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Shapiro JA, Gaonkar KS, Spielman SJ, Savonen CL, Bethell CJ, Jin R, Rathi KS, Zhu Y, Egolf LE, Farrow BK, Miller DP, Yang Y, Koganti T, Noureen N, Koptyra MP, Duong N, Santi M, Kim J, Robins S, Storm PB, Mack SC, Lilly JV, Xie HM, Jain P, Raman P, Rood BR, Lulla RR, Nazarian J, Kraya AA, Vaksman Z, Heath AP, Kline C, Scolaro L, Viaene AN, Huang X, Way GP, Foltz SM, Zhang B, Poetsch AR, Mueller S, Ennis BM, Prados M, Diskin SJ, Zheng S, Guo Y, Kannan S, Waanders AJ, Margol AS, Kim MC, Hanson D, Van Kuren N, Wong J, Kaufman RS, Coleman N, Blackden C, Cole KA, Mason JL, Madsen PJ, Koschmann CJ, Stewart DR, Wafula E, Brown MA, Resnick AC, Greene CS, Rokita JL, Taroni JN. OpenPBTA: The Open Pediatric Brain Tumor Atlas. Cell Genom 2023;3:100340. [PMID: 37492101 PMCID: PMC10363844 DOI: 10.1016/j.xgen.2023.100340] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 02/28/2023] [Accepted: 05/04/2023] [Indexed: 07/27/2023]

Affiliation(s)

Joshua A. Shapiro Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
Krutika S. Gaonkar 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 Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
Stephanie J. Spielman Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA Rowan University, Glassboro, NJ 08028, USA
Candace L. Savonen Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
Chante J. Bethell Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
Run Jin 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
Komal S. Rathi Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
Yuankun Zhu 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
Laura E. Egolf Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
Bailey K. Farrow 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
Daniel P. Miller 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
Yang Yang Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
Tejaswi Koganti 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
Nighat Noureen Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA
Mateusz P. Koptyra 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
Nhat Duong Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
Mariarita Santi Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
Jung Kim Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA
Shannon Robins 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
Phillip B. Storm 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
Stephen C. Mack Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
Jena V. Lilly 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
Hongbo M. Xie Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
Payal Jain 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
Pichai Raman Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
Brian R. Rood Children’s National Research Institute, Washington, DC 20012, USA George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
Rishi R. Lulla Division of Hematology/Oncology, Hasbro Children’s Hospital, Providence, RI 02903, USA Department of Pediatrics, The Warren Alpert School of Brown University, Providence, RI 02912, USA
Javad Nazarian Children’s National Research Institute, Washington, DC 20012, USA George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA Department of Pediatrics, University of Zurich, Zurich, Switzerland
Adam A. Kraya 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
Zalman Vaksman Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
Allison P. Heath 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
Cassie Kline Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
Laura Scolaro Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
Angela N. Viaene Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
Xiaoyan Huang 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
Gregory P. Way Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO 80045, USA
Steven M. Foltz Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
Bo Zhang 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
Anna R. Poetsch Biotechnology Center, Technical University Dresden, Dresden, Germany National Center for Tumor Diseases, Dresden, Germany
Sabine Mueller Department of Neurology, Neurosurgery and Pediatrics, University of California, San Francisco, San Francisco, CA 94115, USA
Brian M. Ennis 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
Michael Prados University of California, San Francisco, San Francisco, CA 94115, USA
Sharon J. Diskin Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA
Siyuan Zheng Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA
Yiran Guo Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
Shrivats Kannan 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
Angela J. Waanders Division of Hematology, Oncology, Neuro-Oncology, and Stem Cell Transplant, Ann & Robert H Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
Ashley S. Margol Division of Hematology and Oncology, Children’s Hospital of Los Angeles, Los Angeles, CA 90027, USA Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, CA 90033, USA
Meen Chul Kim 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
Derek Hanson Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA Hackensack University Medical Center, Hackensack, NJ 07601, USA
Nicholas Van Kuren 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
Jessica Wong 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
Rebecca S. Kaufman Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
Noel Coleman 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
Christopher Blackden 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
Kristina A. Cole Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
Jennifer L. Mason 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
Peter J. Madsen 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
Carl J. Koschmann Department of Pediatrics, University of Michigan Health, Ann Arbor, MI 48105, USA Pediatric Hematology Oncology, Mott Children’s Hospital, Ann Arbor, MI 48109, USA
Douglas R. Stewart Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA
Eric Wafula Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
Miguel A. Brown 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
Adam C. Resnick 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
Casey S. Greene Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO 80045, USA Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
Jo Lynne Rokita 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 Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
Jaclyn N. Taroni Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
Children’s Brain Tumor Network Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA 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 Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA Rowan University, Glassboro, NJ 08028, USA Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA Children’s National Research Institute, Washington, DC 20012, USA George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA Division of Hematology/Oncology, Hasbro Children’s Hospital, Providence, RI 02903, USA Department of Pediatrics, The Warren Alpert School of Brown University, Providence, RI 02912, USA Department of Pediatrics, University of Zurich, Zurich, Switzerland Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO 80045, USA Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA Biotechnology Center, Technical University Dresden, Dresden, Germany National Center for Tumor Diseases, Dresden, Germany Department of Neurology, Neurosurgery and Pediatrics, University of California, San Francisco, San Francisco, CA 94115, USA University of California, San Francisco, San Francisco, CA 94115, USA Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA Division of Hematology, Oncology, Neuro-Oncology, and Stem Cell Transplant, Ann & Robert H Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA Division of Hematology and Oncology, Children’s Hospital of Los Angeles, Los Angeles, CA 90027, USA Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, CA 90033, USA Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA Hackensack University Medical Center, Hackensack, NJ 07601, USA Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA Department of Pediatrics, University of Michigan Health, Ann Arbor, MI 48105, USA Pediatric Hematology Oncology, Mott Children’s Hospital, Ann Arbor, MI 48109, USA Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
Pacific Pediatric Neuro-Oncology Consortium Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA 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 Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA Rowan University, Glassboro, NJ 08028, USA Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA Children’s National Research Institute, Washington, DC 20012, USA George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA Division of Hematology/Oncology, Hasbro Children’s Hospital, Providence, RI 02903, USA Department of Pediatrics, The Warren Alpert School of Brown University, Providence, RI 02912, USA Department of Pediatrics, University of Zurich, Zurich, Switzerland Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO 80045, USA Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA Biotechnology Center, Technical University Dresden, Dresden, Germany National Center for Tumor Diseases, Dresden, Germany Department of Neurology, Neurosurgery and Pediatrics, University of California, San Francisco, San Francisco, CA 94115, USA University of California, San Francisco, San Francisco, CA 94115, USA Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA Division of Hematology, Oncology, Neuro-Oncology, and Stem Cell Transplant, Ann & Robert H Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA Division of Hematology and Oncology, Children’s Hospital of Los Angeles, Los Angeles, CA 90027, USA Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, CA 90033, USA Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA Hackensack University Medical Center, Hackensack, NJ 07601, USA Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA Department of Pediatrics, University of Michigan Health, Ann Arbor, MI 48105, USA Pediatric Hematology Oncology, Mott Children’s Hospital, Ann Arbor, MI 48109, USA Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA

