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Cancer is the second leading cause of death in the United States. A cancer cell is genetically unstable and hence can mutate faster. They can also modify their microenvironment and escape immune surveillance. The difficulties in treating cancer are further compounded by the emergence of rapid resistance to anticancer drugs. The most common ways to attain resistance in cancer cells include alteration in drug transport and metabolism, modification of drug target, elevated DNA damage response, or...
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Updated: Sep 9, 2025

Detection and Monitoring of Tumor Associated Circulating DNA in Patient Biofluids
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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.

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Summary
This summary is machine-generated.

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.

Keywords:
DockerOpenPedCanmultiomicsopen sciencepediatric cancerreproducibility

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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.