Expansion of the CAVATICA Platform to Australia Enables Harmonized Analysis of Geographically Separated and Jurisdictionally Protected Data Resources
BOSTON, June 2, 2020—Seven Bridges, the industry-leading bioinformatics ecosystem provider, today announced a collaborative partnership between The Gabriella Miller Kids First Data Resource Center (Kids First DRC), ZERO Childhood Cancer (ZERO), the Children’s Brain Tumor Tissue Consortium (CBTTC), the Australian BioCommons and the Australian Research Data Commons (ARDC). The multinational genomic cancer research project aims to establish internationally federated computational infrastructure that will enable the harmonization of pediatric cancer data from ZERO Australia with the extensive genomic datasets from CBTTC and Kids First DRC. Through this collaboration, researchers hope to better understand rare pediatric brain cancer subtypes and improve interventions for patients and their families.
Large-scale cancer whole genome sequencing (WGS), RNA-Seq and methylome analyses have made a substantial impact on our understanding of many cancers, including their etiology, identifying disease subtypes, novel pathways and new drug targets. While there are a number of extensive genomic cancer research programs globally, most focus on adult cancer; however, as all high-risk pediatric cancer subtypes are rare diseases, statistically significant correlation between subtype and genomic variation is inherently dependent on large sample numbers.
“Childhood cancer kills more children than any other disease in Australia and every week three children and adolescents in Australia die because of cancer,” said Mark Cowley, Ph.D., Associate Professor of the Children’s Cancer Institute. “Every child is different, every cancer is unique, so treatment has to be tailored for each individual. Through an international data collaboration on pediatric cancer subtypes, we hope to better understand how to treat the cancers we find in Australia, based on information that was previously unaccessible.”
Research will be done on the CAVATICA Platform, a cloud-based system for collaboratively accessing, sharing and analyzing childhood cancer data. The CAVATICA Platform, powered by Seven Bridges, allows clinicians and 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 analyze data. Complex and comparative analyses can be achieved using various open source R and Python packages; and through the Data Cruncher feature, data can be shared through interactive Jupyter Notebooks.
“The CAVATICA Platform enables us to seamlessly collaborate, share, interoperate and connect with other researchers studying pediatric cancer, driving improved outcomes and novel research,” said Adam Resnick, Ph.D., Kids First Data Resource Principal Investigator. “The platform has enabled us to harmonize and process over 15,000 whole genomes, whole exomes and RNA-seq, including alignment, somatic variant calling, copy number calls, structural variants, RNA expression and fusions. Additionally, integrations with the Kids First Data Resource Center portal allow users to create cohorts and manage their analysis in secure, cloud-based projects in CAVATICA.”
To enable this multinational collaboration, the CAVATICA Platform is being expanded to enable harmonized analyses across geographically separated and jurisdictionally protected data datasets, in this case across Australia and the United States. The extended CAVATICA orchestration engine will allow ZERO and Kids First workflows and analysis tools to be used interchangeably and seamlessly across both datasets. From the researcher’s perspective, the platform aggregates the separate datasets into a single virtual pan-continental dataset that is highly accessible through a global best practice analysis platform.
“By connecting pediatric researchers across international borders through the CAVATICA platform, we are also breaking down borders between data silos through the use of the global standard Common Workflow Language (CWL) and the ease of multi-cloud computing,” said Brandi Davis-Dusenbery, Ph.D., Chief Scientific Officer of Seven Bridges. “This enables our researchers to focus on treatments for kids with rare cancers rather than data challenges.”
About Seven Bridges
Seven Bridges enables researchers to extract meaningful insights from genomic and phenotypic data in order to advance precision medicine. Our complete bioinformatics ecosystem consists of a compliant analytics platform, seamless data and automation, and expert scientific services. This holistic approach to bioinformatics is enabling researchers — at the world’s leading academic, biotechnology, government, medical centers, and pharmaceutical entities — to increase R&D efficiency, enhance the hypothesis resolution process, isolate critical biomarkers, and even turn a failing clinical trial around while also reducing computational workflow times and data storage costs. To learn more, visit sevenbridges.com or follow us on LinkedIn and Twitter.
