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Genomics Coordination Center Groningen

Contact Details

University Medical Center Groningen & University of Groningen

p/a Dept. of Genetics CB50 University Medical Center Groningen P.O. Box 30001 9700 RB GRONINGEN

Prof. M.A. Swertz

0031 (0)50 3617100

Hotel Description

The Genomics Coordination Center Groningen is a rapidly growing bioinformatics hotel of 15 researchers, programmers and system managers headed by Dr. Morris Swertz. Research, consultancy and services include:
• Catalogues and integrative analysis portals that are developed and hosted for cataloguing and access to biobank datasets, large model-organism consortia, patient registries, multi-omics data;
• ‘Big Data analysis infrastructure’ to develop and run large analysis pipelines for next generation sequencing, GWAS imputation, and multi-omics QTL analysis;
• Data stewardship and project/consortium analysis support including BBMRI-NL Genome of the Netherlands (a whole genome sequencing panel of 769 Dutch), BBMRI-NL imputation (>20.000 samples), LifeLines biobank (165.000 individuals) and WormQTL (> 30 set multi-omics data integration).

In the past five years GCC is organized as a data coordination hub that combines the expertise’s of:
• UMCG Dept. of Genetics providing bioinformatics for next generation sequencing (Prof. C. Wijmenga);
• RuG Centre for Information Technology towards ‘petabyte’ scale storage and compute infrastructure;
• UMCG department of epidemiology providing support to large epidemiological studies (Prof. R. Stolk);
• RUG department of analytical biochemistry and proteomics (Dr. P. Horvatovich);
• Groningen Bioinformatics Center developing methods for high-throughput data (Prof. R.C. Jansen).

With sophisticated data management and processing environment in place (with respect to both hardware and software) and with strong collaborating partners in our network we aim to develop further our strong domain specific tool library and workflows and most importantly combine these and realize multiomics (multidomain) large scale projects for example multi-level NGS, proteogenomics combined with imaging, and realize translational research towards personalized genomics and diagnostics. Therefore the Genomics Coordination Center is (co-)leading in several national and international infrastructure development and standardization projects (see below). As a principle, all GCC tools are freely shared in the open source MOLGENIS software project for wider life sciences community to build on (http://www.github.com/molgenis).

  • Next-generation whole genome sequencing, whole exome sequencing, custom capture design, RNA sequencing, genome wide association studies
  • Genome wide linkage studies, GWAS imputation, QTL analysis, multi-omics experiments
  • Applied methylation, gene expression, proteomics, metabolomics
  • Biobanking
  • Genetics
  • xQTLs
  • Natural populations (human)
  • Experimental populations (plant, mouse, worm, wasp)
  • Gene expression

Expertise and Track Record

Unique capabilities include:
• Host to largest genomics research project in NL (GoNL)
• Portable analysis infrastructure to local servers, computer clusters and national BigGrid
• Leading biobank catalogue working groups of BBMRI-NL and BBMRI-EU
• Most used multi-omics database platform in NL (>20 installations)
• Part of world-leading P3G and BioSHARE data integration and harmonization project

• BBMRI.NL – Project lead of BBMRI-NL Bioinformatics analysis (GoNL, NGS, imputation)
• LifeLines – Developing IT research infrastructure for 30yr/165.000 people cohort study
• EU-PANACEA – Complete data management for FP7 EU model organism project

