Fighting Cancer; how supercomputing is helping to make the impossible, possible
Researchers within the University of South Wales’ Genomics and Computational Biology research group are making use of HPC Wales’ supercomputing technology and services to help them revolutionise the way in which cancer is treated. Dr Tatiana Tatarinova and her team use mathematical modelling and computational simulation to help them understand the biological processes that occur within a cell, translating the genetic information stored in our DNA into observable physical characteristics and traits.
Dr Tatarinova is confident that an improved understanding of the genetic factors underlying the onset of cancer in each individual patient will lead to the development of improved – and personalised – methods for that patient’s treatment. There is a very personal reason behind her quest:
“One of the saddest moments of my life was when my mother was diagnosed with cancer. She had surgery, but developed secondary cancer and subsequently died five years later. One of the problems with cancer treatment is that drugs are not made specifically for individual patients: medicine should take into account a person’s genotype, not just age and gender, and should be tailored to their needs.
“Computational biology has the potential to do this. It is a tool used to rigorously and mathematically describe and investigate biological processes, impacting our understanding of genetics and healthcare. Computational biology has the potential to become one of the most important areas of scientific research in the twenty-first century.
“I will dedicate my life to trying to prevent tragedies like this happening to other families. Although I couldn't save my mother, maybe I can save other people.”
Recent advances in medical sensing devices provide an opportunity to realise Dr Tatarinova’s dream. By automating experiments, so that large-scale repetition becomes feasible, large volumes of data can be generated and used to characterise biological systems. As Dr Tatarinova explains, this means doctors will soon have access to detailed genetic information about a patient, enabling them to rapidly identify the optimal treatment regime and improve the patient’s prognosis:
“We are currently seeing a revolution in laboratory-based sciences and computing technologies. We can process enormous volumes of diverse data very cheaply. At the same time, new experimental techniques are continuously being developed. Integrating these two sets of advances provides access to an unprecedented amount of information about biological processes.
“In the very near future, when every person is genotyped, the notion of personalised medicine will become a reality. Healthcare decisions and practices will be tailored to the individual patient by integrated use of genotypic and phenotypic information as well as medical and family history. At the University of South Wales we have developed a novel method for identifying a person's ancestry based on DNA analysis. Understanding an individual’s origins is essential to choosing the correct medical treatments and the best diet for that person.”
Personalised medicine is fuelling rapid growth in the global bioinformatics market, which is expected to grow from £1.9 billion in 2012 to £5 billion in 2017. Wales’ thriving life sciences sector employs 15,000 people in more than 300 companies and contributes over £1.3 million to the economy – representing around 10% of the total life sciences employment in the UK. This existing reservoir of expertise within Wales means that the country is very well positioned to capture a significant share of the growth in the bioinformatics market.
However, access to the wealth of newly available biological information comes at the cost of challenges in analysing, managing, storing and transferring this information. Overcoming these challenges requires the use of high performance computing, as Dr Tatarinova explains:
“High performance computing is an essential part of computational biology research. Our research would be slow and difficult – maybe even impossible – without access to it. HPC Wales have given us training, support and access to their technology and services. They have motivated me to aim higher and to make my projects more ambitious. They have installed all of the software that we required, fixed any problems that we had with our codes and scripts, and even liaised with third-party software developers to improve their codes.
“To give an example, we were recently operating under a strict deadline to deliver results to our collaborators in the USA. The program that we were using was able to handle small chromosomes, but failed with the larger ones that we were interested in. The software developers did not have access to a system of the size of HPC Wales, so they had never attempted to analyse large chromosomes. HPC Wales’ support staff discussed the bug with the software developers, a fix was implemented and we finished our project on time.”
HPC Wales is giving life sciences businesses and researchers across Wales access to the high performance computing technology required to develop new techniques for personalised medicine that will change the way in which cancer is treated in future, improving the chances of survival for each patient and providing an opportunity for further growth and employment in an area in which the Welsh economy is already strong.