St. Jude team creates tool to visualize pediatric cancer mutations

A team at St. Jude Children's Research Hospital has created a tool to visualize the mutations that lead to pediatric cancers. The free application, called ProteinPaint, displays genetic lesions such as sequence mutations and gene fusion alongside RNA expression.

Xin Zhou, a senior bioinformatics research scientist at St. Jude, designed the tool in collaboration with other hospital employees to fill a perceived gap in the existing ecosystem of cancer genome data repositories. While offerings such as BioPortal and the Catalogue of Somatic Mutations in Cancer have improved access to data on cancers that affect adults, the team at St. Jude identified a lack of equivalent portals focused on the genetics of pediatric oncology. ProteinPaint, which was presented in a letter to the Nature Genetics editor this week, is intended to be such a pediatric-focused portal.

"ProteinPaint's focus on pediatric cancer and presentation of mutations at the gene level complements existing cancer genome data portals," Jinghui Zhang, chair of St. Jude's department of computational biology, said in a statement. The team at St. Jude plans to use the current version of ProteinPaint as a launchpad for the creation of a comprehensive repository of pediatric cancer data. "For St. Jude, the application is the foundation for developing a global reference database for information about pediatric cancer," Zhang said.

As it stands, ProteinPaint covers 27,000 somatic coding lesions, 252 germline lesions found in more than 1,000 patients and RNA sequencing data from more than 900 pediatric tumors. The name "ProteinPaint" is derived from what St. Jude has done with this data. Annotated information is "painted" over the top of protein mutations to provide users with additional details. Users can pull up information on the pediatric cancer subtype in which a mutation has been validated and links to the relevant research by clicking on the section of interest.

- read the release
- here's the letter (sub. req.)