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 RNA-seq data, and develop a software tool for identifying fractions of error in the total amount of RNA of a cancer sample. After aligning RNA sequences to genome sequences, the student will search for sequences not matching RNA from healthy cells. These RNA sequences are errors made by cancer cells, and we will attempt to define the fraction of such aberrant RNA structures per cancer, similar to what we have done previously from non-sequencing based genome technologies (see our paper in BMC Genomics and our paper in Genome Medicine). As a possible next step, the project will work to integrate these RNA-results with DNA sequencing. Here, we will search for associations between DNA errors (somatic mutations) and changes in the RNA patterns. 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-supervisor Ole Christian Lingjærde. The work may - if desired - 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).