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Koptyra MP, Rahti K, Zhu Y, Farrow B, Miller D, Kraya A, Guo Y, Madsen P, Van Kuren N, Huang X, Brown MA, Mason JL, Kim MC, Heath AP, Ennis BM, Zhang B, Lilly JV, Rokita JL, Friedman C, Cuellar XP, Sullivan CA, Coleman N, Duros T, Nguyen TQ, Drake EC, Helili Z, Frenkel BA, Trooskin GR, Familiar A, Viswanathan K, Beck CM, Hollawell ML, Baubet VP, Kline C, Santi M, Patton TS, Stefankiewicz S, Kamnaa A, Velasco RA, Cardona D, Storm PJ, Resnick AC, Network OCBT. Abstract 3566: Expansion of the Pediatric Brain Tumor Atlas: Children's Brain Tumor Network, Kids First Data Resource and Childhood Cancer Data Initiative Open Science effort. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]

Abstract Abstract Pediatric central nervous system (CNS) cancers are the leading disease-related cause of death in children and there is urgent need for curative therapeutic strategies for these tumors. To address the urgency, Children’s Brain Tumor Network (CBTN) has advanced an open science model to accelerate the research discovery for pediatric brain tumors. In first phase of Open Pediatric Brain Tumor Atlas (OpenPBTA) effort CBTN together with Pacific Pediatric Neuro-Oncology Consortium (PNOC) with support of Gabriella Miller Kids First Data Resource Center (KFDRC) created and comprehensively characterized over 1000 clinically annotated pediatric brain tumors. In the second phase of the OpenPBTA effort, through resource awards and collaboration across KFDRC, the NCI Childhood Cancer Data Initiative (CCDI), NCI’s Clinical Proteomic Tumor Analysis Consortium (CPTAC), NCI Center for Cancer Research and additional partnered institutions and foundations, CBTN has expanded OpenPBTA to support high throughput molecular characterization for an additional 1900 pediatric brain tumor patients and their families. This includes the processing and characterization of over 8000 specimens across >50 brain tumor diagnoses. The cohort expansion builds on >1000 previously characterized samples with a portfolio of multimodal data including whole genome sequencing, RNA sequencing, miRNA sequencing, methylation sequencing, proteomics, lipidomics and/or metabolomics. Molecular data is linked to patient longitudinal clinical data, imaging data (MRIs and radiology reports), histology slide images, and pathology reports. To inform novel discovery and clinical implementation of genomic approaches for diagnostic/therapeutic purposes, the data is deposited the cloud-based research environment of the NCI’s CCDI and the KFDRC to provide near real-time integration, dissemination, processing, and sharing of associated petabyte-scale harmonized data. The approach leverages the DRC platform’s cloud-based computational environment in CAVATICA. Processed annotations are facilitated via CAVATICA-enabled shareable pipelines and can be explored through PedcBioPortal, a data visualization/analysis application further integrating additional public and deposited datasets. This expansion phase of OpenPBTA is released with no embargo period and provides one of the largest deeply characterized cohorts of pediatric brain tumor samples and associated clinical data for >3000 pediatric brain tumor patients. CBTN’s open-science, rapid-release model aims to advance novel biomarkers and therapeutic exploratory research, supporting new clinical trial development and accelerated discovery on behalf of changing the outcome for kids with brain tumors. Citation Format: Mateusz P. Koptyra, Komal Rahti, Yuankun Zhu, Bailey Farrow, Daniel Miller, Adam Kraya, Yiran Guo, Peter Madsen, Nicholas Van Kuren, Xiaoyan Huang, Miguel A. Brown, Jennifer L. Mason, Meen Chul Kim, Allison P. Heath, Brian M. Ennis, Bo Zhang, Jena V. Lilly, Jo Lynne Rokita, Christopher Friedman, Ximena P. Cuellar, Catherine A. Sullivan, Noel Coleman, Trang Duros, Thinh Q. Nguyen, Emmett C. Drake, Zeinab Helili, Beth A. Frenkel, Gerri R. Trooskin, Ariana Familiar, Karthik Viswanathan, Christopher M. Beck, Madison L. Hollawell, Valerie P. Baubet, Cassie Kline, Mariarita Santi, Tatiana S. Patton, Stephanie Stefankiewicz, Arya Kamnaa, Ryan A. Velasco, Dani Cardona, Phillip J. Storm, Adam C. Resnick, o/b/o Children's Brain Tumor Network. Expansion of the Pediatric Brain Tumor Atlas: Children's Brain Tumor Network, Kids First Data Resource and Childhood Cancer Data Initiative Open Science effort. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3566. Collapse

