Collaborative Corner

PedcBioPortal Cancer Visualization

pedcbioportal_logo

 

 

June 6, 2016

Contributing Authors: Pichai Raman,  Angela J Waanders, Sabine Mueller, Adam C Resnick,  and John Maris on behalf of the CBTTC, PNOC and SU2C-St. Baldrick’s Pediatric Cancer Dream Team

The pediatric cancer genome is severely under-represented in genomic databases as existing data portals have primarily focused on adult cancers. Furthermore, large-scale data sets like TARGET remain devoid of pediatric brain tumor data. PedcBioPortal was developed to address this unmet need. (http://pedcbioportal.org).

PedcBioPortal is an instance of cBioPortal supporting the curation and pan-cancer integration of published pediatric cancer data and consortia-based efforts including the Children’s Brain Tumor Tissue Consortium (CBTTC), the Pediatric NeuroOncology Consortium (PNOC), and the SU2C- St. Baldrick’s Pediatric Cancer Dream Team.

Open Access to Genomic Data

The aim of PedcBioPortal is to lower the barrier to large-scale pediatric and pan-cancer genomics analysis by providing rich visualizations and detailed statistics/summaries that integrate multi-dimensional data sets. Key functionalities include the ability to view mutations and copy number aberrations along the genome, correlations between gene expression profiles, and protein-protein interaction networks. Clinical trials data, pharmacological agent information, pathology reports, and tissue images are all incorporated, demonstrating the platform’s ability to store both structured and unstructured data. Researchers can also download data for further investigation and discovery efforts.  Additionally, API’s that support access to data for large-scale analyses projects are also available to bioinformaticians and data scientists.

The PedcBioPortal is part of an evolving cloud-based eco-system of applications dedicated to the empowered use of pediatric large-scale data that encompass and integrate the translational cancer research workflow through 1) bio-specimen availability, 2)processing of raw data, and 3) the interpretation of summarized data.  As such, users can easily move between samples in PedcBioPortal to raw data files and even to physical specimens.

PedcBioportal software is developed and maintained by a multi-institutional team including Memorial Sloan-Kettering Cancer Center, Dana Farber Cancer Institute, Princess Margaret Cancer Centre in Toronto, The Children’s Hospital of Philadelphia, The Hyve in the Netherlands, and Bilkent University in Ankara, Turkey.

 

 

Leave a comment

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.