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Park JW, Lee K, Kim EE, Kim SI, Park SH. Brain Tumor Classification by Methylation Profile. J Korean Med Sci 2023; 38:e356. [PMID: 37935168 PMCID: PMC10627723 DOI: 10.3346/jkms.2023.38.e356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 09/12/2023] [Indexed: 11/09/2023] Open
Abstract
The goal of the methylation classifier in brain tumor classification is to accurately classify tumors based on their methylation profiles. Accurate brain tumor diagnosis is the first step for healthcare professionals to predict tumor prognosis and establish personalized treatment plans for patients. The methylation classifier can be used to perform classification on tumor samples with diagnostic difficulties due to ambiguous histology or mismatch between histopathology and molecular signatures, i.e., not otherwise specified (NOS) cases or not elsewhere classified (NEC) cases, aiding in pathological decision-making. Here, the authors elucidate upon the application of a methylation classifier as a tool to mitigate the inherent complexities associated with the pathological evaluation of brain tumors, even when pathologists are experts in histopathological diagnosis and have access to enough molecular genetic information. Also, it should be emphasized that methylome cannot classify all types of brain tumors, and it often produces erroneous matches even with high matching scores, so, excessive trust is prohibited. The primary issue is the considerable difficulty in obtaining reference data regarding the methylation profile of each type of brain tumor. This challenge is further amplified when dealing with recently identified novel types or subtypes of brain tumors, as such data are not readily accessible through open databases or authors of publications. An additional obstacle arises from the fact that methylation classifiers are primarily research-based, leading to the unavailability of charging patients. It is important to note that the application of methylation classifiers may require specialized laboratory techniques and expertise in DNA methylation analysis.
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Affiliation(s)
- Jin Woo Park
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Kwanghoon Lee
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Eric Eunshik Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Seong-Ik Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Institute of Neuroscience, Seoul National University College of Medicine, Seoul, Korea.
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2
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Yamaguchi J, Ohka F, Motomura K, Saito R. Latest classification of ependymoma in the molecular era and advances in its treatment: a review. Jpn J Clin Oncol 2023; 53:653-663. [PMID: 37288489 DOI: 10.1093/jjco/hyad056] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/19/2023] [Indexed: 06/09/2023] Open
Abstract
Ependymoma is a rare central nervous system (CNS) tumour occurring in all age groups and is one of the most common paediatric malignant brain tumours. Unlike other malignant brain tumours, ependymomas have few identified point mutations and genetic and epigenetic features. With advances in molecular understanding, the latest 2021 World Health Organization (WHO) classification of CNS tumours divided ependymomas into 10 diagnostic categories based on the histology, molecular information and location; this accurately reflected the prognosis and biology of this tumour. Although maximal surgical resection followed by radiotherapy is considered the standard treatment method, and chemotherapy is considered ineffective, the validation of the role of these treatment modalities continues. Although the rarity and long-term clinical course of ependymoma make designing and conducting prospective clinical trials challenging, knowledge is steadily accumulating and progress is being made. Much of the clinical knowledge obtained from clinical trials to date was based on the previous histology-based WHO classifications, and the addition of new molecular information may lead to more complex treatment strategies. Therefore, this review presents the latest findings on the molecular classification of ependymomas and advances in its treatment.