Affiliation(s)

Mateusz P. Koptyra 1Children's Hospital of Philadelphia, Philadelphia, PA
Komal Rahti 1Children's Hospital of Philadelphia, Philadelphia, PA
Yuankun Zhu 1Children's Hospital of Philadelphia, Philadelphia, PA
Bailey Farrow 1Children's Hospital of Philadelphia, Philadelphia, PA
Daniel Miller 1Children's Hospital of Philadelphia, Philadelphia, PA
Adam Kraya 1Children's Hospital of Philadelphia, Philadelphia, PA
Yiran Guo 1Children's Hospital of Philadelphia, Philadelphia, PA
Peter Madsen 1Children's Hospital of Philadelphia, Philadelphia, PA
Nicholas Van Kuren 1Children's Hospital of Philadelphia, Philadelphia, PA
Xiaoyan Huang 1Children's Hospital of Philadelphia, Philadelphia, PA
Miguel A. Brown 1Children's Hospital of Philadelphia, Philadelphia, PA
Jennifer L. Mason 1Children's Hospital of Philadelphia, Philadelphia, PA
Meen Chul Kim 1Children's Hospital of Philadelphia, Philadelphia, PA
Allison P. Heath 1Children's Hospital of Philadelphia, Philadelphia, PA
Brian M. Ennis 1Children's Hospital of Philadelphia, Philadelphia, PA
Bo Zhang 1Children's Hospital of Philadelphia, Philadelphia, PA
Jena V. Lilly 1Children's Hospital of Philadelphia, Philadelphia, PA
Jo Lynne Rokita 1Children's Hospital of Philadelphia, Philadelphia, PA
Christopher Friedman 1Children's Hospital of Philadelphia, Philadelphia, PA
Ximena P. Cuellar 1Children's Hospital of Philadelphia, Philadelphia, PA
Catherine A. Sullivan 1Children's Hospital of Philadelphia, Philadelphia, PA
Noel Coleman 1Children's Hospital of Philadelphia, Philadelphia, PA
Trang Duros 1Children's Hospital of Philadelphia, Philadelphia, PA
Thinh Q. Nguyen 1Children's Hospital of Philadelphia, Philadelphia, PA
Emmett C. Drake 1Children's Hospital of Philadelphia, Philadelphia, PA
Zeinab Helili 1Children's Hospital of Philadelphia, Philadelphia, PA
Beth A. Frenkel 1Children's Hospital of Philadelphia, Philadelphia, PA
Gerri R. Trooskin 1Children's Hospital of Philadelphia, Philadelphia, PA
Ariana Familiar 1Children's Hospital of Philadelphia, Philadelphia, PA
Karthik Viswanathan 1Children's Hospital of Philadelphia, Philadelphia, PA
Christopher M. Beck 1Children's Hospital of Philadelphia, Philadelphia, PA
Madison L. Hollawell 1Children's Hospital of Philadelphia, Philadelphia, PA
Valerie P. Baubet 1Children's Hospital of Philadelphia, Philadelphia, PA
Cassie Kline 1Children's Hospital of Philadelphia, Philadelphia, PA
Mariarita Santi 1Children's Hospital of Philadelphia, Philadelphia, PA
Tatiana S. Patton 1Children's Hospital of Philadelphia, Philadelphia, PA
Stephanie Stefankiewicz 1Children's Hospital of Philadelphia, Philadelphia, PA
Arya Kamnaa 1Children's Hospital of Philadelphia, Philadelphia, PA
Ryan A. Velasco 1Children's Hospital of Philadelphia, Philadelphia, PA
Dani Cardona 1Children's Hospital of Philadelphia, Philadelphia, PA
Phillip J. Storm 1Children's Hospital of Philadelphia, Philadelphia, PA
Adam C. Resnick 1Children's Hospital of Philadelphia, Philadelphia, PA
o/b/o Children's Brain Tumor Network 1Children's Hospital of Philadelphia, Philadelphia, PA

