OpenPBTA

Crowdsourcing expertise of pediatric brain cancer experts from across the world to gain a deeper understanding of one of the leading causes of death in children and young adults.

It is estimated that 4,630 new cases of pediatric brain tumors will be diagnosed in the U.S. in 2021. Brain tumors, more than any type of tumors, have a long lasting and life-altering impact on the patient, physically, cognitively, and psychologically. Despite advances in biomedical research, there is no approved drug to specifically treat pediatric brain tumors. (Source)

Organized in collaboration with Center for Data-Driven Discovery in Biomedicine at Children’s Hospital of Philadelphia, OpenPBTA analyzes a vast collection of pediatric brain tumor data, comprising data from over 1,000 tumors. It is analyzed in the open and the results are made available publicly in real-time on GitHub.

Chart: Co-occurrence and mutual exclusivity of nonsynonymous mutations between genes.

Co-occurrence and mutual exclusivity of nonsynonymous mutations between genes.

Collaborative

46 contributors across 18 institutions have made contributions to setting up infrastructure, managing, and analyzing PBTA data within the first year of the project.

Real Time and Publicly Available

It usually takes 6 months for the results of an analysis to become public through the peer review and publishing process.  Even then, analysis code and data may not be publicly available.

We make the data, the analysis code, and the results publicly available in real time on GitHub, as each analysis passes the review process.

Reusable Workflows

The workflows are reusable. They will continue to be applied as the PBTA data grows to include additional samples and can be reused to study other pediatric cancers.

Transferable Practices and Skills

The project helps contributing researchers cultivate skills and best practices for robust and reproducible analysis, so they may utilize this knowledge in their own research projects.