Bulk whole genome sequencing (WGS) enables the analysis of tumor evolution but, because of depth limitations, can only identify old mutational events. The discovery of current mutational processes for predicting the tumor’s evolutionary trajectory requires dense sequencing of individual clones or single cells. Such studies, however, are inherently problematic because of the discovery of excessive false positive mutations when sequencing picogram quantities of DNA. Data pooling to increase the confidence in the discovered mutations, moves the discovery back in the past to a common ancestor. Here we report a robust whole genome sequencing and analysis pipeline (DigiPico/MutLX) that virtually eliminates all false positive results while retaining an excellent proportion of true positives. Using our method, we identified, for the first time, a hyper-mutation (kataegis) event in a group of ∼30 cancer cells from a recurrent ovarian carcinoma. This was unidentifiable from the bulk WGS data. Overall, we propose DigiPico/MutLX method as a powerful framework for the identification of clone-specific variants at an unprecedented accuracy.

The Wellcome Trust have funded a new HDRUK-Turing Wellcome PhD programme in Health Data Science which will be jointly directed by Christopher Yau. Applications for entry October 2020 coming soon.

A paper by Kaspar Martens and group alumni Kieran Campbell Covariate GPLVM has been accepted for presentation at the International Conference on Machine Learning.

Project Title: clinAIcan - developing clinical applications of artificial intelligence for cancer

Track Record [max 2 pages]

I am an Artificial Intelligence (AI) researcher with a focus on developing computational and statistical methodologies for problems within the biomedical and health sciences.