The SYSCID consortium brings together top-level European and EU-associated research teams with a strong track record in quantitative and mechanistic studies of immune-related disorders using systems-level and/or OMICs approaches (including leading roles in IHEC, ICGC, TwinsUK and Meta-HIT).
Kiel University with University Hospital Schleswig Holstein
Philip Rosenstiel (SYSCID coordinator), Andre Franke, Stefan Schreiber, Konrad Aden
Inflammation research is one of the three major foci of the Medical Faculty of the Christian-Albrechts-University Kiel (CAU). The Institute of Clinical Molecular Biology (ICMB) at the University Kiel is a recognized leader in translational genomic research in inflammatory barrier diseases. Main interests are in the complex interactions between human barrier organs and the environment in health and disease. This includes the generation of genetic risk maps and biomarker detection using cohort-based approaches (applicant AF) as well as research on epigenetic/transcriptomal alterations and their validation in cell biological experiments in vitro, in standardized mouse models in vivo (Applicant PR). Ultimately, we aim to translate the findings into the human diagnostic or therapeutic experiment (Applicant SS). The institute operates the largest university based next generation sequencing centre in Germany, commands a high throughput genotyping facility and is partner in the popgen biobank program with more than 80.000 patients in Schleswig-Holstein under long-term follow up.Address
Institute of Clinical Molecular Biology (IKMB)
University Hospital Schleswig-Holstein
King’s College London
Massimo Mangino, Timothy Spector
The TwinsUK is based at the Department of Twin Research and Genetic Epidemiology at King’s College, one of the world's leading research and teaching universities based in the heart of London. The study, started in 1992, is probably the most phenotypically and genomically detailed population resource in the world. It comprises about 12,000 adult twins with thousands of clinical phenotypes, GWAS, WGS, methylation, expression, metabolomics, and glycomics information which can now be combined with new immune and microbiome phenotypes. The extensive collaborative network and publications of the department and Twin resource (over 70 per year) prove the track record of both the environment and the principal investigator’s team. In particular, in the field relating to this project, we have produced novel twin data showing multiple genetic associations with canonical immune traits of all major immune cell subsets, and uncovered novel insights into the genetic control for regulatory T cells (Roederer et al. Cell 2015, Mangino et al. Nat. Comm. 2017). In addition the department has a track record in developing and allowing research access to novel omics data using the twin resource.
Basic research in life sciences is VIB’s raison d’être. On the one hand, we are pushing the boundaries of what we know about molecular mechanisms and how they rule living organisms such as human beings, animals, plants and microorganisms. On the other, we are creating tangible results for the benefit of society. Based on a close partnership with five Flemish universities – Ghent University, KU Leuven, University of Antwerp, Vrije Universiteit Brussel and Hasselt University – and supported by a solid funding program, VIB unites the expertise of 75 research groups in a single institute. VIB’s technology transfer activities translate research results into new economic ventures which, in time, lead to new products that can be used in medicine, agriculture and other applications. VIB also engages actively in the public debate on biotechnology by developing and disseminating a wide range of science-based information about all aspects of biotechnology.
KU Leuven (University of Leuven) is a leading European research university dedicated to excellent research, education and service to society. It is a founding member of the League of European Research Universities and has a strong European and international orientation. Its sizeable academic staff conducts basic and applied research in a comprehensive range of disciplines. University Hospitals Leuven, its network of research hospitals, provides high-quality healthcare and develops new therapeutic and diagnostic insights with an emphasis on translational research. The university welcomes more than 57,000 students from over 140 countries. Its doctoral schools organise internationally oriented PhD programmes for over 4,500 doctoral students.Address
The Chancellor, Masters and Scholars of the University of Cambridge
The University of Cambridge is one of the oldest universities and leading academic centres world-wide. As an institution it is committed to achieving excellence in research, and to ensuring that its research output contributes to the well-being of society. The Department of Medicine provides high quality research, teaching and patient care. It is the largest Department in the School of Clinical Medicine, and is comprised of 11 divisions, each aligned to a clinical specialty within the NHS. It houses 25 professors, and over 750 directly employed and affiliated members of staff and students. The research interests of the 11 divisions are necessarily broad, although many groups work in the general area of immunity, inflammation and infection. The Department aims to perform high quality basic scientific as well as translational research, and to do this maximizes synergies with other scientists on the Cambridge Biomedical Campus and throughout the region. The research is focused on areas of relevance to human disease, to understand the mechanisms of disease and to deliver novel therapeutic approaches to the clinic.
