Genomic Medicine and Statistics
Marieke Oudelaar (2014 - present)
Marieke Oudelaar gained a BSc degree at Utrecht University with a 3-month research project and studied for a Masters in Biomedicine at the Karolinska Institute prior to joining the Genomic Medicine and Statistics (GMS) Programme. With interests in genetics and epigenetics she was already thinking of working with her supervisors, Jim Hughes and Doug Higgs, when she applied, and the rotations in the first year of the Programme gave her the opportunity to experience both labs. Now in her 4th year, Marieke is studying how chromatin structure relates to transcriptional activity using chromosome conformation capture (“3C”) methods to map regions with close nuclear proximity. This approach generates massive amounts of data – using proximity ligation to allow the sequencing of structural junctions within the packed chromatin – and this means that there is a major bioinformatics aspect to the project alongside lab work. In this sense, hers is a model GMS project – and it is addressing a complex area of science which is a kind of chicken-and-egg problem: is the sub-organisation of the nucleus the basis of gene activity or determined by gene activity? It’s looking like the two influence one another, and Marieke’s work should take the field forward significantly.
Along the way Marieke has learnt new approaches and techniques, especially in computational analysis of her complex datasets. The more basic courses in the first year allow the different students in the GMS cohort, who come from a wide range of backgrounds, to gain a common skillset. But the most important thing in choosing a DPhil is, she says, to have a project that interests you and which you enjoy studying, and supervisors who will support you. When she completes her DPhil Marieke will spend some time thinking about the research challenges she would like to address next, and the expertise she will need to develop for the future.
Warren Kretzschmar (2011 - 2016)
After studying biochemistry at Beloit College, WI, USA, and post-baccalaureate research at the National Human Genome Research Institute, MD, USA, Warren obtained a Master in Applied Statistics at the University of Oxford, UK. Subsequently, he joined the Genomic Medicine and Statistics program in 2011. Under the supervision of Jonathan Marchini, Warren's DPhil work focused on the development of statistical methods to call genotypes from very large sets of low coverage sequencing data. For the CONVERGE consortium, he wrote the pipeline to create analysis-ready genotypes that were used to discover the first replicated genome-wide association hit for major depression. Warren also developed a statistical method to call the genotypes for the Haplotype Reference Consortium. After submitting his thesis, he will be joining a startup in San Francisco.
Matthias Thurner (2012 - 2016)
Matthias is from Austria and came to the UK to obtain a BSc in Biological Sciences at UCL in 2009. He graduated with a first class degree in 2012 and received an offer from the Wellcome Trust Genomic Medicine and Statistics DPhil programme at the University of Oxford. In the first year the programme provided Matthias with the opportunity to conduct both wet and dry lab research as part of two rotational research projects: The first project focussed on analysing mutations of the tumour suppressor protein FBXW7 in colorectal and endometrial cancer using wet lab techniques. During the second rotation he developed computational methods for identifying exonic deletions using exome chip arrays and testing these deletions for their contribution to the development of Type 2 Diabetes (T2D). For his DPhil Matthias decided to work with Prof Mark McCarthy and Prof Anna Gloyn to determine the role of novel genetic (exonic Copy number variants) and epigenetic (DNA methylation and open chromatin modifications) mechanisms in the role of the development of T2D.