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St. Jude Team Introduces Interactive Tool for Assessing Pediatric Cancer Cases

NEW YORK (GenomeWeb) – In a correspondence article published in this week's issue of Nature Genetics, a St. Jude Children's Research Hospital team describes an interactive web application known as ProteinPaint that is designed to visualize the impact of gene mutations and fusions in pediatric cancer genomes.

ProteinPaint currently houses information on nearly 27,188 validated somatic mutations — along with more than 250 pathogenic or loss-of-function mutation detected in the germline — of more than 1,000 children with cancer assessed through the St. Jude Children's Research Hospital-Washington University Pediatric Cancer Genome Project (PCGP), the National Cancer Institute's Therapeutically Applicable Research to Generate Effective Treatments initiative, and other pediatric cancer efforts.

Infographics within ProteinPaint present features such as mutation sites in a particular gene, information on the number of samples containing a given mutation, mutant allele frequencies, and so on, coupled with relevant RNA expression profiles generated for more than 900 pediatric tumors from three-dozen cancer subtypes, the researchers explained.

The tool not only distinguishes between germline and pediatric mutations, they noted, but also provides information on whether mutations have been detected in diagnostic tumor samples or during cancer progression and relapse.

"ProteinPaint's focus on pediatric cancer and presentation of mutations at the gene level complements existing cancer genome data portals," first author Xin Zhou, a computational biology researcher at St. Jude, said in a statement. "For St. Jude, the application is the foundation for developing a global reference database for information about pediatric cancer."

The method is intended to complement and expand on existing cancer databases and visualization tools, many of which focus on adult cancer genomes, he and his colleagues explained. "[E]xisting cancer genome data portals … lack features for exploring pathogenic germline mutations, gene fusions, and mutation stratification by cancer subtype, all of which are of great importance in pediatric cancer," they wrote.

For example, Zhou and other members of the PCGP applied the approach in a recent study published in the New England Journal of Medicine, which described cancer-related germline mutations identified by genome and/or exome sequencing in samples from 1,120 children affected by a wide range of cancer subtypes.

Zhou noted that a similar approach is expected to prove useful for studying other diseases involving protein-impacting mutations such as sickle cell disease. A ProteinPaint demonstration is available through the St. Jude Pediatric Cancer Data Portal, or PeCan. The application is freely available to academic researchers.

"Data in mutation annotation format generated by studies such as The Cancer Genome Atlas or individual research laboratories can be uploaded to ProteinPaint to enable data visualization and cross-study comparison for the broad genetic research community," the authors wrote.