Developing Personalised Treatment for Kids With Cancer

CAVATICA is a cloud-based platform for collaboratively accessing, sharing, and analysing childhood cancer data.

Childhood cancer kills more children than any other disease in Australia and tragically, every week three children and adolescents in Australia currently die because of cancer.

Every child is different, every cancer is unique, and so treatment has to be tailored for each individual. To personalise medicine, doctors and researchers need to use the latest innovations and technologies that can provide a unique insight into an individual child’s cancer to enable identification of the drugs likely to target their cancer most effectively.

graphic of cancer cells

Enter CAVATICA

The platform allows scientists worldwide to rapidly access large amounts of genomic data and workflows within a computation and storage environment where they can share, process, integrate, and analyse data. Complex and comparative analyses can be achieved using various open source R and Python packages; and through CAVATICA’s Data Cruncher, data can be shared through interactive Jupyter Notebooks and RStudio.

The Australian Research Data Commons (ARDC), in partnership with Bioplatforms Australia, the Australian BioCommons, Children’s Cancer Institute in Australia, the Centre for Data Driven Discovery in Biomedicine (D3b) in the USA, and Seven Bridges, have been working to expand CAVATICA to utilise Amazon Web Services in Sydney and piloting new capabilities to support Australian initiatives such as Zero Childhood Cancer *.

A/Prof Mark Cowley, Computational Biology Group Leader at Children’s Cancer Institute, says the expansion of CAVATICA has already enhanced international collaboration by providing easier and faster approaches to sharing data and analysing rare childhood cancer data.

“Since we know so little about many paediatric cancer subtypes, it is essential that we share data globally. We may be able to better understand how to treat an Australian patient’s tumour by comparing it to larger numbers of American patients.

“The innovative technology of CAVATICA enables researchers from Australia and the United States to seamlessly share data and novel analysis methods with ease, driving improved outcomes and novel research,” A/Prof Cowley said.

The ARDC, the Australian BioCommons, and the Children’s Cancer Institute hosted a series of workshops and a webinar in early February 2020. Presented by Dr Allison Heath, Director of Data Technology and Innovation, D3b at the Children’s Hospital of Philadelphia, the webinar and a training workshop provided:

  • an overview of CAVATICA
  • how to use CAVATICA to create tools for data analysis and sharing
  • how to access and leverage existing production workflows.

The Gabriella Miller Kids First Data Resource Center (Kids First DRC) manages genomic data across structural birth defects and pediatric cancers. Kids First DRC has used CAVATICA to harmonise and process over 15,000 whole genomes, whole exomes, and RNA-seq, including alignment, somatic variant calling, structural variants, RNA expression and fusions.

Head over to CAVATICA’s dedicated website to find out more about the platform and read more about how the ARDC are collaborating with national and international organisations to help Australian researchers cure kids with cancer.

*The Zero Childhood Cancer Program is a joint initiative of Children’s Cancer Institute and Kids Cancer Centre, Sydney Children’s Hospital, Randwick.

Researchers at the CAVATICA training workshop

The Outcome: Improving the lives of children with rare cancer

Sydney Children’s Hospital recently implemented a new clinical trial program called the Zero Childhood Cancer Program. It uses rapid data access and sharing through the CAVATICA platform, allowing medical staff to quickly access global data related to new cancer cases.

As soon as a child is diagnosed and enrolled in the trial, researchers analyse the genetic and molecular make-up of their cancer cells and test hundreds of options to identify which drugs are most likely to be effective. Once a promising drug is identified, it is tested in living laboratory models to see how it performs. The results are used to develop a personalised treatment plan.

The trial is showing promising results. During the first 12 months, nearly 70 per cent of participating children were able to benefit from these rapidly produced treatment plans.

For some, the trial has been life saving.

Eleven-month-old Ellie was admitted to the hospital with a tumour in her chest and was enrolled in the program. A team rapidly identified the likely cause of her cancer and compared her genetic information with global data. They identified a new US anti-cancer drug that specifically targeted her case. After several weeks, Ellie was able to leave intensive care.

“The innovative technology of CAVATICA enables researchers from Australia and the United States to seamlessly share data and novel analysis methods with ease, driving improved outcomes and novel research,” said A/Prof Mark Cowley, Computational Biology Group Leader at Children’s Cancer Institute.

Support for the program continues to build. The Australian Government and the Minderoo Foundation recently announced an additional $67 million to expand the Zero program. This enables all Australian children and young adults who have been diagnosed with cancer to access targeted treatment through the collaborative research and clinical program.

