ProteinPaint: Web Application for Visualizing Genomic Data (SJ-15-0021)

St. Jude Reference #SJ-15-0021

Description

Researchers at St. Jude have invented a better way to visualize mutations in the context of human genes and proteins. This web application assimilates complex genomic data and associated phenotypic information in a way that is far superior to currently available applications.  A demo of this application, which can be manipulated by the user, is available at https://pecan.stjude.org/proteinpaint/TP53.

The software developed for this project highlights critical attributes about the mutations, including the form of protein variant (e.g. the new amino acid as a result of missense mutation), the name of sample from which the mutation was identified, whether the mutation is somatic or germline, and whether the mutation appears during the relapse phase of treatment. The software was developed to far exceed existing standards for user interface by, among other things, maintaining legibility when showing large amount of mutation data, displaying the mutational profiles of the same protein across multiple data sets for the purpose of cross-project comparison, and by showing the relevant expression level of the same gene in the biological samples in which the mutations were discovered. Novel 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. That information provides clues about how a change might contribute to cancer’s start, progression or relapse.

The application “paints” RNA-sequencing data from 928 pediatric tumors from 36 subtypes to track how mutations affect gene expression. While whole genome sequencing reveals the complete DNA makeup of an organism, RNA sequencing provides a snapshot of how instructions encoded in DNA are transcribed into RNA molecules. The information is essential for developing and delivering individualized cancer therapies.

In addition to data from the St. Jude Children’s Research Hospital—Washington University Pediatric Cancer Genome Project, the National Cancer Institute’s Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative and other published pediatric cancer studies can be incorporated as well. It currently includes information on almost 27,500 mutations discovered in more than 1,000 pediatric patients with 21 cancer subtypes, with more data to be uploaded as information is published. Additionally, it is not limited to this data or even to humans, as it can also be used for all animal and plant genomes.


 

Keywords

Protein, gene, mutation, gene expression, visualization


 

Granted Patents or Published Applications

© Copyright 2015 St. Jude Children’s Research Hospital. This software is also protected by a pending United States patent application.


 

Related Scientific References

Watch a demo, explore and use the tool here: https://pecan.stjude.org/proteinpaint/TP53
(For a full demo, scroll to the bottom of the page and on the far side of “2015 © St. Jude Children's Research Hospital — Pediatric Cancer Data Portal” click the up arrow to minimize the paint tool, and display the demo screen.)

Exploring genomic alteration in pediatric cancer using ProteinPaint
Jinghui Zhang, Ph.D. and Xin Zhou, Ph.D., Nature Gen  Dec 29, 2015. doi:10.1038/ng.3466.

The tool was used to study the role played by germline mutations in pediatric cancer. The research appeared in the November 19 edition of the New England Journal of Medicine.


 

Licensing Opportunities

This software is provided freely for nonclinical academic research use only. Anyone interested in any other use of this software, including commercial use or sale, should contact Chad Riggs at chad.riggs@stjude.org.

Related Links

Contact the Office of Technology Licensing (Phone: 901-595-2342, Fax: 901-595-3148) for more information.