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Affiliation(s)
- Junya Yamaguchi
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Fumiharu Ohka
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuya Motomura
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ryuta Saito
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
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3
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Cardoni A, Barresi S, Piccirilli E, Alesi V, Miele E, Giovannoni I, Genovese S, Del Baldo G, Diomedi-Camassei F, Antonelli M, Giangaspero F, Puggioni C, Carai A, Colafati GS, Mastronuzzi A, Gessi M, Alaggio R, Rossi S. A non-hemispheric transtentorial ZFTA fusion-positive ependymoma in a 6-month-old boy. Neuropathol Appl Neurobiol 2023; 49:e12886. [PMID: 36709981 DOI: 10.1111/nan.12886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/23/2022] [Accepted: 01/21/2023] [Indexed: 01/31/2023]
Affiliation(s)
- Antonello Cardoni
- Pathology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Sabina Barresi
- Pathology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Eleonora Piccirilli
- Imaging Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.,Department of Neuroscience, Imaging and Clinical Sciences (DNISC), University "Gabriele D'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Viola Alesi
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Evelina Miele
- Department of Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Silvia Genovese
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giada Del Baldo
- Department of Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Manila Antonelli
- Department of Radiology, Oncology and Anatomic Pathology, University La Sapienza, Rome, Italy
| | - Felice Giangaspero
- Department of Radiology, Oncology and Anatomic Pathology, University La Sapienza, Rome, Italy.,IRCCS Neuromed, Pozzilli, Italy
| | - Chiara Puggioni
- Pathology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Carai
- Neurosurgery Unit, Department of Neuroscience and Neurorehabilitation, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giovanna Stefania Colafati
- Imaging Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.,Department of Neuroscience, Imaging and Clinical Sciences (DNISC), University "Gabriele D'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Angela Mastronuzzi
- Department of Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Marco Gessi
- Neuropathology Unit, Pathology Division Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica S. Cuore, Rome, Italy
| | - Rita Alaggio
- Pathology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Sabrina Rossi
- Pathology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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Tran S, Bielle F. WHO 2021 and beyond: new types, molecular markers and tools for brain tumor classification. Curr Opin Oncol 2022; 34:670-675. [PMID: 36093875 DOI: 10.1097/cco.0000000000000903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW The fifth edition of the WHO classification of central nervous system tumors was published in 2021. It implemented major advances in the current diagnostic practice such as DNA methylation profiling. The review addresses how our understanding of the diversity of brain tumors has recently much improved through omics analysis and derived molecular biomarkers. RECENT FINDINGS Latest impactful studies identifying new diagnostic or prognostic biomarkers in frequent tumors and describing new rare tumor types are summarized about adult and pediatric gliomas, rare neuroepithelial tumors, ependymomas, medulloblastomas and meningiomas. Some controversies are debated. The role of methylation classes and surrogate immunohistochemical markers is highlighted. SUMMARY New diagnostic criteria and better definitions of tumor types aim at improving the management of brain tumor patients and at better evaluating new treatments in clinical trials. The rapidly evolving field of brain tumor classification opens exciting perspectives and many challenges to integrate clinical, radiological, histological and molecular information into a framework relevant for care and research.
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Affiliation(s)
- Suzanne Tran
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, AP-HP, Hôpital Universitaire La Pitié Salpêtrière, DMU Neurosciences, Department of Neuropathology
| | - Franck Bielle
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, AP-HP, Hôpital Universitaire La Pitié Salpêtrière, DMU Neurosciences, Department of Neuropathology
- Sorbonne Université, AP-HP, SIRIC CURAMUS, Paris, France
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Park SH, Won JK, Kim CH, Phi JH, Kim SK, Choi SH, Chung CK. Pathological Classification of the Intramedullary Spinal Cord Tumors According to 2021 World Health Organization Classification of Central Nervous System Tumors, a Single-Institute Experience. Neurospine 2022; 19:780-791. [PMID: 36203303 PMCID: PMC9537827 DOI: 10.14245/ns.2244196.098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/25/2022] [Indexed: 12/14/2022] Open
Abstract
According to the new 2021 World Health Organization (WHO) classification of tumors of the central nervous system (CNS) the classification of the primary intramedullary spinal cord tumors (IM-SCT) follows that of CNS tumors. However, since the genetics and methylation profile of ependymal tumors depend on the location of the tumor, the 'spinal (SP)' should be added for the ependymoma (EPN) and subependymoma (SubEPN). For an evidence-based review, the authors reviewed SCTs in the archives of the Seoul National University Hospital over the past decade. The frequent pathologies of primary IM-SCT were SP-EPN (45.1%), hemangioblastoma (20.0%), astrocytic tumors (17.4%, including pilocytic astrocytoma [4.6%] and diffuse midline glioma, H3 K27-altered [4.0%]), myxopapillary EPN (11.0%), and SP-subEPN (3.0%) in decreasing order. IDH-mutant astrocytomas, oligodendrogliomas, glioneuronal tumors, embryonal tumors, and germ cell tumors can occur but are extremely rare in the spinal cord. Genetic studies should support for the primary IM-SCT classification. In the 2021 WHO classifications, extramedullary SCT did not change significantly but contained several new genetically defined types of mesenchymal tumors. This article focused on primary IM-SCT for tumor frequency, age, sex difference, pathological features, and genetic abnormalities, based on a single-institute experience.