Dr Stuart Newman

Therapeutic Innovation Australia

Since completing a PhD in Antarctic Biology from the University of Tasmania, Stuart has built up considerable experience of science policy, pharmaceutical R&D, grant funding, IP management, business development and commercialisation in the university and not-for-profit sectors.|

Stuart joined TIA as CEO in 2017. Under his leadership, TIA has focussed investment on the gap between research and development of high-value therapeutics, including pharmaceuticals, biologics, vaccines and cell & gene therapies. He also devised an innovative infrastructure access voucher scheme. He is a graduate of the Australian Institute of Company Directors

Beryl Morris

Terrestrial Ecosystem Research Network

Merran Smith

Population Health Research Network

Merran is the inaugural Chief Executive of Australia’s Population Health Research Network and chairs the PHRN Participant Council. She is a past Director of the International Population Data Linkage Network (2019-2020) and current member of the Pawsey Supercomputing Centre Board.

Merran has an extensive background in science, health, and economics with strengths in strategic leadership and many years’ experience in Australia’s health and research infrastructure systems.  She is well versed in data management and oversaw the WA Department of Health’s Health Information Centre for more than 10 years. While with the Department, she established data linkage as a core service and served on Australia’s peak national health information committees. 

Prof Michael Dobbie

Phenomics Australia

Prof. Michael Dobbie has worked to establish and operate Phenomics Australia since its foundation in 2007, serving as CEO since 2013. Prior to leading the development and implementation of these national research infrastructures, Michael was a biomedical research with a PhD in Neurochemistry from the University of London and gained over 20 Years’ experience at the bench in field including genetics, vascular biology, cancer angiogenesis, neuroscience, metabolism, developmental biology, malaria and oxidative stress.

Mark Stickells

Pawsey Supercomputing Centre

Mark is a research executive with more than 20 years’ experience working at a senior level in innovative research and business development roles in complex, multi-stakeholder environments. Through national and international programs and joint-ventures, Mark had successfully led initiatives to accelerate the impact of research, development and education programs for Australia’s key energy, mining and agricultural sectors.
He is a former Chief Executive of an LNG research and development alliance of CSIRO, Curtin University and UWA, partnering with Chevron, Woodside and Shell. Prior to his appointment at Pawsey Mark led the innovation and industry engagement portfolio at The University of Western Australia. In addition, Mark is the current Chair of the Board of All Saints’ College and was appointed an adjunct Senior Fellow of the Perth USAsia Centre (an international policy think tank) in 2017.

Craig Humphrey

National Sea Simulator

Craig Humphrey has worked at AIMS for more than 25 years. He presently serves as the Director of the National Sea Simulator, a position he has held for the last two years. During the ten years preceding his directorial role, Craig was instrumental in the initial conceptualisation, creation, and implementation of the SeaSim. Prior to joining the SeaSim team, Craig worked as an experimental scientist at AIMS for 15 years, where he conducted research on various projects including fish ecotoxicology, inshore reef biological indicators of water quality, and coral reef climate-related studies.

Wojtek Goscinski

National Imaging Facility

Prof Wojtek Goscinski, with over two decades of leadership in research and innovation, heads the National Imaging Facility (NIF), Australia’s premier imaging network. As CEO, he oversees NIF’s collaboration among universities, research institutes, and government agencies. An Adjunct Professor at Monash University, he contributes to the Faculty of Medicine, Nursing and Health Sciences. Prof Goscinski’s notable past roles include founding MASSIVE, a high-impact national analytics facility. He also serves on the Scientific Advisory Committee for Euro Bioimaging ERIC and has led significant international neuroinformatics programs.

Prof Sean Smith

National Computational Infrastructure

Sean Smith commenced as Director of the NCI in January 2018 and is conjointly Professor of Computational Nanomaterials Science and Technology at ANU. He has extensive theoretical and computational research experience in chemistry, nanomaterials and nano-bio science and technology.

Dr Lisa Yen

Microscopy Australia

Lisa is currently Microscopy Australia’s Chief Operating Officer and has over 15 years of experience in university administration, strategic research management in Centres of Excellence, and operations and management of national collaborative research infrastructure. She has been with Microscopy Australia since 2019. Lisa has a doctorate in cognitive science and a first–class honours degree in psychology.

Tamin Darwish

National Deuteration Facility (ANSTO)

Tamim leads the National Deuteration Facility at ANSTO, managing its operations and scientific advancements. With a Ph.D. in Chemistry, his expertise spans deuterium labeling, NMR spectroscopy, and organic synthesis. Tamim’s research focuses on creating deuterated molecules for advanced analytical techniques. His career includes postdoctoral fellowships and contributions to the field as a member of prestigious science communities and committees. His dedication to chemistry and material science is evident in his extensive work and achievements in the field.

