A collaborative effort between a research team at the University of California, San Francisco (UCSF) and ISB Cancer Gateway in the Cloud (ISB-CGC) enhanced the cloud-based data infrastructure needed to conduct a large breast cancer research consortium study, leveraging Google BigQuery data tables and analytical tools. Amrita Basu, PhD, was an integral part of the UCSF/ISB-CGC collaboration and continues to use the tables and tools developed through this work in ongoing clinical trial studies. 

The UCSF/ISB-CGC collaboration built upon the data infrastructure required for the Investigation of Serial Studies to Predict Your Therapeutic Response with Imaging and Molecular Analysis (I-SPY 2 Trial), a long-running, multi-site clinical trial that focuses on improving treatment outcomes.The I-SPY 2 research consortium seeks to identify new drug agents that are most effective for specific breast cancer tumor types, using genomic, proteomic, and pathology imaging data to uncover biomarkers and early indicators of therapeutic response. Dr. Laura Esserman, Director of the UCSF Breast Care Center, serves as the principal investigator of the I-SPY Trial program.  

The UCSF/ISB-CGC collaboration resulted in the Patient Repository of Biomolecular Entities (PRoBE) toolkit, which streamlined the collection, management, and sharing of complex, large-scale data across multiple clinical sites within the I-SPY 2 consortium. The authors published about the PRoBE toolkit in their paper titled PRoBE the Cloud Toolkit: Finding the Best Biomarkers of Drug Response within a Breast Cancer Clinical Trial. The data tables and tools developed through this collaboration are accessible to researchers who meet the data security requirements for accessing I-SPY 2 data.

Commenting on her current work using the tools developed through this collaboration, Dr. Basu explains, “The earlier work with ISB-CGC has supported my work to add more data fields related to specific therapeutic combinations, side effects over time, and patient outcomes. For busy clinicians evaluating both patient-reported quality of life metrics and treatment response, data collection and sharing process must be straightforward. The work done years ago is proving invaluable as we now incorporate additional data into the I-SPY 2 datasets and compare them with data from newly recruited patients."

Dr. Basu’s current research aims to refine the use of targeted drugs based on known biomarkers—the original focus of I-SPY 2—while also prioritizing the avoidance of serious side effects, a factor often overlooked in large-scale studies. She highlights the lack of a standard methodology in clinical trial studies for effectively tracking patient-centered data, which requires coordinated data collection, management, and analysis across diverse teams in multi-site trials. Her team is testing this methodology with a group of I-SPY 2 patients, as well as a distinct cohort from UCSF. 

The ISB-CGC team that worked on the PRoBE toolkit represents one of three NCI Cloud Resources. ISB-CGC is dedicated to training research teams in the Google platform and BigQuery tables and tools. David Gibbs, PhD, Senior Research Scientist at ISB-CGC and co-author of the PRoBE paper, notes that the teams overcame numerous technical challenges between 2015 and 2019 in preparation for the publication. “We focused on data compatibility and security, which are now all standard procedures. We also prototyped processes and tools to make pathology images from multiple sources accessible through a standardized imaging format."

In developing these tools and infrastructure enhancements, the UCSF/ISB-CGC team ensured that I-SPY 2 consortium members with varying levels of data science expertise could contribute and use the data for follow-on studies. Dr. Basu is now enabling clinical researchers to share more types of data, including quality-of-life measures. As she notes, this expanded approach opens new possibilities for advancing precision and personalized medicine.

Learn more about I-SPY 2 Consortium

Find the biosketch for Dr. Basu, Professor of Surgery, University of California San Francisco (UCSF) 

Find the biosketch for Dr. Esserman, MD, PhD, Principal Investigator on the I-SPY Trial program and co-author on the PRoBE paper  

Find the biosketch for David Gibbs, PhD, co-author of the PRoBE paper and part of the USCF/ISB-CBC collaboration

Find datasets used by ISPY-2 within ISB-CGC: 

• TCGA
• Pan Cancer Atlas

Find I-SPY 2 imaging data available through the CRDC Imaging Data Commons:

Find the code used to execute the RShiny applications in the cloud by the UCSF team:

• Gene expression
• Drug Response
• Clinical Data Cohorts