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Ellen de Jong

Bioinformatics analyst
Ellen de Jong

Setting up state-of-the-art pipelines to process WGS, WES, RNA-Seq and DNA methylation data.

After successfully graduating from Hogeschool Leiden (University of applied sciences) as a bioinformatician in 2017, I started working at the Princess Máxima Center as a bioinformatics analyst. Here, I have been working together with colleagues to set-up an automated pipeline (for both diagnostics and research) to process DNA methylation data in a fast, robust and standardized way. The pipeline includes tasks to predict or explore distinct tumor (sub)types. We designed an inhouse QC report to identify poor quality data which can negatively influence downstream analysis steps. To identify possible sample swaps, we have developed a task to fingerprint samples. Currently, classification of samples into tumor specific subtypes is the final task of the pipeline. For diagnostic purposes, a central nervous system (CNS) specific classifier is used. Whereas in a research setting, a classifier is being developed to distinguish prognosis related subgroups in rhabdomyosarcoma. As a member of the bioinformatics expertise core, I am also helping my colleagues with the implementation of other pipelines, currently focusing on a RNA sequencing pipeline for the detection of gene-fusion events.