{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,19]],"date-time":"2026-10-19T16:36:38Z","timestamp":1792427798995,"version":"4.5.0"},"reference-count":81,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2025,9,2]],"date-time":"2025-09-02T00:00:00Z","timestamp":1756771200000},"content-version":"vor","delay-in-days":244,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["75N91019D00024"],"award-info":[{"award-number":["75N91019D00024"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U24OD038422"],"award-info":[{"award-number":["U24OD038422"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>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 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).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Findings<\/jats:title>\n                    <jats:p>We 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\u2019s 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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/gigascience\/giaf093","type":"journal-article","created":{"date-parts":[[2025,7,19]],"date-time":"2025-07-19T11:56:26Z","timestamp":1752926186000},"source":"Crossref","is-referenced-by-count":13,"title":["The Open Pediatric Cancer Project"],"prefix":"10.1093","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-6883-0691","authenticated-orcid":false,"given":"Zhuangzhuang","family":"Geng","sequence":"first","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8073-3797","authenticated-orcid":false,"given":"Eric","family":"Wafula","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Department of Biomedical and Health Informatics, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3478-0784","authenticated-orcid":false,"given":"Ryan J","family":"Corbett","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children's National Hospital Center for Cancer and Immunology Research, , Washington, DC 20010 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanchao","family":"Zhang","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Department of Biomedical and Health Informatics, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8958-9266","authenticated-orcid":false,"given":"Run","family":"Jin","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0838-2405","authenticated-orcid":false,"given":"Krutika S","family":"Gaonkar","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Department of Biomedical and Health Informatics, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3727-9602","authenticated-orcid":false,"given":"Sangeeta","family":"Shukla","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Department of Biomedical and Health Informatics, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5534-6904","authenticated-orcid":false,"given":"Komal S","family":"Rathi","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Department of Biomedical and Health Informatics, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1337-1789","authenticated-orcid":false,"given":"Dave","family":"Hill","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Department of Biomedical and Health Informatics, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9352-1312","authenticated-orcid":false,"given":"Aditya","family":"Lahiri","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Department of Biomedical and Health Informatics, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2032-4358","authenticated-orcid":false,"given":"Daniel P","family":"Miller","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7830-7537","authenticated-orcid":false,"given":"Alex","family":"Sickler","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children's National Hospital Center for Cancer and Immunology Research, , Washington, DC 20010 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7451-5117","authenticated-orcid":false,"given":"Kelsey","family":"Keith","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Department of Biomedical and Health Informatics, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4928-090X","authenticated-orcid":false,"given":"Christopher","family":"Blackden","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonia","family":"Chroni","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6782-1442","authenticated-orcid":false,"given":"Miguel A","family":"Brown","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8526-5694","authenticated-orcid":false,"given":"Adam A","family":"Kraya","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7207-6608","authenticated-orcid":false,"given":"Kaylyn L","family":"Clark","sequence":"additional","affiliation":[{"name":"Children's National Hospital Center for Cancer and Immunology Research, , Washington, DC 20010 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian R","family":"Rood","sequence":"additional","affiliation":[{"name":"Children's National Hospital Center for