Powerful interactive tool to mine data from cancer genome

Powerful interactive tool to mine data from cancer genome

St. Jude Children's Research Hospital scientists have developed a web application and data set that gives researchers worldwide a powerful interactive tool to advance understanding of the mutations that lead to and fuel pediatric cancer. The freely available tool, called ProteinPaint, is described in today's issue of the scientific journal Nature Genetics.

ProteinPaint provides users with a gene-by-gene snapshot of mutations from pediatric cancer that alters genetic instructions for encoding proteins. The application provides critical information unavailable with existing visualization tools. For example, ProteinPaint shows whether mutations are present at diagnosis or just at relapse, or whether mutations occur in almost every cell (germline) or just cancer cells (somatic).

ProteinPaint's novel interactive infographics also 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.

There are multiple types of mutations that disrupt the structure of protein-coding genes and lead to cancer. ProteinPaint integrates mutation information from multiple data sets, which boosts its power as a research tool. 

ProteinPaint currently includes information on almost 27,500 mutations discovered in more than 1,000 pediatric patients with 21 cancer subtypes. The data will be updated as new information is published.

The application also '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.

The application also '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.

https://www.stjude.org/media-resources/news-releases/2015-medicine-science-news/st-jude-researchers-develop-powerful-interactive-tool-to-mine-data-from-cancer-genome.html
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