A National Approach to Data Federation and Analysis

Program 2 – A National Approach to Data Federation and Analysis

Knowledge gained from a patient’s genome will increasingly inform diagnoses and clinical management. However, realising the full benefits of genomics in healthcare, and ensuring accuracy of genomic testing, depends on access to high-quality, annotated genotype and phenotype data.

This Program is developing data standards and processes to capture and use clinical and genomic data, to support Australian Genomics’ clinical Flagships research activities. It’s activity is also informing a coordinated, national approach to the generation, processing, curation, storage and sharing of genomic and related clinical data.

We are developing:

  • Infrastructure for genomic data storage and access
  • Policies and processes for ethical access to data for research purposes
  • Tools to capture and use clinical information in a standardised, machine-readable format
  • A system for Australian diagnostic labs to share variant classifications and evidence
  • A national genotype-phenotype database

Looking for data tools & policies?

Visit our Tools pages

Leads Program 2

Dr David Hansen
Australian e-Health Research Centre, CSIRO

A/Prof Oliver Hofmann
The University of Melbourne

Dr Natalie Thorne
Melbourne Genomics Health Alliance

Program 2 Manager

Dr Marie-Jo (MJ) Brion
Australian Genomics & QIMR Berghofer Medical Research Institute

Working Group

A/Prof Ainsley Newson
The University of Sydney

Allan Williams
The Australian National University

Dr Alejandro Metke
Australian e-Health Research Centre, CSIRO

A/Prof Amanda Spurdle
QIMR Berghofer Medical Research Institute

Dr Boris Guennewig
The University of Sydney

David Bunker
Queensland Genomics

David Lawrence
SA Pathology & University of South Australia

Dr Denis Bauer
CSIRO

Emma Tudini
Australian Genomics & QIMR
Berghofer Medical Research Institute

Dr Hardip Patel
The Australian National University

James Andrews
SA Pathology & University of South Australia

Prof John Christodoulou
Murdoch Children’s Research Institute

John Pearson
QIMR Berghofer Medical Research Institute

Dr Karin Kassahn
SA Pathology

Dr Ken Doig
Peter MacCallum Cancer Centre

Lavinia Gordon
The University of Melbourne

A/Prof Mark Cowley
Children’s Cancer Institute

Maureen Turner
Biogrid Australia

Dr Nic Waddell
QIMR Berghofer Medical Research Institute

Dr Philip Wu
The Australian National University

Matilda Jackson
Australian Genomics & SA Pathology

Dr Sebastian Lunke
Victorian Clinical Genetics Services

Dr Simon Sadedin
Murdoch Children’s Research Institute

Dr Stefanie Elbracht-Leong
Australian Genomics

Dr Tessa Mattiske
Australian Genomics

Tiffany Boughtwood
Australian Genomics

Dr Uwe Dressel
Australian Genomics & The University of Queensland

Dr Warren Kaplan
Garvan Institute of Medical Research

Our Projects

A national Genomic Data Repository is being established to enable storage, sharing, retrieving and archiving of genomic data from the Australian Genomics’ clinical Flagship studies.

The genomic data, produced by diagnostic laboratories, will be available for clinical and research access. Australian Genomics develops and manages data systems that balance security, data integrity and access for researchers.

As these rich data sets expand, a Data Governance Framework will define and guide access principles and policies, draft agreements and terms of research access. To align with international standards, the tools of the Global Alliance for Genomics and Health (GA4GH) are being integrated, within our procedures for mapping consent, data user authentication and approvals and data sharing.

See more on our data access policy below.

Project Lead

A/Prof Oliver Hofmann
The University of Melbourne

Data Co-ordinator

Dr Stefanie Elbracht-Leong
Australian Genomics

Technical Host

The University of Melbourne

Technical Lead

Lavinia Gordon
The University of Melbourne

Clinical information can come from many different sources, with inconsistent terms and complex formats that make it challenging to combine for genomic research and clinical tools.

To efficiently capture and use high-quality clinical information to power genomic research and clinical activities, adopting common language systems (such as SNOMED-CT and HPO) to describe patient conditions and clinical histories are required. These common languages use computer-readable terminologies and codes rather than relying on natural language which is difficult to compute, and prone to variation.

