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Daniel Stekhoven
Clinical Bioinformatics Unit
ETH Zurich
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What do we do?

The Clinical Bioinformatics Unit of NEXUS Personalized Health Technologies – a technology platform of ETH Zurich – offers customized bioinformatics and statistics services for analyses and projects in the field of biomedical research. We maintain close collaborations with hospitals in Zurich and Basel, introducing and enabling state-of-the-art multi-omics data analyses. Based on a fee-for-service model, our aim is to meet individual project goals and establish close interaction with our customers. Our ambition is to help the end user understand what the results mean. However, our services are not limited to analysis alone. We also offer support in writing and reviewing manuscript texts, as well as delivery of manuscript-ready tables and figures.

Highlights 2016

Building on its previous successes over the course of 2015, CBU’s second year went well. The newly launched Molecular Tumor Board Zurich shaped the opinion of molecular cancer diagnostics in clinics both in Zurich and in Basel towards comprehensive analysis – with, on the one hand, comprehensive sequencing using WES and WGS for profiling tumors, and on the other hand, the comprehensive mining of public databases, clinical trial registries and research literature. While comprehensive sequencing and variant calling still have a more fundamental research characteristic, comprehensive mining is directly relevant for patients in the clinics today.
Together with the University of Zurich and the University Hospital of Zurich we were involved in a project which established the first in vivo mouse model for ccRCC, accurately capitulating the cellular and molecular features of clear cell renal cell carcinoma (ccRCC). This project combined RNA-Seq, WES and public data from TCGA, and we showed how well the mouse model represented human data. The project was finished and submitted at the end of 2016.
CBU planned and performed a workshop on the topic of Clinical Bioinformatics as a Service as part of the annual ECCB 2016 in Den Haag. The workshop was conceived together with Niko Beerenwinkel (ETHZ), Wolfgang Huber (EMBL) and Simon Tavaré (CRUK). There was great interest in the topics and a large common ground between European core facilities providing bioinformatics in a clinical setting was identified. Given this success we are intending to organize another workshop covering the same topic soon.

Main Publications 2016

  • Thurnherr T, Franziska Singer F, Stekhoven DJ, Beerenwinkel N. Genomic variant annotation workflow for clinical applications. F1000Research 2016;5:1963
  • Lukamowicz-Rajska M, Mittmann C, Prummer M, Zhong Q, Bedke J, Hennenlotter J, et al. MiR-99b-5p expression and response to tyrosine kinase inhibitor treatment in clear cell renal cell carcinoma patients. Oncotarget 2016 Oct 12. doi: 10.18632/oncotarget.12618

Our research topics: