Partners
MOLGENIS tools and services are driven by many partners and their user communities:
CardioResource
2026 - 2031
CardioResource will be the first national registry for patients with Heritable Cardiac Conditions such as the cardiomyopathies and cardiac electrical disorders. By bringing together the resources of all seven largest Dutch University Medical Centers, it will enable breakthrough research into these diseases by combining cutting edge (AI-based) analysis in genetics, imaging and the integration of clinical data. MOLGENIS leads action line 1, the federated data infrastructure including local FAIR portals and the central catalogue.
MOLGENIS tools used: catalogue registry
UNCAN-connect
2025 - 2030
The EU-funded UNCAN-Connect project (Horizon 101215206) will establish a decentralised collaborative network for cancer research, focusing on paediatric cancers, lymphoid malignancies, pancreatic, ovarian, lung, and prostate cancers. MOLGENIS delivers building blocks for the data platform, leading the catalogue and deposition tasks, and participating in federated analysis platform, with UMCG also involved via OncoLifes.
MOLGENIS tools used: catalogue armadillo registry
INTERCEPT IHI
2025 - 2030
At INTERCEPT, we are transforming the landscape of Crohn’s disease research by shifting from reactive symptom management to proactive early detection and prevention by using biomarkers to identify individuals at risk before symptoms develop, making diagnosis earlier than early. In other words, the aim is to stop Crohn’s disease. MOLGENIS leads the data infrastructure work package. This project is supported by the Innovative Health Initiative Joint Undertaking (IHI JU) under grant agreement No 101194780.
MOLGENIS tools used: catalogue hpc
STAGE
2024 - 2030
STAGE is a European Research and Innovation project studying healthy ageing and multi-morbidity using a life-course approach. It tackles the gaps in knowledge to understand life-long processes and their connections with biological, environmental, social, historical and infrastructural factors. MOLGENIS leads the WP9 STAGE lifecourse intelligence portal which is built on MOLGENIS catalogue. (EU Horizon 101137146).
MOLGENIS tools used: catalogue armadillo
INTEGRATE-LMedC
2024 - 2026
The INTEGRATE-LMedC consortium will develop a new concept to guide and support decision-making for the next-generation research infrastructure (RI) to facilitate efficient utilization and harmonization of large medical cohorts (LMedC). MOLGENIS participates in the workpackages for data infrastructure in particular catalogue and federated analysis.
MOLGENIS tools used: catalogue armadillo
IHEN
2024 - 2030
The International Human Exposome Network (IHEN) project aims to build a world-wide network to collaborate and improve human exposome research. The network will bring together researchers, policymakers, and independent experts to enhance the impact of future studies in this field. The MOLGENIS team contributes to the IHEN toolbox, in particular the EHEN/IHEN data catalogue.
MOLGENIS tools used: catalogue armadillo
ERDERA
2024 - 2031
ERDERA aims to provide better prevention, better diagnosis, better treatment to the over 30 million people living with a rare disease in Europe. ERDERA represents over 180 organisations from 36 countries working closely together with a shared vision of making Europe a world leader in rare diseases research and innovation to ultimately support concrete health benefits to rare diseases patients through improved prevention, diagnosis and treatment. MOLGENIS leads the datasharing infrastructure work package in the data services work stream and contributes to the genome diagnostics work stream, providing meta data registry, variant interpretation pipeline and high performance computing. Funding: EU Horizon 101156595.
MOLGENIS tools used: registry vip hpc
NESTOR
2023 - 2028
All University Medical Centers (UMCs) and the Netherlands Cancer Institute (NKI) will collaborate under the leadership of Nicoline Hoogerbrugge to build a large database of individuals with a proven hereditary predisposition to cancer, funded by KWF. MOLGENIS delivers the federated data infrastructure, with for each center a patient registry and a central aggregator.
MOLGENIS tools used: registry
GDI
2022 - 2026
The Genomic Data Infrastructure (GDI) project is enabling access to genomic and related phenotypic and clinical data across Europe. It is doing this by establishing a federated, sustainable and secure infrastructure to access the data. It builds on the outputs of the Beyond 1 Million Genomes (B1MG) project and is realising the ambition of the 1+Million Genomes (1+MG) initiative. MOLGENIS team has led the pilot site for infrastructure deployment in GDI-NL, lead the report on semantic interoperability and co-leads the FAIR data model work (Joeri van der Velde).
