Publications

PedcBioPortal: A Cancer Data Visualization Tool for Integrative Pediatric Cancer Analyses

Neuro-Oncology

November 7, 2016
Pichai Raman, Adam C Resnick, Phillip B Storm, Sabine Mueller, Nikolaus Schultz, Ethan Cerami, John M Maris, Angela J Waanders.

Summary

The pediatric cancer genome is severely under-represented in genomic databases as existing data portals have primarily focused on adult cancers. Furthermore, large-scale datasets like TARGET remain devoid of pediatric brain tumor data. To address this unmet need, we have developed a new cancer visualization tool (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 St. Baldrick’s Pediatric Stand Up 2 Cancer Dream Team. 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 datasets. 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. Importantly, 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, application program interfaces (APIs) that support bioinformatics and data scientist access to data for large-scale analyses projects are available. PedcBioPortal is part of an evolving cloud-based eco-system of applications dedicated to the empowered use of pediatric largescale data that encompass and integrate the translational cancer research workflow from a biospecimen availability, to processing of raw data, and 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, consisting of Memorial Sloan-Kettering Cancer Center, Dana Farber Cancer Institute, Princess Margaret Cancer Centre in Toronto, Children’s Hospital of Philadelphia, The Hyve in the Netherlands, and Bilkent University in Ankara, Turkey.