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Familiar AM, Kazerooni AF, Anderson H, Lubneuski A, Viswanathan K, Breslow R, Khalili N, Bagheri S, Haldar D, Kim MC, Arif S, Madhogarhia R, Nguyen TQ, Frenkel EA, Helili Z, Harrison J, Farahani K, Linguraru MG, Bagci U, Velichko Y, Stevens J, Leary S, Lober RM, Campion S, Smith AA, Morinigo D, Rood B, Diamond K, Pollack IF, Williams M, Vossough A, Ware JB, Mueller S, Storm PB, Heath AP, Waanders AJ, Lilly J, Mason JL, Resnick AC, Nabavizadeh A. A multi-institutional pediatric dataset of clinical radiology MRIs by the Children's Brain Tumor Network. ArXiv 2023:arXiv:2310.01413v1. [PMID: 38106459 PMCID: PMC10723526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Pediatric brain and spinal cancers remain the leading cause of cancer-related death in children. Advancements in clinical decision-support in pediatric neuro-oncology utilizing the wealth of radiology imaging data collected through standard care, however, has significantly lagged other domains. Such data is ripe for use with predictive analytics such as artificial intelligence (AI) methods, which require large datasets. To address this unmet need, we provide a multi-institutional, large-scale pediatric dataset of 23,101 multi-parametric MRI exams acquired through routine care for 1,526 brain tumor patients, as part of the Children's Brain Tumor Network. This includes longitudinal MRIs across various cancer diagnoses, with associated patient-level clinical information, digital pathology slides, as well as tissue genotype and omics data. To facilitate downstream analysis, treatment-naïve images for 370 subjects were processed and released through the NCI Childhood Cancer Data Initiative via the Cancer Data Service. Through ongoing efforts to continuously build these imaging repositories, our aim is to accelerate discovery and translational AI models with real-world data, to ultimately empower precision medicine for children.
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Affiliation(s)
- Ariana M. Familiar
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Anahita Fathi Kazerooni
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hannah Anderson
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Aliaksandr Lubneuski
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Karthik Viswanathan
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rocky Breslow
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nastaran Khalili
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sina Bagheri
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Debanjan Haldar
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Meen Chul Kim
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sherjeel Arif
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rachel Madhogarhia
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Thinh Q. Nguyen
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elizabeth A. Frenkel
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Zeinab Helili
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jessica Harrison
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Marius George Linguraru
- Sheikh Zayed Institute for Pediatric Surgical Innovation, Children’s National Hospital, Washington, DC, USA
- Departments of Radiology and Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Ulas Bagci
- Department of Radiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yury Velichko
- Department of Radiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jeffrey Stevens
- Department of Hematology and Oncology, Seattle Children’s, Seattle, WA, USA
| | - Sarah Leary
- Department of Hematology and Oncology, Seattle Children’s, Seattle, WA, USA
| | - Robert M. Lober
- Division of Neurosurgery, Dayton Children’s Hospital, Dayton, OH, USA
| | - Stephani Campion
- Department of Pediatric Hematology & Oncology, Orlando Health Arnold Palmer Hospital for Children, Orlando, FL, USA
| | - Amy A. Smith
- Department of Pediatric Hematology & Oncology, Orlando Health Arnold Palmer Hospital for Children, Orlando, FL, USA
| | - Denise Morinigo
- Department of Hematology-Oncology, Children’s National Hospital, Washington, DC, USA
| | - Brian Rood
- Department of Hematology-Oncology, Children’s National Hospital, Washington, DC, USA
| | - Kimberly Diamond
- Department of Pediatric Neurosurgery, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Ian F. Pollack
- Department of Pediatric Neurosurgery, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Melissa Williams
- Division of Hematology, Oncology, NeuroOncology, and Transplant, Ann & Robert H Lurie Children’s Hospital of Chicago, Chicago, IL, USA
| | - Arastoo Vossough
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Radiology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jeffrey B. Ware
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sabine Mueller
- Department of Neurology, Division of Child Neurology, University of San Francisco, San Francisco, CA, USA
| | - Phillip B. Storm
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Allison P. Heath
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Angela J. Waanders
- Division of Hematology, Oncology, NeuroOncology, and Transplant, Ann & Robert H Lurie Children’s Hospital of Chicago, Chicago, IL, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jena Lilly
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jennifer L. Mason
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Adam C. Resnick
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ali Nabavizadeh
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Fathi Kazerooni A, Arif S, Madhogarhia R, Khalili N, Haldar D, Bagheri S, Familiar AM, Anderson H, Haldar S, Tu W, Kim MC, Viswanathan K, Muller S, Prados M, Kline C, Vidal L, Aboian M, Storm PB, Resnick AC, Ware JB, Vossough A, Davatzikos C, Nabavizadeh A. Automated Tumor Segmentation and Brain Tissue Extraction from Multiparametric MRI of Pediatric Brain Tumors: A Multi-Institutional Study. Neurooncol Adv 2023; 5:vdad027. [PMID: 37051331 PMCID: PMC10084501 DOI: 10.1093/noajnl/vdad027] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
Abstract
Background
Brain tumors are the most common solid tumors and the leading cause of cancer-related death among all childhood cancers. Tumor segmentation is essential in surgical and treatment planning, and response assessment and monitoring. However, manual segmentation is time-consuming and has high interoperator variability. We present a multi-institutional deep learning-based method for automated brain extraction and segmentation of pediatric brain tumors based on multi-parametric MRI scans.