  • Fehrmann RS, Jansen RC, et al, Franke L. (2011) Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA. PLoS Genet 7(8):e1002197 GCC collaborates on daily basis with experts from different research Depts such as Genetics and the Groningen to develop novel experimental designs and analytical methods. One of the spearheads are multi-omics QTL analyses (transcriptomics, epigenetics, proteomics, metabolomics) in human natural populations and experimental model organism populations, such as the example paper cited here. In collaboration GCC takes such new methods and implements suitable software infrastructure to apply these methods routinely.
  • Swertz MA, Dijkstra M, et al (2010) The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button. BMC Bioinformatics. GCC has developed >20 database applications for many research projects. All these database are developed using a common platform and as open source to maximize reuse and development of new features. This package is known as the ‘Molecular Genetics Information System’ (MOLGENIS) and is currently installed amongst others in Leicester (gwas central), European Bioinformatics Center (phenoflow), Finnish institute for molecular medicine (FIMM, Findis and Nordic gwas database). GCC regularly uses it to develop new custom databases for its collaborators and customers.
  • Adamusiak T, Parkinson H, Muilu J, et al, Swertz MA (2012) Observ-OM and Observ-TAB: Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information. Hum Mutat. 33(5):867-73. GCC was invited to join the EU-GEN2PHEN consortium on a mission to develop a data exchange model and format for complex phenotype and genotype data. GCC lead the development of the standard, and bridges teams from GEN2PHEN, EU-BIOSHARE, P3G, BBMRI. This model is now highly successful and being adopted in other projects including Vario-ML (published by Muilu et al), and BBMRI, CTMM, LifeLines, BioMedBridges biobank catalogues.
  • Snoek LB, Van der Velde KJ, et al, Swertz MA (2013) WormQTL--public archive and analysis web portal for natural variation data in Caenorhabditis spp. Nucleic Acids Research 41. GCC was data integration center for EU-PANACEA consortium, developed their data integration tools and hosted data and compute (together with GBIC). The resulting WormQTL web portal for integration of multi-omics QTL data is popular in the worm community and is currently being cloned by communities in plants and rodents. The platform can be downloaded independently, and was published in Bioinformatics (Arends D, van der Velde, et al, Swertz MA (2012) xQTL workbench: a scalable web environment for multi-level QTL analysis).
  • Boomsma DI, Wijmenga C, Slagboom EP, Swertz MA, et al (2013) The Genome of the Netherlands: design, and project goals. Eur J Hum Genet. GCC is data stewardship center for all GoNL data (500 Tb) of the national BBMRI-NL consortium. We coordinated the analyses, realised the project management, host raw, intermediate and result data and developed and run the necessary compute pipelines (together with CIT, BigGrid, eBioGrid, NBIC). The resulting state-of-the-art NGS and imputation pipeline can be easily ported to new computer clusters and grids and are available as service.

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GCC is strongly rooted in national and international including BBMRI-NL, NFU Data4Lifesciences, DTL, BBMRI-ERIC, RD-connect, CORBEL, EXCELERATE, European Bioinformatics Institute. 

IT advisor to the BBMRI-NL steering committee (open-ended); PI of the NBIC Biobanking taskforces in BBMRI-NL and BioAssist (2010 – 2013);PI of the BBMRI-NL national ‘big data’ bioinformatics infrastructure project (2009-2014);PI of the BBMRI-NL national biobank catalogues project (2013-2016);Lead of the Dutch biobank catalogue and the EU-BioMedBridges catalogue workgroup (open-ended);co-PI of the Genome of the Netherlands whole genome sequencing project (2009-2014);co-PI of the Biobank data harmonization work-packages in EU-BioSHARE (2010 – 2014);co-PI LifeLines genomics research IT and biobank catalogue (2008-2014);Partner in Target big data infrastructure project (2008 – 2014);Partner in eBioGrid the BigGrid project that bridges life sciences (2009-2012);Partner Top Institute Food & Nutrition as data steward and host of biomarker research (2010-2014);Partner in CTMM/Translational IT (TraIT) for catalogue, NGS pipelines and analysis portal (2010-2014);Partner in EU-BioMedBridges for biobank data standards and personalized medicine (2011 – 2015);Partner in EU-PANACEA hosting all data integration in EU-PANACEA (C. elegans, 2008 – 2012);Database host for international rare disease databases (deb-central.org, chd7.org);Associate partner in EU-GEN2PHEN responsible for pheno/genotype data standards (2008-2013);Associate partner in EU-CASIMIR responsible for database standards in mouse (2007 – 2010);Associate partner in COST-EU-SYSGENET systems genetics on IT infrastructure (mouse, 2008 – 2012);Associate partner in Centre for Genome Diagnostics (2011-2013)

Hotel Characteristics

  • GCC is a growing team of 25 researchers, programmers and system managers headed by Professor Morris Swertz.