Cancer and Immunology Research, , Washington, DC 20010 ,","place":["USA"]},{"name":"George Washington University School of Medicine and Health Sciences Department of Pediatrics, , Washington, DC 20052 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0436-4189","authenticated-orcid":false,"given":"Adam C","family":"Resnick","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7414-9516","authenticated-orcid":false,"given":"Nicholas","family":"Van\u00a0Kuren","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John M","family":"Maris","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Division of Oncology, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"University of Pennsylvania Department of Pediatrics, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1087-9840","authenticated-orcid":false,"given":"Alvin","family":"Farrel","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Department of Biomedical and Health Informatics, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Center for Childhood Cancer Research, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3857-6633","authenticated-orcid":false,"given":"Mateusz P","family":"Koptyra","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gerri R","family":"Trooskin","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6454-1285","authenticated-orcid":false,"given":"Noel","family":"Coleman","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2455-9525","authenticated-orcid":false,"given":"Yuankun","family":"Zhu","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephanie","family":"Stefankiewicz","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zied","family":"Abdullaev","sequence":"additional","affiliation":[{"name":"National Cancer Institute Laboratory of Pathology, , Bethesda, MD 20892 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7831-3996","authenticated-orcid":false,"given":"Asif T","family":"Chinwalla","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Department of Biomedical and Health Informatics, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6728-3450","authenticated-orcid":false,"given":"Mariarita","family":"Santi","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Department of Pathology and Laboratory Medicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"University of Pennsylvania Perelman School of Medicine Department of Pathology and Laboratory Medicine, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ammar S","family":"Naqvi","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer L","family":"Mason","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0825-7615","authenticated-orcid":false,"given":"Carl J","family":"Koschmann","sequence":"additional","affiliation":[{"name":"University of Michigan Health Department of Pediatrics, , Ann Arbor, MI 48105 ,","place":["USA"]},{"name":"Mott Children\u2019s Hospital Pediatric Hematology Oncology, , Ann Arbor, MI 48109 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7267-4512","authenticated-orcid":false,"given":"Xiaoyan","family":"Huang","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7200-8939","authenticated-orcid":false,"given":"Sharon J","family":"Diskin","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Division of Oncology, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"University of Pennsylvania Department of Pediatrics, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kenneth","family":"Aldape","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6727-6333","authenticated-orcid":false,"given":"Bailey K","family":"Farrow","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiping","family":"Ma","sequence":"additional","affiliation":[{"name":"Icahn School of Medicine at Mount Sinai Department of Genetics and Genomic Sciences, , New York, NY 10029 ,","place":["USA"]},{"name":"Icahn School of Medicine at Mount Sinai Tisch Cancer Institute, , New York, NY 10029 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0743-5379","authenticated-orcid":false,"given":"Bo","family":"Zhang","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2653-5009","authenticated-orcid":false,"given":"Brian M","family":"Ennis","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Tasian","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Division of Oncology, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"University of Pennsylvania Department of Pediatrics, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2771-2572","authenticated-orcid":false,"given":"Saksham","family":"Phul","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-7370-102X","authenticated-orcid":false,"given":"Matthew R","family":"Lueder","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Department of Pathology and Laboratory Medicine, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2406-2735","authenticated-orcid":false,"given":"Chuwei","family":"Zhong","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph M","family":"Dybas","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pei","family":"Wang","sequence":"additional","affiliation":[{"name":"Icahn School of Medicine at Mount Sinai Tisch Cancer Institute, , New York, NY 10029 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3302-4610","authenticated-orcid":false,"given":"Deanne","family":"Taylor","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Department of Biomedical and Health Informatics, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"University of Pennsylvania Perelman Medical School Department of Pediatrics, , Philadelphia, PA 19104 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2171-3627","authenticated-orcid":false,"given":"Jo Lynne","family":"Rokita","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of Philadelphia Center for Data-Driven Discovery in Biomedicine, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Division of Neurosurgery, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children\u2019s Hospital of Philadelphia Department of Biomedical and Health Informatics, , Philadelphia, PA 19104 ,","place":["USA"]},{"name":"Children's National Hospital Center for Cancer and Immunology Research, , Washington, DC 20010 ,","place":["USA"]},{"name":"George Washington University School of Medicine and Health Sciences Department of Pediatrics, , Washington, DC 20052 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,9,2]]},"reference":[{"key":"2025090211224930500_bib1","author":"Molecular Targets Platform"},{"key":"2025090211224930500_bib2","author":"Children's Brain Tumor Network"},{"key":"2025090211224930500_bib3","doi-asserted-by":"publisher","first-page":"100846","DOI":"10.1016\/j.neo.2022.100846","article-title":"The Children's Brain Tumor Network (CBTN)\u2014accelerating research in pediatric central nervous system tumors through collaboration and open science","volume":"35","author":"Lilly","year":"2023","journal-title":"Neoplasia"},{"key":"2025090211224930500_bib4","author":"Gabriella Kids First Pediatric Research Program Data Resource Center"},{"key":"2025090211224930500_bib5","author":"Pediatric Neuro-Oncology Consortium"},{"issue":"7","key":"2025090211224930500_bib6","doi-asserted-by":"publisher","first-page":"100340","DOI":"10.1016\/j.xgen.2023.100340","article-title":"OpenPBTA: the Open Pediatric Brain Tumor Atlas","volume":"3","author":"Shapiro","year":"2023","journal-title":"Cell Genomics"},{"key":"2025090211224930500_bib7","volume-title":"TARGET: Therapeutically Applicable Research to Generate Effective Treatments dbGaP Study","author":"National Cancer Institute (NCI)"},{"key":"2025090211224930500_bib8","article-title":"Discovering the genetic basis of human neuroblastoma: a Gabriella Miller Kids First Pediatric Research Program (Kids First) Project dbGaP Study"},{"key":"2025090211224930500_bib9","volume-title":"Molecular characterization across pediatric brain tumors and other solid and hematologic malignancies for research, diagnostic, and precision medicine dbGaP study","author":"Childhood Cancer Data Initiative (CCDI)"},{"key":"2025090211224930500_bib10","author":"Chordoma Foundation"},{"key":"2025090211224930500_bib11","author":"Pediatric Preclinical In Vivo Testing Consortium (PIVOT)"},{"issue":"6","key":"2025090211224930500_bib12","doi-asserted-by":"publisher","first-page":"1675","DOI":"10.1016\/j.celrep.2019.09.071","article-title":"Genomic profiling of childhood tumor patient-derived xenograft models to enable rational clinical trial design","volume":"29","author":"Rokita","year":"2019","journal-title":"Cell Rep"},{"key":"2025090211224930500_bib13","author":"Pediatric Preclinical Testing Consortium (PPTC) dbGaP Study"},{"key":"2025090211224930500_bib14","doi-asserted-by":"publisher","first-page":"170033","DOI":"10.1038\/sdata.2017.33","article-title":"Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines","volume":"4","author":"Harenza","year":"2017","journal-title":"Sci Data"},{"key":"2025090211224930500_bib15","author":"Michigan Center for Translational Pathology"},{"key":"2025090211224930500_bib16","author":"The Genotype Tissue Expression (GTEx) Portal"},{"key":"2025090211224930500_bib17","author":"National Institutes of Health. The Cancer Genome Atlas (TCGA) dbGaP Study"},{"issue":"7","key":"2025090211224930500_bib18","doi-asserted-by":"publisher","first-page":"1962","DOI":"10.1016\/j.cell.2020.10.044","article-title":"Integrated proteogenomic characterization across major histological types of pediatric brain cancer","volume":"183","author":"Petralia","year":"2020","journal-title":"Cell"},{"issue":"4","key":"2025090211224930500_bib19","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1016\/j.ccell.2021.01.006","article-title":"Proteogenomic and metabolomic characterization of human