Methods
Multi-parametric scans (T1w, T1w-CE, T2, and T2-FLAIR) of 244 pediatric patients (n=215 internal and n=29 external cohorts) with de novo brain tumors, including a variety of tumor subtypes, were preprocessed and manually segmented to identify the brain tissue and tumor subregions into four tumor subregions, i.e., enhancing tumor (ET), non-enhancing tumor (NET), cystic components (CC), and peritumoral edema (ED). The internal cohort was split into training (n=151), validation (n=43), and withheld internal test (n=21) subsets. DeepMedic, a three-dimensional convolutional neural network, was trained and the model parameters were tuned. Finally, the network was evaluated on the withheld internal and external test cohorts.
Results
Dice similarity score (median±SD) was 0.91±0.10/0.88±0.16 for the whole tumor, 0.73±0.27/0.84±0.29 for ET, 0.79±19/0.74±0.27 for union of all non-enhancing components (i.e., NET, CC, ED), and 0.98±0.02 for brain tissue in both internal/external test sets.
Conclusions
Our proposed automated brain extraction and tumor subregion segmentation models demonstrated accurate performance on segmentation of the brain tissue and whole tumor regions in pediatric brain tumors and can facilitate detection of abnormal regions for further clinical measurements.
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Affiliation(s)
- Anahita Fathi Kazerooni
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia , PA, USA
- AI2D Center for AI and Data Science for Integrated Diagnostics, University of Pennsylvania, Philadelphia , PA, USA
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA, USA
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia , PA, USA
| | - Sherjeel Arif
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia , PA, USA
| | - Rachel Madhogarhia
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia , PA, USA
| | - Nastaran Khalili
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia , PA, USA
| | - Debanjan Haldar
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia , PA, USA
- Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA, USA
| | - Sina Bagheri
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia , PA, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA, USA
| | - Ariana M Familiar
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia , PA, USA
| | - Hannah Anderson
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia , PA, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA, USA
| | - Shuvanjan Haldar
- Department of Biomedical Engineering, Rutgers University, New Brunswick , NJ, USA
| | - Wenxin Tu
- College of Arts and Sciences, University of Pennsylvania, Philadelphia , PA, USA
| | - Meen Chul Kim
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia , PA, USA
| | - Karthik Viswanathan
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia , PA, USA
| | - Sabine Muller
- Department of Neurology and Pediatrics, University of California San Francisco, San Francisco , CA, USA
| | - Michael Prados
- Department of Neurological Surgery and Pediatrics, University of California San Francisco, San Francisco , CA, USA
| | - Cassie Kline
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia , PA, USA
| | - Lorenna Vidal
- Division of Radiology, Children’s Hospital of Philadelphia, Philadelphia , PA, USA
| | - Mariam Aboian
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven , CT, USA
| | - Phillip B Storm
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia , PA, USA
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA, USA
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia , PA, USA
| | - Adam C Resnick
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia , PA, USA
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia , PA, USA
| | - Jeffrey B Ware
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA, USA
| | - Arastoo Vossough
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia , PA, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA, USA
- Division of Radiology, Children’s Hospital of Philadelphia, Philadelphia , PA, USA
| | - Christos Davatzikos
- AI2D Center for AI and Data Science for Integrated Diagnostics, University of Pennsylvania, Philadelphia , PA, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA, USA
| | - Ali Nabavizadeh
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia , PA, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA, USA
