The Open Pediatric Cancer Project.

bioRxiv

Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA · Funded by NCI/NIH Contract No. 75N91019D00024, Task Order No. 75N91020F00003.

Published: July 2024

AI Article Synopsis

  • The Open Pediatric Cancer (OpenPedCan) Project builds upon the earlier Open Pediatric Brain Tumor Atlas, analyzing data from over 6,000 pediatric cancer patients and providing a vast multi-omic dataset from various tumor types.
  • The project integrates multiple genomic and proteomic data types, allowing researchers to access harmonized data through platforms like GitHub, CAVATICA, and AWS.
  • OpenPedCan enhances molecular subtyping of tumors by incorporating methylation information, facilitating research that supports more accurate diagnosis and treatment strategies in pediatric cancer.

Article Abstract

Background: In 2019, the Open Pediatric Brain Tumor Atlas (OpenPBTA) was created as a global, collaborative open-science initiative to genomically characterize 1,074 pediatric brain tumors and 22 patient-derived cell lines. Here, we extend the OpenPBTA to create the Open Pediatric Cancer (OpenPedCan) Project, a harmonized open-source multi-omic dataset from 6,112 pediatric cancer patients with 7,096 tumor events across more than 100 histologies. Combined with RNA-Seq from the Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA), OpenPedCan contains nearly 48,000 total biospecimens (24,002 tumor and 23,893 normal specimens).

Findings: We utilized Gabriella Miller Kids First (GMKF) workflows to harmonize WGS, WXS, RNA-seq, and Targeted Sequencing datasets to include somatic SNVs, InDels, CNVs, SVs, RNA expression, fusions, and splice variants. We integrated summarized CPTAC whole cell proteomics and phospho-proteomics data, miRNA-Seq data, and have developed a methylation array harmonization workflow to include m-values, beta-vales, and copy number calls. OpenPedCan contains reproducible, dockerized workflows in GitHub, CAVATICA, and Amazon Web Services (AWS) to deliver harmonized and processed data from over 60 scalable modules which can be leveraged both locally and on AWS. The processed data are released in a versioned manner and accessible through CAVATICA or AWS S3 download (from GitHub), and queryable through PedcBioPortal and the NCI's pediatric Molecular Targets Platform. Notably, we have expanded PBTA molecular subtyping to include methylation information to align with the WHO 2021 Central Nervous System Tumor classifications, allowing us to create research- grade integrated diagnoses for these tumors.

Conclusions: OpenPedCan data and its reproducible analysis module framework are openly available and can be utilized and/or adapted by researchers to accelerate discovery, validation, and clinical translation.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11257555PMC
http://dx.doi.org/10.1101/2024.07.09.599086DOI Listing

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