MOLGENIS tools used: catalogue hpc
EOSC4Cancer
2022 - 2025
EOSC4Cancer (Horizon 101058427) will make diverse types of cancer data accessible: genomics, imaging, medical, clinical, environmental and socio-economic. It will use and enhance federated and interoperable systems for securely identifying, sharing, processing and reusing FAIR data across borders and offer them via community-driven analysis environments. EOSC4Cancer’s well curated data sets will be essential input for reproducible and robust analytics and computational methods – including machine learning and artificial intelligence. EOSC4Cancer’s five use cases will cover the patient journey from cancer prevention over diagnosis to treatment, laying the foundation of data trajectories and workflows for future European Cancer Mission projects. MOLGENIS provided the catalogue and the federated analysis demonstrator in collaboration with EBI and GDI.
MOLGENIS tools used: catalogue armadillo hpc
Health-RI
2021 - 2026
Health-RI is an organization in the Netherlands dedicated to improving the reuse of health data for policy, research, and innovation to achieve a learning healthcare system. Our mission is: better health for citizens and patients by reusing health and life sciences data with an integrated data infrastructure to enable data-driven research, innovation, and policy.
MOLGENIS tools used: catalogue
MINERVA
2020 - 2021
the MINERVA (Metadata for data dIscoverability aNd study rEplicability in obseRVAtional studies) project (EUPAS39322) was initiated in response to the HMA–EMA joint Big Data Task Force recommendation on “the identification of metadata” for regulatory decision-making on the choice of data source. The MINERVA Consortium included 18 institutions and worked in collaboration with the EMA. MOLGENIS co-lead the metadata model definition and lead the pilot implementation for HMA-EMA Catalogues of real-world data sources and studies. This project was funded by the European Medicines Agency (EMA) through the framework contract No. EMA/2017/09/PE/16.
MOLGENIS tools used: catalogue
LongITools
2020 - 2025
The LongITools European research project studied the interactions between environmental, lifestyle and biological factors to determine the risks of chronic cardiovascular and metabolic diseases data variables on over 11 million European and UK citizens, from 24 different studies. The data variables are wide ranging and include, for example, height, weight, blood composition, employment, lifestyle factors, cholesterol and many more. Where possible, researchers harmonised the variables in their data sets to an agreed LongITools definition (harmonised model or common data model). MOLGENIS lead the data infrastructure work package, with focus on the data and harmonisation catalogue.
MOLGENIS tools used: catalogue armadillo
FORCE
2020 - now
FORCE Infrastructure for rare cancers in the Netherlands is a consortium comprising patients, clinicians, and researchers working collaboratively. The primary goal of FORCE is to improve treatment outcomes for rare cancers by developing a data warehouse containing clinicopathological data, imaging data, and a large-scale biobank of samples from donors with rare cancers. This comprehensive repository enables high-quality research on rare cancers. MOLGENIS leads the infrastructure development.
MOLGENIS tools used: vip hpc catalogue
EHEN
2020 - 2025
The European Human Exposome Network combines nine research projects funded under Horizon 2020, the EU Framework Programme for Research and Innovation: EXPANSE / EQUAL-LIFE / LONGITOOLS ATHLETE / EXIMIOUS / HEDIMED HEAP / REMEDIA / EPHOR. Together, they represent 106 M€ funding from the EU over 5 years. The Human Exposome is the study of how elements we are exposed to via our diet, lifestyle and the environment we live and work in, affect our health. MOLGENIS participated in ATHLETE and LongITools and provided the integrated catalogue for the network.
MOLGENIS tools used: catalogue
ATHLETE
2020 - 2025
ATHLETE (Advancing Tools for Human Early Lifecourse Exposome Research and Translation) is a European-funded project that aims to better understand and prevent health effects of numerous environmental hazards and their mixtures, starting from the earliest stages of life. The project aims to develop a human exposome toolbox that can be used to evaluate the effects of a large number of environmental exposures in individuals, as well as in communities, in order to design policies and interventions to prevent or reduce their health impact. MOLGENIS lead the data infrastructure work package, with focus on the data and harmonisation catalogue.
MOLGENIS tools used: catalogue armadillo
SKIN-ERN
2019 - now
SKIN ERN is the European Reference Network for rare, complex and undiagnosed skin disorders in children and adults. Most of them are exclusively cutaneous/sub-cutaneous and often present a severe prognosis, because of the intensity of the cutaneous/mucosal involvement, the risk of cancer for some of them, or the frequent multisystemic involvement directly or secondary to skin damages. MOLGENIS delivers on their patient registry
MOLGENIS tools used: catalogue registry
ReCONNET-ERN
2019 - now
CRANIO ERN is the European Reference Network for Connective Tissue and Musculoskeletal Diseases. MOLGENIS delivers on their patient registry (planned).