Université de Liège
The SYSCID research will be carried out by the team of Prof Michel Georges in collaboration with Prof Edouard Louis at the GIGA research institute of the University of Liège. The GIGA interdisciplinary research institute, which was founded in 2007, is committed to excellence in the biomedical sciences. It is located adjacent to the CHU-Liège university hospital and is comprised of some 583 members originating from > 40 countries and affiliated to six faculties who are actively conducting research in the fields of neuroscience, oncology, infection-inflammation-immunity, cardiovascular sciences, molecular pathology, medical genomics and in silico medicine. GIGA operates nine core facilities that provide cost effective access to state- of-the-art technologies in genomics, proteomics, in vivo and in vitro imaging, flow cytometry, immuno-histochemistry, viral vector design and production, and rodent and zebrafish model systems. Since its inception, GIGA scientists have produced > 1,000 publications in peer reviewed journals, now including ∼8 % in journals with IF ≥ 10. The GIGA community has graduated > 200 PhD students, filed > 140 patents and spawned/hosted >60 spin-off and start-up companies in dedicated facilities. The group of Prof Michel Georges is one of the leading research groups in the field of genetics and genomics. Through the group’s participation in the International Inflammatory Bowel Disease Genetics Consortium, they have contributed to the comprehensive investigation of GWAS disease loci in Crohn’s disease and ulcerative colitis.Address
GIGA Research Institute
CHU - B34
Avenue de l’Hôpital, 11
Université de Genève
The laboratory of Prof. Dermitzakis at the University of Geneva is internationally recognized for their expertise in the analysis and interpretation of gene expression data and other cellular phenotypes and will contribute genetic analysis of cellular phenotypes in the project. Prof. Dermitzakis has participated in a number of important international research projects such as HapMap ENCODE, 1000genenomes and GTEx and the EU FP7 grants EuroBATS, SYSCOL, GEUVADIS, BLUEPRINT and DIRECT and had an ERC consolidator grant.
The laboratory has extensive experience and track record in omics data analysis and omics data generation. The participants have direct access to two HiSEQ2000 instruments, soon to be upgraded to HISEQ4000s, and other extensive laboratory facilities. The lab of Prof Dermitzakis has participated in many projects and has generated transcriptome sequence data for more than 15,000 RNA samples over the last 6 years. The laboratory has privileged access to a large computational resource, VITAL- IT.
Comma Soft AG
Comma Soft AG is a software and IT consulting company, founded in 1989 and located in Bonn, Germany. The company belongs to the most successful German innovation drivers at the interface between business and IT. With innovative products, sustainable IT strategy consulting and consistent focus on value propositions, Comma Soft provides IT solutions to numerous small-scale companies and DAX enterprises. The Data Science department at Comma Soft consists of a team of 15 data scientists with a very strong scientific background in computer science, bioinformatics, physics or mathematics. The team strives to develop analytical software that helps domain experts to explore data on their own and to level their expertise with the help of interactive analytical tools. This is achieved by utilizing an in-memory-based data management system developed by Comma Soft, configuration of suitable big data technologies according to the customers’ requirements, and design and implementation of machine learning algorithms and interactive visualizations.Address
Comma Soft AG
Pützchens Chaussee 202
Rheinische Friedrich-Wilhelms-Universität Bonn
Joachim Schultze & Marc Beyer
Basic and translational immunology research is one of the major foci of the Life & Medical Sciences (LIMES) Institute at the Faculty of Mathematics and Natural Sciences at the University of Bonn. The Department for Genomics and Immunoregulation at the LIMES Institute is a recognized leader in transcriptomic and epigenomic research in immunology. Main interest is the integration of complex signals within immune cells resulting in transcriptional and epigenetic reprogramming of immune cells through homeostatic, infectious and environmental cues in health and disease with the aim to translate the findings to novel diagnostic or therapeutic strategies in humans. To this end, the department jointly with the German Center for Neurodegenerative Diseases (DZNE) operates the platform for single-cell genomics and epigenomics (PRECISE) in combination with a flow cytometry unit which allows the integrated analysis of immune cell phenotypes with single-cell transcriptional and epigenetic profiles.
The Department is a partner in the Excellence Cluster “Immunosensation” and several local comprehensive research center initiatives and is linked to major networks on the national and international level including the IHEC epigenomics project DEEP.Address
Rheinische Friedrich-Wilhelms-Universität Bonn
Université du Luxembourg
The Luxembourg Centre for Systems Biomedicine (LCSB) is an interdisciplinary research centre at the University of Luxembourg. It is accelerating biomedical research by closing the link between systems biology and medical research. Collaboration between biologists, medical and computer scientists, physicists, engineers as well as mathematicians is offering new insights in complex systems like cells, organs and organisms. Neurodegenerative diseases like Parkinson’s disease and description of diseases as networks are in the focus of LCSB’s research.
The Bioinformatics Core, led by Dr Reinhard Schneider, is responsible for the efficient data flow between the experimental groups and the theoretical and medical oriented groups. The group focuses on the development of (clinical) data management and storage systems and sets up cost- and time-efficient data analysis pipelines. The group develops new algorithms in various fields including data mining and visualisation to help understand and interpret the data.
Based at the University of Southern Denmark, Inflammation Research is a major focus area at the Institute of Molecular Medicine. Researchers are working internationally with the most recent techniques by using innovative molecular and biomedical technologies to increase the understanding of mechanisms within important chronic inflammatory diseases, and furthermore develop new and more individualized treatments for these diseases.
