Department of Bioinformatics – BiGCaT

BiGCaT Science Cafe


Schedule 2019

Date Time Room Presenter Topic Abstract Slides
28 Feb 16:00-17:00 UNS50/4.140a Chris Evelo / Friederike Ehrhart European Joint Programme on Rare Diseases (EJP-RD) Abstract  Slides
14 Mar 16:00-17:00 UNS50/4.140a
04 Apr 16:00-17:00 UNS50/4.140a
18 Apr 16:00-17:00 UNS50/4.140a
02 Mar 16:00-17:00 UNS50/4.140a

Schedule 2018
Schedule 2017
Schedule 2016
Previous schedule

Abstracts

28 Feb 2019 – Prof. Dr. Chris. Evelo / Dr. Friederike Ehrhart

Title: A cross-omics analysis work package in the European Joint Programme on Rare Diseases (EJP-RD)
The day after this talk, February 29, is #RareDiseaseDay (yes, a rare day indeed đŸ˜‰ ). We thought this would be a nice occasion to tell you about the new EJP-RD, a large project that will support research in rare disease aiming to substantially improve diagnosis and treatment. EJP RD is a 5-year project, it has 85 partners in 33 different European and non-European countries and the total budget is about 110M Euro; part of that reserved for calls opened by the project itself. One of the main pillars of this project will develop and test a bioinformatics framework and infrastructure for rare diseases. It will use earlier ELIXIR experiences on FAIR data and BBMRI experiences with private patient data catalogues, and EJP RD was already selected as a new driver project for the Global Alliance for Genomics and Health (GA4GH). After all that data organisation we will apply bioinformatics interoperability approaches for integrative data evaluation. The work package on this latter cross-omics and data integration approach is lead by the Department for Bioinformatics at UM.
Next to tool development, this work will include the following steps:

  • Create disease-specific pathways on a new WikiPathways rare disease portal (see http:///raredisease.wikipathways.org for the first version). This will be done based on database and literature evaluation and in collaboration with existing European expert networks (ERNs), quite a few of these are also active in our MUMC.
  • Evaluate omics and other relevant data-availability on selected rare diseases and perform pathway (enrichment) analysis (likely already improving understanding of disease mechanisms. Omics data types already identified include genomics (largely exomes and single gene variants), transcriptomics and metabolomics.
  • We will combine affected pathways into data and knowledge supported rare disease networks, evaluate these for things like active nodes and make them available on NDEX.
  • Allow extension of these networks with relevant regulatory information (e.g. transcription factors and miRNAs) and where available evaluate data on such regulatory factors.
  • Use the networks to evaluate drug targets and thus come up with ideas for drug repurposing with some special interest in orphan drugs (building on our IMI collaborations).
  • Evaluate the network for intrinsic lifestyle factors (e.g. micronutrients present in or known to affect the networks) or processes known to be affected by exercise (building on our NuGO and other nutrition-related collaborations).
  • Allow extension with external environmental factors like chemical exposure (toxicology) and evaluate overlap with so-called adverse outcome pathways (building on toxicology collaborations).
  • Create complete workflows and make these available, including component containers and specific networks resulting from the analysis.

In this project, we will collaborate with various partners, The ones with central roles are: Franz Schaefer (WP co-lead, Heidelberg representing the ERN research group, Peter-Bram t Hoen (leads proof of principle task, RUMC Nijmegen, Marco Roos (link to FAIR work, LUMC Leiden), Anais Baudot (nutrient evaluation in networks, INSERM-AMU, Aix en Provence), Alberto Mantovani (toxicology evaluation, Istituto Superiore di Sanita (ISS), Rome), plus currently about 20 other participants. It will probably be clear that the project also links to most, if not all, activities that we currently have at BiGCaT. We expect that this project can thus also become a driver project for the department as a whole making the interlinks between various activities more tangible.