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Qi P, Yao QL, Lao IW, Ren M, Bai QM, Cai X, Xue T, Wei R, Zhou XY. A custom next-generation sequencing panel for 1p/19q codeletion and mutational analysis in gliomas. J Neuropathol Exp Neurol 2024; 83:258-267. [PMID: 38408388 DOI: 10.1093/jnen/nlae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024] Open
Abstract
The World Health Organization has updated their classification system for the diagnosis of gliomas, combining histological features with molecular data including isocitrate dehydrogenase 1 and codeletion of chromosomal arms 1p and 19q. 1p/19q codeletion analysis is commonly performed by fluorescence in situ hybridization (FISH). In this study, we developed a 57-gene targeted next-generation sequencing (NGS) panel including 1p/19q codeletion detection mainly to assess diagnosis and potential treatment response in melanoma, gastrointestinal stromal tumor, and glioma patients. Loss of heterozygosity analysis was performed using the NGS method on 37 formalin-fixed paraffin-embedded glioma tissues that showed 1p and/or 19q loss determined by FISH. Conventional methods were applied for the validation of some glioma-related gene mutations. In 81.1% (30 of 37) and 94.6% (35 of 37) of cases, 1p and 19q were found to be in agreement whereas concordance for 1p/19q codeletion and no 1p/19q codeletion was found in 94.7% (18 of 19) and 94.4% (17 of 18) of cases, respectively. Overall, comparing NGS results with those of conventional methods showed high concordance. In conclusion, the NGS panel allows reliable analysis of 1p/19q codeletion and mutation at the same time.
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Affiliation(s)
- Peng Qi
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Qian-Lan Yao
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - I Weng Lao
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Min Ren
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Qian-Ming Bai
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Xu Cai
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Tian Xue
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Ran Wei
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Xiao-Yan Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
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2
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Satgunaseelan L, Sy J, Shivalingam B, Sim HW, Alexander KL, Buckland ME. Prognostic and predictive biomarkers in central nervous system tumours: the molecular state of play. Pathology 2024; 56:158-169. [PMID: 38233331 DOI: 10.1016/j.pathol.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 01/19/2024]
Abstract
Central nervous system (CNS) tumours were one of the first cancer types to adopt and integrate molecular profiling into routine clinical diagnosis in 2016. The vast majority of these biomarkers, used to discriminate between tumour types, also offered prognostic information. With the advent of The Cancer Genome Atlas (TCGA) and other large genomic datasets, further prognostic sub-stratification was possible within tumour types, leading to increased precision in CNS tumour grading. This review outlines the evolution of the molecular landscape of adult CNS tumours, through the prism of World Health Organization (WHO) Classifications. We begin our journey in the pre-molecular era, where high-grade gliomas were divided into 'primary' and 'secondary' glioblastomas. Molecular alterations explaining these clinicopathological observations were the first branching points of glioma diagnostics, with the discovery of IDH1/2 mutations and 1p/19q codeletion. Subsequently, the rigorous characterisation of paediatric gliomas led to the unearthing of histone H3 alterations as a key event in gliomagenesis, which also had implications for young adult patients. Simultaneously, studies investigating prognostic biomarkers within tumour types were undertaken. Certain genomic phenotypes were found to portend unfavourable outcomes, for example, MYCN amplification in spinal ependymoma. The arrival of methylation profiling, having revolutionised the diagnosis of CNS tumours, now promises to bring increased prognostic accuracy, as has been shown in meningiomas. While MGMT promoter hypermethylation has remained a reliable biomarker of response to cytotoxic chemotherapy, targeted therapy in CNS tumours has unfortunately not had the success of other cancers. Therefore, predictive biomarkers have lagged behind the identification of prognostic biomarkers in CNS tumours. Emerging research from new clinical trials is cause for guarded optimism and may shift our conceptualisation of predictive biomarker testing in CNS tumours.
