Related Experiment Video
Updated: Sep 9, 2025
06:53
Detection and Monitoring of Tumor Associated Circulating DNA in Patient Biofluids
Published on: June 8, 2019
8.8K
The Open Pediatric Cancer Project
Zhuangzhuang Geng1,2, Eric Wafula3, Ryan J Corbett1,2,4
1Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Gigascience
|September 2, 2025
Summary
The Open Pediatric Cancer (OpenPedCan) Project provides a harmonized multiomic dataset for 6,112 pediatric cancer patients. This open-source resource accelerates pediatric cancer research and clinical translation through accessible, reproducible data and analysis tools.
Area of Science:
- Genomics
- Oncology
- Bioinformatics
Background:
- The Open Pediatric Brain Tumor Atlas (OpenPBTA) initiative characterized 1,074 pediatric brain tumors.
- The Open Pediatric Cancer (OpenPedCan) Project extends this by creating a harmonized multiomic dataset.
Purpose of the Study:
- To establish a comprehensive, open-source multiomic dataset for pediatric cancers.
- To provide reproducible analysis workflows for researchers.
Main Methods:
- Harmonized whole-genome sequencing (WGS), whole exome sequencing (WXS), RNA-seq, and targeted sequencing data.
- Integrated proteomics, phospho-proteomics, miRNA sequencing, and methylation array data.
- Developed dockerized, reproducible workflows for data processing and analysis.
Main Results:
- The OpenPedCan dataset includes 6,112 pediatric cancer patients with 7,096 tumor events across diverse histologies.
- Nearly 48,000 total biospecimens (tumor and normal) are available.
- Expanded molecular subtyping for brain tumors using methylation data, aligning with WHO 2021 classifications.
Conclusions:
- OpenPedCan data and analysis framework are openly available.
- Facilitates accelerated discovery, validation, and clinical translation in pediatric cancer research.
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