The Open Pediatric Cancer Project
Rattachement africain : us. Niveau de preuve : code pays fourni par la source.
Le résumé fourni par la source
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 present an extension of the OpenPBTA called 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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Le contrôle bibliographique ouvert
DOI retrouvé dans Crossref DOI retrouvé ; titre concordant.
- Titre Crossref
- The Open Pediatric Cancer Project
- Date Crossref
- 11/07/2024
- Éditeur
- openRxiv
- Type
- posted-content
Ce recoupement confirme des métadonnées liées au DOI. Il ne confirme ni la méthode ni les conclusions de l’étude, et il ne compte pas comme une seconde source scientifique indépendante.
Où se fait cette recherche
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Children's Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine pays non établi dans la noticeOrganisme public
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Children's National Center for Cancer and Immunology Research pays non établi dans la noticeÉtablissement de santé
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C. S. Mott Children's Hospital Pediatric Hematology Oncology pays non établi dans la noticeÉtablissement de santé
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George Washington University Children's National Research Institute pays non établi dans la noticeUniversité ou école supérieure
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National Cancer Institute pays non établi dans la noticeOrganisme public
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University of Pennsylvania Department of Pediatrics pays non établi dans la noticeUniversité ou école supérieure
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Icahn School of Medicine at Mount Sinai Department of Genetics and Genomic Sciences pays non établi dans la noticeUniversité ou école supérieure
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University of Michigan Department of Pediatrics pays non établi dans la noticeUniversité ou école supérieure
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Michigan Medicine pays non établi dans la noticeÉtablissement de santé
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Laboratory of Pathology pays non établi dans la noticeStructure de recherche
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Department of Pathology and Laboratory Medicine pays non établi dans la noticeStructure de recherche
Center for Data-Driven Discovery in Biomedicine — Children's Hospital of Philadelphia, Center for Cancer and Immunology Research — Children's National et Pediatric Hematology Oncology — C. S. Mott Children's Hospital, avec 8 autres affiliations.
Une affiliation ne permet pas de déduire la nationalité d’un auteur.