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Lilly JV, Rokita JL, Mason JL, Patton T, Stefankiewiz S, Higgins D, Trooskin G, Larouci CA, Arya K, Appert E, Heath AP, Zhu Y, Brown MA, Zhang B, Farrow BK, Robins S, Morgan AM, Nguyen TQ, Frenkel E, Lehmann K, Drake E, Sullivan C, Plisiewicz A, Coleman N, Patterson L, Koptyra M, Helili Z, Van Kuren N, Young N, Kim MC, Friedman C, Lubneuski A, Blackden C, Williams M, Baubet V, Tauhid L, Galanaugh J, Boucher K, Ijaz H, Cole KA, Choudhari N, Santi M, Moulder RW, Waller J, Rife W, Diskin SJ, Mateos M, Parsons DW, Pollack IF, Goldman S, Leary S, Caporalini C, Buccoliero AM, Scagnet M, Haussler D, Hanson D, Firestein R, Cain J, Phillips JJ, Gupta N, Mueller S, Grant G, Monje-Deisseroth M, Partap S, Greenfield JP, Hashizume R, Smith A, Zhu S, Johnston JM, Fangusaro JR, Miller M, Wood MD, Gardner S, Carter CL, Prolo LM, Pisapia J, Pehlivan K, Franson A, Niazi T, Rubin J, Abdelbaki M, Ziegler DS, Lindsay HB, Stucklin AG, Gerber N, Vaske OM, Quinsey C, Rood BR, Nazarian J, Raabe E, Jackson EM, Stapleton S, Lober RM, Kram DE, Koschmann C, Storm PB, Lulla RR, Prados M, Resnick AC, Waanders AJ. The children's brain tumor network (CBTN) - Accelerating research in pediatric central nervous system tumors through collaboration and open science. Neoplasia 2023;35:100846. [PMID: 36335802 PMCID: PMC9641002 DOI: 10.1016/j.neo.2022.100846] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]

Affiliation(s)

