Partners meet to start building the digital infrastructure needed for human genomics research though GUARDIANS

A diverse group came together, including special guest Dr Melissa Konopko from ELIXIR who is standing here with BioCommons’ Prof Bernie Pope.

Australian researchers are set to make significant strides in discovering, accessing, and analysing human genomics data. The first in-person meeting of a significant new collaboration brought together partners who are committed to implementing the Australian BioCommons’ GUARDIANS program.

The meeting in Sydney represented the start of two years of implementation work as part of the GUARDIANS mission to empower Australian researchers to easily and securely discover, access, analyse and use human genomics data across national infrastructure, using the latest tools and resources.

The project brings Australian BioCommons together with Australian Access Federation, Children's Cancer Institute / ZERO, Garvan Institute of Medical Research, National Computational Infrastructure (NCI), QIMR Berghofer Institute of Medical Research, University of Melbourne, and University of Sydney. The project builds on years of foundational work in the Human Genomes Platform Project which also included a funded program and contracted schedules of work with partners. 

This first GUARDIANS meeting helped to build a sense of shared purpose as the group established effective ways of working together across their diverse organisations. Explorations into the policies, processes, and technologies that will be required during the project were driven by the open exchange of ideas, and collaborative discussions on solutions to potential challenges.

Scientific Product Manager at ELIXIR, Dr Melissa Konopko, travelled from the UK to share her insights into the Genomic Data Infrastructure (GDI). There were many parallels to learn from this project which is enabling access to genomic and related phenotypic and clinical data across Europe through establishing a federated, sustainable and secure infrastructure to access the data. 

Explore how GUARDIANS is accelerating human genomics and related omics research in Australia through the development of world-class digital infrastructure.

Contact us if you’d like to learn more.

First batch of clinical data arrives in new data platform

A large collaborative effort striving to take the next leap toward protecting Australians at risk of coronary artery disease recently made significant progress. The first batch of clinical data for the Australian Cardiovascular disease Data Commons (ACDC) has arrived and is now loaded onto the project’s secure staging environment.

The dataset is from the Baker Heart and Diabetes Institute’s Australian Diabetes, Obesity and Lifestyle Study (AusDiab), a national population-based survey of 11,247 adults which is examining the natural history of diabetes, pre-diabetes, heart disease and kidney disease among Australian participants. AusDiab began in 1999 and is still following up with participants - making it Australia's largest longitudinal study in the field.

The ACDC project has drawn together an amazing array of clinicians, researchers, digital infrastructure experts, and consumer representatives. Work on the platform is ongoing, with data modelling, testing and validation continuing with partners from Baker Heart and Diabetes Institute, ACvA, The University of Sydney, 23Strands, CSL Limited and 18 cohort custodians. In the years to come, the platform will improve the capacity for Australian medical researchers to undertake discovery and translational research, specifically cardiovascular risk assessment and treatment.

Australian BioCommons is leading the implementation of the digital infrastructure underpinning ACDC, using the Gen3 data commons platform. Ultimately, the ACDC will become a critical data infrastructure housing pooled data from approximately 400,000 individuals representing up to 18 clinical cohorts from across Australia. 

Learn more about how we are building the ACDC.

Australian meeting strengthens international ties in human genomics

Australian BioCommons recently brought together a global group of research infrastructure specialists working at the forefront of genomics data sharing and management. Seizing the rare opportunity to meet face-to-face created by the GA4GH Plenary held in Melbourne, members gathered to explore shared challenges, common interests and opportunities to deepen ties for mutual benefit.

