The effect of splicing mutations in prostate cancer
Next generation sequencing of DNA and RNA is commonly performed in cancer research. Sequencing of nucleic acids from cancerous and healthy cells yields enormous amounts of biological data with large potential for identification of cancer-causing mutations. In order to translate such data into meaningful information and knowledge, working out analysis pipelines and informatics strategies is needed. However, computational analysis of sequencing data is currently a major bottleneck.
Objective and challenges
The student will search for mutations in particular splice sites of DNA sequences from prostate cancer patients and look for associations with aberrant RNA transcripts. Splice sites are positioned at the boundary of exon and intron regions, and play an important role in splicing where pre-mRNAs are processed into mature mRNAs. Mutations in these parts of the genes can disrupt the splicing process and alter the protein-coding sequence. The master project will be to develop a software tool for identification of associations between DNA splice site mutations and RNA variants. The necessary raw sequence data for the project has been generated by researchers at the Oslo University Hospital. Publicly available data sets will also be applied for validation of results.
Main supervisor will be Bjarne Johannessen and co-supervisors Rolf I. Skotheim and Torbjørn Rognes. The work will include time at the Oslo University Hospital, Radiumhospitalet. 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/Linux environment, which are widely used in bioinformatics.
This master project is offered as a long master project (60 study points).