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App Integrates Mutation Data for Pediatric Cancer Research

"For St. Jude, the application is the foundation for developing a global reference database for information about pediatric cancer."

By Frank Irving

A new web application and data set brings the power of visualization to health data exchange in pediatric cancer research. Scientists at St. Jude Children’s Research Hospital developed the freely available tool, ProteinPaint, which aims to advance understanding of the mutations that lead to and fuel childhood cancer.

An article describing ProteinPaint appears in the Dec. 29 online version of Nature Genetics. The app provides researchers with gene-by-gene snapshots of mutations that alter genetic instructions for encoding proteins. It shows whether mutations are present at diagnosis or just at relapse, and whether mutations occur in most cells (germline) or strictly cancer cells.

Interactive infographics let researchers “see at a glance all mutations in individual genes and their corresponding proteins, including detailed information about mutation type, frequency in cancer subtype and location in the protein domain,” according to a statement issued by St. Jude. “That information provides clues about how a change might contribute to cancer’s start, progression or relapse.”

Corresponding author Jinghui Zhang, PhD, chair of the the St. Jude Department of Computational Biology, said ProteinPaint is intended to be an intuitive tool easily usable by any scientist working on cancer genomics.

ProteinPaint integrates mutation information from multiple data sets and incorporates findings from St. Jude, Washington University Pediatric Cancer Genome Project, the National Cancer Institute and other published pediatric cancer studies.

The app currently includes information on nearly 27,500 mutations discovered in more than 1,000 pediatric patients with 21 cancer subtypes. The project calls for the data to be updated as new information is published.

The app’s developers use the curated data to overlay detailed, annotated information about each mutation on the affected protein. First author Xin Zhou, PhD, senior bioinformatics research scientist at St. Jude, developed the infographics to display the range of genomic information in an interactive format. “A click of the mouse gives users additional details about the mutations, including the pediatric subtype where the change has been validated, and a link to the publication,” the St. Jude statement says.

In addition, the app “paints” RNA-sequencing data from 928 pediatric tumors from 36 subtypes to track how mutations affect gene expression. The RNA-sequencing information is used to develop and deliver individualized cancer therapies.

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

The software also has the potential to help researchers studying other disorders, such as sickle cell disease, that involve a mutation affecting protein function, according to Zhou.

Academic researchers can use ProteinPaint to analyze their own data at no cost. The app also lets researchers compare pediatric and adult cancer genomes by providing a parallel view of data from COSMIC, a large database of mutations primarily from adult cancer.

Previous research, which appeared in the Nov. 18 online edition of the New England Journal of Medicine, described the tool’s use in studying the role of germline mutations in pediatric cancer.

Photo credit: St. Jude Children’s Research Hospital / Peter Barta





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