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Haldar D, Kazerooni AF, Arif S, Familiar A, Madhogarhia R, Khalili N, Bagheri S, Anderson H, Shaikh IS, Mahtabfar A, Kim MC, Tu W, Ware J, Vossough A, Davatzikos C, Storm PB, Resnick A, Nabavizadeh A. Unsupervised machine learning using K-means identifies radiomic subgroups of pediatric low-grade gliomas that correlate with key molecular markers. Neoplasia 2023; 36:100869. [PMID: 36566592 PMCID: PMC9803939 DOI: 10.1016/j.neo.2022.100869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/21/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Despite advancements in molecular and histopathologic characterization of pediatric low-grade gliomas (pLGGs), there remains significant phenotypic heterogeneity among tumors with similar categorizations. We hypothesized that an unsupervised machine learning approach based on radiomic features may reveal distinct pLGG imaging subtypes. METHODS Multi-parametric MR images (T1 pre- and post-contrast, T2, and T2 FLAIR) from 157 patients with pLGGs were collected and 881 quantitative radiomic features were extracted from tumorous region. Clustering was performed using K-means after applying principal component analysis (PCA) for feature dimensionality reduction. Molecular and demographic data was obtained from the PedCBioportal and compared between imaging subtypes. RESULTS K-means identified three distinct imaging-based subtypes. Subtypes differed in mutational frequencies of BRAF (p < 0.05) as well as the gene expression of BRAF (p<0.05). It was also found that age (p < 0.05), tumor location (p < 0.01), and tumor histology (p < 0.0001) differed significantly between the imaging subtypes. CONCLUSION In this exploratory work, it was found that clustering of pLGGs based on radiomic features identifies distinct, imaging-based subtypes that correlate with important molecular markers and demographic details. This finding supports the notion that incorporation of radiomic data could augment our ability to better characterize pLGGs.
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Affiliation(s)
- Debanjan Haldar
- Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania, USA; Center for Data-Driven Discovery in Biomedicine (D3b), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Anahita Fathi Kazerooni
- Center for Data-Driven Discovery in Biomedicine (D3b), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Radiology, Hospital of University of Pennsylvania, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sherjeel Arif
- Center for Data-Driven Discovery in Biomedicine (D3b), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Radiology, Hospital of University of Pennsylvania, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ariana Familiar
- Center for Data-Driven Discovery in Biomedicine (D3b), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Rachel Madhogarhia
- Center for Data-Driven Discovery in Biomedicine (D3b), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Radiology, Hospital of University of Pennsylvania, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nastaran Khalili
- Center for Data-Driven Discovery in Biomedicine (D3b), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Radiology, Hospital of University of Pennsylvania, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sina Bagheri
- Center for Data-Driven Discovery in Biomedicine (D3b), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Radiology, Hospital of University of Pennsylvania, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hannah Anderson
- Center for Data-Driven Discovery in Biomedicine (D3b), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Radiology, Hospital of University of Pennsylvania, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Aria Mahtabfar
- Center for Data-Driven Discovery in Biomedicine (D3b), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Neurological Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Meen Chul Kim
- Center for Data-Driven Discovery in Biomedicine (D3b), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Wenxin Tu
- College of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jefferey Ware
- Department of Radiology, Hospital of University of Pennsylvania, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arastoo Vossough