Jena V Lilly Children's Hospital of Philadelphia, Philadelphia, PA, USA
Jo Lynne Rokita Children's Hospital of Philadelphia, Philadelphia, PA, USA
Jennifer L Mason Children's Hospital of Philadelphia, Philadelphia, PA, USA
Tatiana Patton Children's Hospital of Philadelphia, Philadelphia, PA, USA
Stephanie Stefankiewiz Children's Hospital of Philadelphia, Philadelphia, PA, USA
David Higgins Children's Hospital of Philadelphia, Philadelphia, PA, USA
Gerri Trooskin Children's Hospital of Philadelphia, Philadelphia, PA, USA
Carina A Larouci Children's Hospital of Philadelphia, Philadelphia, PA, USA
Kamnaa Arya Children's Hospital of Philadelphia, Philadelphia, PA, USA
Elizabeth Appert Children's Hospital of Philadelphia, Philadelphia, PA, USA
Allison P Heath Children's Hospital of Philadelphia, Philadelphia, PA, USA
Yuankun Zhu Children's Hospital of Philadelphia, Philadelphia, PA, USA
Miguel A Brown Children's Hospital of Philadelphia, Philadelphia, PA, USA
Bo Zhang Children's Hospital of Philadelphia, Philadelphia, PA, USA
Bailey K Farrow Children's Hospital of Philadelphia, Philadelphia, PA, USA
Shannon Robins Children's Hospital of Philadelphia, Philadelphia, PA, USA
Allison M Morgan Children's Hospital of Philadelphia, Philadelphia, PA, USA
Thinh Q Nguyen Children's Hospital of Philadelphia, Philadelphia, PA, USA
Elizabeth Frenkel Children's Hospital of Philadelphia, Philadelphia, PA, USA
Kaitlin Lehmann Children's Hospital of Philadelphia, Philadelphia, PA, USA
Emily Drake Children's Hospital of Philadelphia, Philadelphia, PA, USA
Catherine Sullivan Children's Hospital of Philadelphia, Philadelphia, PA, USA
Alexa Plisiewicz Children's Hospital of Philadelphia, Philadelphia, PA, USA
Noel Coleman Children's Hospital of Philadelphia, Philadelphia, PA, USA
Luke Patterson Children's Hospital of Philadelphia, Philadelphia, PA, USA
Mateusz Koptyra Children's Hospital of Philadelphia, Philadelphia, PA, USA
Zeinab Helili Children's Hospital of Philadelphia, Philadelphia, PA, USA
Nicholas Van Kuren Children's Hospital of Philadelphia, Philadelphia, PA, USA
Nathan Young Children's Hospital of Philadelphia, Philadelphia, PA, USA
Meen Chul Kim Children's Hospital of Philadelphia, Philadelphia, PA, USA
Christopher Friedman Children's Hospital of Philadelphia, Philadelphia, PA, USA
Alex Lubneuski Children's Hospital of Philadelphia, Philadelphia, PA, USA
Christopher Blackden Children's Hospital of Philadelphia, Philadelphia, PA, USA
Marti Williams Children's Hospital of Philadelphia, Philadelphia, PA, USA
Valerie Baubet Children's Hospital of Philadelphia, Philadelphia, PA, USA
Lamiya Tauhid Children's Hospital of Philadelphia, Philadelphia, PA, USA
Jamie Galanaugh Children's Hospital of Philadelphia, Philadelphia, PA, USA
Katie Boucher Children's Hospital of Philadelphia, Philadelphia, PA, USA
Heba Ijaz Children's Hospital of Philadelphia, Philadelphia, PA, USA
Kristina A Cole Children's Hospital of Philadelphia, Philadelphia, PA, USA
Namrata Choudhari Children's Hospital of Philadelphia, Philadelphia, PA, USA
Mariarita Santi Children's Hospital of Philadelphia, Philadelphia, PA, USA
Robert W Moulder Children's Hospital of Philadelphia, Philadelphia, PA, USA
Jonathan Waller Children's Hospital of Philadelphia, Philadelphia, PA, USA
Whitney Rife Children's Hospital of Philadelphia, Philadelphia, PA, USA
Sharon J Diskin Children's Hospital of Philadelphia, Philadelphia, PA, USA
Marion Mateos Sydney Children's Hospital, Sydney, Australia
Donald W Parsons Texas Children's Hospital, Houston, TX, USA
Ian F Pollack UPMC The Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
Stewart Goldman Phoenix Children's Hospital, Phoenix AZ, USA; University of Arizona College of Medicine, Phoenix AZ, USA
Sarah Leary Seattle Children's Hospital, Seattle, WA, USA
Chiara Caporalini Meyer Children's Hospital, Floerence, Italy
Anna Maria Buccoliero Meyer Children's Hospital, Floerence, Italy
Mirko Scagnet Meyer Children's Hospital, Floerence, Italy
David Haussler University of California Santa Cruz, Santa Cruz, CA, USA
Derek Hanson Joseph M. Sanzari Children's Hospital at Hackensack University Medical Center, Hackensack, NJ, USA
Ron Firestein Hudson Institute of Medical Research, Victoria, Australia
Jason Cain Hudson Institute of Medical Research, Victoria, Australia
Joanna J Phillips University of California San Francisco & Benioff Children's Hospitals, San Francisco, CA, USA
Nalin Gupta University of California San Francisco & Benioff Children's Hospitals, San Francisco, CA, USA
Sabine Mueller University of California San Francisco & Benioff Children's Hospitals, San Francisco, CA, USA
Gerald Grant Duke University Medical Center, Durham, NC USA
Michelle Monje-Deisseroth Lucille Packard Children's Hospital Stanford, Stanford, CA, USA
Sonia Partap Lucille Packard Children's Hospital Stanford, Stanford, CA, USA
Jeffrey P Greenfield Weill Cornell Medicine Pediatric Brain and Spine Center, New York, NY, USA
Rintaro Hashizume Ann and Robert Lurie Children's Hospital, Chicago, IL, USA
Amy Smith Orlando Health Arnold Palmer Hospital for Children, Orlando, FL, USA
Shida Zhu China National Genebank (Beijing Genomics Institute), China
James M Johnston University of Alabama at Birmingham, Children's of Alabama, Birmingham, AL, USA
Jason R Fangusaro Children's Healthcare of Atlanta, Atlanta, GA, USA
Matthew Miller Doernbecher Children's Hospital at Oregon Health & Science University (OHSU), Portland, OR, USA
Matthew D Wood Doernbecher Children's Hospital at Oregon Health & Science University (OHSU), Portland, OR, USA
Sharon Gardner Hassenfeld Children's Hospital at NYU Langone, New York, NY, USA
Claire L Carter Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
Laura M Prolo Lucille Packard Children's Hospital Stanford, Stanford, CA, USA
Jared Pisapia Maria Fareri Children's Hospital at Westchester Medical Center, Valhalla, NY, USA
Katherine Pehlivan Maria Fareri Children's Hospital at Westchester Medical Center, Valhalla, NY, USA
Andrea Franson C.S. Mott Children's Hospital, University of Michigan, Ann Arbor, MI, USA
Toba Niazi Nicklaus Children's Hospital, Miami, FL, USA
Josh Rubin St. Louis Children's Hospital, St. Louis, MO
Mohamed Abdelbaki St. Louis Children's Hospital, St. Louis, MO
David S Ziegler Kids Cancer Centre, Sydney Children's Hospital, High St, Randwick, NSW, Australia; Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, Australia; School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
Holly B Lindsay Texas Children's Cancer and Hematology Center, Baylor College of Medicine, Houston, TX, USA
Ana Guerreiro Stucklin University Children's Zürich, Zürich, Switzerland
Nicolas Gerber University Children's Zürich, Zürich, Switzerland
Olena M Vaske University of California Santa Cruz, Santa Cruz, CA, USA
Carolyn Quinsey UNC Chapel Hill, Chapel Hill, NC, USA; North Carolina Children's Hospital, Chapel Hill, NC, USA
Brian R Rood Children's National Hospital, Washington, DC, USA
Javad Nazarian University Children's Zürich, Zürich, Switzerland; Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA; The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
Eric Raabe Johns Hopkins University School of Medicine, Baltimore, MD USA
Eric M Jackson Johns Hopkins University School of Medicine, Baltimore, MD USA
Stacie Stapleton Johns Hopkins University School of Medicine, Baltimore, MD USA
Robert M Lober Dayton Children's Hospital, Dayton, OH, USA
David E Kram UNC Chapel Hill, Chapel Hill, NC, USA; North Carolina Children's Hospital, Chapel Hill, NC, USA
Carl Koschmann C.S. Mott Children's Hospital, University of Michigan, Ann Arbor, MI, USA
Phillip B Storm Children's Hospital of Philadelphia, Philadelphia, PA, USA
Rishi R Lulla Hasbro Children's Hospital, Brown University
Michael Prados University of California San Francisco Benioff Children's Hospital, San Franscisco, CA, USA
Adam C Resnick Children's Hospital of Philadelphia, Philadelphia, PA, USA
Angela J Waanders Ann and Robert Lurie Children's Hospital, Chicago, IL, USA.