Michael Steer

Southern Coastal Research Vessel Fleet

Professor Mike Steer is the Research Director at the South Australian Research and Development Institute (SARDI), with over 20 years of expertise in marine science. He specialises in fish biology, fisheries science, cephalopod ecology, and fishery reform. Dr. Steer has led numerous research initiatives that have significantly advanced Australia’s seafood industry. He is known for fostering collaborations between academia and industry to address challenges in aquatic ecosystems. Prof. Steer holds a PhD from the University of Tasmania and serves on several national committees, including the National Coastal Research Vessels Working Group and the National Marine Science Committee.

Toni Moate

Marine National Facility (CSIRO)

Toni Moate is Director of the Marine National Facility and Director of CSIRO’s National Collections and Marine Infrastructure business unit. 

Toni is responsible for ensuring CSIRO’s national collections and marine infrastructure programs and research areas are effectively positioned, managed and utilised for long term financial sustainability and support science delivery in the national interest. 

Toni has extensive experience in strategic, financial, project and stakeholder management and has worked for CSIRO for over 30 years. In 2015 Toni was awarded the Public Service Medal for outstanding public service in Australian marine and atmospheric science, as part of the Queen’s Birthday Honours List. This was followed in 2017 when Toni was awarded the Tasmanian Telstra Business Woman of the Year. 

Dr Michelle Heupel

Integrated Marine Observing System

Michelle Heupel, with over two decades in marine science, leads Australia’s Integrated Marine Observing System (IMOS) at the University of Tasmania. Her work, pivotal in deploying oceanic observing equipment, supports marine and climate research. Heupel’s expertise in marine predator ecology, especially sharks, is recognized globally. She has a BSc in Zoology and a PhD in Marine Science, contributing to over 160 scientific papers. Her roles have included Vice Chair of Strategy for the IUCN Shark Specialist Group and advisor for the Ocean Tracking Network. Heupel’s dedication to marine conservation and management reflects her profound impact on the field.

Thomas McGoram

Heavy Ion Accelerators

James Whisstock

European Molecular Biology Laboratory Australia

Professor James Whisstock is based at Monash University, where he is currently an Australian Research Council Laureate Fellow, an Honorary National Health and Medical Research Council Senior Principal Research Fellow and Deputy Dean Research in the Faculty of Medicine Nursing and Health Sciences.

Ceri Brenner

Centre for Accelerator Science (ANSTO - Nuclear Science Facilities)

Andrew Gilbert

Bioplatforms Australia

Andrew Gilbert has been Bioplatforms Australia’s general manager since its inception in 2007.
He is a graduate of the Australian Institute of Company Directors. Andrew oversees the investment of $300 million in Commonwealth Government research infrastructure funding in the discovery sciences of genomics, proteomics and metabolomics.
Andrew has an extensive network of contacts from Commonwealth and State Governments, along with prominent universities, medical research institutes, agricultural research institutes and commercial entities. The Bioplatforms Australia network now supports 4500 users per annum across the spectrum of pure research to commercial production. In addition to managing the national infrastructure network, Andrew has also catalysed the formation of a series of strategic national scientific collaborations.
Each of these projects is by design multi-disciplinary, multi-institutional and contain both discovery implications and pathways to end use.

Prof Pascal Perez

Aurin

Professor Pascal Perez is a specialist of Integrative Social Simulation, using Multi-Agent Systems technologies to explore complex infrastructure systems. He is a Fellow of the Royal Society of NSW and the Modelling and Simulation Society of Australia and New Zealand (MSSANZ). 

Professor Perez has published 200 refereed articles and book chapters. In 2002, he received an ARC-International Linkage Fellowship to develop social modelling research at the Australian National University. In 2006, he co-edited with his colleague David Batten the book ‘Complex Science for a Complex World’ (ANU E Press).

Rosie Hicks

Australian Research Data Commons

Rosie has 20 years’ experience working in Australia’s research infrastructure sector. With a career spanning every aspect of scientific instrumentation from product development and technical marketing to managing multi-user facilities, she works across academic and industry domains to drive innovation and research translation.

Richard Dichmann

Australian Plant Phonemics Facility

Richard is committed to advancing Australian agriculture through strengthening sustainable industry partnerships and creating new business opportunities which capitalise on innovation. His career with Bayer spans more than 25 years and five countries in roles ranging from marketing, technology scouting and sustainability. Hailing from rural Victoria and educated in Melbourne, Richard obtained an honours degree in Forestry from Melbourne University and a master’s degree in Agriculture, focusing on satellite remote sensing, from the University of Sydney. Richard is a graduate of the Australian Institute of Company Directors. As Head of Public and Government Affairs ANZ for Bayer Australia and New Zealand, Richard is dedicated to increasing awareness and understanding among political stakeholders of the critical role innovation plays in meeting the food supply and health challenges of the future. Richard is a proud ambassador for Australian agriculture and is married with four children.

