Applied Bioinformatics of Cancer

Overview

High-throughput genomic techniques allow the simultaneous measurement of thousands of DNA sequences, mRNA transcripts, peptides or metabolites giving us a holistic view of the machinations of cellular processes. They enable us to ask fundamentally different experimental questions, such as “which genes change?”, rather than “does gene X change?” - enabling data-driven rather than hypothesis-driven experiments to be performed.

Breast cancer is an extremely complex disease, with a huge number of variables. Risk factors range from unavoidable genetic predisposition, through to lifestyle choices such as diet and exercise. Breast tumours are also highly heterogeneous with many different clinical and pathological characteristics. The ABC research group utilise the latest data analysis methods to interpret the results of genome-wide studies to improve our understanding of the effects of treatments and risk factors.  By doing so, we hope to be able to evaluate and select the most appropriate treatments and prevention methods.

Our focus

The ABC research group is an integral part of the Edinburgh Breakthrough Research Unit. We aim to bridge the gap between basic and clinical research using high-throughput genomic approaches. These allow us to test and generate hypotheses which further our understanding of the molecular mechanisms and cellular changes responsible for cancer development and the implications they have for treatment. Bioinformatics provides us with the tools needed to comprehend and interpret the latest techniques.

To maximise the value of high throughput ‘-omics’ studies, they must be considered within the wider context of cancer biology, accepting the complexity and heterogeneity. The ABC research group conduct both carefully designed experiments to look at the specific effects of single factors and meta-analyses which bring together several studies to place laboratory findings into the wider context of patients and treatment.

There is now a greater understanding that there are many more subtle molecular mechanisms which can contribute to the disregulation of genes in cancer, including chromatin structure regulation, DNA methylation, differential splicing, microRNAs and post-translational modifications of proteins. These can all be assessed using different high-throughput techniques. We need to acknowledge that the additional intricacies of these mechanisms have a role to play a role in the complexity of cancer. The ABC research group aims to integrate and compare different layers of molecular data with the vast amount of information already present in the public domain, in order to further our understanding of cancer.