< Terug naar vorige pagina

Organisatie

Computationele Kankerbiologie en Epigenomica

Division

Hoofdorganisatie:Departement Oncologie
Tijdsduur:1 okt 2022 →  Heden
Organisatieprofiel:

 

Cancers are highly heterogeneous entities, both within a single tumor and across patients. Intratumoral heterogeneity stems from the spectrum of cancer cell clones and the dynamic cellular composition of the tumour microenvironment. Cross-patient heterogeneity is based on the multitude of cancer cells-of-origin and patient-specific combinations of germline and somatic genetic variants driving the tumorigenesis. Despite recent major advances in cancer genomics, genetic analyses cannot characterize non-malignant cells in the tumour microenvironment and lack cell type-resolved and patient-specific context for cancer-driving mutations. In contrast, epigenetic modifications – specific molecular barcodes reflecting the individuality of each cell – can help unravel cellular composition and altered cell type-specific regulatory landscapes in each patient. 

The Laboratory of Computational Cancer Biology and Epigenomics focuses on computational approaches for understanding tumor heterogeneity and origins based on high-throughput single-cell and spatial omics technologies. Molecularly, our major interest are epigenetic modifications, in particular DNA methylation for which we have created numerous bioinformatic methods and software in the past. In particular, we used tailored matrix factorization methods to enable reference-free deconvolution of DNA methylation profiles of cellular mixtures (Lutsik et al., Genome Biology, 2017; Scherer et al., Nat Protocols, 2020). More recently we are working on novel methods to understand DNA methylomes at single-molecule level using conventional and novel long-read sequencing methods, such as that of Oxford Nanopore Technologies (ONT) that enable DNA modification mapping across tens to hundreds of kilobases. Due to the fast turnover times, ONT can facilitate ultra-rapid clinical pipelines down to intraoperative analysis. ONT reads can help phase and thereby functionally link genetic variants e.g. single-nucleotide (SNVs) and structural variants (SVs) with the epigenetic domains at single-molecule resolution, shedding light upon the functional effects of complex genetic variants.

Trefwoorden:epigemonica
Disciplines:Bio-informatica en computationele biologie, Oncologie