The organisations and projects represented included:

• Australian BioCommons

• Australian Genomics

• BROAD Institute

• Canadian Distributed Infrastructure for Genomics (CanDIG)

• ELIXIR

• EMBL's European Bioinformatics Institute (EMBL-EBI)

• European Genomic Data Infrastructure (GDI)

• Global Alliance for Genomics and Health (GA4GH)

• IT Centre for Science, Finland (CSC)

• McGill University

• Murdoch Children’s Research Institute (MCRI)

• National Computational Infrastructure (NCI)

• Ontario Institute for Cancer Research (OICR)

• University Health Network

• University of Melbourne Centre for Cancer Research (UMCCR)

The two day meeting opened with presentations detailing the genomics landscapes in Europe, Canada and Australia, showcasing the tools and techniques deployed by each organisation. These presentations uncovered significant convergence on technology solutions across the globe. Dr Mallory Freeberg, Human Genomics Team Lead at EMBl-EBI, noted that:

The chance to meet in person made it abundantly clear that challenges faced in human genomics are shared worldwide, and that we can learn so much from each other through our collaborations. The meeting significantly strengthened our existing relationships, and I look forward to continuing to grow our global human genomics community.

The Australian BioCommons Human Genome Informatics team relished the chance to dive into the finer details. Discussions around common technology solutions, such as GA4GH’s Beacon for handling data discovery, and using metadata standards like HPO and OMOP, were a clear standout that the team will apply to their ongoing work. Dr Conrad Leonard, Technical Lead of the Human Genome Informatics team, said:

I’m very excited for the potential of future collaborations. The opportunity to partner with the worlds’ leading scientists and technologists in this space is invaluable in our efforts to deliver genomic data sharing solutions for Australian researchers.

Overall, the meeting strengthened connections between Australian, European, and North American human genome informatics organisations, and set the stage for potential future partnerships that will drive research progress through provision of critical research infrastructure.

Read more about Australian BioCommons’ human genome informatics activities.

ZERO Childhood Cancer Data Portal launched

Researchers can now access a large bank of paediatric genomic data collected as part of the ZERO Childhood Cancer program, including molecular, phenotypic, multi-omics, and clinical data, plus physical biospecimens across 38 diseases. Housed within the newly launched ZERO Childhood Cancer Data Portal, the datasets represent tumour samples from 1,019 participants in the ZERO2 clinical trial, which includes all children with cancer in Australia and Aotearoa/New Zealand.

The Human Genome Informatics team at the Australian BioCommons was thrilled to recently partner with the Children’s Cancer Institute (CCI) and the ZERO program to support their efforts in establishing the data portal, which formed part of a national, multi-institutional project called the Human Genomes Platform Project (HGPP). The HGPP was designed to enhance capability for securely and responsibly sharing human genome research data nationally and internationally, ensuring maximum value can be derived from these assets. Along with CCI and ZERO, HGPP was a successful partnership between Australian Access Federation, Australian BioCommons, Australian Genomics, Garvan Institute of Medical Research, National Computational Infrastructure, QIMR Berghofer Medical Research Institute, and University of Melbourne Centre for Cancer Research. 

The HGPP team adapted GA4GH’s Beacon network for implementation in Australia, with Beacon v2 now supporting the ZERO Childhood Cancer Data Portal. To learn more about key outcomes and outputs of the HGPP, watch the final showcase on the BioCommons YouTube channel.

The development of the ZERO Childhood Cancer Data Portal was supported by the Australian BioCommons' Human Genomes Platform Project and funded through NCRIS investments from Bioplatforms Australia and the Australian Research Data Commons, and investment by the ZERO Childhood Cancer Program and Children's Cancer Institute.

Human Genomes Platform Project delivers collaborative vision for a national human omics research data ecosystem

The Human Genomes Platform Project (HGPP) wrapped up in November 2023, having investigated and prototyped a toolbox of services designed to enhance Australian capabilities for secure and responsible sharing of human omics research data.

Extensive investigations since January 2021 into global best practice technologies for human omics in Australia focused on:

• A customised user interface for discovering virtual cohorts, using a GA4GH Beacon (version 2) network

• An online management system that removes the burden associated with data access committee approvals

• Finely controlled identity and access management enabled by CILogon and COmanage

• A comprehensive report and proposal for the development of a national repository for human omics data aligned with international efforts, such as the Federated European Phenome Genome Archive (FEGA).

To learn more about the toolbox contents and the project more generally, watch the final HGPP showcase.