This project is developing tools to directly capture patient information in coded form, rather than in free-text, and transform patient phenotype data from the Australian Genomics clinical Flagship studies into a common format, based on FHIR, a new international standard that will be available in many electronic health record systems.

Read more on our Tools page.

Project Lead

Dr David Hansen
Australian e-Health Research Centre, CSIRO

Technical Host

CSIRO

Technical lead

Dr Alejandro Metke
Australian e-Health Research Centre (CSIRO)

Technical Contributors

Hugo Leroux
Australian e-Health Research Centre (CSIRO)

Madonna Kemp
Australian e-Health Research Centre (CSIRO)

Establishing unified systems and standards across Australian testing laboratories is important to ensure that specific genetic variations are given the same definitions, and medical interpretations.

This project has created an online communication platform and variant registry for automated and real-time sharing of variant classifications, evidence and expertise between pathology service providers.

The platform, called Shariant, allows laboratories to share curated variant classification information across Australia.

The world leading software will ensure greater efficiency and consistency in how we diagnose and treat disease. Shariant will also simplify exchange of information with international variant databases such as ClinVar.

This project works closely with the clinical variant re-classification group within Program 1.

Read more about Shariant on our tools page.

Project Lead

A/Prof Amanda Spurdle
QIMR Berghofer Medical Research Institute

Coordinator

Emma Tudini
QIMR Berghofer Medical Research Institute

Technical Hosts

University of South Australia and SA Pathology

Technical Leads

David Lawrence
SA Pathology & University of South Australia

James Andrews
SA Pathology & University of South Australia

Technical Contributors

Anthony Marty & James U
Melbourne Genomics Health Alliance

The value of genomic data is greatly enhanced by the ability to seamlessly analyse it together with patient’s clinical information and medical records.

This will depend on bringing together genotype and phenotype data from large numbers of patients in a way that is powerful but user-friendly, and in a secure and access-controlled environment.

This project has developed a genotype-phenotype data platform, called Variant Atlas, to manage and gather these large data sets and enable visualisations and query functions to support clinical decision making and research.

Read more on Variant Atlas on our Tools page.

Project and Technical Lead

Dr Warren Kaplan
Garvan Institute of Medical Research

Technical Host

Garvan Institute of Medical Research

Technical Contributors

Dmitry Degrave
Garvan Institute of Medical Research

Andre Hermanto
Garvan Institute of Medical Research

Evan Benn
Garvan Institute of Medical Research

Data Access

The purpose of this policy is to generate a framework around reasonable access to the data collected through clinical flagship projects in the Australian Genomic Health Alliance (Australian Genomics) for the purpose of secondary research use.

This policy is designed to reflect the opinions of flagships investigators, and respect the wishes of flagships participants: data collected will strictly be used in accordance with a participant’s consent for collection, use and data sharing.

Some participants will dynamically and granularly update their consent preferences through an online platform (CTRL). The expressed or withdrawn consent is taken into account during the data access process.

Dynamic Consent

Australian Genomics has developed a new online research consent and engagement platform for our participants called CTRL (control), to improve the experience of participants enrolled in genomic research programs and undergoing genomic testing.

The platform is based on dynamic consent – an emerging mechanism which enables study participants to choose from more granular consent options, and to give and revoke consent in real time.

Lead

Dr Matilda Haas
Australian Genomics

Working Group

Adam Walczak
Canteen

Bronwyn Terrill
Garvan Institute of Medical Research

David Bunker
Queensland Genomics

Working Group

Dr Harriet Teare
University of Oxford

Prof Jane Kaye
The University of Melbourne & University of Oxford

Dr Jessica Bell
The University of Melbourne

Keri Finlay
Australian Genomics

Kirsten Boggs
Australian Genomics & Sydney Children’s Hospital Network

Lindsay Fowles
Genetic Health Queensland & Australian Genomics

Lyn Hunter
Patient Advocate

Working Group

Dr Megan Prictor
The University of Melbourne

Dr Miranda Vidgen
QIMR Berghofer Medical Research Institute

Nada Mirkovic
University of New South Wales

Norah Grewal
The University of Sydney

Sean Murray
Mito Foundation

Tiffany Boughtwood
Australian Genomics

A/Prof Zornitza Stark
Victorian Clinical Genetics Services & Australian Genomics