The focus of my research is cancer evolution and heterogeneity. Cancers are made up of a heterogeneous mix of cells, each bearing a different set of mutations in its DNA. We aim to characterise groups of cells, or ‘subclones’, according to their mutational profiles and to study the interaction between subclones.
Tumours are difficult to treat because they change over time, gaining mutations that enable them to metastasise to distant organs or that result in resistance to treatment. By comparing multiple samples, we can identify those mutations that cause relapse and progression. Using genetic markers, we can also track the spread of disease, giving us insights into the mechanisms and processes involved in cancer growth and metastasis.
We have developed software packages for the purpose of studying tumour evolution and heterogeneity, including:
- The Battenberg algorithm, which identifies clonal and subclonal copy number aberrations. The Battenberg package may be downloaded from here.
- DPClust clusters mutations into subclones, identifying the Cancer Cell Fraction (CCF) and number of mutations within each subclones. DPClust may be downloaded from here.
- Octopus, a mapping-based variant caller that calls single nucleotide variants (SNVs) and small insertions and deletions (indels) using a haplotype-aware framework. Octopus may be downloaded from here.