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  • 1
    Online Resource
    Online Resource
    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
    American Association for Cancer Research (AACR) ; 2023
    In:  Cancer Research Vol. 83, No. 7_Supplement ( 2023-04-04), p. 3566-3566
    Details
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 83, No. 7_Supplement ( 2023-04-04), p. 3566-3566
    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 & gt;50 brain tumor diagnoses. The cohort expansion builds on & gt;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 & gt;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.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    URL: Article
    DOI: 10.1158/1538-7445.AM2023-3566
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
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    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 2
    Online Resource
    Online Resource
    The children's brain tumor network (CBTN) - Accelerating research in pediatric central nervous system tumors through collaboration and open science
    Elsevier BV ; 2023
    In:  Neoplasia Vol. 35 ( 2023-01), p. 100846-
    Details
    In: Neoplasia, Elsevier BV, Vol. 35 ( 2023-01), p. 100846-
    Type of Medium: Online Resource
    ISSN: 1476-5586
    URL: Article
    DOI: 10.1016/j.neo.2022.100846
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2023
    detail.hit.zdb_id: 2008231-9
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  • 3
    Online Resource
    Online Resource
    MODL-30. Children’s Brain Tumor Network preclinical tumor models development and sharing platform: collaborative model empowering pediatric brain tumor discovery and global research.
    Oxford University Press (OUP) ; 2022
    In:  Neuro-Oncology Vol. 24, No. Supplement_1 ( 2022-06-03), p. i175-i176
    Details
    In: Neuro-Oncology, Oxford University Press (OUP), Vol. 24, No. Supplement_1 ( 2022-06-03), p. i175-i176
    Abstract: Pediatric brain tumor preclinical field suffered for years from the lack of in vitro and in vivo models. With the explosion of novel therapy approaches for solid and brain tumors, including the immunotherapies it is essential to maximize the access to preclinical models for preclinical specificity, efficacy as well and safety. One of the many ways the Children’s Brain Tumor Network (CBTN) accelerates the pediatric brain tumor research and discovery is through support of the tumor model development program. This program focuses on the generation, characterization, and distribution of diverse models to investigators worldwide provided free of charge. Here we present the resource platform with over 150 cell lines, organoids and patient derived xenografts (PDX) developed and/or propagated at D3b at CHOP on behalf of CBTN. This platform maximizes the tumor tissue use to generate a combination of cell line, organoids and/or xenograft models grown in animals. In recent years, consortium supported over 40 requests for cells lines used in basic biology and translational studies internationally. Current efforts focusing also on supporting large-scale data generation and testing through its collaborative model (Childhood Cancer Model Atlas, Procan, National Center for Advancing Translational Sciences) to maximize the molecular information available for each tumor model essential in preclinical screenings. The generated and returned to consortia data are bound with the deidentified patient clinical information and genomic data and freely available through Kid’s First Data, Cavatica and PedcBio portals. These efforts have already attracted interest from pharma stakeholders previously not observed in pediatric brain environment. This open-source repository model is an example of a unique research partnership supported by patients and their families and built with one mission to bring fast change to kids suffering from brain tumors.
    Type of Medium: Online Resource
    ISSN: 1522-8517 , 1523-5866
    URL: Article
    DOI: 10.1093/neuonc/noac079.653
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2094060-9
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  • 4
    Online Resource
    Online Resource
    RARE-17. Multi-institutional craniopharyngioma cohort highlights need for more comprehensive data collection on comorbidities and quality of life
    Oxford University Press (OUP) ; 2022
    In:  Neuro-Oncology Vol. 24, No. Supplement_1 ( 2022-06-03), p. i13-i13
    Details
    In: Neuro-Oncology, Oxford University Press (OUP), Vol. 24, No. Supplement_1 ( 2022-06-03), p. i13-i13
    Abstract: BACKGROUND: Pediatric craniopharyngioma is associated with long-term survival, but tumor- and therapy-related complications often negatively impact quality of life (QoL). Standard treatments include resection and radiation, but institutional practices vary and recurrence rates remain high. In this review, we utilized a cohort from the Children’s Brain Tumor Network (CBTN) to evaluate outcomes for craniopharyngioma. METHODS: CBTN provides clinical and genomic data for pediatric patients diagnosed with primary central nervous system tumors across 25+ institutions. We collected data for 124 patients, ages 0-21, diagnosed with craniopharyngioma between 2012-2020. Variables collected included treatment, recurrence/progression, and comorbidities. RESULTS: Excluding patients without confirmed pathologic diagnosis (n=10) or follow-up data (n=39), 75 patients remained. For initial treatment, most (n=46, 61%) received surgery alone (9 partial, 33 near-total resection). Twenty-six (35%) underwent both surgery and radiation, with 9 receiving both therapies upfront and 17 receiving radiation at progression/recurrence. Four (5%) patients received chemotherapy. Over half of the cohort (n=39, 52%) had at least one progression/recurrence, and four died (5%). Significantly higher rates of progression/recurrence (84% vs. 32%, p=4.0e-5) were identified in patients that had surgery and radiation, compared to surgery alone. Time to recurrence, progression, or death was shorter for the surgery and radiation group (HR=4.1, p & lt;1.0e-4), and for those that underwent partial versus near-total resection (HR=2.7, p=0.1.2e-2). Comorbidities were likely underreported, based on low rates of visual (32%), neuroendocrine (27%), and neurologic (28%) deficits at diagnosis, and 29 patients (39%) with unspecified medical history. CONCLUSIONS: CBTN provides a robust repository of information on treatment and survival of craniopharyngioma patients. However, we found a paucity of data on associated comorbidities and QoL outcomes. We advocate that future datasets and clinical trials routinely collect functional outcomes alongside therapy and survival data, particularly in craniopharyngioma where long-term survival is balanced with future QoL.