- Center for Data-Driven Discovery in Biomedicine (D3b), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Radiology, Hospital of University of Pennsylvania, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Christos Davatzikos
- Department of Radiology, Hospital of University of Pennsylvania, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Phillip B Storm
- Center for Data-Driven Discovery in Biomedicine (D3b), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Division of Neurological Surgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Adam Resnick
- Center for Data-Driven Discovery in Biomedicine (D3b), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ali Nabavizadeh
- Center for Data-Driven Discovery in Biomedicine (D3b), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Radiology, Hospital of University of Pennsylvania, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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Kazerooni AF, Arif S, Madhogarhia R, Khalili N, Haldar D, Bagheri S, Familiar AM, Anderson H, Haldar S, Tu W, Kim MC, Viswanathan K, Muller S, Prados M, Kline C, Vidal L, Aboian M, Storm PB, Resnick AC, Ware JB, Vossough A, Davatzikos C, Nabavizadeh A. Automated Tumor Segmentation and Brain Tissue Extraction from Multiparametric MRI of Pediatric Brain Tumors: A Multi-Institutional Study. medRxiv 2023:2023.01.02.22284037. [PMID: 36711966 PMCID: PMC9882407 DOI: 10.1101/2023.01.02.22284037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Background Brain tumors are the most common solid tumors and the leading cause of cancer-related death among all childhood cancers. Tumor segmentation is essential in surgical and treatment planning, and response assessment and monitoring. However, manual segmentation is time-consuming and has high interoperator variability. We present a multi-institutional deep learning-based method for automated brain extraction and segmentation of pediatric brain tumors based on multi-parametric MRI scans. Methods Multi-parametric scans (T1w, T1w-CE, T2, and T2-FLAIR) of 244 pediatric patients (n=215 internal and n=29 external cohorts) with de novo brain tumors, including a variety of tumor subtypes, were preprocessed and manually segmented to identify the brain tissue and tumor subregions into four tumor subregions, i.e., enhancing tumor (ET), non-enhancing tumor (NET), cystic components (CC), and peritumoral edema (ED). The internal cohort was split into training (n=151), validation (n=43), and withheld internal test (n=21) subsets. DeepMedic, a three-dimensional convolutional neural network, was trained and the model parameters were tuned. Finally, the network was evaluated on the withheld internal and external test cohorts. Results Dice similarity score (median±SD) was 0.91±0.10/0.88±0.16 for the whole tumor, 0.73±0.27/0.84±0.29 for ET, 0.79±19/0.74±0.27 for union of all non-enhancing components (i.e., NET, CC, ED), and 0.98±0.02 for brain tissue in both internal/external test sets. Conclusions Our proposed automated brain extraction and tumor subregion segmentation models demonstrated accurate performance on segmentation of the brain tissue and whole tumor regions in pediatric brain tumors and can facilitate detection of abnormal regions for further clinical measurements. Key Points We proposed automated tumor segmentation and brain extraction on pediatric MRI.The volumetric measurements using our models agree with ground truth segmentations. Importance of the Study The current response assessment in pediatric brain tumors (PBTs) is currently based on bidirectional or 2D measurements, which underestimate the size of non-spherical and complex PBTs in children compared to volumetric or 3D methods. There is a need for development of automated methods to reduce manual burden and intra- and inter-rater variability to segment tumor subregions and assess volumetric changes. Most currently available automated segmentation tools are developed on adult brain tumors, and therefore, do not generalize well to PBTs that have different radiological appearances. To address this, we propose a deep learning (DL) auto-segmentation method that shows promising results in PBTs, collected from a publicly available large-scale imaging dataset (Children's Brain Tumor Network; CBTN) that comprises multi-parametric MRI scans of multiple PBT types acquired across multiple institutions on different scanners and protocols. As a complementary to tumor segmentation, we propose an automated DL model for brain tissue extraction.
