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Jeroen de Ridder

Cyclomics: ultra-sensitive nanopore sequencing of cell free tumor DNA

About Jeroen de Ridder

Dr. Jeroen de Ridder is a Principal Investigator and Associate Professor at the Center for Molecular Medicine of the University Medical Center Utrecht, as well as a junior PI at the Oncode Institute. He runs a bioinformatics lab which aims to create and apply innovative data science methods to advance our understanding of disease biology. His research efforts are always inspired by a biological question and typically deal with big data, such as large-scale genomics and epigenomics datasets. As a result, much of the research floats on machine learning and data integration algorithms. Recently, Dr. de Ridder, along with Dr. Kloosterman and Dr. Marcozzi, founded a start-up company Cyclomics, which aims to provide ultra-sensitive sequencing of cell free tumor DNA. 

Abstract

In many types of cancer, tumor cells shed small (~150bp) DNA molecules in the blood or other body fluids. Detecting mutations in the cell-free DNA (cfDNA) content of liquid biopsies in cancer patients thus offers a unique opportunity for non-invasive diagnostics for the purpose of e.g. treatment monitoring treatment response or detecting recurrent disease. Reliably detecting mutations from minute amounts of tumor derived cfDNA is, however, highly challenging. To address this, we developed CyclomicsSeq, a novel sequencing approach leveraging the long-read nanopore platform to achieve single molecule detection accuracy. We have demonstrated proof of concept on head and neck cancer (HNC) patient samples and found that CyclomicsSeq can detect mutations anywhere in the TP53 gene with single-molecule accuracy. CyclomicsSeq thus offers a reliable liquid biopsy diagnostic assay which can be cost-effectively implemented in routine clinical workflows. 

Jeroen de Ridder

Jeroen de Ridder

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