About The Gabriella Miller Kids First Pediatric Research Program Data Resource Center
The NIH Common Fund-supported Gabriella Miller Kids First Data Resource Center (Kids First DRC) is a collaborative pediatric research effort created to accelerate data-driven discoveries and the development of novel precision-based approaches for children diagnosed with cancer or a structural birth defect using large genomic datasets. The Kids First DRC is comprised of integrated core teams that support development of leading-edge big data infrastructure and provide the necessary resources and tools to empower researchers and clinicians.
As part of the Common Fund’s Gabriella Miller Kids First Pediatric Research Program, the Kids First DRC is charged with:
- Developing data-driven platforms that integrate large amounts of genomic and clinical data from different disease types.
- Empowering the collaborative discovery, engagement, and necessary partnerships across disease communities that are crucial for progress in our biological understanding of diseases.
- Enabling rapid translation to personalized treatments for patients diagnosed with childhood cancer or structural birth defects.
- Accelerating discovery of genetic causes and shared biologic pathways within and across these conditions.
About the Children’s Brain Tumor Tissue Consortium
The mission of the Children’s Brain Tumor Tissue Consortium (CBTTC) is to find cures and improve treatments for children diagnosed with brain tumors. To that end, the CBTTC collects high-quality brain tumor biospecimens and associated clinical data to facilitate the genomic analysis of biospecimens. Cell lines are developed and transplantable tumor models are then created from tumor specimens. These models allow researchers to share their findings with other CBTTC member institutions and with the world-wide scientific community. The CBTTC has established a collaborative multi-institutional tissue and data repository to enable the collection and analysis of high-quality brain tumor specimens. In addition to specimen data, the repository also links to clinical data to provide a comprehensive snapshot of each unique tumor.
Additionally, the CBTTC is committed to the advancement of tissue-based research, allowing researchers throughout the world to access molecular analysis of brain tumor specimens. These initiatives will allow for improvements in therapeutic treatment of patients diagnosed with a brain tumor.
About the Australian BioCommons
The Australian BioCommons is building digital capability for Australian life science research through the coordination and provision of bioinformatics and bioscience data infrastructures at a national scale. With a focus on active engagement with research communities, shared digital infrastructures are being developed and maintained in partnership with international peer infrastructures. The Australian BioCommons is tailoring services that provide sophisticated analysis capabilities, including both software and hardware platforms. Training and support solutions are streamlining access to the digital techniques, data and tools that are essential to environmental, agricultural and biomedical research. For more information online about the Australian BioCommons or follow us on Twitter.
About Children’s Cancer Institute
Originally founded by two fathers of children with cancer in 1976, Children’s Cancer Institute is the only independent medical research institute in Australia wholly dedicated to research into the causes, prevention and cure of childhood cancer. Forty years on, our vision is to save the lives of all children with cancer and improve their long-term health, through research. The Institute has grown to now employ over 300 researchers, operational staff and students, and has established a national and international reputation for scientific excellence. Our focus is on translational research, and we have an integrated team of laboratory researchers and clinician scientists who work together in partnership to discover new treatments which can be progressed from the lab bench to the beds of children on wards in our hospitals as quickly as possible. These new treatments are specifically targeting childhood cancers, so we can develop safer and more effective drugs and drug combinations that will minimise side-effects and ultimately give children with cancer the best chance of a cure with the highest possible quality of life. More at www.ccia.org.au.
About Zero Childhood Cancer (ZERO)
The Zero program is led by Children’s Cancer Institute and the Kids Cancer Centre at Sydney Children’s Hospital, Randwick bringing together all major Australian clinical and research groups working in childhood cancer to offer Australia’s first ever personalised medicine program for children with high-risk or relapsed cancer.
About the Australian Research Data Commons
The Australian Research Data Commons (ARDC) is a transformational initiative that enables Australian research community and industry access to nationally significant, leading edge data intensive eInfrastructure, platforms, skills and collections of high-quality data. Our purpose is to provide Australian researchers competitive advantage through data. For more information visit online or follow us on LinkedIn and Twitter.
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