Computational analyses of transcriptome instability in cancer

In the past few decades, bioinformatics has become an important part of medical research, providing the means to perform heavy computational analyses on increasingly large biomedical datasets, yielding new insights into the development of complex diseases such as cancer. The Oslo University Hospital - Norwegian Radium Hospital is conducting research addressing the underlying factors of cancer in an effort to advance towards the goal of preventing, detecting and treating this disease. The current master’s project is a collaboration between the Department of Molecular Oncology at the Radium Hospital and the group for Biomedical Informatics at the Department of Informatics at the University of Oslo. The hereditary information in the human body is prone to different kinds of errors which are sometimes associated with cancer. We have investigated the expression levels of genomic features called exons in the context of alternative splicing, a central component of the fundamental biological process of translating the genetic code of ribonucleic acids (RNA) into proteins, the functional components in our genetic makeup. We have utilized a combination of existing methods as well as introduced novel approaches to analyze RNA from cancer in the search for information that can lead to a better understanding of the underlying biological processes of cancer development. An initial goal for the project has been to provide new biological insight on alternative and aberrant RNA splicing in cancer, based on novel analyses, as well as to develop a software tool to aid other groups in performing similar analyses. We have developed a script that measures transcriptome instability from RNA-sequencing data. Further, we have developed a toolbox that can be utilized to perform various analyses of total amounts of alternative splicing events in cancer samples based on output from a software called SpliceSeq. We also provide examples of its utilization, serving as a proof of concept of potential applications of the software.