    Type of Medium: Online Resource
    ISSN: 1522-8517 , 1523-5866
    URL: Article
    DOI: 10.1093/neuonc/noac079.042
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2094060-9
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  • 5
    Online Resource
    Online Resource
    METB-11. EXPANSION OF THE PEDIATRIC BRAIN TUMOR ATLAS: AN OPEN SCIENCE EFFORT OF CHILDREN’S BRAIN TUMOR NETWORK, KIDS FIRST DATA RESOURCE AND CHILDHOOD CANCER DATA INITIATIVE
    Oxford University Press (OUP) ; 2023
    In:  Neuro-Oncology Vol. 25, No. Supplement_1 ( 2023-06-12), p. i32-i32
    Details
    In: Neuro-Oncology, Oxford University Press (OUP), Vol. 25, No. Supplement_1 ( 2023-06-12), p. i32-i32
    Abstract: Pediatric central nervous system 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) and Gabriella Miller Kids First Data Resource Center (KFDRC) created and characterized over 1000 clinically annotated pediatric brain tumors. The second phase of the OpenPBTA, through resource awards and collaboration across KFDRC, the NCI Childhood Cancer Data Initiative (CCDI), Clinical Proteomic Tumor Analysis Consortium (CPTAC), Center for Cancer Research and partnered institutions and foundations has expanded molecular characterization for an additional 1900 pediatric brain tumor patients and their families. This includes the processing and characterization of & gt;8000 specimens across & gt;50 brain tumor diagnoses. This expansion builds off multimodal data including whole genome, RNA, miRNA and methylation sequencing, proteomics, lipidomics and/or metabolomics. Molecular data is linked to longitudinal clinical data, imaging data, histology images, and pathology reports. The data deposition in the cloud-based environment of the NCI’s CCDI and KFDRC to provide near real-time integration, dissemination, processing, and sharing capability. The approach leverages the DRC platform’s cloud-based computational environment through CAVATICA portal shareable pipelines. Data can be explored via PedcBioPortal, a data visualization/analysis application integrating additional public and deposited datasets. This OpenPBTA expansion released with no embargo provides one of the largest deeply characterized cohorts of samples and associated clinical data for & gt;3000 pediatric brain tumor patients. CBTN’s open-science, rapid-release model aims to accelerate pediatric biomarker and drug discovery research and supports clinical trial development on behalf of changing the outcome for kids with brain tumors.
    Type of Medium: Online Resource
    ISSN: 1522-8517 , 1523-5866
    URL: Article
    DOI: 10.1093/neuonc/noad073.128
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2094060-9
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  • 6
    Online Resource
    Online Resource
    BIOL-22. CHILDREN’S BRAIN TUMOR NETWORK PRECLINICAL TUMOR MODELS DEVELOPMENT AND SHARING PLATFORM: COLLABORATIVE MODEL EMPOWERING PEDIATRIC BRAIN TUMOR DISCOVERY AND GLOBAL RESEARCH
    Oxford University Press (OUP) ; 2023
    In:  Neuro-Oncology Vol. 25, No. Supplement_1 ( 2023-06-12), p. i10-i11
    Details
    In: Neuro-Oncology, Oxford University Press (OUP), Vol. 25, No. Supplement_1 ( 2023-06-12), p. i10-i11
    Abstract: Pediatric brain tumor preclinical development has suffered from the lack of robust in vitro and in vivo models that span the large number of brain tumor histologies. Opportunities for precision medicine approaches for solid and brain tumors are expanding, including immunotherapies, so it is essential to maximize access to preclinical models for studies of specificity, efficacy, and safety of treatments in ways that align patient models to patient samples and their clinical course. The Children’s Brain Tumor Network (CBTN) seeks to accelerate pediatric brain tumor research and discovery through support of the tumor model development program paired with molecularly characterized patient samples and longitudinal clinical data. This program focuses on the generation, characterization, and distribution of diverse models to investigators worldwide. Here we present currently available preclinical model resources comprising over 150 cell lines, organoids, and patient derived xenografts (PDX) developed and/or propagated at D3b at CHOP on behalf of CBTN. This platform maximizes the use of tumor tissue to generate a combination of cell lines, organoids and/or xenograft models grown in animals. To date, consortium-supported lines have been provided internationally to over 50 projects, encompassing basic biology and translational studies. Molecular data (whole genome sequencing and RNAseq) is currently available for over 80 models and a substantial portion of that cohort undergoes additional large-scale data generation and drug testing through collaborative work with Childhood Cancer Model Atlas, ProCan, and National Center for Advancing Translational Sciences. All models’ data are accompanied with patient molecular and clinical longitudinal information accessible through Kids First Data Resource, CAVATICA and PedcBio portals. This open-source repository model is an example of a unique research partnership supported by patients and their families and built with one mission – to accelerate therapeutic discovery for children suffering from brain tumors.
    Type of Medium: Online Resource
    ISSN: 1522-8517 , 1523-5866
    URL: Article
    DOI: 10.1093/neuonc/noad073.041
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2094060-9
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