Genome of Europe

Topic description

ExpectedOutcome:

• Joint or coordinated sequencing (WGS), as described under Scope.
• New WGS data for a large number of representative European citizens, to be further specified in the call document, generated in accordance with the guidance, specifications and standards agreed within 1+MG (1+MG Trust Framework).
• Integration of eligible population-based WGS data generated independently of the GoE and made available to the project.
• The Genome of Europe federated reference database established and accessible through the federated European genomic data infrastructure and the European Health Data Space (EHDS) infrastructure for secondary use of health data (HealthData@EU).

This action will support the implementation of the Genome of Europe (GoE) multi-country project and contribute to achieving the objectives and long-term ambition of the 1+Million Genomes (1+MG) initiative. GoE aims to establish and launch a European reference genome database of genetic variation obtained by whole genome sequencing (WGS) for at least 500,000 citizens based on population-based national reference genome collections, collectively representative of the European population. GoE has the potential to foster break-through advances in research, innovation, disease prevention and healthcare delivery, widely spread across clinical disciplines, beyond current use cases (disease areas). Moreover, creation of a reference database will allow meaningful savings in healthcare systems as it will enable data imputation and enrichment of genotype information. A concerted genome sequencing effort is necessary to achieve a critical mass of WGS data across Europe. By fostering it, this action is expected to bring major efficiencies due to economies of scale and should enable all GoE countries to contribute with WGS data. It will also ensure consistent application of agreed common data requirements and quality measures across all national datasets, enabling the creation of a high-value European reference dataset.

The objective is also to support the initiative taking into account the potential creation of a European Digital Infrastructure Consortium (EDIC).

The focus of the action is on whole genome sequencing at clinical grade depth necessary for clinical application. This can be achieved by coordinated WGS sequencing expected to enable massive new data collection in all GoE countries. WGS data for the GoE must be generated following the 1+MG Trust Framework that brings together a set of minimal recommendations to enable secure cross-border access to genomic data in Europe, in particular as regards ethical and legal aspects, data standards, data quality and technical inter-operability. To this end, sequencing specifications should follow the available 1+MG guidance and align closely with that initiative.

The biological samples needed to generate the data, i.e., to sequence the genomes, can either originate from existing population-based cohorts and national biobanks, or be collected from participants recruited specifically for the national and European GoE reference databases. The participants will be selected at the national level to be representative of the respective population, including a contribution of relevant minorities. To ensure uniform approach, the exact inclusion and selection principles need to be agreed at the European GoE level.

In parallel to data generating activities (WGS sequencing), the architecture, hardware and software necessary to aggregate national reference databases into a European reference database (The Genome of Europe) need to be designed, developed and implemented in cooperation with the Genomic Data Infrastructure (GDI) project. As well as newly generated GoE data, this should ensure effective integration of available national population-based WGS collections established before or independently of the GoE. The GoE database must be interoperable with and accessible through the 1+MG data infrastructure and equally aligned with the European Health Data Space (EHDS), in particular the infrastructure for secondary use of health data (HealthData@EU).

For data security reasons, sample transport, all WGS activities and genomic data transfer and storage must take place within the territory of eligible countries.

The GoE project forms an integral part of 1+MG and GoE data will be accessible via the European federated genomics data infrastructure (GDI) deployed under the Digital Europe topic DIGITAL-2021-CLOUD-AI-01-FEI-DS-GENOMICS. Besides Digital Europe’s Data Spaces, the topic is also synergetic with the RRF support for the GoE multi-country project as stipulated in the national recovery and resilience plans of several Member States. Cooperation with other relevant European initiatives, and due consideration of other projects and infrastructures, for example those funded under the Horizon 2020 and Horizon Europe research and innovation programmes and the EU4Health Programme (e.g. Genomics for Public Health), will be strongly recommended to build on and bring forward their results as well as to ensure a good use of synergies and complementarities.

The awarded project will use, in so far as possible, the smart cloud-to-edge middleware platform Simpl, and have to work in partnership with the Data Spaces Support Centre deployed under the first W in order to ensure alignment with the rest of the ecosystem of data spaces implemented with the support of Digital Europe Programme. The joint work will target the definition of:

• the data space reference architecture, building blocks and common toolboxes;
• the common standards, including semantic standards and interoperability protocols, both domain-specific and crosscutting;

The data governance models, business models and strategies for running data spaces.