St. Jude ProteinPaint adopted by the National Cancer Institute for cancer data visualization

The St. Jude ProteinPaint platform provides comprehensive data analysis and dynamic viewing capabilities for cancer research. In recognition of the platform’s excellence as a leader in data visualization, the National Cancer Institute (NCI) recently adopted the platform as the new visualization program for their large cancer genetic data portal.

“ProteinPaint is suddenly front and center on this global cancer research stage,” said Xin Zhou, PhD, St. Jude Department of Computational Biology, who designed and developed ProteinPaint over the last nine years. “Previously, we were just in the pediatric cancer space. Now, it is part of the Genomic Data Commons, a national government-maintained database for all human cancers, including pediatric and adult disease.”

Historically, visualizing cancer-derived genetic data has been complicated. Cancer DNA is different from normal human DNA. Many modifications can occur, especially in adult cancer. From deletions or duplications of chromosomes to fused genes, point mutations to novel complex interacting aberrances — cancer genomes can be complex. 

As such, the NCI has struggled to create a digital portal that could help investigators study, understand and visualize the data. The Genomic Data Commons (GDC) has attempted several variations. In 2020, they created a temporary contract with St. Jude to enhance the portal. That contract has been extended every year since, and now GDC is adopting ProteinPaint as its primary visualization and analysis tool.

“NCI wanted to generate a new portal version and support ProteinPaint integration there,” Zhou explained. “It included multiple distinct tools — all from our end — that are part of the ProteinPaint software system. The work was intensive, but we finally launched it early this year.”

ProteinPaint will propel oncology research

“Xin Zhou’s ProteinPaint is a remarkable software package that we are thrilled to include in the NCI Genomic Data Commons; it will accelerate progress in cancer research by enabling discoveries by scientists around the world using cancer genomic data,” said Louis M. Staudt, MD, PhD, NCI Center for Cancer Genomics director.

The inherent complexity of oncology genomes prohibited the previous creation of a universal visual language that enabled analysis. GDC previously catered to a highly accessible but lower information visual format. ProteinPaint consists of both a visual representation and an analytical platform with a high information density. It can visually summarize even some of the most complex genetic alternations and related information. 

“Before ProteinPaint, there was no proper way to visualize this data at the genomic, sample and patient levels while considering the demographics and other datasets associated with the patient,” said Karishma Gangwani, PhD, St. Jude Department of Computational Biology, a postdoctoral research associate in Zhou’s lab. “The platform enables scientists to combine many multivariable datasets.”

To use ProteinPaint, researchers can click information, segregating data as they need. For example, they can specify a cancer subtype and then focus on a specific gene, zooming in on one or a set of mutations within that gene. All subsequent analyses can be run within GDC’s cloud service. That ease of use enables scientists from more resource-limited settings the opportunity to work with that data. The final analyzed results are provided in a compelling visual representation.

“We want the visualizations to be as self-explanatory as possible,” Gangwani said. “We want researchers to take these images straight from the portal to strike their audience with what each chart is trying to communicate.”

Put on the finishing touches

Collaboration is the reason ProteinPaint has worked so well and attracted GDC. From when Zhou started creating the original version, he worked together with oncologists. Every feature was taken to the actual researchers who may use such a portal and then revised based on their feedback for more than five years. With that knowledge, it is perhaps unsurprising that NCI’s oncology researchers saw ProteinPaint as an opportunity.

Going forward, Zhou’s group will be collecting feedback from the greater oncology field as they use the portal. The GDC is currently available for use so scientists can make their foray into visual artistry, empowered by ProteinPaint to push oncology research into the future.