Garvan and Deakin University join forces to accelerate precision medicine through machine learning

28 March 2017

The Garvan Institute of Medical Research and the Centre for Pattern Recognition and Data Analytics (PRaDA) at Deakin University have launched the Garvan-Deakin Program in Advanced Genomic Investigation (PAGI).

The program is an Australian-first and will use machine learning and artificial intelligence to uncover unprecedented insights from genomic and clinical information.

The pioneering new program aims to set the intellectual and technological framework for a new way of thinking in medical research, in healthcare and in health systems management. It also aims to usher in an era in which big data and its analysis transform our understanding of human biology and disease.

The program was launched by Dr Amanda Caples, Victoria's Lead Scientist, at Deakin Downtown, in the company of Deakin University Vice Chancellor Professor Jane den Hollander AO, Garvan Executive Director Professor John Mattick AO FAA and PRaDA Director Professor Svetha Venkatesh.

In the future, researchers in the program aim to bring together thousands and ultimately millions of genome sequences and clinical information from individuals who have consented. They will integrate the two kinds of information and explore them through machine learning and pattern recognition.

The Program seeks to learn more from the vast amounts of human genome sequence data that are now being generated in Australia and worldwide. Already, Garvan has sequenced almost 14,000 whole human genomes, and the speed of genome sequencing continues to increase rapidly.

In parallel, large clinical datasets - which contain remarkably rich multilayered information about an individual’s medical history - are being developed and are reaching maturity.

The new Program draws on Garvan's position as one of the world's leading centres for genome sequencing and analysis, and on PRaDA's expertise in applying machine learning and pattern recognition to datasets of many kinds. It is the result of close collaboration between Professors Mattick and Venkatesh, who share a vision for a new "data ecology" that will transform healthcare.

"This is an important inflection point," Professor Mattick said. "We now have the capacity to sequence human genomes increasingly cheaply, so we're going to have, for the very first time in history, access to thousands, and eventually millions, of genomes along with matched clinical information.

"The amount of clinically relevant information that is encoded in those datasets is almost unimaginable - and so far, we have only scratched the surface of what genome sequences can tell us."

Professor Venkatesh said, "With approaches such as machine learning, we now have the power to detect patterns and motifs within that very rich, multidimensional data, to make connections that no one has been able to make before.

"These data present enormous challenges, as the number of individuals for whom we have data is much smaller than the enormous numbers of variants we find in the genomic data. We need to develop new methods to look at the variability between individuals, especially when some variants may be very rare but of great impact.

"Handling these subtle differences will open up new ways of analysing and identifying patterns to ultimately understand, at the individual and population level, the factors that contribute to disease.”

In the first instance, researchers in the Program will develop tools and approaches, using genomic and clinical datasets already in existence in Australia, to uncover effective approaches to interrogation of linked datasets.

Professor Venkatesh said, "Our program is ambitious and extremely exciting. I am delighted that we will be pushing the frontiers at the nexus of biology and computer science with this talented multi-disciplinary team."

Professor Mattick said, "We are taking the first steps into a new world which will fundamentally change the way discoveries are made, the way people manage their health, and the way the health system is organised.

"The integration of genomic data is at the heart of what is coming to be known as precision medicine, where everyone's individual information, including genetic information, guides their healthcare.

"It is the next great technological and social advance. It will transform medicine from the art of crisis management to the science of health management, create new data industries and jobs in the largest and most important industry in the world, and have a major impact on the national economy, national prosperity and national wellbeing into the future."

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Media release Faculty of Science Engineering and Built Environment, School of Information Technology Pattern Recognition and Data Analytics (PRaDA)