glioblastoma","volume":"39","author":"Wang","year":"2021","journal-title":"Cancer Cell"},{"key":"2025090211224930500_bib20","author":"Kids First Tumor Only Workflow v0.3.0-beta"},{"key":"2025090211224930500_bib21","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1186\/s13059-016-0974-4","article-title":"The Ensembl variant effect predictor","volume":"17","author":"McLaren","year":"2016","journal-title":"Genome Biol"},{"key":"2025090211224930500_bib22","doi-asserted-by":"publisher","first-page":"591","DOI":"10.1038\/s41592-018-0051-x","article-title":"Strelka2: fast and accurate calling of germline and somatic variants","volume":"15","author":"Kim","year":"2018","journal-title":"Nat Methods"},{"key":"2025090211224930500_bib23","doi-asserted-by":"publisher","DOI":"10.1101\/861054","article-title":"Calling somatic SNVs and indels with Mutect2","author":"Benjamin","year":"2019","journal-title":"bioRxiv."},{"key":"2025090211224930500_bib24","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1038\/s42003-018-0023-9","article-title":"Genome-wide somatic variant calling using localized colored de Bruijn graphs","volume":"1","author":"Narzisi","year":"2018","journal-title":"Commun Biol"},{"issue":"11","key":"2025090211224930500_bib25","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1093\/nar\/gkw227","article-title":"VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research","volume":"44","author":"Lai","year":"2016","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"2025090211224930500_bib26","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1093\/bioinformatics\/btr670","article-title":"Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data","volume":"28","author":"Boeva","year":"2011","journal-title":"Bioinformatics"},{"issue":"2","key":"2025090211224930500_bib27","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/bioinformatics\/btq635","article-title":"Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization","volume":"27","author":"Boeva","year":"2010","journal-title":"Bioinformatics"},{"issue":"4","key":"2025090211224930500_bib28","doi-asserted-by":"publisher","first-page":"e1004873","DOI":"10.1371\/journal.pcbi.1004873","article-title":"Genome-wide copy number detection and visualization from targeted DNA sequencing","volume":"12","author":"Talevich","year":"2016","journal-title":"PLoS Comput Biol"},{"key":"2025090211224930500_bib29","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res"},{"key":"2025090211224930500_bib30"},{"key":"2025090211224930500_bib31"},{"key":"2025090211224930500_bib32"},{"key":"2025090211224930500_bib33"},{"issue":"8","key":"2025090211224930500_bib34","doi-asserted-by":"publisher","first-page":"1220","DOI":"10.1093\/bioinformatics\/btv710","article-title":"Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications","volume":"32","author":"Chen","year":"2015","journal-title":"Bioinformatics"},{"issue":"20","key":"2025090211224930500_bib35","doi-asserted-by":"publisher","first-page":"3572","DOI":"10.1093\/bioinformatics\/bty304","article-title":"AnnotSV: an integrated tool for structural variations annotation","volume":"34","author":"Geoffroy","year":"2018","journal-title":"Bioinformatics"},{"key":"2025090211224930500_bib36","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2025090211224930500_bib37"},{"key":"2025090211224930500_bib38"},{"key":"2025090211224930500_bib39"},{"key":"2025090211224930500_bib40","doi-asserted-by":"publisher","first-page":"448","DOI":"10.1101\/gr.257246.119","article-title":"Accurate and efficient detection of gene fusions from RNA sequencing data","volume":"31","author":"Uhrig","year":"2021","journal-title":"Genome Res"},{"key":"2025090211224930500_bib41","doi-asserted-by":"publisher","DOI":"10.1101\/120295","article-title":"STAR-Fusion: fast and accurate fusion transcript detection from RNA-seq","author":"Haas","year":"2017","journal-title":"bioRxiv"},{"key":"2025090211224930500_bib42","unstructured":"Rokita J, Marini F, Gaonkar K, et al. AnnoFuseData: v1.0.0. Zenodo. 10.5281\/zenodo.13152566. Accessed 01 May 2022."},{"key":"2025090211224930500_bib43","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1186\/s12859-020-03922-7","article-title":"annoFuse: an R package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions","volume":"21","author":"Gaonkar","year":"2020","journal-title":"BMC Bioinf"},{"key":"2025090211224930500_bib44","unstructured":"Marini F, Gaonkar K, Rokita JL. annoFuse v0.90.0. Zenodo. 2020. 10.5281\/zenodo.4036788."