State
of the art
Genome-wide
association
studies (GWAs) in complex diseases have identified many single
nucleotide polymorphisms (SNPs) associated with disease susceptibility.
However, a large fraction of genetic markers associated with complex
disease pathogenesis are part of larger haploblocks with high linkage
disequilibrium (LD) and many are located within non-coding regions or
even so-called gene deserts, adding further difficulty to the decoding
of pathological molecular processes underlying complex diseases.
Identifying disease loci and genes causal for disease pathogenesis
would improve understanding of the disease on a molecular level as well
as opening possibilities for therapy optimization, new drug development
or repurposing of existing drugs.
As the cost for genomic studies continues to decrease with
high-throughput sequencing and imputation, the amount of data generated
also increases, requiring advanced bioinformatic tools for
processing. In the current post-GWAs era, greater emphasis is placed on
fine mapping the true causal variant within a haploblock, elucidating
how it affects gene expression and thus determining what role the
variant plays in disease pathogenesis. To this end, expression
quantitative trait loci (eQTL) studies are performed to link suspected
disease susceptibility variants to gene expression data in select
tissues. The recent advent of RNAseq technology has enabled full
transcriptome studies, providing immense insight in how complex
diseases work on the RNA level, increasing the rate at which eQTL are
discovered and also allowing discovery of new, disease-specific gene
transcript variants.
Furthermore, genome and transcriptome studies enable identification of
DNA and RNA markers of drug response. Identifying drug response
biomarkers and translating them into clinical praxis would fulfill the
ideal of personalized medicine. By using the patient's characteristics
on the molecular level, it would be possible to select the correct
drug, administer it at the optimal dosage and maximize the chance of a
successful treatment outcome while minimizing the severity and
likelihood of adverse side effects. Advanced statistics and the
principles of machine learning are employed to create accurate
biomarker prediction models.
Research areas
To
this end, the centre is collecting an extensive bank of biological
samples from clinically well characterized patients. The centre researches
foremost on immune-mediated complex diseases such as inflammatory bowel
disease, rheumatoid arthritis and asthma, but we also research certain
types of cancers, ex. breast cancer. For most studies, peripheral
venous blood is collected to obtain serum, peripheral blood mononuclear
cells (PBMCs) and erythrocytes. If possible, we also collect relevant
tissue biopsies. In some cases, saliva and stool samples are also
collected.
Currently, the centre is focused mainly on identification of diagnostic and
prognostic biological markers in immune-mediated diseases and cancer.
To see a list of completed and ongoing research projects, click here.
To see a list publications, click here.
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