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Updated: Jun 20, 2025

Detection and Monitoring of Tumor Associated Circulating DNA in Patient Biofluids

Detection and Monitoring of Tumor Associated Circulating DNA in Patient Biofluids

Published on: June 8, 2019

The Open Pediatric Cancer Project.

Zhuangzhuang Geng^1,2, Eric Wafula³, Ryan J Corbett^4,1,2

¹Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.

Biorxiv : the Preprint Server for Biology

|July 19, 2024

Summary

This summary is machine-generated.

The Open Pediatric Cancer (OpenPedCan) Project provides a harmonized, open-source multi-omic dataset for 6,112 pediatric cancer patients. This extensive resource, including genomic and proteomic data, aims to accelerate pediatric cancer research and discovery.

Keywords:

Docker OpenPedCan Pediatric cancer multi-omics open science reproducibility

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Area of Science:

Pediatric Oncology
Genomics
Multi-omics Data Integration

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 large-scale, harmonized dataset for pediatric cancers.

Purpose of the Study:

To establish a comprehensive, open-source, multi-omic dataset for pediatric cancer research.
To integrate diverse molecular data types for enhanced analysis and discovery.

Main Methods:

Harmonized whole genome sequencing (WGS), whole exome sequencing (WXS), RNA-seq, and targeted sequencing data.
Integrated proteomics, phospho-proteomics, miRNA-Seq, and developed methylation array harmonization.
Utilized Gabriella Miller Kids First (GMKF) workflows and reproducible, dockerized analysis modules.

Main Results:

The OpenPedCan dataset includes 6,112 pediatric cancer patients with 7,096 tumor events across over 100 histologies.
Combined with GTEx and TCGA, the dataset comprises nearly 48,000 total biospecimens (tumor and normal).
Expanded molecular subtyping with methylation data aligns with WHO 2021 classifications, enabling integrated diagnoses.

Conclusions:

OpenPedCan provides openly available data and reproducible analysis frameworks for researchers.
The project aims to accelerate discovery, validation, and clinical translation in pediatric cancer research.