Wouter Maessen Email & Phone Number

Nijmegen, Ge, Nl

Burjassot, Valencia, Spanje

During my internship my goal is to evaluate and improve SQANTI3 (https://doi.org/10.1038/s41592-024-02229-2) which is used to complete challenges for the LRGASP (Long Read Genome Annotation and Association Project - https://doi.org/10.1038/s41592-024-02298-3). SQANTI3 allows long-read sequencing pipelines to be analysed with specific metrics. Long-read RNA sequencing provides the ability to capture full-length transcripts, enabling transcript-level identification and quantification. This is crucial for understanding isoform-specific expression, alternative splicing, and transcript diversity across various biological contexts. Transcript quantification can be approached in two ways: (1) constructing transcript models from the data, which can be computationally intensive due to noisy reads, or (2) using reference annotations for direct quantification, though these often miss sample-specific isoforms.Existing tools for transcript identification and quantification include cluster-based (e.g., FLAIR, Mandalorion), graph-based (e.g., IsoQuant, StringTie2), and class-based methods (e.g., ESPRESSO, TALON), each with their own strengths and weaknesses, particularly concerning reliance on reference genomes or annotations. In the LRGASP project, only transcript identification and quantification tools are currently available. Therefore, benchmarking direct quantification tools, such as Oarfish and lr-kallisto, is essential for understanding this new approach for transcript quantification.Direct quantification methods heavily depend on reference annotations to assign reads to transcripts. However, incomplete reference annotations may result in many reads being unassigned. One alternative is to build a transcriptome model from unassigned reads and perform quantification based on this model. This approach introduces challenges related to computational cost and accuracy, and it is important to assess how complete a reference annotation needs to be to efficiently run these tools

Nijmegen, Gelderland, Nederland

Vaccination of melanoma subjects with dendritic cells that present melanoma antigens is an expertimental cellular immunotherapy against cancer. Yet the systemic effects of such vaccination have never been measured. The goal of the project is to determine which genes and pathways are differentially regulated upon vaccination, and which of these pathways correlate with recurrence free survival of the subjects and/or with immunological parameters that have been measured. The project encompasses the analysis of the RNA seq data, from the quality control, mapping to genes, and determining read counts of the genes to the using of mixed effects models to disentangle the effect of the various covariates, including the immunological relevant ones, on gene expression.

Sittard-Geleen, Limburg, Nederland

Op de afdeling P&O worden alle belangrijke digitale documenten en papieren verwerkt. Zo worden ziektemeldingen, of nieuwe contracten in het systeem gezet. Dit vereist veel focus omdat de kleinste foutjes hier al cruciaal zijn. Vanwege de vele papieren is een combinatie van efficiëntie en foutloos werken nodig. Bovendien worden klanten op deze afdeling geholpen met eventuele informatie over bijbehorende papieren, waardoor veel kennis over alle soorten document zijn vergaard.

Sittard-Geleen, Limburg, Nederland

Alle printers binnen de organisatie Zuyderland te Sittard-Geleen en Heerlen, moeten worden geïnventariseerd. Dit betekent dat elke kamer waar mogelijk een printer staat moet worden gecheckt. Bovendien moeten ook operationele kamers worden bekeken. Dit is nodig om zoveel mogelijk te kunnen bezuinigen op printers.

Maastricht, Limburg, Nederland

Preimplantation genetic testing (PGT) is a genetic testing method to avoid the transfer of a genetically affected embryos, including families with risk of having children with severe genetic disorders. To be able to perform PGT, an IVF treatment is needed. After 5/6 days of development, a trophectoderm (TE) biopsy is taken consisting of 5-10 cells. These cells will then be further analysed to select against embryos that carry genetic abnormality. During the in vitro (IVF) culture of an embryo, it releases genetic material in the culture medium, called cell-free DNA (cfDNA). Even though, taking the TE biopsy seems to be safe for offspring, taking the biopsy can hamper embryo development and is labor intensive, as a cascade of highly skilled personnel and specific equipment is needed. We are interested in this cfDNA as this allows us to analyse embryonic DNA without the need of performing a biopsy. After whole-genome amplification (WGA) and sequencing the spent culture medium, we are able to analyse single-nucleotide polymorphisms (SNPs) and copy number variations (CNVs). However, it is challenging to generate a CNV profile from single-cell or cell-free DNA sequencing data from human embryos due to WGA artefacts and low tolerance for sample contamination and degeneration. Multiple methods are available to profile CNVs e.g. QDNAseq, Ginkgo, FREEC, and CANVAS. However, it is unclear which method is optimal for cfDNA CNV profiling. During this internship, I will apply and optimize these methods on sequencing data obtained from embryonic cfDNA sequencing. I will be testing (at least one) method(s) available, and see how well the CNVs can be profiled. In case our method could accurately profile the CNVs from cfDNA, this could be implemented to use for non-invasive PGT (niPGT). Therefore, my research question of the project will be: ‘Comparison of different Copy number profiling methods for Copy Number profiling in niPGT’.

Sittard-Geleen, Limburg, Nederland

Patiënten verwelkomen bij het Zuyderland ziekenhuis te Sittard-Geleen en Heerlen. Hierbij worden de patiënten begeleid met een nieuw aanmeldprocedure, mochten zij hier zelf niet uit komen. Zo is goede en duidelijke communicatie nodig, ook voor niet-nederlands-sprekende mensen.

Master Of Science - Ms, Medical Biology

Bachelor'S Degree, Biomedical Sciences, General

Education record