PhD Student for applied wet- and dry-lab research in translational epigenomics

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We are looking for a highly motivated and enthusiastic PhD student to contribute to our recently funded research within the Applied Epigenomics group of the Department of Genetic Identification at Erasmus MC, led by Dr. Athina Vidaki. The successful applicant will work on a project aiming at developing a novel and innovative epigenomic method that will assist the translation of epigenomic findings to the clinic and court.

Human epigenomic research has yielded numerous biomarkers predictive of personalized health- and disease-related outcomes, such as in cancer diagnosis and management. These personalized signatures can also be useful for specialized non-medical applications, such as in forensics. Over the years, epigenetic biomarker discovery has become possible via DNA methylation microarrays for epigenome-wide screening of hundreds of thousands of biomarkers (CpG sites), provided that the analysed DNA is of sufficiently high quantity and quality, which in many clinical and forensic applications it is not. Therefore, clinical and forensic epigenomic applications have suffered thus far from small-scale targeted tests (no more than 20-30 CpG fragments), despite the need of many more CpGs to address these questions. Currently, translation in epigenomic applications has come to a halt due to the lack of suitable large-scale targeted methods, in terms of sensitivity, multiplex capability, flexibility, and costs.

In this project, we aim to tackle this major and timely technical limitation by developing and thoroughly testing a new method for the simultaneous targeted analysis of hundreds to thousands of CpGs, pre-selected for different applications. We aim to achieve this via novel technological innovation that will allow for tailored and large-scale targeted epigenomic testing from just 100-1,000 cells, typically obtained in clinical settings that use liquid and need biopsies, but also in forensics that deal with trace evidence from crime scenes. The project will include method development, thorough validation and direct application to selected clinical and forensic questions.

As a Ph.D. student you will be part of an interdisciplinary research group working in the field of applied (epi)genomics. You will directly be responsible for the development, optimization, validation and testing of the proposed novel and innovative method, which includes both laboratory and computational tools. It is therefore essential that you have experience and expertise with both wet- and dry-lab analysis methods. Evidence of a deep understanding of prior research topics and of independent intellectual and practical contributions to previous research projects will be considered as good indicators that such attributes can be brought into the present project. This position also entails close collaborative and interdisciplinary work involving other departments at Erasmus MC and international partners. For eventually fulfilling the PhD requirements at Erasmus MC, several first-author publications in international peer-reviewed scientific journals are required together with education achievements within the 4-year PhD period.

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