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Affiliation(s)
- Laveniya Satgunaseelan
- Department of Neuropathology, Royal Prince Alfred Hospital, Sydney, NSW, Australia; Sydney Medical School, Faculty of Medicine and Health Sciences, The University of Sydney, Sydney, NSW, Australia; Department of Neurosurgery, Chris O'Brien Lifehouse, Sydney, NSW, Australia
| | - Joanne Sy
- Department of Neuropathology, Royal Prince Alfred Hospital, Sydney, NSW, Australia; Sydney Medical School, Faculty of Medicine and Health Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Brindha Shivalingam
- Sydney Medical School, Faculty of Medicine and Health Sciences, The University of Sydney, Sydney, NSW, Australia; Department of Neurosurgery, Chris O'Brien Lifehouse, Sydney, NSW, Australia
| | - Hao-Wen Sim
- Sydney Medical School, Faculty of Medicine and Health Sciences, The University of Sydney, Sydney, NSW, Australia; Department of Medical Oncology, Chris O'Brien Lifehouse, Sydney, NSW, Australia; Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Kimberley L Alexander
- Department of Neuropathology, Royal Prince Alfred Hospital, Sydney, NSW, Australia; Department of Neurosurgery, Chris O'Brien Lifehouse, Sydney, NSW, Australia; School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Michael E Buckland
- Department of Neuropathology, Royal Prince Alfred Hospital, Sydney, NSW, Australia; Sydney Medical School, Faculty of Medicine and Health Sciences, The University of Sydney, Sydney, NSW, Australia.
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Kanayama T, Tomita H, Hara A. In Situ Hybridization of Brain Slices. Methods Mol Biol 2024; 2794:13-19. [PMID: 38630216 DOI: 10.1007/978-1-0716-3810-1_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
In situ hybridization (ISH) is an important technique for identifying gene expression at the cellular level in various organs, including brain slices. This approach hybridizes nucleic acid probes to cellular mRNA, allowing the detection of transcriptional products. Recent advances have enabled RNA preservation in formalin-fixed paraffin-embedded (FFPE) samples, making ISH applicable to brain tumor diagnosis and research. Here, we provide a concise overview of the standard application of chromogenic ISH in neuroscience research and neuropathology practice using FFPE blocks of brain slice sections.
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Affiliation(s)
- Tomohiro Kanayama
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Gifu, Japan.
| | - Hiroyuki Tomita
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Akira Hara
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Gifu, Japan
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Penkova A, Kuziakova O, Gulaia V, Tiasto V, Goncharov NV, Lanskikh D, Zhmenia V, Baklanov I, Farniev V, Kumeiko V. Comprehensive clinical assays for molecular diagnostics of gliomas: the current state and future prospects. Front Mol Biosci 2023; 10:1216102. [PMID: 37908227 PMCID: PMC10613994 DOI: 10.3389/fmolb.2023.1216102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/04/2023] [Indexed: 11/02/2023] Open
Abstract
Glioma is one of the most intractable types of cancer, due to delayed diagnosis at advanced stages. The clinical symptoms of glioma are unclear and due to a variety of glioma subtypes, available low-invasive testing is not effective enough to be introduced into routine medical laboratory practice. Therefore, recent advances in the clinical diagnosis of glioma have focused on liquid biopsy approaches that utilize a wide range of techniques such as next-generation sequencing (NGS), droplet-digital polymerase chain reaction (ddPCR), and quantitative PCR (qPCR). Among all techniques, NGS is the most advantageous diagnostic method. Despite the rapid cheapening of NGS experiments, the cost of such diagnostics remains high. Moreover, high-throughput diagnostics are not appropriate for molecular profiling of gliomas since patients with gliomas exhibit only a few diagnostic markers. In this review, we highlighted all available assays for glioma diagnosing for main pathogenic glioma DNA sequence alterations. In the present study, we reviewed the possibility of integrating routine molecular methods into the diagnosis of gliomas. We state that the development of an affordable assay covering all glioma genetic aberrations could enable early detection and improve patient outcomes. Moreover, the development of such molecular diagnostic kits could potentially be a good alternative to expensive NGS-based approaches.
