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Trans eQTL paper by Westra et al. in Nature Genetics

Systematic identification of trans eQTLs as putative drivers of known disease associations, Westra et al. Harm-Jan Westra, … Alexandra Zhernakova, Daria V Zhernakova, … Juha Karjalainen, Sebo Withoff, … Yang Li, Ritsert C Jansen, … Lude Franke, of Dept of Genetics, UMCG, Groningen Published in Nature Genetics online: 08 September 2013 Lude Franke and colleagues report the results of a large expression QTL study performed on peripheral blood samples from 5,311 individuals. They identify trans-eQTL effects for 103 independent loci that were previously associated with complex traits at genome-wide significance, suggesting that this approach can provide insights into the downstream effects of many trait-associated variants.

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VENI grant for Yang Li

Dr. Yang Li, a postdoc working in the Wijmenga group, has been awarded an NWO VENI grant (€250,000) to perform systems genetics analyses on metabolic fluxes using yeast as a model system. Genetic analyses on multiple molecular levels can provide insight into how a genotype relates to a phenotype. She will use this approach to look for heritable causes of metabolite flow rate (flux) through metabolic pathways. See her homepage

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Genome of the Netherlands, Eur J Hum Genet, 2013

The Dept of Genetics (UMCG, Groningen, NL) is the coordinator, and the Genomics Coordination Center (GCC) is the data stewardship center, for all GoNL data (500 TB) generated by the Dutch BBMRI-NL national consortium. We coordinated the analyses; managed the project; hosted raw, intermediate and result data; and developed and now run all the necessary computing 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 is available as a service from the GCC. See: Boomsma DI, Wijmenga C, Slagboom EP, Swertz MA, et al

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WormQTL, Nucleic Acid Research, 2013

The GCC was the data integration center for the EU-PANACEA consortium. We developed their data integration tools and hosted the data and computing (together with GBIC). The resulting WormQTL web portal for integrating multi-omics QTL data is popular in the worm community and is currently being cloned by other research communities working on plants and rodents. The platform can be downloaded independently and was published in Bioinformatics (Arends D, van der Velde KJ, … Swertz MA (2012) xQTL workbench: a scalable web environment for multi-level QTL analysis). See: Snoek LB, Van der Velde KJ, … Swertz MA (2013) WormQTL–public archive and

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MOLGENIS toolkit, Bioinformatics, 2012

The GCC has developed >20 database applications for many research projects. All these databases have been developed using a common platform and as open source software to maximize their use and the development of new features. This package is known as the ‘Molecular Genetics Information System’ (MOLGENIS) and is currently installed in Leicester (GWAS central), the European Bioinformatics Center (phenoflow), and the Finnish Institute for Molecular Medicine (FIMM, Findis and Nordic GWAS databases). GCC uses MOLGENIS to develop new, custom-made databases for its collaborators and clients. See: Swertz MA, Dijkstra M, et al (2010) The MOLGENIS toolkit: rapid prototyping of biosoftware

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Observ-OM, Human Mutation, 2013

The 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. The GCC led the development of the standard, and bridges teams from GEN2PHEN, EU-BIOSHARE, P3G, and BBMRI. This model was highly successful and is being adopted for other projects, including Vario-ML (published by J Muilu et al), BBMRI, CTMM, LifeLines, and BioMedBridges biobank catalogues. See: Adamusiak T, Parkinson H, Muilu J, … 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.

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