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Petralia F, Tignor N, Reva B, Koptyra M, Chowdhury S, Rykunov D, Krek A, Ma W, Zhu Y, Ji J, Calinawan A, Whiteaker JR, Colaprico A, Stathias V, Omelchenko T, Song X, Raman P, Guo Y, Brown MA, Ivey RG, Szpyt J, Guha Thakurta S, Gritsenko MA, Weitz KK, Lopez G, Kalayci S, Gümüş ZH, Yoo S, da Veiga Leprevost F, Chang HY, Krug K, Katsnelson L, Wang Y, Kennedy JJ, Voytovich UJ, Zhao L, Gaonkar KS, Ennis BM, Zhang B, Baubet V, Tauhid L, Lilly JV, Mason JL, Farrow B, Young N, Leary S, Moon J, Petyuk VA, Nazarian J, Adappa ND, Palmer JN, Lober RM, Rivero-Hinojosa S, Wang LB, Wang JM, Broberg M, Chu RK, Moore RJ, Monroe ME, Zhao R, Smith RD, Zhu J, Robles AI, Mesri M, Boja E, Hiltke T, Rodriguez H, Zhang B, Schadt EE, Mani DR, Ding L, Iavarone A, Wiznerowicz M, Schürer S, Chen XS, Heath AP, Rokita JL, Nesvizhskii AI, Fenyö D, Rodland KD, Liu T, Gygi SP, Paulovich AG, Resnick AC, Storm PB, Rood BR, Wang P. Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer. Cell 2020;183:1962-1985.e31. [PMID: 33242424 PMCID: PMC8143193 DOI: 10.1016/j.cell.2020.10.044] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 06/19/2020] [Accepted: 10/26/2020] [Indexed: 02/06/2023]

Affiliation(s)

