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Swertz Group – Big data bioinformatics

The Genomics Coordination Center (GCC) Groningen is a rapidly growing bioinformatics hotel of 25 researchers, programmers and system managers, headed by Prof. Morris Swertz.  In the past five years the GCC has become a data coordination hub that combines the expertise of the UMCG’s Dept of Genetics (host) with providing bioinformatics for next generation sequencing (Prof. C. Wijmenga), the University of Groningen’s Centre for Information Technology working towards  ‘petabyte’-scale storage and compute infrastructure, the University’s Dept of Analytical Biochemistry and Proteomics (Dr. P. Horvatovich) and the Groningen Bioinformatics Center for developing methods for high-throughput data (Prof. R.C. Jansen).

May 2016: Morris Swertz was awarded an NWO-VIDI grant for a proposal on “Scalable ‘big data’ methods towards personalized genome diagnostics”. New NGS techniques can now measure all the DNA variations in an individual in one experiment. Unfortunately, this is not yet leading to more diagnoses bacause genetic labs are drowning in the amount of data produced. Previously, tests were performed only on single genes. This VIDI project will develop personalized whole genome diagnostics (patient-oriented techniques to find damaging mutations more quickly and better).

Research and services

  • Big Data Analysis Infrastructure with the ability to develop and run large-scale analysis pipelines for next generation sequencing, whole genome, exome, RNA, GWAS imputation, and multi-omics QTL analysis towards multi-omics phenotype analysis.
  • Big Data Integration Infrastructure with the ability to rapidly create integrative database portals that are developed and hosted for cataloguing and providing access to biobank datasets, clinical datasets, large model-organism consortia, patient registries, multi-omics data, translational medicine sets, towards personalized medicine (>40 projects).
  • Big Data Stewardship and Project/Consortium Hosting, including analysis protocols for BBMRI-NL’s Genome of the Netherlands (a whole genome sequencing panel of 769 Dutch individuals), BBMRI-NL’s imputation set (>20,000 samples), LifeLines biobank (165,000 individuals) and WormQTL (integrating >30 sets of multi-omics data) on a mission to create the biggest biomedical research resource in the Netherlands.

GCC’s unique capabilities

  • Hosts largest genomics research project in NL, Genome of the Netherlands
  • Hosts several international databases for rare diseases (e.g. deb-central.org; chd7.org)
  • Target/CIT partner 2 petabyte high-performance storage, 1000 core UMCG clusters & 3000 core University of Groningen clusters
  • Portable analysis infrastructure, portable over local servers, computer clusters and national BigGrid
  • Leading national and international biobank catalogue working groups of BBMRI-NL and BBMRI-EU
  • Host to the most used multi-omics database platform in the Netherlands (MOLGENIS >20 installations)
  • Part of leading-edge data integration and harmonization projects for P3G, BioSHARE and BioMedBridges

Collaborations

  • BBMRI
  • BBMRI-ERIC
  • BBMRI-NL catalogue group (Hs)
  • BigGrid (info)
  • CORBEL, EU-BioMedBridges consortium (all)
  • DTL/DISC
  • EGI Competence Centre
  • ERCET European Research Centre for Exascale Technology
  • EU-BioSHARE consoritum (Hs)
  • EU-CASIMIR consortium (Mm)
  • EU-GEN2PHEN consortium (Hs)
  • EU-PANACEA consortium (Ce)
  • Learning from Nature (At)
  • LifeLines cohort study (Hs)
  • NBIC/BioAssist consortium (bioinfo)
  • NFU data 4 life sciences
  • NL Brassica Nutr. consortium (At)
  • Rd-Connect (EU)
  • Target + CIT (info)
  • TIFN Top Institute Food and Nutrition (Hs)
  • VKGL data sharing WG

Morris Swertz is also:

  • IT advisor to the BBMRI-NL steering committee (open-ended)
  • Lead of the Dutch biobank catalogue and the EU-BioMedBridges catalogue working group (open-ended)

Key publications by GCC

here

Swertz Group – Big data bioinformatics website

Team members

Associated projects