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VIDI grants for Sasha Zhernakova and Iris Jonkers

May 2017 – Departmental researchers Dr. Iris Jonkers and Dr. Sasha Zhernakova have both been awarded 2017 Vidi grants! These awards from the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO – The Netherlands Organisation for Scientific Research) provide €800,000 for excellent original research programs that can be used to fund up to five years of research. Dr. Jonkers will be using newly developed techniques to identify which single nucleotide polymorphisms truly play a causal role in immune mediated disease using celiac disease as a model. Dr. Zhernakova will characterize the breast milk microbiome and the role it plays in baby health in the LifeLines Next cohort of

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BBMRI-NL2.0 awarded €9.8 million

BBMRI-NL2.0: building on the Dutch biobank On Tuesday 1st July, BBMRI-NL2.0 was awarded €9.8 million as part of the National Roadmap of Large Research Infrastructures. It is one of six facilities receiving a grant from NWO. The award was announced during a ceremony at Leiden University Medical Centre. Professor Cisca Wijmenga (UMCG) is director of this large-scale biobanking project. (BBMRI stands for Biobanking and Biomolecular Research Infrastructure) BBMRI-NL will join forces with EPI2 and CTMM-TraIT in July 2014  │   BBMRI-NL embarks upon its second phase: BBMRI-NL2.0 The new endeavour will comprise BBMRI-NL and all the biobanks connected with it.

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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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Enlighten Your Research Global Award: Virtual Machine Images for Life Science Research

Denver (USA), 18 November 2013 – One of the four prestigious “Enlighten Your Research Global” awards has been given to an idea developed by an ELIXIR working group for the sharing of virtual machines over research and education networks. The concept, which was developed from an ELIXIR pilot action, makes it much easier for scientists in many different countries to find meaning in massive volumes of biomedical data in a secure manner, such as 1000 Genomes, Genome of the Netherlands, and GWAS/epidemiological data in the BBMRI biobank network. The working group is a collaboration of institutions involved in the ICT

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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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