Visualisation of chimeric RNA; sequences originating from two individual genes
Genomic DNA rearrangements are common in cancer and may result in so-called fusion genes which are hybrid genes formed from two previously separate genes. Identification of fusion genes has become important in characterization of cancer genomes, both for research and for genome-based precision medicine. RNA transcripts composed of exons from two or more genes are similarly referred to as fusion transcripts, or chimeric RNA. These have the potential to encode novel proteins. New high-throughput sequencing of RNA (RNA-seq) has revealed that many chimeric RNA-molecules exist in cancer cells, and even in healthy cells (see our paper in Translational Oncology).
Objective and challenges
To evaluate which of the chimeric RNA-molecules observed in cancer cells are relevant for the development of the cancer, good prioritisation of the results are important. This can be helped by a visualization system of integrated DNA and RNA data of the fused genes. However, such a structured visualisation framework has not been established due to high complexity of genomic/transcriptomic features. In this master project, the student is challenged to develop a new visualisation strategy for chimeric RNA-molecules: a system which presents the chimeras together with common types of biological and medical data (e.g. DNA-mutations, RNA expression, protein domain/motif architectures and clinical/biospecimen information).
Automated generation of user-friendly visualisations will enable effective prioritisations of which fusion transcripts that are likely to be important. The necessary raw sequence data for the project are in place - both generated by researchers at the Oslo University Hospital - Radium Hospital and publicly available data generated elsewhere.
This master project is suitable for a student with interests in both programming and creative art work. 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 master project will be offered as a long master project (60 study points).