},{"key":"2025090211224930500_bib45"},{"key":"2025090211224930500_bib46"},{"key":"2025090211224930500_bib47","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1038\/nmeth.4256","article-title":"MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry\u2013based proteomics","volume":"14","author":"Kong","year":"2017","journal-title":"Nat Methods"},{"issue":"23","key":"2025090211224930500_bib48","doi-asserted-by":"publisher","first-page":"3838","DOI":"10.1093\/bioinformatics\/btv437","article-title":"Correcting systematic bias and instrument measurement drift with mzRefinery","volume":"31","author":"Gibbons","year":"2015","journal-title":"Bioinformatics"},{"key":"2025090211224930500_bib49","doi-asserted-by":"publisher","first-page":"5277","DOI":"10.1038\/ncomms6277","article-title":"MS-GF+ makes progress towards a universal database search tool for proteomics","volume":"5","author":"Kim","year":"2014","journal-title":"Nat Commun"},{"issue":"Suppl 1","key":"2025090211224930500_bib50","doi-asserted-by":"publisher","first-page":"S9","DOI":"10.1186\/1471-2164-15-s1-s9","article-title":"Spectral probabilities of top-down tandem mass spectra","volume":"15","author":"Liu","year":"2014","journal-title":"BMC Genomics"},{"key":"2025090211224930500_bib51","doi-asserted-by":"publisher","first-page":"1285","DOI":"10.1038\/nbt1240","article-title":"A probability-based approach for high-throughput protein phosphorylation analysis and site localization","volume":"24","author":"Beausoleil","year":"2006","journal-title":"Nat Biotechnol"},{"issue":"4","key":"2025090211224930500_bib52","doi-asserted-by":"publisher","first-page":"558","DOI":"10.1093\/bioinformatics\/btw691","article-title":"Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi","volume":"33","author":"Fortin","year":"2016","journal-title":"Bioinformatics"},{"key":"2025090211224930500_bib53","doi-asserted-by":"publisher","first-page":"1394","DOI":"10.1038\/bjc.2013.496","article-title":"Review of processing and analysis methods for DNA methylation array data","volume":"109","author":"Wilhelm-Benartzi","year":"2013","journal-title":"Br J Cancer"},{"key":"2025090211224930500_bib54","doi-asserted-by":"publisher","first-page":"1003","DOI":"10.1186\/s12864-015-2202-0","article-title":"Impact of SNPs on methylation readouts by Illumina Infinium HumanMethylation450 BeadChip Array: implications for comparative population studies","volume":"16","author":"Daca-Roszak","year":"2015","journal-title":"BMC Genomics"},{"key":"2025090211224930500_bib55","doi-asserted-by":"publisher","first-page":"469","DOI":"10.1038\/nature26000","article-title":"DNA methylation-based classification of central nervous system tumours","volume":"555","author":"Capper","year":"2018","journal-title":"Nature"},{"issue":"6","key":"2025090211224930500_bib56","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1016\/j.cels.2015.12.004","article-title":"The molecular signatures database hallmark gene set collection","volume":"1","author":"Liberzon","year":"2015","journal-title":"Cell Syst"},{"key":"2025090211224930500_bib57","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/1471-2105-14-7","article-title":"GSVA: gene set variation analysis for microarray and RNA-seq data","volume":"14","author":"H\u00e4nzelmann","year":"2013","journal-title":"BMC Bioinf"},{"key":"2025090211224930500_bib58","doi-asserted-by":"publisher","first-page":"R41","DOI":"10.1186\/gb-2011-12-4-r41","article-title":"GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers","volume":"12","author":"Mermel","year":"2011","journal-title":"Genome Biol"},{"key":"2025090211224930500_bib59","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1186\/s13059-016-0893-4","article-title":"deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution","volume":"17","author":"Rosenthal","year":"2016","journal-title":"Genome Biol"},{"key":"2025090211224930500_bib60","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1038\/nature12477","article-title":"Signatures of mutational processes in human cancer","volume":"500","author":"Alexandrov","year":"2013","journal-title":"Nature"},{"issue":"8","key":"2025090211224930500_bib61","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1002\/gcc.22733","article-title":"Tumor mutational burden standardization initiatives: recommendations for consistent tumor mutational burden assessment in clinical samples to guide immunotherapy treatment decisions","volume":"58","author":"Stenzinger","year":"2019","journal-title":"Genes Chromosomes Cancer"},{"key":"2025090211224930500_bib62"},{"issue":"12","key":"2025090211224930500_bib63","doi-asserted-by":"publisher","first-page":"1626","DOI":"10.1016\/j.annonc.2021.09.016","article-title":"Aligning tumor mutational burden (TMB) quantification across diagnostic platforms: phase II of the Friends of Cancer Research TMB Harmonization Project","volume":"32","author":"Vega","year":"2021","journal-title":"Ann Oncol"},{"issue":"8","key":"2025090211224930500_bib64","doi-asserted-by":"publisher","first-page":"1231","DOI":"10.1093\/neuonc\/noab106","article-title":"The 2021 WHO Classification of Tumors of the Central Nervous System: a summary","volume":"23","author":"Louis","year":"2021","journal-title":"Neurooncology"},{"key":"2025090211224930500_bib65","doi-asserted-by":"publisher","first-page":"4343","DOI":"10.1038\/s41467-019-12187-5","article-title":"Alterations