Netherlands X-omics InitiativeGlobally renowned Dutch leaders in the field of genomics, proteomics, metabolomics and data integration & analysis join forces to realize the Netherlands X-omics Initiative. The initiative will realise a truly integrated X-omics research infrastructure across the Netherlands that enables researchers from universities, academic hospitals and companies to answer their questions by:
- pushing technological boundaries in each omics field by improving sensitivity, coverage, and quality of analysis,
- studying smaller sample volumes and larger sample numbers at reduced costs,
- integrating data from different omics approaches,
- providing direct access to the most advanced omics facilities in the world.
- BBMRI-NL – The Biobanking and BioMolecular resources Research Infrastructure - Netherlands – represents over 200 biobanks in the Netherlands that facilitate studying population-based cohorts. In the last decades, BBMRI-NL has collected valuable phenotypic and molecular data on over 1,000,000 Dutch individuals and a catalogue of available phenotype data is available here. The X-omics cores and nodes will closely collaborate with BBMRI-NL to provide researchers with both well-defined cohorts and available data collections (role BBMRI-NL) and the tools to assess biological samples at a much more comprehensive and detailed molecular level (role X-omics).
- ELIXIR-NL, the Dutch node of the European Life Sciences Infrastructure for Biological Information, is setting up standard 'rules' on data-sharing, provides the data-sharing infratructure and accomodates virtual workspaces. The infrastructure guides the full research data lifecycle, from data acquisition to publication and data re-use. ELIXIR interacts with X-omics on three levels:
- Cloud (data storage) orchestration with user interfaces (findable)
- Data orchestration (interoperable), access, and publication (accessible)
- Tool orchestration and application store (re-usable)
- Health RI, an interconnected data infrastructure for Dutch personalized medicine and health research. This facility was designed by the Dutch Techcentre for Life Sciences, together with ELIXIR-NL, BBMRI-NL, EATRIS-NL, NFU, VSNU and Health-Holland and is supported by 60+ stakeholders.
- Bioscopy, a multi-disciplinary research ambition towards mapping molecular and structural processes in cells, to elucidate cell function and its relation to human biology and function.
- Proteomics: Between 2011 and 2015 the Utrecht core-facility was the coordinating hub of the European Large-Scale Infrastructure in Proteomics (PRIME-XS), which supported access and running costs but did not support hardware. A follow-up project is currently in preparation in response to a call for a proteomics infrastructure in the EU H2020 framework program. The Dutch proteomics facilities provide access to a very wide range of both academic and industrial partners. The Utrecht core-facility is also involved in the highly prestigious FET-Open project MSmed (project ID 686547). The proteomics community collaborates with other large-scale facilities such as the European Bioinformatic Institute (EBI), and the ESFRI landmark project INSTRUCT for integrated structural biology.
- Metabolomics: The Netherlands was one of the drivers behind the MetabolomeXchange, a portal for metabolomics studies, and is heavily involved in establishing metabolomics for BBMRI-NL and to establish an Elixir metabolomics network in Europe. Additionally, Leiden University is also part of the EU H2020 PhenoMeNal consortium, which aims to establish a virtual metabolomics and phenomics infrastructure together with EBI and others European metabolomics groups. Hankemeier recently submitted MetaStar as coordinator, a H2020 infrastructure proposal to start a metabolomics community for a joint effort of the major metabolomics labs and facilities in Europe to standardize metabolomics. The MetaStar consortium will also address the training needs of new users and enable collaboration with other large-scale metabolomics and Phenome facilities. PIs are involved or leading many multi-omics H2020 projects on neurodegenerative diseases and cancer (CamPaC, CoSTREAM, SysMedPD).
- Genomics: In the area of sequencing technologies no real European consortia have been established, but there are coordinated efforts in specific NGS application areas. Radboudumc was also in the lead of the EU FP6 TECHNGENE project in which standards for genomic diagnostics were set (CITE recommendations/standards). The genomics community, like the proteomics community does also collaborate with other large-scale facilities such as the European Bioinformatic Institute (EBI), and is represented in the NWO Gravitation program CancerGenomics.nl (CGC.nl), contributes genetic analyses for the national organoid icon project (Clevers) and the Center for Personalized Cancer Treatment (CPCT). When it comes to rare diseases, involved partners have direct links to nearly all European Reference Networks (ERNs), and coordinate several of them.
- Data integration and analysis: The genomics, proteomics and metabolomics experts in X-omics are taking part in multiple European research consortia (funded for instance by H2020 and IMI) where they apply their technological skills in collaboration with other omics or bioinformatics scientists and life science researchers. The Biomarker Development Center recently initiated the COST action CliniMARK, in which over 25 countries and industries are assembled to exchange knowledge on optimal translation of X-omics information to validated biomarkers and impact in healthcare. The members of the X-omics consortium take part in the major translational European Research Infrastructures EATRIS, BBMRI-NL and ELIXIR (e.g. van Gool chairs the Biomarker Platform of EATRIS covering 34 translational medicine institutes across Europe). Collaborative steps being taken by these infrastructures towards definition and implementation of Good Biomarker Practice guidelines3.
Nederlandse samenvattingDe chemie van het leven is ongekend complex. De grootste uitdaging van biologen en artsen is dan ook om goed te begrijpen hoe ziektes ontstaan en hoe deze beter en vroegtijdiger ontdekt en behandeld kunnen worden. Daarvoor gebruiken zij een groot aantal moleculaire technologieën zoals genomics, proteomics, metabolomics en bio-informatica. Deze technologieën maken het mogelijk om in meer detail naar de complexe en dynamische processen in cellen en weefsels te kijken. In dit project worden al deze technologieën gebundeld ten behoeve van onderzoek op het gebied van kanker, Alzheimer en andere ziektes. Met geavanceerde bioinformatica methodes worden vervolgens alle onderzoeksdata geïntegreerd en geanalyseerd. De resultaten uit dit project geven inzicht in de moleculaire mechanismen die een belangrijke rol spelen in het ontstaan en verloop van deze ziektes en bieden mogelijke aangrijpingspunten voor preventie en behandeling hiervan.
Training and OutreachThe Netherlands X-omics Initiative will have a strong focus on training and outreach. We will develop a portfolio of user trainings, in particular to educate new omics users in experimental design, sampling and data integration and interpretation. At the same time we will develop and provide trainings for omics practitioners including young talent and technicians at the different sites on understanding better the other omics techniques, on the implementation of (quality) protocols and FAIR data standards and on biostatistics, data integration, and modelling. As part of the X-omics Initiative website we will provide moderated discussion forums, instruction videos (for instance on sampling techniques), and on guidelines on best practices in analytical procedures and data integration and interpretation.
Alain van Gool - TEST, WERKT NIET PhD