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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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Spinoza award for Cisca Wijmenga

At NWO’s Bessensap event on 12th June, it was announced that Cisca Wijmenga is one of four NWO Spinoza prize winners for 2015. The NWO Spinoza prize in brief The NWO Spinoza prize is the highest award in the Netherlands science arena and can be seen as the ‘Dutch Nobel Prize’. Each year, NWO awards Spinoza prizes to three or four researchers working in the Netherlands who, according to international standards, belong at the very top of their scientific field. NWO Spinoza laureates perform ground-breaking research that has a major impact and they are a source of inspiration to younger researchers. The prize winners

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The genetics of coeliac disease

Read an interview with Cisca Wijmenga about some of her work. She “is fascinated by the study of coeliac disease; here, she discusses her close connection to the history of the field, the changes brought about by new sequencing methods and the importance of collaboration”. Read about:   Navigating the non-coding regions of the genome  –  Genome of the Netherlands   —  Non-coding RNA  –  Coeliac disease the facts  –  Genetic risk profiling The project “Coeliac disease: from lincRNAs to disease mechanism (CD-Link)”  is supported by an ERC Advanced Investigator grant. By Josh Gabbatiss. Published courtesy of International Innovation – a leading scientific dissemination service. Link to full

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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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