in ALK\/ROS1\/NTRK\/MET drive a group of infantile hemispheric gliomas","volume":"10","author":"Guerreiro\u00a0Stucklin","year":"2019","journal-title":"Nat Commun"},{"issue":"5","key":"2025090211224930500_bib66","doi-asserted-by":"publisher","first-page":"613","DOI":"10.1093\/neuonc\/noz235","article-title":"Molecular subgrouping of atypical teratoid\/rhabdoid tumors\u2014a reinvestigation and current consensus","volume":"22","author":"Ho","year":"2019","journal-title":"Neurooncology"},{"issue":"10","key":"2025090211224930500_bib67","doi-asserted-by":"publisher","first-page":"e1008263","DOI":"10.1371\/journal.pcbi.1008263","article-title":"A transcriptome-based classifier to determine molecular subtypes in medulloblastoma","volume":"16","author":"Rathi","year":"2020","journal-title":"PLoS Comput Biol"},{"issue":"1","key":"2025090211224930500_bib68","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1016\/j.celrep.2018.03.076","article-title":"Genomic and molecular landscape of DNA damage repair deficiency across the cancer genome atlas","volume":"23","author":"Knijnenburg","year":"2018","journal-title":"Cell Rep"},{"issue":"2","key":"2025090211224930500_bib69","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1158\/2159-8290.cd-17-0321","article-title":"Accelerating discovery of functional mutant alleles in cancer","volume":"8","author":"Chang","year":"2018","journal-title":"Cancer Discov"},{"key":"2025090211224930500_bib70","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1038\/nbt.3391","article-title":"Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity","volume":"34","author":"Chang","year":"2015","journal-title":"Nat Biotechnol"},{"key":"2025090211224930500_bib71","doi-asserted-by":"publisher","first-page":"890","DOI":"10.1038\/sj.cdd.4401904","article-title":"The functional domains in p53 family proteins exhibit both common and distinct properties","volume":"13","author":"Harms","year":"2006","journal-title":"Cell Death Differ"},{"key":"2025090211224930500_bib72","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1038\/ng0593-42","article-title":"Gain of function mutations in p53","volume":"4","author":"Dittmer","year":"1993","journal-title":"Nat Genet"},{"issue":"4","key":"2025090211224930500_bib73","doi-asserted-by":"publisher","first-page":"a026187","DOI":"10.1101\/cshperspect.a026187","article-title":"Inherited TP53 mutations and the Li\u2013Fraumeni syndrome","volume":"7","author":"Guha","year":"2017","journal-title":"Cold Spring Harb Perspect Med"},{"issue":"11","key":"2025090211224930500_bib74","doi-asserted-by":"publisher","first-page":"e103","DOI":"10.1093\/nar\/gkx193","article-title":"NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types","volume":"45","author":"Lee","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2025090211224930500_bib75","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1186\/s13073-020-00761-2","article-title":"Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches","volume":"12","author":"Pedersen","year":"2020","journal-title":"Genome Med"},{"key":"2025090211224930500_bib76","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1038\/s41597-019-0096-4","article-title":"Barriers to accessing public cancer genomic data","volume":"6","author":"Learned","year":"2019","journal-title":"Sci Data"},{"key":"2025090211224930500_bib77"},{"key":"2025090211224930500_bib78","unstructured":"Rokita J, Wafula E, Jin R, et al., Accessed 2025 July 20 \u00a0OpenPedCan-analysis GitHub repository v2.5.1. Zenodo. 10.5281\/zenodo.6473912."},{"key":"2025090211224930500_bib79","author":"The National Cancer Institute Genomic Data Commons Portal"},{"key":"2025090211224930500_bib80","author":"National Cancer Institute Proteomic Data Commons"},{"key":"2025090211224930500_bib81","author":"PedcBioPortal for Integrated Childhood Cancer Genomics"}],"container-title":["GigaScience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/gigascience\/article-pdf\/doi\/10.1093\/gigascience\/giaf093\/64189242\/giaf093.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gigascience\/article-pdf\/doi\/10.1093\/gigascience\/giaf093\/64189242\/giaf093.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,2]],"date-time":"2025-09-02T15:23:02Z","timestamp":1756826582000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gigascience\/article\/doi\/10.1093\/gigascience\/giaf093\/8245684"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025]]},"references-count":81,"URL":"https:\/\/doi.org\/10.1093\/gigascience\/giaf093","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.07.09.599086","asserted-by":"object"}]},"ISSN":["2047-217X"],"issn-type":[{"value":"2047-217X","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025]]},"published":{"date-parts":[[2025]]},"article-number":"giaf093"}}