Genome4Brussels by Emma Verkinderen

2022, G4BXL / Thursday, March 24th, 2022

The Fondation 101 génomes has been participating since 2019 in the Genomes4Brussels project co-financed by the Brussels region (Innoviris).

This project brings together the Foundation and three organisations specialising in bioinformatics, genetics and algorithms: theInteruniversity Institute of Bioinformatics Brussels (IB)², theULB Center of Human Genetic (CHG) and theULB Machine Learning Group (MLG).

This consortium has established an ecosystem to optimise the development of bioinformatics tools for genome analysis to assist physicians and researchers in the field of rare diseases.

Emma Verkinderen, bioinformatician at the (IB)², answers Ludivine's questions and explains her role in this unique project.

Ludivine - Emma, can you tell us about your academic career?

Emma - I obtained a BSc in Bioengineering Sciences and an MSc in Bioinformatics at the KU Leuven. After graduation, I did a five-month internship in a start-up company specialising in human genetics and rare diseases.

L. - How is your past experience an asset for the Genome4Brussels project?

E.- During my internship, I was trained in genetics, variant analysis and Machine learning in the context of rare diseases, which are of course very relevant areas of expertise for the Genome4Brussels project. In addition, I gained technical experience, learning the main concepts and best practices of web application development. This internship has greatly fuelled my interest in bioinformatics software development, so I am very happy to continue working on a project where biomedicine and informatics meet as a technical bioinformatician for the Genome4Brussels project.

L.- Can you tell us more about the tools you are working on at the moment?

E.- Until now, I have mainly worked on ORVAL, a bioinformatics tool developed at the Interuniversity Institute of Bioinformatics in Brussels (IB)². ORVAL is an online oligogenic variant analysis platform where users can submit the variants they have found in a patient's genome. ORVAL then creates all possible digenic combinations (a pair of variants in two different genes) and annotates them with data from public bioinformatics resources. The annotations are then used to run the machine learning predictor (VarCoPP) which produces for each digenic combination the probability that it causes the disease. Finally, the results are presented in a comprehensive manner, and the user can perform further analysis on the digenic variant combinations of interest.

As part of the Genome4Brussels project, we want to transfer this tool from the (IB)² infrastructure to the FairGX cloud to ensure its sustainability. I am currently preparing ORVAL for this transfer.

L.- What do you think of the Genome4Brussels project?

E.- I think it is very interesting to see how the Genome4Brussels project creates an ecosystem that centralises genomic data (and its collection) and bioinformatics analysis tools. This helps to stimulate research on rare diseases and, potentially, to make more effective diagnoses.

The fact that all the tools and data are hosted in the cloud is an essential additional advantage, as the cloud can accommodate a large volume of genomic data while respecting the requirements for transparency according to the FAIR principles in data processing and scientific analysis.

I am therefore delighted to be part of this innovative project!

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