OpenPBTA: The Open Pediatric Brain Tumor Atlas

Joshua A. Shapiro, Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA.
Krutika S. Gaonkar, Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Stephanie J. Spielman, Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA.
Candace L. Savonen, Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA.
Chante J. Bethell, Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA.
Run Jin, Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Komal S. Rathi, Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Yuankun Zhu, Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Laura E. Egolf, Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
Bailey K. Farrow, Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Daniel P. Miller, Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Yang Yang, Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA.
Tejaswi Koganti, Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Nighat Noureen, Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA.
Mateusz P. Koptyra, Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Nhat Duong, Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Mariarita Santi, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Jung Kim, Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA.
Shannon Robins, Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Phillip B. Storm, Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Stephen C. Mack, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
Jena V. Lilly, Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Hongbo M. Xie, Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Payal Jain, Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Pichai Raman, Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Brian R. Rood, Children's National Research Institute, Washington, DC 20012, USA.
Rishi R. Lulla, Division of Hematology/Oncology, Hasbro Children's Hospital, Providence, RI 02903, USA.
Javad Nazarian, Children's National Research Institute, Washington, DC 20012, USA.
Adam A. Kraya, Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Zalman Vaksman, Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Allison P. Heath, Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Cassie Kline, Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.

Document Type

Journal Article

Publication Date

7-12-2023

Journal

Cell genomics

Volume

3

Issue

7

DOI

10.1016/j.xgen.2023.100340

Keywords

brain tumors; classification; open science; pediatric cancer; reproducibility; somatic variation; tumor atlas

Abstract

Pediatric brain and spinal cancers are collectively the leading disease-related cause of death in children; thus, we urgently need curative therapeutic strategies for these tumors. To accelerate such discoveries, the Children's Brain Tumor Network (CBTN) and Pacific Pediatric Neuro-Oncology Consortium (PNOC) created a systematic process for tumor biobanking, model generation, and sequencing with immediate access to harmonized data. We leverage these data to establish OpenPBTA, an open collaborative project with over 40 scalable analysis modules that genomically characterize 1,074 pediatric brain tumors. Transcriptomic classification reveals universal dysregulation in mismatch repair-deficient hypermutant high-grade gliomas and loss as a significant marker for poor overall survival in ependymomas and H3 K28-mutant diffuse midline gliomas. Already being actively applied to other pediatric cancers and PNOC molecular tumor board decision-making, OpenPBTA is an invaluable resource to the pediatric oncology community.

Department

Pediatrics

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