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

The Garvan Institute of Medical Research and the Centre for Pattern Recognition and Data Analytics (PRaDA) at Deakin University will today launch the Garvan-Deakin Program in Advanced Genomic Investigation (PAGI).
Media Release: 28 March 2017

The PAGI 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 will be 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 to explore it 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.”

The launch will take place at 9am today (Tuesday 28 March) at Deakin Downtown, Level 12, Tower 2, 727 Collins Street, Melbourne. 


 Media enquiries:  Meredith Ross (Garvan) – – 0439 873258

 Notes for editors

 About Deakin University

With a focus on excellence in teaching and research, and a commitment to give back to the domestic and international communities it serves, Deakin is ranked among the top two per cent of universities globally, and is one of the world’s top universities under 50 years old.

About PRaDA

PRaDA is a world-class Strategic Research Centre based at Deakin University. Researchers work on discovering patterns in big and lean data to solve real-world problems. Exploiting sophisticated machine learning, PRaDA researchers develop new tools and technologies for practical use in sectors such as health care, security, social media, advanced manufacturing and more.

PRaDA's work has resulted in two start-ups that are being used around the world. The TOBY Autism Therapy is an app that provides tailored learning for children with autism, and iCetana is intelligent video surveillance software that detects potential security threats in large data sets.

 About the Garvan Institute of Medical Research

The Garvan Institute of Medical Research is one of Australia's largest medical research institutions and is at the forefront of next-generation genomic sequencing in Australia. Garvan’s main research areas are: cancer, diabetes and metabolism, immunology and inflammation, osteoporosis and bone biology, and neuroscience. Garvan’s mission is to make significant contributions to medical science that will change the directions of science and medicine and have major impacts on human health. In 2012, Garvan established Australia’s first purpose‐built facility for undertaking clinical-grade genome sequencing and large-scale research projects. The Kinghorn Centre for Clinical Genomics (KCCG) researchers undertake collaborative projects and genome‐based studies to improve genome interpretation, with the aim of advancing the use of genomic information in patient care.

What is machine learning?

Machine learning is a type of artificial intelligence that enables computers to learn without being explicitly programmed, so they can grow when exposed to new data. It is used in Google, Bing, computer vision, self-driving cars and fraud detection, with new applications emerging in many fields.

What is a genome?

Your genome is the entire complement of genetic information contained within the DNA in your cells. Your genome is a combination of genetic material you have inherited from your parents, totaling more than six thousand million DNA units or bases. 

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