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Kazerooni AF, Madhogarhia R, Arif S, Ware JB, Bagheri S, Haldar D, Anderson H, Familiar A, Vidal L, Aboian M, Storm PB, Resnick AC, Vossough A, Davatzikos C, Nabavizadeh A. NIMG-102. RAPNO-DEFINED SEGMENTATION AND VOLUMETRIC ASSESSMENT OF PEDIATRIC BRAIN TUMORS ON MULTI-PARAMETRIC MRI SCANS USING DEEP LEARNING; A ROBUST TOOL WITH POTENTIAL APPLICATION IN TUMOR RESPONSE ASSESSMENT. Neuro Oncol 2022. [PMCID: PMC9660634 DOI: 10.1093/neuonc/noac209.720] [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] Open
Abstract
Abstract
Volumetric measurements of whole tumor and its components on MRI scans, facilitated by automatic segmentation tools, are essential to reduce inter-observer variability in monitoring tumor progression and response assessment for pediatric brain tumors. Here, we present a fully automatic segmentation model based on deep learning that reliably delineates the tumor components recommended by the Response Assessment in Pediatric Neuro-Oncology (RAPNO) working group for evaluation of treatment response. Multi-parametric MRI (mpMRI) scans (T1-pre, T1-post, T2, and T2-FLAIR), acquired on multiple MRI scanners with different field strengths and vendors, for a cohort of 218 pediatric patients with a variety of histologically confirmed brain tumor subtypes were collected. The mpMRI scans were co-registered and manually segmented by experienced neuroradiologists in consensus to identify the tumor subregions including the enhancing tumor (ET), non-enhancing tumor (NET), cystic components (CC), and peritumoral edema (ED) regions. A convolutional neural network model based on DeepMedic architecture was trained using mpMRI scans as the inputs for segmentation of the whole tumor and subregions. The trained model showed excellent performance in segmentation of the whole tumor, as suggested by median dice of 0.90/0.85 for validation (n = 44)/independent test (n = 22) sets. ET and non-enhancing components (union of NET, CC, and ED) were segmented with median dice scores of 0.78/0.84 and 0.76/0.74 for validation/test sets, respectively. The automated and manual segmentations demonstrated strong agreement in estimating VASARI (Visually AcceSAble Rembrandt Images) MRI features with Pearson’s correlation coefficient R > 0.75 (p < 0.0001) for ET, NET, CC, and ED components. Our proposed automated segmentation method developed based on MRI scans acquired with different protocols, equipment, and from a variety of brain tumor subtypes, shows potential application for reliable and generalizable volumetric measurements which can be used for treatment response assessment in clinical trials.
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Affiliation(s)
- Anahita Fathi Kazerooni
- Center for Biomedical Image Computing and Analytics and Department of Radiology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
| | | | | | - Jeffrey B Ware
- Hospital of the University of Pennsylvania , Philadelphia , USA
| | - Sina Bagheri
- Hospital of the University of Pennsylvania , Philadelphia , USA
| | | | - Hannah Anderson
- Hospital of the University of Pennsylvania , Philadelphia , USA
| | | | - Lorenna Vidal
- Children's Hospital of Philadelphia , Philadelphia , USA
| | | | | | - Adam C Resnick
- Children's Hospital of Philadelphia , Philadelphia , USA
| | | | - Christos Davatzikos
- Center for Biomedical Image Computing and Analytics and Department of Radiology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
| | - Ali Nabavizadeh
- Hospital of the University of Pennsylvania , Philadelphia , USA
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Kazerooni AF, Kraya AA, Kim MC, Khalili N, Arif S, Jin R, Rathi K, Familiar A, Madhogarhia R, Haldar D, Bagheri S, Anderson H, Shaikh IS, Haldar S, Ware JB, Vossough A, Storm PB, Resnick AC, Davatzikos C, Nabavizadeh A. NIMG-74. RADIOIMMUNOMIC SIGNATURES IN PEDIATRIC LOW-GRADE GLIOMA BASED ON MULTIPARAMETRIC MRI SCANS. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac209.692] [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] Open
Abstract
Abstract
Understanding the immune microenvironment in pediatric low-grade glioma (pLGG) patients may help in identification of the patients who benefit from anti-tumor immunotherapies. However, surgical resection is not feasible for many pLGG tumors in certain anatomical locations. Therefore, developing non-invasive tools that characterize the tumor microenvironment prior to therapeutic interventions could contribute to stratification and enrollment of the patients into relevant clinical trials. In this work, we derived radiomic signatures of immune profiles (radioimmunomics) based on machine learning (ML) analysis of readily available conventional MRI scans. Transcriptomic data for a cohort of 197 subjects was retrospectively collected from Open Pediatric Brain Tumor Atlas (OpenPBTA). The patients were categorized into three groups (Group1-3) based on their immunological profiles using consensus clustering algorithm. This analysis revealed greater immune cell infiltration in non-BRAF mutated pLGGs. Group1 showed more enrichment in M1 macrophages, and microenvironment and immune scores compared to Group2 and Group3. Elevated tumor inflammation score (TIS), as a predictor of clinical response to anti-PD-1 blockade, was observed in Group1 compared to Group2 (p= 1.4e-7) and Group3 (p= 0.0054). Radiomic features, including volumetric, morphologic, histogram, and texture descriptors, were extracted from the segmented tumor regions on multiparametric MRI (mpMRI) scans of 71 (of 197) patients. Multivariate ML models were trained to predict the three immunological groups based on radiomic features using cross-validated random forest classifier along with recursive feature elimination, which yielded AUC of 0.72 for this multi-class classification problem. Our findings indicate the presence of distinct immunological groups in pLGG tumors, with possibly more favorable response to immunotherapies in Group1 tumors. Furthermore, we developed radioimmunomic signatures based on pre-operative conventional mpMRI that can potentially stratify the patients based on their immune tumor microenvironment. Based on these initial promising results, we are exploring additional features to increase the accuracy of radioimmunomics model.
