I am a molecular biologist interested in (epi)genetic alterations underlying disease development. After my PhD (2013) on ‘Genomic profiling of high-grade cervical intraepithelial neoplasia’ I started working as power-user for the Center for Translational Molecular Medicine, Translational Research-IT (CTMM-TraIT) project in the group of Gerrit Meijer (currently at the Netherlands Cancer Institute, Amsterdam). The project aim is to provide sustainable data-management solutions for translational research data types. I have evaluated tools for their capability of accommodating research data and work with IT developers to improve the chosen tools. I am also a data consultant and member of a data-team, which is tasked with getting data of TraIT customers onto the data-integration platform for easy view and query.
TITLE: Querying, viewing and analyzing colorectal cancer translational research studies in tranSMART
All translational research projects basically share the same design, which is correlating variation in disease phenotype to variation in underlying biology. Typical questions to be addressed are: ‘Which (out of thousands) biomarkers predict good/bad outcome?’ and ‘Which (out of thousands) biomarkers predict whether a patient will benefit from a particular therapy?’. In line with this concept, many research teams have generated large amounts of experimental molecular data from patient samples, yet generally this information is inaccessible for examination due to local storage of both (meta)data and the data processing workflows used. Alternatively, data stored in central databases may only be available for exploration and interpretation by data specialists, provided that the processing workflow has been published and is available. Thus, if data is not recorded and easily retrievable, validation of obtained results (e.g. promising biomarkers) may be virtually impossible. Additionally, it will be difficult to query existing data sets to answer new questions, which may lead to experiments being unnecessarily repeated and biological materials being wasted.