessly form part of the European Health Data Space.
Examples/description of the type of research
The infrastructure supports the research of genetic aspects of rare diseases, complex and common disease, cancer, and infectious disease. It supports research into population genetics. It supports the inclusion of people into randomized clinical trials. All of these are supported in a national and an international context: through connection to the international infrastructure Dutch researchers will be able to use genomic data from subjects all over Europe through a single integrated infrastructure, and researchers all over Europe will be able to get secure and privacy preserving access to data of Dutch citizens under the same conditions.
How to access the infrastructure?
Access to the data is to be provided in a secure processing environment.