Projects
Statistical Methods for Improved Base-calling and Integration of Massive Parallel Sequencing Data Ghent University
In virology research, massively parallel sequencing (MPS) has great opportunity to study viral quasispecies in HIV-1 and HCV-infected patients, which is essential for the understanding of the pathways to resistance and can substantially improve treatment. In this project statistical methods are developed for the identification and quantification of viral variants using the Illumnia MPS technology.
The study of mutations in the mitochondrial genome of human pluripotent stem cells by massive parallel sequencing Vrije Universiteit Brussel
Identification of causal variants for psychiatric diseases through massive parallel resequencing methods. University of Antwerp
Massive parallel de novo design of biological nanopores. Vrije Universiteit Brussel
IMPLEMENTATION OF GENOME-WIDE CELL-FREE DNA SEQUENCING FOR THE EARLY IDENTIFICATION AND EFFICIENT MANAGEMENT OF HIGH-RISK PREGNANCIES KU Leuven
IMPLEMENTATION OF GENOME-WIDE CELL-FREE DNA SEQUENCING FOR THE EARLY IDENTIFICATION AND EFFICIENT MANAGEMENT OF HIGH-RISK PREGNANCIES
In prenatal diagnosis, NIPT (non-invasive prenatal testing) has been introduced as a safe and reliable screening test for common fetal chromosomal aneuploidies (trisomy 21, 18 and 13). The test is based on sequencing fetal cell-free DNA (cffDNA) in the maternal circulation of pregnant women. In 2013, ...
Deep learning based synthetic design and massively parallel reporter assays to characterize and exploit cell type specific enhancers KU Leuven
Gene regulation in eukaryotes is controlled by an interplay of regulatory elements, among which genomic enhancers play a major role. The DNA sequence of an enhancer determines which transcription factors can bind to it. The combined actions of these regulatory elements form a gene regulatory network, which determines a cell's identity. Understanding how the cell type specific activity of enhancers is encoded in their sequence remains a major ...
Mapping genetic interaction networks underlying complex traits via massively parallel precision genome editing KU Leuven
Finding all sequence variants that give rise to diversity among individuals and understanding how they affect specific traits is a key challenge in genetics. Through advances in genome sequencing we now know what the variants are that differ among individuals. However, with current methods it is difficult to pinpoint which of these variants contribute to a trait. Variants can also interact to mask or enhance each other’s effect, further ...
Nanopore sequencing of complete pharmacogenes after CRISPR/Cas9 enrichment in tamoxifen and clopidogrel patients allowing enhanced haplotyping and continuous scale machine learning efficacy prediction. Ghent University
Pharmacogenetics (PGx) studies how genes influence individual response to drug therapies. Current massively parallel short-read DNA sequencing (SR-MPS) technologies provide limited haplotype information. We want to alleviate this by developing full-gene long-read MPS on PGx genes using an amplification-free CRISPR/Cas9 target enrichment method. Completely-phased genotype data and metadata from 2 cohorts will be used to train a machine ...
PromethION: nanopore sequencer for high-throughput and long read high-fidelity DNA and RNA sequencing allowing fast decoding of (epi)genomes and (epi)transcriptomes Ghent University
The PromethION (Oxford Nanopore) is a standalone benchtop instrument designed for highthroughput, high-sample number nanopore sequencing. This third generation sequencing technology allows unprecedented opportunities such as direct epitranscriptome analysis, sequencing of extremely long reads and real-time data analysis. This groundbreaking technology differs from the
mostly used second generation short-read sequencing and allows ...