Francesca Petralia Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Nicole Tignor Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Boris Reva Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Mateusz Koptyra Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
Shrabanti Chowdhury Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Dmitry Rykunov Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Azra Krek Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Weiping Ma Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Yuankun Zhu Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
Jiayi Ji Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Anna Calinawan Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Jeffrey R Whiteaker Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
Antonio Colaprico Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA
Vasileios Stathias Department of Pharmacology, Institute for Data Science and Computing, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33146, USA
Tatiana Omelchenko Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
Xiaoyu Song Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Pichai Raman Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
Yiran Guo Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
Miguel A Brown Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
Richard G Ivey Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
John Szpyt Thermo Fisher Scientific Center for Multiplexed Proteomics, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
Sanjukta Guha Thakurta Thermo Fisher Scientific Center for Multiplexed Proteomics, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
Marina A Gritsenko Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
Karl K Weitz Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
Gonzalo Lopez Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Selim Kalayci Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Zeynep H Gümüş Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Seungyeul Yoo Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Felipe da Veiga Leprevost Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
Hui-Yin Chang Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
Karsten Krug Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02412, USA
Lizabeth Katsnelson Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
Ying Wang Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
Jacob J Kennedy Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
Uliana J Voytovich Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
Lei Zhao Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
Krutika S Gaonkar Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
Brian M Ennis Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
Bo Zhang Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
Valerie Baubet Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
Lamiya Tauhid Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
Jena V Lilly Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
Jennifer L Mason Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
Bailey Farrow Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
Nathan Young Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
Sarah Leary Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Cancer and Blood Disorders Center, Seattle Children's Hospital, Seattle, WA 98105, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
Jamie Moon Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
Vladislav A Petyuk Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
Javad Nazarian Children's National Research Institute, George Washington University School of Medicine, Washington, DC 20010, USA; Department of Oncology, Children's Research Center, University Children's Hospital Zürich, Zürich 8032, Switzerland
Nithin D Adappa Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, PA 19104, USA
James N Palmer Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, PA 19104, USA
Robert M Lober Department of Neurosurgery, Dayton Children's Hospital, Dayton, OH 45404, USA
Samuel Rivero-Hinojosa Children's National Research Institute, George Washington University School of Medicine, Washington, DC 20010, USA
Liang-Bo Wang Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
Joshua M Wang Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
Matilda Broberg Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
Rosalie K Chu Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
Ronald J Moore Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
Matthew E Monroe Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
Rui Zhao Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
Richard D Smith Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
Jun Zhu Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Ana I Robles Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
Mehdi Mesri Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
Emily Boja Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
Tara Hiltke Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
Henry Rodriguez Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
Bing Zhang Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
Eric E Schadt Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
D R Mani Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02412, USA
Li Ding Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
Antonio Iavarone Institute for Cancer Genetics, Department of Neurology, Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
Maciej Wiznerowicz Poznan University of Medical Sciences, 61-701 Poznań, Poland; International Institute for Molecular Oncology, 61-203 Poznań, Poland
Stephan Schürer Department of Pharmacology, Institute for Data Science and Computing, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33146, USA
Xi S Chen Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
Allison P Heath Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
Jo Lynne Rokita Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
Alexey I Nesvizhskii Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
David Fenyö Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
Karin D Rodland Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA
Tao Liu Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
Steven P Gygi Thermo Fisher Scientific Center for Multiplexed Proteomics, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
Amanda G Paulovich Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
Adam C Resnick Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Phillip B Storm Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Brian R Rood Children's National Research Institute, George Washington University School of Medicine, Washington, DC 20010, USA.
Pei Wang Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.

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Zhu Y, Guo Y, Heath AP, Raman P, Appert E, Mason J, Zhang B, Kalletla K, Brown MA, Singh N, Farrow BK, Killada P, Kim MC, Felmeister A, Koptyra MP, Mueller S, Prados M, Lilly JV, Lulla R, Resnick AC, Nazarian J, Storm PB, Waanders AJ. Abstract 3667: The Pediatric Brain Tumor Atlas - Transforming the landscape of research. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]

Abstract Abstract The Pediatric Brain Tumor Atlas (PBTA) is a cloud-based, cross-platform, and data-rich collaborative effort to accelerate discoveries for therapeutic intervention in children diagnosed with brain tumors. Pediatric brain tumors are the leading cause of disease-related death in children and despite advances in therapy, morbidity and mortality rates remain poor. There have been large scale efforts to genomically profile these cancers in the past, however public access to the resulting datasets are limited at best. In contrast, the PBTA, created as a multi-center effort by Children’s Brain Tumor Tissue Consortium (CBTTC) and Pacific Pediatric Neuro-Oncology Consortium (PNOC), has a goal of characterizing over 1,600 pediatric brain tumor samples and making the data publicly available to cancer researchers world-wide. PBTA comprises comprehensive clinical data in addition to whole exome sequencing, whole genome sequencing (WGS), RNA sequencing (RNASeq), miRNA sequencing, and proteomics. To address the need to inform novel discovery and clinical implementation of genomic approaches for diagnostic/therapeutic purposes, PBTA utilizes a cloud-based scientific environment, the CAVATICA portal. CAVATICA provides near real-time integration, dissemination, processing, and sharing of associated PetaByte-sized data by leveraging Amazon Web Services and powerful genomic workflows. It also enables dbGaP approved users to access TCGA and other datasets hosted by NCI’s Cancer Genomics’ Cloud, allowing for cross-disease studies. While CAVATICA manages raw sequencing data, processed annotations and biospecimen querying is enabled for PBTA via PedcBioPortal, a data visualization/analysis application further integrating additional public and deposited datasets. PBTA data can further be accessed via the KidsFirst platform, which integrates both CAVATICA and PedcBioPortal, and allows for querying of cancer and non-cancer genomic data for subsequent analytics, visualization, and discovery. The 1st dataset release of PBTA occurred on September 10th, 2018. In this release there are over 30 different types of pediatric brain tumors representing over 1,000 subjects. This data is available on CAVATICA, KidsFirst, and PedcBioPortal and users can seamlessly move between applications. Data types include those for matched tumor/normal samples, such as WGS, RNASeq, proteomics, longitudinal clinical data, imaging data (MRIs and radiology reports), histology slide images, and pathology reports. CBTTC/PNOC promote real time data release with no embargo period, allowing PBTA to have is up-to-date data releases with no embargo. The combination of cloud-based analytic platforms such as KidsFirst/CAVATICA/PedcBioPortal with data from both genomics and clinical practice serves to define a new paradigm for pediatric cancer research and collaborative discovery. Citation Format: Yuankun Zhu, Yiran Guo, Allison P. Heath, Pichai Raman, Elizabeth Appert, Jennifer Mason, Bo Zhang, Karthik Kalletla, Miguel A. Brown, Natasha Singh, Bailey K. Farrow, Parimala Killada, Meen Chul Kim, Alex Felmeister, Mateusz P. Koptyra, Sabine Mueller, Michael Prados, Jena V. Lilly, Rishi Lulla, Adam C. Resnick, Javad Nazarian, Phillip B. Storm, Angela J. Waanders. The Pediatric Brain Tumor Atlas - Transforming the landscape of research [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3667. Collapse

