Elisabeth D. Chen

PhD Student


This person is a member of Sanger Institute Alumni.

Liz conducted her PhD research in Mathew Garnett's group between 2015-2018. There, she worked on creating and annotation and functional characterisation of gene fusions in human cancer cell lines.

My work is built on the extensive genomic characterisation and drug screening of human cancer cell lines completed within the Garnett lab. To date, our group has screened over 1,000 anti-cancer drugs across a genomicaly annotated panel of > 1,000 human cancer cell lines with the goal to identify therapeutic biomarkers that can predict response to anti-cancer drugs.

On top of these resources, I worked on creating an annotation of gene fusions for that panel of >1,000 cancer cell lines. In recent years, RNA sequencing technology has made the identification of gene fusions relatively cheap and convenient, however the next challenge is to separate gene fusions that drive cancer initiation, progression and maintenance from those that are passenger events. Therefore, I developed computational methods that leverage the extensive drug screening and CRISPR-Cas9 whole genome screening data available for our cell lines to ask which gene fusions are associated with a sensitivity to a given drug, and which are selectively essential for the survival of cancer cell lines. My analysis uncovered evidence for novel oncogenic driver fusions, known driver fusions in a new tissue context and opportunities for drug repurposing.

Prior to coming to the Sanger Institute, I obtained my BSc from Imperial College London, during which I completed a year-long research internship at the Royal Botanic Gardens, Kew, where I looked at the evolution of the morphology of plant stomata. After completing my PhD, I will be taking on a new role as management consultant in London, UK.

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