New St. Jude software explores sources of pediatric cancer mutations
Researchers at St. Jude Children's Research Hospital have developed an interactive web application and dataset that puts pediatric cancer mutations and growth under a microscope, a new article from Nature Genetics reveals.
ProteinPaint includes information of about 27,500 mutations from more than 1,000 pediatric patients, with 21 types of cancer subtypes. Data is updated as new information is published.
Datasets are incorporated from findings of St. Jude's Children's Research Hospital, Washington University Pediatric Cancer Genome Project, the National Cancer Institute's Therapeutically Applicable Research to Generate Effective Treatments initiative and various published pediatric cancer studies.
Developers use this curated data to create layers of information about mutations on affected proteins. The first author of the study, Xin Zhou, St. Jude senior bioinformatics research scientist, developed the infographics to display a range of genomic data in an interactive format.
"ProteinPaint's focus on pediatric cancer and presentation of mutations at the gene level complements existing cancer genome data portals," said one of the study's authors, Jinghui Zhang, chair of the St. Jude Department of Computational Biology.
"For St. Jude, the application is the foundation for developing a global reference database for information about pediatric cancer," she added.
The software gives users a gene-by-gene snapshot of pediatric cancer mutations that alter genetic encoding proteins and features interactive infographics and creates a detailed snapshot of all individual mutations and proteins - including mutation type, cancer subtype frequency and its precise location.
All of this data crucial to determining what the changes mean in terms of the start, progression or relapse of cancer.
Multiple types of mutations disrupt protein-coding genes that lead to cancer, but ProteinPaint integrates mutation information from various datasets increasing research information to target the cause.
Users can interact with the platform to learn more about the mutation, its subtype and are directed to applicable publications for additional information. The software can also potentially be used for other conditions that affect protein function mutations, such as sickle cell disease.
"Each day brings new information about mutations that drive human cancer. Novel tools are essential to help scientists use this wealth of genomic data to advance research and find new cures," Zhang said.
"We developed ProteinPaint as an intuitive tool any scientist can easily use to explore the vast amount of information now available on cancer genomics," she added.
ProteinPaint can also create images of RNA-sequencing of over 900 pediatric tumors from 36 sub-types to track the path of mutations and how it affects genes – data crucial to helping providers create individualized treatment plans for their patients.
Academics from around the world can access ProteinPaint for free to analyze their own datasets, can also allow researchers to compare cancer information from COSMIC, the largest database of somatic mutations - mostly of adult cancer. This information can help interpret rare mutations.