Dr Susie Cooke is a cancer genomics and bioinformatics expert, bridging the gap between biological and clinical questions about cancer and the computational methods needed to solve them – and then working to ensure the successful application of the resulting methods and technologies in the healthcare system. Dr Cooke has extensive knowledge of cancer genomics and applies this in work with industry, academic research and clinical/drug trials.
At GPOL she manages multidisciplinary teams across ‘wet’ laboratories that test and analyse DNA, or other biological materials, and ‘dry’ laboratories, where computers or computer-generated models are used for analysis.
Following a PhD in 2007 on cancer genomics that focused on alterations of chromosome 8 in breast cancer, Dr Cooke became a research fellow at Cancer Research UK’s Cambridge Institute, where she began doing experiments using next-generation sequencing, a technology that generates millions (or even billions) of data points for each sample. The tools hadn’t yet been invented to analyse this type and scale of data, so Dr Cooke started working with bioinformaticians, who wrote computer code to process the data.
In 2011, Dr Cooke took up a research fellowship in the Cancer Genome Project at the Wellcome Sanger Institute, where she continued to bridge between the data – how it’s generated and what properties it has from a biological sense – and what that means in terms of what a computer needs to do to it. She also began transitioning herself into bioinformatics.s a member of the External Quality Assessment (EQA) Specialist Advisory Group (SAG) for Next Generation Sequencing (NGS), and contributes to Scottish and national working groups for the advancement of genomics in healthcare.
Dr Cooke explained: ‘Next-generation sequencing technologies for studying genomics came to market during my PhD and first post-doc, so my career has grown up with them. They’ve really changed a lot in that time (as anyone who remembers nebulising DNA, size selecting on gels and getting excited about 30bp reads on a Genome Analayzer will confirm!). By understanding how things are done in the lab from my past experience, and how the technology has evolved, I know how to make the most of the data and a lot of the pitfalls to avoid – a classic case of being in the right place at the right time!’
In 2014 Dr Cooke joined the Sanger Institute cancer genomics startup, 14M Genomics, where she worked creating cancer tests and analysis pipelines and partnering with people doing drug trials to deliver genomic cancer test reports for patients.
In 2016, Professor Andrew Biankin established the Glasgow Precision Oncology Laboratory at the University of Glasgow to support his work in pancreatic and other cancers, with Dr Cooke as Head of Medical Genomics, managing a team in the next-generation sequencing and bioinformatics facility and delivering sequencing, analysis and interpretation of cancer genomic data for national projects, such as the Scottish Genomes Partnership, and drug trials, including the UK-wide Precision-Panc trials for patients with pancreatic cancer, as well as collaborating with local academic investigators.
‘We’re working in that gap after translational research, where you’re taking research that has potential to be translated into the healthcare system, and actually translating it’, said Dr Cooke. ‘Essentially, it’s solving a gigantic and complex problem to deliver a product that’s not just a good product, but the right product. It’s never going to be perfect, but the right compromises have to be made in the right places. It has to do the best job it can do for the purpose for which it’s intended, whilst still being practical, with the extra pressure that people’s lives are on the other end of it.’
Dr Cooke has authored the Cancer and Bioinformatics chapters of the Scottish Science Advisory Council’s Report on ‘Informing the Future of Genomic Medicine in Scotland’, and co-authored the Scottish Genomes Partnership’s response to the House of Commons Science and Technology Committee Inquiry on Genomics and Genome Editing in the NHS. She led GPOL’s contribution to the National Institute for Biological Standards and Control’s preparation of the proposed WHO 1st International Standards for Cancer Genomes and is chair of the ACGS Driver Working Group, drafting national best practice guidelines.
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