Despite a desire to share data for research use, there are many siloed collections of human omics data in Australia that are often difficult for outside users to access. With this challenge in mind, the HGPP assembled a network of experts across biomedical research and digital infrastructure domains. The group explored and tested a selection of foundational infrastructure to pave the way for human omics data in Australia to be findable, searchable, shareable, and linkable to analytical capabilities, all while ensuring the privacy of individuals is protected and data processing is performed ethically, securely and safely.

Looking to the future and building on the HGPP, the Australian BioCommons Human Genome Informatics initiative has ambitious plans to continue exploring and establishing national infrastructure to propel human omics research in Australia. New HGI pursuits include building the Australian Cardiovascular disease Data Commons and the recently announced GUARDIANS project.

Key Outputs from HGPP

• Flyer describing the HGPP
• Webinar - establishing Gen3 to enable better human genome data sharing in Australia
• Webinar - Protection of genomic data and the Australian Privacy Act: is genomic data ‘personal information’?
• Webinar - Improving discovery and access management of genomic data
• Subproject reports including:
• Virtual Cohort Assembly discovery phase and pilot phase reports
• Data Access Committee Management Systems discovery phase and candidate solutions evaluation reports
• Federated Identity and Access Management discovery phase and candidate solutions evaluation reports
• Data and Metadata Archiving feasibility report
• Documentation for infrastructure managers including:
• REMS deployment in Amazon Web Services
• GA4GH Beacon
• Gen3 deployment
• CILogon and COmanage

The HGPP formed part of the Human Genome Informatics initiative and was funded by NCRIS via the Australian Research Data Commons (https://doi.org/10.47486/PL032) and Bioplatforms Australia. Contributions were also made by partner organisations: Australian Access Federation, Garvan Institute for Medical Research, National Computational Infrastructure, QIMR Berghofer Medical Research Institute, The University of Melbourne Centre for Cancer Research, Children’s Cancer Institute, and ZERO Childhood Cancer.

Creative collisions: Bio Day a hit at Supercomputing Asia 2024

This month's Supercomputing Asia (SCA) conference featured a dedicated ‘Bio Day’ which focused on the intersection of biology and computing. Life scientists were enthusiastically invited to interact with the Asia Pacific high performance computing (HPC) community at the Sydney event. The conference organisers offered special access to almost 40 researchers and research infrastructure providers who were keen to participate in the biology-focused sessions. This extra support to add the unique voice of life scientists to the HPC forum was generously provided through Bioplatforms Australia's platinum sponsorship of the event.

Bio Day commenced with Prof Alex Brown, Director - National Centre for Indigenous Genomics, delivering a keynote presentation ‘Towards a National Indigenous genomics Ecosystem within Australia.’ As Professor of Indigenous Genomics at the Telethon Kids Institute and The Australian National University, Alex is an internationally leading Aboriginal clinician/researcher who has worked his entire career in Aboriginal health in the provision of public health services, infectious diseases and chronic disease care, health care policy and research.

Later, sessions titled ‘Building the Foundation: Genomic Data Infrastructure for Precision Medicine and Beyond’ showcased several key pieces of research infrastructure that Australian BioCommons has developed to support life scientists including:

• The Australian BioCommons Leadership Share (ABLeS)

• The Australian Alphafold Service

• The newly funded GUARDIANS project

• A pilot program bringing Seqera Platform to Australian researchers

Some of BioCommons’ significant national partners such as the Australian Amphibian and Reptile Genomics Initiative (AusARG) and international collaborators ELIXIR were also showcased on Bio Day. Additionally, Dr Kate Michie’s (UNSW) talk revealed the ‘Transformative Impact of Deep Learning on Accelerating Molecular Research: A Focus on AlphaFold2 and its Implementation Challenges.’ The Skills and Training Track on the same day also featured our training guru, Dr Melissa Burke, presenting our unique Training Cooperative model.

Sessions held on Bio Day illuminated the unique challenges that bioinformatics research brings to HPC, including:

• Episodic and extended access is required for compute resources

• Compute use is reliant on experimental outcomes, and difficult to predict in advance

• Software is diverse, rapidly evolving, and in many cases not optimised for HPC

• Researchers may have limited experience working in HPC environments

The light shone on these unique challenges stimulated some uncommon conversations at SCA, which aim to improve life science researchers' access to appropriate and scalable bioinformatics methods and compute resources. Dr Johan Gustafsson, Bioinformatics Engagement Officer at BioCommons said:

The conference was a unique opportunity to bring two worlds together - researchers working hard in their particular field of biology don’t normally attend HPC conferences, and vice versa. So it was great to see them starting to speak the same language!