The department operates between the clinical departments at the Hospitals of Southern Denmark and the basic science departments at the Faculty of Health Science. The close collaboration between university and hospitals in the region has focused on translational research. At the department translational research is not only translation of knowledge into implementation for the individual patient but is also seen as a method of collaboration reaching out to citizens, decision makers, patient organisations and other stakeholders.Address
5230 Odense M
Universität des Saarlandes
As part of the Human and Molecular Biology Center of the Saarland University, the institute of genetics focuses its research on epigenetics of human cells in development and disease. Jörn Walter’s group develops experimental tools and bioinformatic approaches to gain a deeper understanding of the epigenetic control mechanisms in human diseased cells. The institute is one of the core centres of the German epigenome programme DEEP applying cutting edge epigenome technologies including a series of methods to map and decompose rare oxidative DNA-modifications and open chromatin (DNAseI-Seq, ATAC-Seq and NOMe-Seq) RNA-Seq and ChIP-Seq. The group has co-developed a number of computational methods and tools for high-level analysis of complex epigenomics data. Furthermore, sophisticated experimental and mathematical approaches to model the mechanism leading to altered epigenetic programs were developed. The group investigates mechanisms of epigenetic reprogramming during stem cell formation being among the first to show that epigenetic programs encounter a genome wide demethylation during germ stem cell formation and in early embryonic development.
Humanitas University (HUNIMED) is an international higher education institution, established in 2014 and recognized by the Italian Ministry of Education, University and Research. HUNIMED is dedicated to basic and translational research in life sciences. Translational studies are carried out in tight collaboration with the Humanitas Research Hospital, a 750 beds hospital devoted to clinical research mainly in the context of immune-related, neurological, cardiovascular and neoplastic diseases. Research activities are carried out by 350 researchers and physicians, divided into more than 22 research groups.
HUNIMED's mission is also to train globally oriented medical doctors through state-of-the-art interactive teaching methods and close integration with the clinical community at the Humanitas Research Hospital.Address
Via Alessandro Manzoni 113
20089 Cascina Perseghetto
Idryma Iatroviologikon Ereunon Akademias Athinon
Autoimmunity-inflammation and genomics - transcriptomics represent key strategic areas of the BRFAA group which includes investigators based bothin Athens (BRFAA, National and Kapodistrian University of Athens, Medical Schooland Attikon University Hospital) and in Crete (University of Crete, Medical School, University Hospital of Heraklion). The group includes physician scientists (G Bertsias, D Boumpas, P Sidiropoulos) and basic scientists with expertise in immunology (P Verginis) and genomics/pharamacogenomics (D Sanoudou). Both places are centres of excellence in autoimmune rheumatic diseases with well characterized longitudinal patient cohorts/registries and biobanks of patients with systemic lupus erythematosus (SLE), rheumatoid arthritis (RA) and spondyloarthritis (SpA). The established cohorts include over 1.260 SLE patients, 2.780 RA patients, and 890 SpA patients.
Genos Doo Za Vjestacenje I Analizu
Genos Ltd is a research intensive SME located in Zagreb, Croatia, specialized in high-throughput glycoanalysis. Their main competitive edge is the know-how and experience in performing high throughput studies, ranging from analytical chemistry to study design and statistical data analysis. The Scientist magazine ranked Genos as the “Best place to work” for researchers in industry in the world. Since 2015 Genos is member of the National Centre of Excellence in Personalised Healthcare, one of 13 national centres of scientific excellence. Researchers in Genos are pioneering high-throughput glycomics. They performed the first large scale studies of the human plasma glycome (in 2009) and human IgG glycome (in 2011), which were the basis for the subsequent first genome wide association studies of the human glycome and several large clinical studies.
Genos is currently global leader in high-throughput glycomics for clinical and epidemiological studies with over 40,000 samples analysed in the last three years and established collaboration with numerous leading research institutions in Europe, USA, China and Australia.
Working in close cooperation with Genos in SYSCID is the group led by Vlatka Zoldoš from the Faculty of Science of the University of Zagreb.
Eurice European Research and Project Office GmbH
Founded in the year 2000, Eurice - European Research and Project Office GmbH - provides comprehensive support services for the planning, initiation, and implementation of large international collaborative projects. EURICE has been involved in EU-Framework Programmes since FP4 and has been supporting researchers in more than 250 EU funded projects to date. Today, EURICE is among Germany’s largest project management offices, with a dedicated team of 40 staff members with different professional and scientific expertise, such as law, social sciences, medicine, biology, chemistry, communications, or computer sciences.
In addition to classical project management, Eurice helps to develop and implement coherent IP strategies and supports consortia through dissemination, networking, training, and capacity building activities. Thus, Eurice accompanies researchers and innovative companies through the entire life cycle of a project – from the first idea to successful project completion – and beyond.Address
European Research and Project Office GmbH
Science Park 1