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Dutch genome deciphered

The family tree of the Dutch people has been deciphered by researchers at 5 Dutch universities under the leadership of Prof. Cisca Wijmenga of the UMCG in Groningen. The early history of the Dutch can be re-written and diseases can be better predicted. The research is described in a Nature Genetics article published yesterday. `Paul de Bakker, Cisca Wijmenga and colleagues report on The Genome of the Netherlands Project, including whole-genome sequencing of 769 individuals of Dutch ancestry from 250 parent-offspring families and construction of a phased haplotype map. Their intermediate-coverage population sequencing data set provides a complementary resource to

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GUT paper on coeliac disease in F1000Prime

A recent paper by the Wijmenga group has been selected for F1000Prime. It was recommended as being of special significance in its field by Faculty Member Piero Portincasa. “Improving coeliac disease risk prediction by testing non-HLA variants additional to HLA variants” by Jihane Romanos, …Vinod Kumar, Gosia Trynka, Lude Franke, Agata Szperl, Javier Gutierrez-Achury, Cleo C van Diemen, Roan Kanninga, Soesma A Jankipersadsing, … Cisca Wijmenga, and the PreventCD Group. Published in Gut, 2014 Mar;63(3):415-22. Open access full text. Epub 2013 May 23. “In this paper, the authors highlight the importance of a more comprehensive genetic test for the diagnosis of

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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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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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