Projects in oncology bioinformatics
For one biologist a project on microarray data from patients with colon cancer lead to a new post in oncology bioinformatics.
The MSc research project ...
The student took our microarray module as one of her optional modules, and so gained experience in using Bioconductor. She was then able to choose a research project requiring the analysis of colonic tissue samples from patients with and without liver metastases.
With additional experience in the use of Bioconductor in oncology bioinformatics, the student was then able to move on the post-graduation job described below.
The new job ...
As a bioinformatician at EMBL-EBI, I am responsible for data management of kidney cancer data, derived from CAGEKID project. Kidney cancer is one of the very few tumour types for which there are currently no biological markers in routine clinical use. The project is the first systematic analysis of this type of cancer comprising of genomics, transcriptomics and epigenetics data. It is a collaboration between 14 EU research partners from 7 countries, including St James's University Hospital in Leeds. In particular, I am involved in data analysis of RNA sequencing data, which include quality control, identifying structural rearrangements, fusion genes, variant analysis and alternative splicing. I mainly analyse the data with standard libraries in Bioconductor and modified R functions. In addition, I apply tools suitable for RNA next generation sequencing data such as Tophat and Cufflinks.