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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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2 VIDI grants awarded

May 2014: NWO (Netherlands Organisation for Scientific Research) has awarded VIDI grants to Jingyuan Fu for her project on “Understanding the causal relationships between the host genome, microbiota and lipids” and to Lude Franke for his project on “A novel approach to understanding how DNA variants cause disease”. (1) Understanding the causal relationships between the host genome, microbiota and lipids - Dr. Jingyuan Fu Lipid composition varies widely between human individuals and is associated with many diseases. Numerous studies have shown that the lipid composition can be affected by an individual’s genetic make-up and intestinal microbial composition. Over millions of years, microbes and humans have formed a truly symbiotic relationship.

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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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