Dr Jane Fitzpatrick

Australian National Fabrication Facility

Jane led ANFF’s Queensland node for a number of years, joining the HQ team as its Chief Operating officer in 2012, before becoming CEO in 2021. Her responsibilities include ensuring the network performs as a cohesive and collaborative community, and maximising ANFF’s ability to support projects from academia and industry.

Prof Andy Hogg

Australian Earth System Simulator (ACCESS-NRI)

Professor Andy Hogg is a distinguished climate scientist leading the ACCESS-NRI, where he oversees the development of Australia’s advanced climate models. As a key figure in COSIMA, he contributes to ocean-sea ice model research. His role as a Chief Investigator at the ARC Centre of Excellence for Climate Extremes underscores his commitment to understanding climate dynamics and extremes. His work is pivotal in shaping Australia’s approach to climate science and modeling, reflecting his dedication to environmental research and innovation.

Jamie Schultz

Australian Centre for Neutron Scattering (ANSTO - Nuclear Science Facilities)

Dr Debbie Eagles

Australian Centre for Disease Preparedness (CSIRO)

Debbie Eagles is currently the Director of CSIRO’s Australian Centre for Disease Preparedness (ACDP). Prior to this, Debbie’s roles with ACDP included 4 years as ACDP Deputy Director and 3 years as the Research Director for the Diagnosis, Surveillance and Response (DSR) Program.

Debbie is a veterinarian by training and a World Organisation for Animal Health (WOAH) Reference Laboratory Expert on Bluetongue Virus. She is also enrolled as a WOAH and Australian Qualified Expert on the UN Secretary-General Mechanism’s (UNSGM) Roster for investigations of Alleged Use of Chemical, Biological or Toxin Weapons, has postgraduate qualifications in veterinary public health and has a special interest in interactions at the field/laboratory interface. Debbie has extensive experience in working in the Asia Pacific region, including in laboratory capacity building projects, in field investigations and through the provision of training courses.

Heath Marks

Australian Access Federation

Heath Marks was appointed by the Council of Australian University Directors of Information Technology (CAUDIT) in July 2009 to head a team to deliver the sustainable operations of Australia’s Trust and Identity services for Research and Education. This includes the national trust authentication framework the Australian Access Federation (AAF), and the Open Researcher and Contributor ID (ORCID) Consortium Lead for Australia. He is an IT professional with a wealth of management experience in the successful delivery of transformational Information Technology within the tertiary education and research sector supporting the National Collaborative Research Infrastructure Strategy (NCRIS). Heath participates in many national and international committees and working groups on trust, identity, cyber security, and company strategy. 

Tim Rawling

AuScope

Tim Rawling is the CEO of AuScope Limited. AuScope is Australia’s provider of research infrastructure to the national geoscience community working on fundamental geoscience questions and grand challenges — climate change, natural resources security and natural hazards. Prior to this role, he was Director of Infrastructure Development for AuScope’s Australian Geophysical Observing System (AGOS). His recent research has involved the development of regional/crustal-scale 3D and 4D geological models as well as new exploration methodologies involving 3D modelling and finite element simulation. Tim’s background is in structural geology and IT and he has previously worked as a consultant exploration geologist, as the manager of the 3D modelling and simulation programs at GeoScience Victoria (DPI), as the MCA funded lecturer at the University of Melbourne, a commercial programmer and as a researcher at Monash University and the University of Arizona.

Dr Andre Zerger

Atlas of living Australia

Dr. Andre Zerger is a key figure at the Atlas of Living Australia (ALA), where he leverages his expertise in spatial sciences and eco-informatics to advance biodiversity research. His work at CSIRO and the Bureau of Meteorology has been instrumental in developing national data infrastructures. At ALA, he’s excited to lead the team in harnessing digital technologies to manage Australia’s largest biodiversity database, fostering collaboration and innovation in the field.

Mark McAuley

Astronomy Australia

Mark McAuley has worked for thirty years in research and development environments, with responsibility for securing investments, facilitating collaborations, and executing projects. As CEO of Astronomy Australia Limited, he is responsible for the NCRIS astronomy programme. Mark has previously worked for CSIRO, and in private industry, including six years in computer-aided engineering. His experience ranges from explaining science to young children to leading financial strategy discussions concerning billion-dollar research infrastructure projects.

Mark holds a Master of Business Administration, Master of Arts (Ancient History), and Bachelor of Science with Honours (Astrophysics). Upon completion of his MBA, he received the Vice-Chancellor’s Medal from the University of Notre Dame, Australia.