MOLGENIS tools used: catalogue registry
ITHACA-ERN
2019 - now
ITHACA is the European Reference Network for Rare Malformation Syndromes, Intellectual and Other Neurodevelopmental Disorders. MOLGENIS delivers on their patient registry
MOLGENIS tools used: catalogue armadillo
GENTURIS-ERN
2019 - now
GENTURIS ERN is the European Reference Network for all patients with one of the rare genetic tumour risk syndromes (genturis). The patients with rare genetic tumour risk syndromes are at very high hereditary risk of developing multiple tumours, which are often located in multiple organ systems. In case they are diagnosed with cancer they may need different treatment and follow-up as compared to non-hereditary cancers. The lifetime risk of cancer can be as high as 100%. MOLGENIS delivers on their patient registry
MOLGENIS tools used: catalogue armadillo
EUCAN-connect
2019 - 2024
EUCAN-Connect brings together science from Europe and Canada to improve the quality of health care through a more efficient use of data. The project aims to promote collaboration and multidisciplinary research in high-value cohort and molecular data on a large scale. As a result statistical power will improve and new discoveries are being facilitated. These discoveries will impact human life course and facilitate the translation of the data into personalized diagnostics, treatment and prevention policies. What is special is that this project focussed on the infrastructure of series of other projects, notably lifecycle, athlete, longitools and united developers of MOLGENIS catalogue, Maelstrom catalogue and DataSHIELD federated analysis, greatly hardening their tools for upscaling. MOLGENIS team lead the consortium and participated in all its tasks.
MOLGENIS tools used: catalogue armadillo
CRANIO-ERN
2019 - now
CRANIO ERN is the European Reference Network for rare and/or complex craniofacial anomalies and ear, nose and throat (ENT) disorders. Most of them are exclusively cutaneous/sub-cutaneous and often present a severe prognosis, because of the intensity of the cutaneous/mucosal involvement, the risk of cancer for some of them, or the frequent multisystemic involvement directly or secondary to skin damages. MOLGENIS delivers on their patient registry
MOLGENIS tools used: catalogue registry
ConcePTION
2019 - 2024
ConcePTION aimed establish a trusted ecosystem that can efficiently, systematically, and in an ethically responsible manner, generate and disseminate reliable evidence-based information regarding effects of medications used during pregnancy and breastfeeding to women and their healthcare providers. This will be achieved by generating, cataloguing, linking, collecting and analysing data from pharmacovigilance, modelling, routine healthcare, breastmilk samples through a large network. MOLGENIS team delivered ConcepTION catalogue.
MOLGENIS tools used: catalogue
CINECA
2019 - 2023
The CINECA project (EU Horizon 825775) aims to establish a common infrastructure for federated data analysis across international human cohorts, particularly in Europe, Canada, and Africa, to advance research on common diseases. It focuses on creating a virtual cohort of 1.4 million individuals from population, longitudinal, and disease studies, enabling federated analyses in the cloud while adhering to ethical and legal standards. The MOLGENIS team contributed to FAIR standards, in collaboration with MOLGENIS catalogue, and implementing a reference pipeline for rare disease, what later would become MOLGENIS VIP.
MOLGENIS tools used: vip hpc catalogue
VKGL
2018 - now
MOLGENIS helps the Dutch Society of Genome diagnostics Laboratories (Vereniging Klinisch Genetische Laboratoriumdiagnostiek, VKGL) with data sharing in particular via the variant sharing registry.
MOLGENIS tools used: registry
Solve-RD
2018 - 2022
The Solve-RD project brings together clinicians, scientists, and patient representatives from 51 institutes spanning 15 countries to collaborate on genetically diagnosing (“solving”) rare diseases (RDs). The project aims to significantly increase the diagnostic success rate by co-analyzing data from thousands of RD cases, including phenotypes, pedigrees, exome/genome sequencing, and multiomics data. The MOLGENIS team lead the ‘analytical sandbox’ and co-lead the work to deliver an interconnected data infrastructure to support large-scale rare disease research.This infrastructure enables users to store, find, connect, and analyze data and metadata in a collaborative manner. Pseudonymized phenotypic and raw experimental data are submitted to the RD-Connect Genome-Phenome Analysis Platform and processed through standardized pipelines. Resulting files and novel produced omics data are sent to the European Genome-Phenome Archive, which adds unique file identifiers and provides long-term storage and controlled access services. MOLGENIS “RD3” and Café Variome “ Discovery Nexus” connect data and metadata and offer discovery services, and secure cloud-based “Sandboxes” support multiparty data analysis. This successfully deployed and useful infrastructure design provides a blueprint for other projects that need to analyze large amounts of heterogeneous data.