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Affiliation(s)
- Alina Penkova
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Olga Kuziakova
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Valeriia Gulaia
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Vladlena Tiasto
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Nikolay V. Goncharov
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
| | - Daria Lanskikh
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Valeriia Zhmenia
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Ivan Baklanov
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
| | - Vladislav Farniev
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Vadim Kumeiko
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
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5
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Rubiano EGO, Baldoncini M, Cómbita AL, Payán-Gómez C, Gómez-Amarillo DF, Hakim F, Figueredo LF, Forlizzi V, Rangel CC, Luzzi S, Campero A, Parra-Medina R. Understanding the molecular profiling of diffuse gliomas classification: A brief overview. Surg Neurol Int 2023; 14:225. [PMID: 37404501 PMCID: PMC10316154 DOI: 10.25259/sni_209_2023] [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: 03/04/2023] [Accepted: 06/04/2023] [Indexed: 07/06/2023] Open
Abstract
Background Gliomas represent almost 30% of all primary brain tumors and account for 80% of malignant primary ones. In the last two decades, significant progress has been made in understanding gliomas' molecular origin and development. These advancements have demonstrated a remarkable improvement in classification systems based on mutational markers, which contribute paramount information in addition to traditional histology-based classification. Methods We performed a narrative review of the literature including each molecular marker described for adult diffuse gliomas used in the World Health Organization (WHO) central nervous system 5. Results The 2021 WHO classification of diffuse gliomas encompasses many molecular aspects considered in the latest proposed hallmarks of cancer. The outcome of patients with diffuse gliomas relies on their molecular behavior and consequently, to determine clinical outcomes for these patients, molecular profiling should be mandatory. At least, the following molecular markers are necessary for the current most accurate classification of these tumors: (1) isocitrate dehydrogenase (IDH) IDH-1 mutation, (2) 1p/19q codeletion, (3) cyclin-dependent kinase inhibitor 2A/B deletion, (4) telomerase reverse transcriptase promoter mutation, (5) α-thalassemia/ mental retardation syndrome X-linked loss, (6) epidermal growth factor receptor amplification, and (7) tumor protein P53 mutation. These molecular markers have allowed the differentiation of multiple variations of the same disease, including the differentiation of distinct molecular Grade 4 gliomas. This could imply different clinical outcomes and possibly impact targeted therapies in the years to come. Conclusion Physicians face different challenging scenarios according to the clinical features of patients with gliomas. In addition to the current advances in clinical decision-making, including radiological and surgical techniques, understanding the disease's molecular pathogenesis is paramount to improving the benefits of its clinical treatments. This review aims to describe straightforwardly the most remarkable aspects of the molecular pathogenesis of diffuse gliomas.
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Affiliation(s)
- Edgar G. Ordóñez Rubiano
- Department of Neurological Surgery, Fundación Universitaria de Ciencias de la Salud, Hospital de San José - Sociedad de Cirugía de Bogotá, Bogotá, Colombia
- School of Medicine, Universidad Nacional de Colombia, Bogotá, Colombia
- Research Institute, Fundación Universitaria de Ciencias de la Salud, Bogotá, Colombia
| | - Matías Baldoncini
- Department of Neurosurgery, San Fernando Hospital, San Fernando, Argentina
| | - Alba Lucía Cómbita
- Departament of Microbiology, Universidad Nacional de Colombia, Bogotá, Colombia
- Translational Research Group in Oncology, Instituto Nacional de Cancerología, Bogotá, Colombia
| | - César Payán-Gómez
- Academic direction, Universidad Nacional de Colombia - Sede de La Paz, La Paz, Colombia
| | - Diego F. Gómez-Amarillo
- Department of Neurosurgery, Hospital Universitario Fundación Santa Fé de Bogotá, Bogotá, Colombia
| | - Fernando Hakim
- Department of Neurosurgery, Hospital Universitario Fundación Santa Fé de Bogotá, Bogotá, Colombia
| | | | - Valeria Forlizzi
- Department of Anatomy, University of Buenos Aires, Buenos Aires, Argentina
| | - Carlos Castillo Rangel
