OpenPBTA: An Open Pediatric Brain Tumor Atlas
Authors: Shapiro Joshua A. , Gaonkar Krutika S. , Savonen Candace L. , Spielman Stephanie J. , Bethell Chante J. , Jin Run , Rathi Komal S. , Zhu Yuankun , Egolf Laura E. , Farrow Bailey K. , Miller Daniel P. , Yang Yang , Koganti Tejaswi , Noureen Nighat , Koptyra Mateusz P. , Duong Nhat , Kraya Adam A. , Kline Cassie , Guo Yiran , Storm Phillip B. , Nazarian Javad , Mack Stephen C. , Raman Pichai , Zheng Siyuan , Madsen Peter J. , Van Kuren Nicholas , Robins Shannon , Huang Xiaoyan , Waanders Angela J. , Kim Jung , Hanson Derek , Koschmann Carl J. , Diskin Sharon J. , Lulla Rishi R. , Brown Miguel A. , Wong Jessica , Mason Jennifer L. , Scolaro Laura , Kim Meen Chul , Xie Hongbo M. , Rood Brian R. , Cole Kristina A. , Margol Ashley S. , Vaksman Zalman , Kaufman Rebecca S. , Heath Allison P. , Ennis Brian M. , Santi Mariarita , Poetsch Anna R. , Viaene Angela N. , Stewart Douglas R. , Foltz Steven M. , Jain Payal , Zhang Bo , Kannan Shrivats , Prados Michael , Lilly Jena V. , Mueller Sabine , Resnick Adam C. , Greene Casey S. , Rokita Jo Lynne , Taroni Jaclyn N. ,   Children’s Brain Tumor Network,   Pacific Pediatric Neuro-Oncology Consortium
Published: September 2022

Pediatric brain and spinal cancer are 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 and Pacific Pediatric Neuro-Oncology Consortium created a systematic process for tumor biobanking, model generation, and sequencing with immediate access to harmonized data. We leverage these data to create OpenPBTA, an open collaborative project which establishes over 40 scalable analysis modules to genomically characterize 1,074 pediatric brain tumors. Transcriptomic classification reveals that TP53 loss is a significant marker for poor overall survival in ependymomas and H3 K28-altered diffuse midline gliomas and further identifies universal TP53 dysregulation in mismatch repair-deficient hypermutant high-grade gliomas. OpenPBTA is a foundational analysis platform actively being applied to other pediatric cancers and inform molecular tumor board decision-making, making it an invaluable resource to the pediatric oncology community.

In Brief

The OpenPBTA is a global, collaborative open-science initiative which brought together researchers and clinicians to genomically characterize 1,074 pediatric brain tumors and 22 patient-derived cell lines. Shapiro, et. al create over 40 open-source, scalable modules to perform cancer genomics analyses and provide a richly-annotated somatic dataset across 58 brain tumor histologies. The OpenPBTA framework can be used as a model for large-scale data integration to inform basic research, therapeutic target identification, and clinical translation.

Highlights

OpenPBTA collaborative analyses establish resource for 1,074 pediatric brain tumors NGS-based WHO-aligned integrated diagnoses generated for 641 of 1,074 tumors RNA-Seq analysis infers medulloblastoma subtypes, TP53 status, and telomerase activity OpenPBTA will accelerate therapeutic translation of genomic insights