Leading genomic data projects to drive a new ‘world of knowledge’

Garvan researchers are key contributors to three genomic data initiatives selected as key Driver Projects by the Global Alliance for Genomics and Health (GA4GH) in a 5-year vision to fully realise the promise of genomic medicine.
18 October 2017

GA4GH, an international alliance formed to accelerate the potential of genomic medicine and research to advance human health, has today struck formal collaborations with fifteen international genomic data initiatives. Three of the fifteen initiatives – the Australian Genomics Health Alliance (AGHA), the Monarch Initiative and Matchmaker Exchange – involve researchers at the Garvan Institute of Medical Research.

The announcement comes as part of the launch of GA4GH Connect, a 5-year vision that aims to promote the GA4GH standards and frameworks for genomic data discovery, analysis, and interpretation to enable responsible sharing of clinical-grade genomic data by 2022. The Driver Projects will share their experience and knowledge in integrating genomics into clinical practice, and will pilot GA4GH data sharing frameworks and standards in real-world healthcare settings. Other Driver Projects named include major national genomic medicine initiatives Genomics England and the U.S. All of Us Research Program.

 

Australian Genomics Health Alliance (AGHA)

AGHA is an NHMRC funded research collaboration of more than 70 organisations committed to integrating genomic medicine into healthcare in Australia. Initially targeting rare disease and cancer, AGHA is building the evidence and piloting solutions for the effective and equitable delivery of genomic medicine in Australia.

Garvan researchers make significant contributions across AGHA research programs. For example, Professor David Thomas, Director of The Kinghorn Cancer Centre and Head of Garvan’s Cancer Division, leads one of the AGHA Cancer Flagships, Managing Patient Risk - Paediatric / Adolescent and Young Adult (AYA). This flagship is studying over 1000 individuals with early-onset cancers: a paediatric cancer cohort (<16 years) and an AYA cohort (16-40 years) at diagnosis, by whole genome sequencing. It aims to identify the spectrum of clinically actionable variants across a broad range of cancers, based on age of onset.

Prof Thomas says, “There are over 5000 young people diagnosed with cancer in Australia every year, and perhaps 250,000 Australians are survivors of cancer arising as children or young adults. The premature mortality from early onset cancer is a major public health issue. Our goal is to reduce premature mortality from cancer through early detection and treatment. 

“We believe there is an important opportunity to use genomics to personalise risk management, to help cancer survivors and their families lead healthy, productive lives.”

Garvan is also playing a leadership role in the National Approach to Data Federation and Analysis research program, which is key to AGHA's new partnership with GA4GH. A/Prof Marcel Dinger, Head of Garvan’s Kinghorn Centre for Clinical Genomics (KCCG) co-leads this Program to develop recommendations for national guidelines and pilot infrastructure for a scalable, shared, and standardised national data repository of clinical genomics information. Program partners are driving the integration of genomic information with other health information – physical characteristics and symptoms that are collectively termed the ‘phenome’.

A/Prof Dinger says, “It’s great to see that the Australian Genomics Health Alliance has been recognised as a strategic partner and a key Driver Project for GA4GH.

“Key to our endeavours is the development of world-class genotype-phenotype databases and interfaces that link to international data sharing initiatives. We see remarkable opportunities to further refine these tools and super-charge their capabilities through closer engagement with GA4GH and with other Driver Projects.”

Garvan has also developed two key data sharing tools for AGHA. Dr Warren Kaplan, KCCG Informatics Program leader, and his team have built the Vectis platform, which provides AGHA members with the capabilities to house, query, filter and analyse genomic data for its diverse cohorts. Dr Tudor Groza, KCCG Phenomics Program leader, and his team have developed the AGHA Patient Archive platform, which enables patient data management, collaborative diagnosis and knowledge exchange.

Other Chief Investigators and Working Group members from Garvan include Prof John Mattick, Prof Deborah Schofield, Dr Tudor Groza, Bronwyn Terrill, Dr Mark Cowley, Dr Mark Pinese, Mary-Anne Young, Dr Stuart Tangye, A/Prof Shane Grey and Dr Amali Mallawaarachchi.

 

The Monarch Initiative and Matchmaker Exchange

The KCCG Phenomics team, led by Dr Tudor Groza, significantly contribute to two of the GA4GH Driver Projects, the Monarch Initiative and Matchmaker Exchange.

“It is truly inspiring to see these initiatives converging and laying the foundation of the next generation of genomic healthcare, which will have an profound impact on the quality of life of patients,” said Dr Groza.

Dr Groza is a principal investigator on the Monarch Initiative, an international collaboration that allows researchers to represent and compare phenotypes within and across species. The Phenomics team contributes data visualisation and text mining tools to this initiative.

Dr Groza also contributed to the design and refinement of Matchmaker Exchange’s API. Matchmaker Exchange helps find diagnoses for patients with rare diseases by connecting people with similar phenotypes and genotypes.

The team’s research direction focuses on developing methods to extract information from diverse sources using natural language processing, then convert it into standardised language.

Standardising the language used to describe phenomic data, like height, blood type and disease symptoms, means it can be used to not only match patients across databases internationally but also enable sophisticated analytics that can identify new genetic associations with clinical characteristics in cohorts.

 

Notes for editors:

About GA4GH: GA4GH is an international alliance formed to accelerate the potential of genomic medicine and research to advance human health. Bringing together 500+ leading organizations working in healthcare, research, patient advocacy, life science, and information technology, GA4GH members are framing policy and developing standards to enable the responsible, voluntary, and secure sharing of genomic data

About Garvan: 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, genomics and epigenetics, 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. 

About the Australian Genomics Health Alliance: AGHA is an NHMRC funded research collaboration of more than 70 organisations committed to integrating genomic medicine into healthcare in Australia. Our goals are to improve diagnostics, enable early intervention and support equitable access to genomic medicine. Our research is developing the knowledge to translate genomic technology sustainably into clinical practice so patients and their families benefit.
australiangenomics.org.au

About Monarch: Monarch isn’t just another data aggregator, it is driven to truly integrate biological information using semantics and present it in a novel way. Their niche is the use of computational reasoning to compare phenotypes both within and across species, with the ultimate goal of improving biomedical research.
monarchinitiative.org

About Matchmaker Exchange: The 'Matchmaker Exchange' project was launched in October 2013 to find genetic causes for patients with rare disease. This involves a growing federated platform (Exchange) to facilitating the matching of cases with similar phenotypic and genotypic profiles (matchmaking) through standardised application programming.