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Affiliation(s)
- Anahita Fathi Kazerooni
- Center for Biomedical Image Computing and Analytics and Department of Radiology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
| | | | | | | | | | | | - Komal Rathi
- Children's Hospital of Philadelphia , Philadelphia , USA
| | | | | | | | - Sina Bagheri
- Hospital of the University of Pennsylvania , Philadelphia , USA
| | - Hannah Anderson
- Hospital of the University of Pennsylvania , Philadelphia , USA
| | | | - Shuvanjan Haldar
- Rutgers University Department of Biomedical Engineering , Newark , USA
| | - Jeffrey B Ware
- Hospital of the University of Pennsylvania , Philadelphia , USA
| | | | | | - Adam C Resnick
- Children's Hospital of Philadelphia , Philadelphia , USA
| | - Christos Davatzikos
- Center for Biomedical Image Computing and Analytics and Department of Radiology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
| | - Ali Nabavizadeh
- Hospital of the University of Pennsylvania , Philadelphia , USA
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Familiar A, Zhao C, Kim MC, Khalili N, Madhogarhia R, Arif S, Bagheri S, Anderson H, Haldar D, Ware JB, Vossough A, Storm PB, Resnick AC, Kazerooni AF, Nabavizadeh A. NIMG-87. CHARACTERIZING IMMUNE PROFILES OF PEDIATRIC MEDULLOBLASTOMA AND THEIR RADIOLOGICAL CORRELATES. Neuro Oncol 2022. [PMCID: PMC9661070 DOI: 10.1093/neuonc/noac209.705] [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] Open
Abstract
Abstract
Recent studies have shown preliminary evidence for differentiation of the tumor microenvironment (TME) and immune landscape between molecularly-defined medulloblastoma (MB) subtypes. Identifying radiological correlates of these TME patterns could establish a non-invasive method of immune profile characterization for guiding patient-centered therapies. Here, we examine immune profiles between MB subtypes using data from Open Pediatric Brain Tumor Atlas (OpenPBTA), and their relationship to tumor measurements from pre-operative MRIs. We identified a retrospective cohort of 94 pediatric MB patients with available molecular subtyping and immune profiles (36 cell types) from bulk gene expression data. A random forest analysis was used to classify the four MB subtypes based on immune profiles. Four cell types had high impact on classification performance: plasmacytoid dendritic cells (PDC; 25.8% accuracy decrease when randomized), hematopoietic stem cells (HSC; 21.9%), plasma B cells (20.3%), and cancer associated fibroblasts (18.8%). Pairwise comparisons revealed SHH and WNT tumors had significantly higher numbers of fibroblasts and HSCs compared to Group3/Group4. We also found novel evidence for significantly lower amounts of plasma B cells in the SHH group, and high PDC levels in Group4, followed by Group3, and low PDC in SHH/WNT. Multi-parametric MRI scans for 39 patients were used to segment tumor volumes. Overall tumor volume was significantly correlated with composite stroma scores (R = 0.34, p = 0.036). Additionally, patients with higher volumes of gadolinium contrast-enhancing compared to non-enhancing components had higher immune (R = 0.42, p = 0.009) and microenvironment (summed immune and stromal cell types; R = 0.44, p = 0.006) scores, regardless of their molecular subtype. Together, our results demonstrate: (1) the use of rich immune profiles for differentiating molecular subtypes of MB and their unique TME characterization; and (2) initial evidence for radiological correlates of these profiles based on pre-operative imaging collected through standard practices.
