SYSTEMS

Seven Bridges has 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 inaccessible."

The 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 becomes, 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."