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Affiliation(s)
- Sung-Hye Park
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea,Institute of Neuroscience, Seoul National University College of Medicine Neuroradiology, Seoul, Korea,Corresponding Author Sung-Hye Park Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul 03080, Korea
| | - Jae Kyung Won
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Chi Heon Kim
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul, Korea
| | - Ji Hoon Phi
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul, Korea
| | - Seung-Ki Kim
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul, Korea
| | - Seung Hong Choi
- Department of Neuroradiology, Seoul National University College of Medicine, Seoul, Korea
| | - Chun Kee Chung
- Institute of Neuroscience, Seoul National University College of Medicine Neuroradiology, Seoul, Korea
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Kim NR, Kim SI, Park JW, Park CK, Chung CK, Choi SH, Yun H, Park SH. Brain parenchymal angiomatoid fibrous histiocytoma and spinal myxoid mesenchymal tumor with FET: CREB fusion, a spectrum of the same tumor type. Neuropathology 2022; 42:257-268. [PMID: 35730186 DOI: 10.1111/neup.12814] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/09/2022] [Accepted: 04/03/2022] [Indexed: 01/22/2023]
Abstract
Angiomatoid fibrous histiocytomas (AFH) is a rare soft tissue tumor of intermediate malignant potential, and its histology is diverse. It can occur in several organs including intracranial and soft tissues. Here, we report two cases of brain parenchymal classic AFH and spinal extramedullary myxoid mesenchymal tumor with clinicopathological and molecular investigations by next-generation sequencing and a comprehensive review. The current brain parenchymal AFH occurred in a 79-year-old woman, and the spinal myxoid mesenchymal tumor arose in the thoracic spine of a 28-year-old woman; both harbored FET:CREB fusion. The current brain parenchymal AFH has not recurred for 15-months follow-up period, but the spinal myxoid mesenchymal tumor recurred three times and metastasized to T8 spine level for 30-months follow-up period. We reviewed 40 reported cases of central nervous system (CNS) AFHs/myxoid mesenchymal tumors including our two cases to identify clinicopathological features and biological behaviors. They occur with a slight female predominance (M:F = 1:1.7) in children and young adults (median age: 17 years; range: 4-79 years old). Approximately 80% of CNS AFHs were younger than 30 year. Most of them were dura-based and were not just intracranial tumors as they occurred anywhere in the CNS including spinal dura. EWSR1 rearrangement was the most common driver (98%), including FET:CREB (33%), EWSR1:ATF1 (30%), and EWSR1:CREM (27%) fusions, but FUS:CREM fusion (2%) was also present. During the follow-up period (median: 27 months), 43% (17/40) of CNS AFHs recurred between two months and 11 years, and multiple recurrences were also observed. One case showed metastases to the lymph nodes and vertebrae, and among 11 cases that resulted in death, four cases provided available clinical data. Because these tumors are identical to soft tissue AFH or primary pulmonary myxoid sarcoma with an FET:CREB fusion in morphological and immunohistochemical spectra, the authors propose incorporating the two tumor terms into one.
