Machine Learning to Help Improve Early Detection and Treatment of Barrett’s Oesophagus

Dr Richard Owen is an upper gastrointestinal researcher based in the Ludwig Institute for Cancer Research, Nuffield Department of Medicine, and the Department of Upper GI Surgery, (Oxford University Hospitals NHS Foundation Trust – OUHFT). He studied as an undergraduate at the University of Liverpool, completed his early surgical training in Liverpool and Manchester, and did his DPhil in Oxford. Richard is currently completing his surgical training in Thames Valley and Oxford.

 

Barrett’s Oesophagus (changes in the cell types in the lower oesophagus) is a risk factor for Oesophageal Cancer. Currently, patients with Barrett’s Oesophagus are regularly checked using endoscopic sampling to allow intervention when early signs of cancer develop and the disease is non-life threatening. However, as relatively few Barrett’s Oesophagus patients progress to cancer, the majority needlessly undergoes endoscopic tests. Furthermore, many cancers develop without the proof that Barrett’s was originally present.

 

Using samples donated by affected patients, Richard utilises single cell and small-sample sequencing, and proteomic analysis to explore the mechanisms by which Barrett’s Oesophagus and Oesophageal Cancer develop. The generated data is analysed using big data analytics methods (such as machine learning) to monitor gene expression, protein expression and gene mutations at each stage of cancer development. By combining the clinical outcome with microscopic images of the tissues Richard and his fellow researchers are trying to identify crucial diagnostic features that relate to molecular findings in their sequencing data (MODI-OC). Ultimately the aim of this work is to enable clinicians to identify at an earlier stage which patients will and will not progress to cancer, sparing those without diseases unnecessary screening, and detecting and treating those with disease earlier. Additionally, in patients who progressed to Oesophageal Cancer, similar scientific methods are used to determine if it is possible to identify which patients may benefit from novel cancer treatments, such as immunotherapy, and how this can be used alongside more traditional cancer therapies such as radiation therapy and surgery (LUD2015-005).

 

Within Oxford Richard is collaborating with researchers from the Ludwig Institute for Cancer Research, Oxford Branch (including Professor Xin Lu and Professor Jens Rittscher), the Department of Oncology, University of Oxford (including Professor Mark Middleton), The Wellcome Centre for Human Genetics (including Professor Simon Leedham)and the Target Discovery Institute, (hosted within the  Nuffield Department of Medicine) (including Dr Roman Fischer).
Further collaborators are Dr Claire Palles (Institute of Cancer and Genomic Sciences, University of Birmingham) and Dr Andrew Roth (Department of Computer Science, University of British Columbia).

 

The research is funded by the Ludwig Institute for Cancer Research, CRUK, the Oxford Biomedical Research Centre, the Oxford Health Services Research Committee, and the Oxford University Clinical Academic Graduate School.