Heath AP, Raman P, Zhu Y, Lilly JV, Taylor D, Storm PB, Waanders AJ, Volchenboum S, Stein L, Ellrott K, Margolin A, Davis-Dusenbery B, Grossman R, Ferretti V, Mueller S, Nazarian J, Resnick AC. TBIO-27. GABRIELLA MILLER KIDS FIRST DATA RESOURCE CENTER ADVANCING GENETIC RESEARCH IN CHILDHOOD CANCER AND STRUCTURAL BIRTH DEFECTS THROUGH LARGE SCALE INTEGRATED DATA-DRIVEN DISCOVERY AND CLOUD-BASED PLATFORMS FOR COLLABORATIVE ANALYSIS. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open

Resnick AC, Storm PB, Waanders AJ, Lilly JV, Lulla RR, Mueller S, Prados M, Sender LS, Heath A, Felmeister AS, Cros A, Zhu Y, Raman P. Abstract LB-008: The Pediatric Brain Tumor Atlas: building an integrated, multi-platform data-rich ecosystem for collaborative discovery in the cloud. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-lb-008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]

Abstract Abstract Pediatric brain tumors are the leading cause of disease-related death in children. However, despite large scale data-driven efforts for pediatric cancers by the NIH (e.g. TARGET, Therapeutically Applicable Research To Generate Effective Treatments), public access to large-scale pediatric brain tumor genomic data remains limited. As a result, precision medicine initiatives and clinical trials in pediatric brain tumors are hampered by the absence of publicly available genomic resources that can dynamically inform novel discovery and clinical implementation of genomic and molecular approaches for diagnostic and therapeutic purposes in affected children. The Pediatric Brain Tumor Atlas is a concerted multi-institution effort by the Children’s Brain Tumor Consortium (CBTTC) and the Pacific Pediatric Neuro-Oncology Consortium to characterize and deeply profile a newly defined cohort of >1600 brain tumor samples across diverse histopathologies via a combination of whole exome sequencing, whole genome sequencing, RNA sequencing and limited proteomic analysis. Importantly, the Atlas initiative provides for near real-time integration, dissemination, and sharing of the associated raw and analyzed data through an ecosystem of data discovery platforms. As data of this size and complexity require a bolus of scalable computational power and storage, a new cloud-based collaborative scientific environment termed CAVATICA (cavatica.org) has been launched to support integrative analysis and open access to data alongside shared computation and algorithms that empower users to further integrate and analyse their own uploaded data. Importantly, CAVATICA provides further portal access to dbGaP approved users to TCGA and other NCI datasets hosted by the NCI’s Cancer Genomics’ Cloud. Additionally, it provides for scalable integration of these and additional disease-specific datasets on the platform via transdisciplinary analyses. Currently, one of the biggest barriers and challenges to collaborative research in large datasets is the transfer and processing of ‘big data’. By committing to the rapid release of these large pediatric brain tumor data and their deposition in CAVATICA’s cloud-based environment supporting shared pipelines, computation, and visualizations, PNOC and the CBTTC’s collaborating membership are seeking to provide a centralized, collaborative rapid discovery environment for researchers to engage new discovery and data reuse. In addition to unprocessed genomic, whole genome and RNA sequencing data in CAVATICA, processed annotations and and additional biospecimen querying is enabled for the Pediatric Brain Tumor Atlas via PedcBioPortal (PedcBioPortal.org), a data visualization and analysis application further integrating across additional public and deposited datasets. The combination of large-scale genomic data and integrative cloud-based analytic platforms with what is one of the largest genomic date cohorts to date for pediatric brain tumors serves to define a new paradigm for pediatric cancer research and collaborative discovery. Citation Format: Adam C. Resnick, Phillip B. Storm, Angela J. Waanders, Jena V. Lilly, Rishi R. Lulla, Sabine Mueller, Michael Prados, Leonard S. Sender, Allison Heath, Alex S. Felmeister, Anthony Cros, Yuankun Zhu, Pichai Raman. The Pediatric Brain Tumor Atlas: building an integrated, multi-platform data-rich ecosystem for collaborative discovery in the cloud [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-008. doi:10.1158/1538-7445.AM2017-LB-008 Collapse

Raman P, Waanders AJ, Storm PB, Lilly JV, Mason J, Heath AP, Felmeister AS, Cros A, Zhu Y, Sender L, Prados M, Mueller S, Lulla R, Nazarian J, Resnick AC. GENE-15. CAVATICA- A PEDIATRIC GENOMIC CLOUD EMPOWERING DATA DISCOVERY THROUGH THE PEDIATRIC BRAIN TUMOR ATLAS. Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox083.086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open