Uwe Winter, BioCloud DevOps Engineer at BioCommons attended a workshop on the recently launched Trillion Parameter Consortium (TPC), a group formed to address the challenges of building large-scale artificial intelligence (AI) systems and advancing trustworthy and reliable AI for scientific research.

Discussions at the TPC workshop brought up a lot of exciting ideas on utilising AI in a fully automated research environment. I was inspired to hear TPC’s future plans and can’t wait to apply them to BioCommons infrastructure for the benefit of Australian researchers!

Overall, Bio Day at SCA was a fantastic chance to continue important conversations around the specialised support and infrastructure that life scientists need. BioCommons extends our thanks to Bioplatforms Australia for their sponsorship and to the conference organisers for running a successful event.

Powering up the ACDC

The Australian Cardiovascular disease Data Commons (ACDC) will pave the way for researchers to make new mechanistic insights and identify potential markers for coronary artery disease (CAD), plus facilitate a translational pipeline to ensure new discoveries are deployed to clinical practice. A new comprehensive, secure, scalable, and internationally integrated data infrastructure will provide access to pooled data from approximately 400,000 individuals across up to 18 clinical cohorts within Australia. 

CAD is the most common type of cardiovascular disease, both in terms of deaths and hospitalisations. Despite developing over several years, CAD is difficult to detect and many patients have no warning symptoms. Developments in data-intensive biomarker research techniques such as genomics, metabolomics, proteomics and immuno-phenotyping, paired with advances in image processing, machine learning, and systems biology pipelines, present opportunities to better understand and identify those at risk through pooled analysis using research infrastructures such as the ACDC.

Work on the ACDC commenced in September, with all stakeholders in the MRFF Critical Research Infrastructure Grant meeting online, including representatives of all 18 clinical cohorts that are planned to be integrated into the ACDC platform. 

It’s a long way to the top, and small working groups will now hold fortnightly ‘sprints’ to keep the ACDC moving forward. You can read more about the ACDC on the BioCommons website.

A formal, in-person, kick off of the ACDC will occur in early December as part of a broader Australian Cardiovascular Alliance Precision Medicine Flagship event hosted by the Baker Heart and Diabetes Institute.

The ACDC project is led by the Baker Heart and Diabetes Institute and funded by the Medical Research Future Fund (MRFF) and Bioplatforms Australia (MRFF 2022 National Critical Research Infrastructure Grant: Building an Australian Cardiovascular disease Data Commons). Additional contributions are being made by the Baker Heart and Diabetes Institute, 23Strands, ACvA, CSL Limited, University of Sydney, Australian BioCommons, data custodians and other partners.

Funding awarded to develop an Australian Cardiovascular disease Data Commons

Development of the Australian Cardiovascular disease Data Commons (ACDC) is underway thanks to a successful Medical Research Future Fund (MRFF) Critical Research Infrastructure bid. As part of the recent funding announcement for new medical technology and research facilities, the project received $3M to develop an Australian Cardiovascular disease Data Commons that is controlled, secure, scalable, internationally integrated and connected with the world's best-practice analysis platforms. The ACDC will pave the way for researchers to make new mechanistic insights and identify potential markers for coronary artery disease, plus facilitate a translational pipeline to ensure new discoveries are deployed to clinical practice. 

Coronary artery disease is the leading cause of premature cardiovascular death in Australia, and results in serious disability for survivors. It is extremely difficult to detect and many patients have no warning symptoms, despite the underlying atherosclerotic plaque developing over several years. The advance of data-intensive biomarker research techniques such as genomics, metabolomics, proteomics and immuno-phenotyping along with image processing, machine learning, and systems biology pipelines is a golden chance to make the next leap in the protection of patients at risk of coronary artery disease. However, there is currently no efficient way to identify cross-study cohorts for combined analysis. The ACDC will enable combined analysis by providing researchers with access to pooled data from over 400,000 individuals across more than 18 clinical cohorts within Australia.

