ArticleGigaScience2025
The Open Pediatric Cancer Project.
Article in GigaScience, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
11 citing papers in PubMed.
- Epigenetic Liquid Biopsy Enables Universal Mutation-Agnostic Molecular Surveillance for High-Risk Neuroblastoma.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- Harnessing MDM2-Mediated Targeted Degradation of Transcriptional and Epigenetic Machinery to Disrupt Oncogenic Addictions in Pediatric Sarcoma.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Unsupervised Deep Representation Learning and Probabilistic Clustering for the Systems-Level Discovery of Germline Mutation Signatures in Pediatric Cancers.Biomedicines · 2026Article
- HLA-Shuttle: A system for enhancing antigen presentation in immunologically cold tumors.Science advances · 2026Article
- Alternative splicing in pediatric central nervous system tumors highlights oncofetal candidateNeuro-oncology pediatrics · 2026Article
- Article
- Germline pathogenic variation impacts somatic alterations and patient outcomes in pediatric central nervous system tumors.Nature communications · 2025Article
- Article
- Claudin 6 is a suitable target for CAR T-cell therapy in atypical teratoid/rhabdoid brain tumors and other pediatric solid tumors.Journal for immunotherapy of cancer · 2025Article
- Single-Cell RNA Sequencing Reveals LEF1-Driven Wnt Pathway Activation as a Shared Oncogenic Program in Hepatoblastoma and Medulloblastoma.Current oncology (Toronto, Ont.) · 2025Article
- LCLAT1 regulates cardiolipin composition, mitochondrial phenotype, Lin28A, and oncogenic signaling networks in ETMR.Neuro-oncology advancesArticle
Corrections and comments
- Update of
Authors and funding
49 authors.
Funding
Abstract
backgroundIn 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 present an extension of the OpenPBTA called the Open Pediatric Cancer (OpenPedCan) Project, a harmonized open-source multiomic dataset from 6,112 pediatric cancer patients with 7,096 tumor events across more than 100 histologies. Combined with RNA sequencing (RNA-seq) from the Genotype-Tissue Expression and The Cancer Genome Atlas projects, OpenPedCan contains nearly 48,000 total biospecimens (24,002 tumor and 23,893 normal specimens).
findingsWe utilized Gabriella Miller Kids First workflows to harmonize whole-genome sequencing (WGS), whole exome sequencing (WXS), RNA-seq, and Targeted Sequencing datasets to include somatic SNVs, indels, copy number variants, structural variants, RNA expression, fusions, and splice variants. We integrated summarized Clinical Proteomic Tumor Analysis Consortium whole-cell proteomics and phospho-proteomics data and miRNA sequencing data, as well as developed a methylation array harmonization workflow to include m-values, beta-values, 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 National Cancer Institute's pediatric Molecular Targets Platform. Notably, we have expanded Pediatric Brain Tumor Atlas molecular subtyping to include methylation information to align with the World Health Organization 2021 Central Nervous System Tumor classifications, allowing us to create research-grade integrated diagnoses for these tumors.
conclusionsOpenPedCan 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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.