Background
Next generation sequencing of DNA and RNA is commonly performed in cancer research. The laboratory tools used for this purpose are fairly new, and they generate terabytes of data from individual biological samples. The computational analysis tools are still immature, and there are many unmet needs in good strategies for integrating data and results from DNA and RNA sequencing.
Objective and challenges
This master project will start out by analysing data from a type of RNA sequencing called RACE-seq (described first in Hoff, Johannessen et al., Oncotarget 2015). Analysis of such data, derived from prostate cancer patients, have already been done by researchers in the group, and several so-called fusion genes have been identified. The master project will be to develop a software tool for identifying DNA variants, from a parallel dataset of the same patient samples, which are associated with particular RNA gene fusions. The student will search for mutations (sequences not matching DNA from healthy cells) which coincide with particular RNA changes. The necessary raw sequence data for the project is in place – both generated by researchers at the Oslo University Hospital - Radium Hospital and publicly available data generated elsewhere.
Practical details
Main supervisor will be Rolf Skotheim and co-supervisors Bjarne Johannessen and Ole Christian Lingjærde. The work will include time at the Oslo University Hospital, Radium Hospital. No prior knowledge of biology is required. The programming will be performed in the languages Perl/Python/Java and R (previous knowledge in at least some of these languages is desirable but not required) under Unix environment, which are widely used in bioinformatics.
This master project is offered as a long master project (60 study points).