The successful funding bid was led by a multi-organisational team comprising the Australian BioCommons, the Baker Heart and Diabetes Institute, Bioplatforms Australia, the University of Melbourne, the University of Sydney, 23Strands, CSL Limited and 18 cohort custodians. The BioCommons team are leading the implementation of the digital infrastructure underpinning ACDC, using software systems such as the Gen3 data commons from the Centre for Translational Data Science at The University of Chicago. The digital infrastructure that ACDC yields will no doubt benefit other data intensive precision medicine programs.

The ACDC project is funded for the next four years, with the first three large datasets soon to be integrated into the platform. The team at Australian BioCommons are extremely excited to be part of the ACDC project and can’t wait to get started! Learn more about the developing Australian Cardiovascular disease Data Commons now.

The international genetics and genomics community comes to Melbourne

Members of the Australian BioCommons team are attending the 23rd International Congress of Genetics (ICG) from 16-21 July in Melbourne. Meet us at booth 27 to find out about our activities in building bioinformatics infrastructure to support human health, agricultural and environmental science research, and discuss the challenges researchers face. We’ll showcase the services that the BioCommons and our partners offer and we would love to hear your feedback!

As well as visiting our booth, keep an eye out for the BioCommons team in the symposia, and the poster and speciality sessions:

• Associate Director - Human Genome Informatics, Bernie Pope: Ultra-sensitive detection of circulating tumour DNA enriches for patients with higher risk disease in clinically localised prostate cancer (talk on 20 July, 11 am)

• Human Genomics Data Specialist, Marion Shadbolt (poster): Advancing human genomics data sharing in Australia: Highlights from the Australian BioCommons

• Community Engagement Officer, Tiff Nelson (poster): Robust public computational services supporting Genome Assembly and Annotation for Australian researchers

• Bernie Pope (poster): Somatic mutation landscape in a cohort of meningiomas that have undergone grade progression

• Deputy Director, Jeff Christiansen will give an overview of BioCommons services supporting genomics research at approximately 1 pm during the Genetics Society of AustralAsia (GSA) annual general meeting on 19 July

While at the congress, you can also visit our partners the Atlas of Living Australia (ALA), who are providing an early look at the new Australian Reference Genome Atlas interface, plus other Bioplatforms Australia supported facilities including the Australian Genome Research Facility, Ramaciotti Centre for Genomics and the Australian National University Biomolecular Research Facility. 

Registration is still open, so come along and chat with the BioCommons team. We can’t wait to see you there!

Gen3 Community Forum to showcase how the BioCommons uses Gen3

Australian BioCommons partners with the team behind Gen3 at the Center for Translational Data Science, University of Chicago, USA to custom build several data commons for use by large Australian national research consortia. 

We help convene the international Gen3 Community Forum, and the next online event ‘Data Modeling in Gen3 Data Commons’ is coming up on Friday July 7, 6.30 am AEST (check in your timezone). Our Human Genomics Data Specialist, Marion Shadbolt, will deliver a presentation on streamlining Gen3 data dictionaries.

Marion’s presentation will outline progress from the BioCommons’ partnership with the Precision Medicine Flagship of the Australian Cardiovascular Alliance (ACvA). The team have been using Gen3 to develop a data dictionary for the Australian Cardiovascular Disease Data Commons, using a google sheet as input and fully automating the workflow to edit, test, validate and publish Gen3 data dictionaries.

Gen3 can be customised for a wide variety of projects and use cases, and there will be three additional presentations from other data commons operators, discussing how they have created their dictionaries and describing the tools or processes they use for updating and configuring them.

The Gen3 platform consists of open-source software services that support the emergence of healthy data ecosystems by enabling the interoperation and creation of cloud-based data resources, including data commons and analysis workspaces. Gen3 aims to accelerate and democratise the process of scientific discovery by making it easy to manage, analyse, harmonise, and share large and complex datasets in the cloud. 

Additional details and registration