About the Lunch Talks

The Biomina Lunch Talks are an initiative of a number of young researchers in the biomina network and is sponsored by the Flemish Government. We aim to stimulate the interaction between researchers from different disciplines who encounter bioinformatics and computational biology, and consequently we focus on a broad and multidisciplinary public. With this informal medium we would like to provide a platform where knowledge and experience can be presented and exchanged, across partners from both academia and industry. In this manner we have had the pleasure to welcome speakers from various institutes such as the University of Antwerp, the Institute of Tropical Medicine, Janssen Pharmaceutica, the Antwerp University Hospital and Open Analytics. Last, but not least, these sessions can provide a great opportunity for young researchers to acquaint themselves with new ideas and methods in the field of bioinformatics and medical informatics.

Speakers

Antonio Mauro Rezende, Institute of Tropical Medicine Antwerp

Title: Metagenomics as diagnostic tool: the Metatropics Project.

Abstract: Specific laboratory tests assist clinicians to identify the etiology of an infection however they require prior suspicion of a particular pathogen, based on symptoms and geography. However, pathogens not tested for and new emerging pathogens will be missed. Metagenomic sequencing provides an attractive alternative to targeted testing as it allows for the untargeted sequencing of all genomic material present in a sample without required prior knowledge on the suspected pathogen. Here, we are developing a wet lab protocol for not target viral enrichment from serum samples coupled to Nanopore sequencing platform and a completely automatic computational pipeline as an untargeted diagnostic approach for viral infectious disease. The pipeline has been developed using NextFlow environment along with several containers (Docker or Singularity) in order to make it easier to be distributed. The whole procedure has been tested with clinical and serum samples where several different spiked in viruses were used (CHIKV, ZIKV, DENV, SARS-Cov-2). Different concentration of spiked in virus have been assessed reflecting Ct values found in clinical samples, such as 25, 29.5 and 35. Therefore, it is worth to mention that even with the highest Ct tested, we were able to recover the complete genome of the pathogen.

Wouter De Coster, VIB-UAntwerp Center for Molecular Neurology

Title: Tandem repeat variability in frontotemporal dementia: a population scale assessment.

Abstract: Tandem repeats are associated with approximately 60 human disorders, primarily neurological, but remain among the most complicated elements in the genome for accurate detection and sizing. In addition, standard short-read sequencing analysis methods are inadequate, especially if repeats expand beyond the read length. However, current methods mitigate this limitation and enable the investigation of tandem repeat lengths across populations. Simultaneously, long-read nanopore sequencing is becoming a routine method for comprehensive genome analysis and dramatically improves the resolution for repeat analysis.

We combine modern analysis methods in large-scale short-read population sequencing with long-read population sequencing for a complete assessment of tandem repeat variability and its role in frontotemporal dementia.