MOLGENIS tools used: catalogue hpc
FAIR Genomes
2018 - now
The FAIR genomes project was initially a Dutch national ZONMW funded national coordination action to unite currently fragmented guidelines & tools to increase ‘FAIR’-ness of DNA data - Findability, Accessibility, Interoperability and Reusability - uniting work from all types of DNA laboratories (rare disease, cancer, research, etc), patients/participants organisations, and has extensive collaborations with (inter)national initiatives. Amongst relevant outputs is NGS semantic metadata data schema that found its way into other projects such as GDI. Read more on the model in van der Velde et al (2022) and the background in Belien et al. (2022). MOLGENIS lead the FAIR genomes project (Prof. Morris Swertz). Now FAIR genomes lives on as a national collaboration.
MOLGENIS tools used: platform
LifeCycle
2017 - 2022
The EU Child Cohort Network, established by the Horizon2020-funded LifeCycle Project (733206), brought together nineteen pregnancy and childhood cohorts, together including more than 250,000 children and their parents. A large set of variables has been harmonised and standardized across these cohorts. The harmonized data are kept within each institution and can be accessed by external researchers through a shared federated data analysis platform using the R-based platform DataSHIELD, which takes relevant national and international data regulations into account, and open access catalogue, both of which were operated by MOLGENIS team.
MOLGENIS tools used: catalogue armadillo
Lifelines
2014 - now
Lifelines is the largest biobank and population cohort study of the Netherlands. that includes over 167,000 participants (10%) from the northern population of the Netherlands. Lifelines includes participants from three generations, who are followed with a lifespan perspective, to obtain insight into healthy ageing. MOLGENIS delivers on their data catalogue including request feature and provides large-scale data access via MOLGENIS high performance compute cluster.
MOLGENIS tools used: catalogue hpc
RD-connect
2012 - 2018
The RD-Connect Project was a multidisciplinary project that united partners from the EU and beyond to create an integrated global infrastructure for Rare Disease research.
MOLGENIS tools used: hpc
UMCG-CBCH
2012 - now
UMCG Cohort and Biobank Coordination Hub (CBCH) serves as a central facilitator and linking pin for all UMCG cohort and biobank activities. We bring together a community of researchers and clinicians, and provide an excellent infrastructure to drive new discoveries. Through our network we are able to connect researchers to the right samples, data, people and knowledge. MOLGENIS contributes through UMCG Research Data Catalogue. Researchers inside and outside the UMCG can use the Research Data Catalogue to search for sample and data collections relevant for their research. You can use the metadata-catalogue to filter on, for example, age groups, data types and available data, such as: lab results, medication and lifestyle. Besides available samples and data, each individual profile page shows the cohort design, contributors, subcohorts, and collection events.
MOLGENIS tools used: catalogue
BBMRI-ERIC
2012 - now
BBMRI-ERIC is a European research infrastructure for biobanking. BBMRI brings together all the main players from the biobanking field – researchers, biobankers, industry, and patients – to boost biomedical research. To that end, BBMRI offer quality management services, support with ethical, legal and societal issues, and a number of online tools and software solutions for biobankers and researchers. Ultimately, our goal is to make new treatments possible. MOLGENIS co-leads BBMRI services for IT and leads BBMRI Directory, the broad catalogue of our biobanks with aggregated information on EU biobank collections. You can browse and filter by country, sample type, quality marks, ICD-10 and more.
MOLGENIS tools used: registry vip hpc
GoNL
2010 - 2015
The Genome of the Netherlands (GoNL) was in its time the largest national Genome sequencing project, funded via the Netherlands Biobanking and Biomolecular Research Infrastructure (BBMRI-NL). By sequencing the genomes of 250 couples and their offspring (the trio’s), this project will map genetic variation in the Netherlands. MOLGENIS co-lead the vast data infrastructure necessary to process all these genome data.
MOLGENIS tools used: hpc
GEN2PHEN
2008 - 2013
The GEN2PHEN project aims to unify human and model organism genetic variation databases towards increasingly holistic views into Genotype-To-Phenotype (G2P) data, and to link this system into other biomedical knowledge sources via genome browser functionality. MOLGENIS contributed to data standards and federated search, in particular patient/mutation databases and Observ-OM standard. GEN2PHEN is made possible by EU Framework VII grant 200754.
MOLGENIS tools used: platform