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Affiliation(s)
- Na Rae Kim
- Department of Pathology, Gachon University Gil Medical Center, Incheon, South Korea
| | - Seong-Ik Kim
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jin Woo Park
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Chul-Kee Park
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Chun Kee Chung
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Seung-Hong Choi
- Department of Radiology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Hongseok Yun
- Department of Genomic Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Institute of Neuroscience, Seoul National University College of Medicine, Seoul, Korea
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7
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Kresbach C, Neyazi S, Schüller U. Updates in the classification of ependymal neoplasms: The 2021 WHO Classification and beyond. Brain Pathol 2022; 32:e13068. [PMID: 35307892 PMCID: PMC9245931 DOI: 10.1111/bpa.13068] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/16/2022] [Accepted: 02/25/2022] [Indexed: 01/23/2023] Open
Abstract
Ependymal neoplasms occur at all ages and encompass multiple tumor types and subtypes that develop in the supratentorial compartment, the posterior fossa, or the spinal cord. Clinically, ependymomas represent a very heterogeneous group of tumors from rather benign subependymomas to very aggressive and often deadly childhood ependymomas of the posterior fossa. Newly identified biological markers and classification schemes, e. g. based on global DNA methylation profiling, have led to the definition of 10 types of ependymal tumors and an improved prediction of patients’ outcome by applying the new classification system. While the exact genetic basis for several ependymoma types still remains unclear, the knowledge about ependymoma driving events has significantly increased within the last decade and contributed to a classification based on molecular characteristics and localization rather than histological features alone. Convincing evidence is now pointing towards gene fusions involving ZFTA or YAP1 causing the development of supratentorial ependymomas. Also, H3, EZHIP, or TERT mutations have been detected in a fraction of infratentorial ependymal tumors. Finally, MYCN amplifications have recently been identified in spinal ependymomas, in addition to the previously known mutations in NF2. This review summarizes how recent findings regarding biology, molecular tumor typing, and clinical outcome have impacted the classification of ependymomas as suggested by the updated 2021 WHO CNS tumor classification system. We focus on changes compared to the previous classification of 2016 and discuss how a formal grading could evolve in the future and guide clinicians to treat ependymoma patients.
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Affiliation(s)
- Catena Kresbach
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, Hamburg, Germany.,Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sina Neyazi
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, Hamburg, Germany.,Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Lim KY, Lee K, Shim Y, Park JW, Kim H, Kang J, Won JK, Kim SK, Phi JH, Park CK, Chung CK, Yun H, Park SH. Molecular subtyping of ependymoma and prognostic impact of Ki-67. Brain Tumor Pathol 2021; 39:1-13. [PMID: 34812989 PMCID: PMC8752536 DOI: 10.1007/s10014-021-00417-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/26/2021] [Indexed: 10/25/2022]
Abstract
Although ependymomas (EPNs) have similar histopathology, they are heterogeneous tumors with diverse immunophenotypes, genetics, epigenetics, and different clinical behavior according to anatomical locations. We reclassified 141 primary EPNs from a single institute with immunohistochemistry (IHC) and next-generation sequencing (NGS). Supratentorial (ST), posterior fossa (PF), and spinal (SP) EPNs comprised 12%, 41%, and 47% of our cohort, respectively. Fusion genes were found only in ST-EPNs except for one SP-EPN with ZFTA-YAP1 fusion, NF2 gene alterations were found in SP-EPNs, but no driver gene was present in PF-EPNs. Surrogate IHC markers revealed high concordance rates between L1CAM and ZFTA-fusion and H3K27me3 loss or EZHIP overexpression was used for PFA-EPNs. The 7% cut-off of Ki-67 was sufficient to classify EPNs into two-tiered grades at all anatomical locations. Multivariate analysis also delineated that a Ki-67 index was the only independent prognostic factor in both overall and progression-free survivals. The gain of chromosome 1q and CDKN2A/2B deletion were associated with poor outcomes, such as multiple recurrences or extracranial metastases. In this study, we propose a cost-effective schematic diagnostic flow of EPNs by the anatomical location, three biomarkers (L1CAM, H3K27me3, and EZHIP), and a cut-off of a 7% Ki-67 labeling index.
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Affiliation(s)
- Ka Young Lim
- Department of Pathology, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Kwanghoon Lee
- Department of Pathology, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Yumi Shim
- Department of Pathology, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Jin Woo Park
- Department of Pathology, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Hyunhee Kim
- Department of Pathology, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Jeongwan Kang
- Department of Pathology, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Jae Kyung Won
- Department of Pathology, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Seung-Ki Kim
- Department of Neurosurgery, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Ji Hoon Phi
- Department of Neurosurgery, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Chul-Kee Park
- Department of Neurosurgery, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Chun-Kee Chung
- Department of Neurosurgery, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Hongseok Yun
- Department of Precision Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea. .,Institute of Neuroscience, Seoul National University College of Medicine, 101 Daehak-ro, Jongo-gu, Seoul, 03080, Republic of Korea.
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