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Affiliation(s)
| | - Chao Zhao
- Children's Hospital of Philadelphia , Philadelphia , USA
| | | | | | | | | | - Sina Bagheri
- Hospital of the University of Pennsylvania , Philadelphia , USA
| | | | | | - Jeffrey B Ware
- Hospital of the University of Pennsylvania , Philadelphia , USA
| | | | | | - Adam C Resnick
- Children's Hospital of Philadelphia , Philadelphia , USA
| | - Anahita Fathi Kazerooni
- Center for Biomedical Image Computing and Analytics and Department of Radiology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
| | - Ali Nabavizadeh
- Hospital of the University of Pennsylvania , Philadelphia , USA
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Kazerooni AF, Arif S, Haldar D, Zhao C, Kim MC, Madhogarhia R, Familiar A, Bagheri S, Anderson H, Ware JB, Vossough A, Storm PB, Resnick AC, Davatzikos C, Nabavizadeh A. NIMG-62. RADIOMIC-BASED PROGRESSION-FREE SURVIVAL STRATIFICATION OF PEDIATRIC LOW-GRADE GLIOMA IS ASSOCIATED WITH MOLECULAR ALTERATIONS. Neuro Oncol 2022. [PMCID: PMC9660652 DOI: 10.1093/neuonc/noac209.680] [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] Open
Abstract
Abstract
Pediatric low-grade glioma (pLGG) encompasses a variety of tumor subtypes with heterogeneous treatment response and relatively long progression-free survival (PFS). Radiomics may serve as a non-invasive and in-vivo tool for early prediction of PFS as a surrogate marker for treatment response and to objectively gauge the efficacy of novel treatment strategies. Here, we present a multivariate model based on radiomic features and clinical variables for risk stratification of pLGGs in terms of PFS and seek associations of the predicted risk groups and mutations in key molecular markers using data from PedCBioportal. Pre-operative multi-parametric MRI scans (T1-pre, T1-post, T2, T2-FLAIR) of 129 patients with newly diagnosed pLGG (median age, 7.76, range, 0.35-19.58 years; median PFS, 28.5, range, 1.1-124.8 months) were collected and quantitative radiomic features (n = 881) were extracted. A multivariate Cox proportional hazard’s (Cox-PH) regression model was fitted based on clinical (age, sex, and extent of tumor resection) and radiomic variables using 4-fold cross-validation. A subset of radiomic features (n = 27) that were most predictive of PFS was selected by applying Elastic Net regularization penalty during Cox-PH model fitting. High-, medium- and low-risk groups were determined based on model predictions. Cox-PH modeling showed excellent performance for prediction of PFS as suggested by the concordance index of 0.78. Radiogenomic assessment (data available in 94/129 patients) showed more enrichment of mutations in NF1 and RB1 genes in the high-risk group, as compared to the low- and medium-risk groups. We showed the potential value of radiomics in providing upfront prediction of PFS, which may further be used as an added treatment arm for early assessment of treatment response of the pLGG patients enrolled in the clinical trials. In the next step of this work, we will expand the cohort and cross-validate these results in an external cohort.
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Affiliation(s)
- Anahita Fathi Kazerooni
- Center for Biomedical Image Computing and Analytics and Department of Radiology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
| | | | | | - Chao Zhao
- Children's Hospital of Philadelphia , Philadelphia , USA
| | | | | | | | - Sina Bagheri
- Hospital of the University of Pennsylvania , Philadelphia , USA
| | - Hannah Anderson
- Hospital of the University of Pennsylvania , Philadelphia , USA
| | - Jeffrey B Ware
- Hospital of the University of Pennsylvania , Philadelphia , USA
| | | | | | - Adam C Resnick
- Children's Hospital of Philadelphia , Philadelphia , USA
| | - Christos Davatzikos
- Center for Biomedical Image Computing and Analytics and Department of Radiology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
| | - Ali Nabavizadeh
- Hospital of the University of Pennsylvania , Philadelphia , USA
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Kazerooni AF, Arif S, Haldar D, Madhogarhia R, Familiar A, Bagheri S, Anderson H, Ware JB, Vossough A, Storm PB, Resnick AC, Davatzikos C, Nabavizadeh A. IMG-15. Radiomic Profiling of Pediatric Low-Grade Glioma Improves Risk Stratification Beyond Clinical Measures. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac079.291] [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: 11/14/2022] Open
Abstract
Abstract
PURPOSE: Treatment response is heterogeneous among patients with pediatric low-grade glioma (pLGG), the most frequent childhood brain tumor. Upfront prediction of progression-free survival (PFS) may facilitate more personalized treatment planning and improve outcomes for the pLGG patients. In this work, we explored the additive value of radiomics to clinical measures for prediction of PFS in pLGGs. We further sought associations between the derived risk groups and underlying alterations in key genomic and transcriptomic variables. METHODS: Quantitative radiomic features were extracted from pre-operative multi-parametric MRI scans (T1, T1-post, T2, T2-FLAIR) of 96 patients with newly diagnosed pLGG (median age, 8.59, range, 0.35-18.87 years; median PFS, 25.23, range, 3.03-124.83 months). Multivariate Cox proportional hazard’s (Cox-PH) regression models were fitted using 5-fold cross-validation on a training cohort of 68 subjects and tested on 28 patients. Three models were generated using (1) only clinical variables (age, sex, and extent of tumor resection), (2) radiomic features, and (3) clinical and radiomic variables. The dimensionality of radiomic features in Cox-PH models was reduced by applying Elastic Net regularization penalty to identify a subset of variables that are most predictive of PFS. The patients were then stratified into three groups of high, medium, and low-risk based on model predictions. RESULTS: Cox-PH modeling resulted in a concordance index (c-index) of 0.55 for clinical data, 0.65 for radiomics, and 0.73 for a combination of clinical and radiomic variables, highlighting the additive value of radiomics to the readily available clinical information in prediction of PFS. Radiogenomic assessments revealed significant differences in expression of BRAF, NF1, TSC1, ALK (p<0.01), and RB1 (p<0.05) genes in the high-risk group, compared to the medium and low-risk groups. CONCLUSION: Our results demonstrate the value of integrating radiomics with clinical measures to improve risk assessment of patients with pLGG through improved pretreatment prediction of PFS.
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Affiliation(s)
- Anahita Fathi Kazerooni
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania , Philadelphia, PA , USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
| | - Sherjeel Arif
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania , Philadelphia, PA , USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
| | - Debanjan Haldar
- Division of Neurosurgery, Children’s Hospital of Philadelphia , Philadelphia, PA , USA
- Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
| | - Rachel Madhogarhia
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania , Philadelphia, PA , USA
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia , Philadelphia, PA , USA
| | - Ariana Familiar
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia , Philadelphia, PA , USA
| | - Sina Bagheri
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia , Philadelphia, PA , USA
| | - Hannah Anderson
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia , Philadelphia, PA , USA
| | - Jeffrey B Ware
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
| | - Arastoo Vossough
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia , Philadelphia, PA , USA
| | - Phillip B Storm
- Division of Neurosurgery, Children’s Hospital of Philadelphia , Philadelphia, PA , USA
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia , Philadelphia, PA , USA
| | - Adam C Resnick
- Division of Neurosurgery, Children’s Hospital of Philadelphia , Philadelphia, PA , USA
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia , Philadelphia, PA , USA
| | - Christos Davatzikos
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania , Philadelphia, PA , USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
| | - Ali Nabavizadeh
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia , Philadelphia, PA , USA
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10
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Madhogarhia R, Haldar D, Bagheri S, Familiar A, Anderson H, Arif S, Vossough A, Storm P, Resnick A, Davatzikos C, Fathi Kazerooni A, Nabavizadeh A. Radiomics and radiogenomics in pediatric neuro-oncology: A review. Neurooncol Adv 2022; 4:vdac083. [PMID: 35795472 PMCID: PMC9252112 DOI: 10.1093/noajnl/vdac083] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The current era of advanced computing has allowed for the development and implementation of the field of radiomics. In pediatric neuro-oncology, radiomics has been applied in determination of tumor histology, identification of disseminated disease, prognostication, and molecular classification of tumors (ie, radiogenomics). The field also comes with many challenges, such as limitations in study sample sizes, class imbalance, generalizability of the methods, and data harmonization across imaging centers. The aim of this review paper is twofold: first, to summarize existing literature in radiomics of pediatric neuro-oncology; second, to distill the themes and challenges of the field and discuss future directions in both a clinical and technical context.
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Affiliation(s)
- Rachel Madhogarhia
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Debanjan Haldar
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sina Bagheri
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ariana Familiar
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hannah Anderson
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sherjeel Arif
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arastoo Vossough
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Radiology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Phillip Storm
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Adam Resnick
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Christos Davatzikos
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anahita Fathi Kazerooni
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ali Nabavizadeh
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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