prof. Katleen De Preter (PhD)

CRIG group leader
Katleen De Preter

Principal investigator - Lab for applied bioinformatics, Center for Medical Genetics (UGent)
Full professor (Faculty of Medicine and Health Sciences, UGent)
Co-founder of CRIG
Partner of BIG (Bioinformatics Institute Ghent)

 

Research focus

The research of the translational bioinformatics group at UGent is focused on the development of bio-informatic pipelines for diagnostic, prognostic and predictive analysis of tumors, enabling a more personalized and precise cancer medicine. In the past we have established m(i)RNA expression signatures that predicted neuroblastoma (NB) patient survival. As the challenge remains to identify patients at ultra-high risk and NB can be considered as a copy number disease, we embarked more recently on an international meta-analysis to identify copy number events that can predict ultra-high risk disease. These results further stress how important it is to analyse the copy number profile in NB, however is challenged by the invasive character of tumor sampling. Therefore, we established a new analytical and bioinformatic pipeline to identify the copy number profile on cfDNA isolated from blood. Assessing the copy number profile of NB tumors is important for prognostic purposes, however these profiles in many cases do not allow to pinpoint druggable driver genes. Many consequences of genetic and epigenetic alterations are reflected in gene expression changes and can be captured using transcriptomic data which we will use to pinpoint druggable targets by mapping pathway activities in primary and circulating tumor cells. Optimized and validated using NB, the developed pipelines will be applicable for individual cancer patients of any tumor type to co-guide therapy stratification.

Research team

Key publications

  • Genomic Amplifications and Distal 6q Loss: Novel Markers for Poor Survival in High-risk Neuroblastoma Patients, JNCI, 2018
  • Shallow whole genome sequencing on circulating cell-free DNA allows reliable non-invasive copy number profiling in neuroblastoma patients. CCR, 2017
  • Upregulation of MAPK Negative Feedback Regulators and RET in Mutant ALK Neuroblastoma: Implications for Targeted Treatment. Clin Cancer Res. 2015 (PMID: 25805801)
  • Mutational dynamics between primary and relapse neuroblastomas. Nature genetics, 2015 (PMID: 26121086 )
  • Histone chaperone CHAF1A inhibits differentiation and promotes aggressive neuroblastoma, Cancer Res., 2014 (PMID: 24335960) 
  • Focal DNA copy number changes in neuroblastoma target MYCN regulated genes, PLoS One, 2013 (PMID: 23308108)
  • Targeted expression of mutated ALK induces neuroblastoma in transgenic mice, Sci. Transl. Med, 2012 (PMID: 22764207)
  • miRNA Expression profiling enables risk stratification in archived and fresh neuroblastoma tumor samples, Clin. Cancer Res. , 2011 (PMID: 22031095)
  • Meta-analysis of neuroblastomas reveals a skewed ALK mutation spectrum in tumors with MYCN amplification, Clin. Cancer Res, 2010 (PMID: 20719933 )
  • Predicting outcomes for children with neuroblastoma using a multigene-expression signature: a retrospective SIOPEN/COG/GPOH study, Lancet Oncol, 2009 (PMID: 19515614 )
  • Human fetal neuroblast and neuroblastoma transcriptome analysis confirms neuroblast origin and highlights neuroblastoma candidate genes, Genome Biol, 2006 (PMID: 16989664 )
  • Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes, Genome Biol, 2002 (PMID: 12184808)

Contact & links

  • Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Medical Research Building (MRB), 2nd floor, room 120.038, Corneel Heymanslaan 10, B-9000 Ghent, Belgium
  • Center for Medical Genetics Ghent
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  • Google Scholar
  • prof. De Preter is interested to receive invitations for presentations or talks