- Department of Neurosurgery, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Mexico City, Mexico
| | - Sabino Luzzi
- Department of Neurosurgery, University of Pavia, Polo Didattico “Cesare Brusotti”, Pavia, Italy
| | | | - Rafael Parra-Medina
- Research Institute, Fundación Universitaria de Ciencias de la Salud, Bogotá, Colombia
- Department of Pathology, Instituto Nacional de Cancerología Bogotá, Bogotá, Colombia
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Tejada Solís S, González Sánchez J, Iglesias Lozano I, Plans Ahicart G, Pérez Núñez A, Meana Carballo L, Gil Salú JL, Fernández Coello A, García Romero JC, Rodríguez de Lope Llorca A, García Duque S, Díez Valle R, Narros Giménez JL, Prat Acín R. Low grade gliomas guide-lines elaborated by the tumor section of Spanish Society of Neurosurgery. NEUROCIRUGIA (ENGLISH EDITION) 2023; 34:139-152. [PMID: 36446721 DOI: 10.1016/j.neucie.2022.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/20/2022] [Accepted: 08/01/2022] [Indexed: 05/06/2023]
Abstract
Adult low-grade gliomas (Low Grade Gliomas, LGG) are tumors that originate from the glial cells of the brain and whose management involves great controversy, starting from the diagnosis, to the treatment and subsequent follow-up. For this reason, the Tumor Group of the Spanish Society of Neurosurgery (GT-SENEC) has held a consensus meeting, in which the most relevant neurosurgical issues have been discussed, reaching recommendations based on the best scientific evidence. In order to obtain the maximum benefit from these treatments, an individualised assessment of each patient should be made by a multidisciplinary team. Experts in each LGG treatment field have briefly described it based in their experience and the reviewed of the literature. Each area has been summarized and focused on the best published evidence. LGG have been surrounded by treatment controversy, although during the last years more accurate data has been published in order to reach treatment consensus. Neurosurgeons must know treatment options, indications and risks to participate actively in the decision making and to offer the best surgical treatment in every case.
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Affiliation(s)
- Sonia Tejada Solís
- Departamento de Neurocirugía, Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain.
| | - Josep González Sánchez
- Departamento de Neurocirugía, Hospital Clínic i Provincial de Barcelona, Barcelona, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Irene Iglesias Lozano
- Departamento de Neurocirugía, Hospital Universitario Puerta del Mar, Cádiz, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Gerard Plans Ahicart
- Departamento de Neurocirugía, Hospital Universitari Bellvitge, Barcelona, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Angel Pérez Núñez
- Departamento de Neurocirugía, Hospital Universitario 12 de Octubre, Madrid, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Leonor Meana Carballo
- Departamento de Neurocirugía, Centro Médico de Asturias, Oviedo, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Jose Luis Gil Salú
- Departamento de Neurocirugía, Hospital Universitario Puerta del Mar, Cádiz, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Alejandro Fernández Coello
- Departamento de Neurocirugía, Hospital Universitari Bellvitge, Barcelona, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Juan Carlos García Romero
- Departamento de Neurocirugía, Hospital Virgen del Rocío, Sevilla, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Angel Rodríguez de Lope Llorca
- Departamento de Neurocirugía, Hospital Virgen de la Salud, Toledo, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Sara García Duque
- Departamento de Neurocirugía, Hospital Universitario La Fe, Valencia, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Ricardo Díez Valle
- Departamento de Neurocirugía, Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Jose Luis Narros Giménez
- Departamento de Neurocirugía, Hospital Virgen del Rocío, Sevilla, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Ricardo Prat Acín
- Departamento de Neurocirugía, Hospital Universitario La Fe, Valencia, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
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7
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Ali RH, Alateeqi M, Jama H, Alrumaidhi N, Alqallaf A, Mohammed EM, Almurshed M, Bahzad S. Evaluation of the Oncomine Comprehensive Assay v3 panel for the detection of 1p/19q codeletion in oligodendroglial tumours. J Clin Pathol 2023; 76:103-110. [PMID: 34489310 DOI: 10.1136/jclinpath-2021-207876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 08/26/2021] [Indexed: 01/24/2023]
Abstract
AIMS Accurate assessment of 1p/19q codeletion status in diffuse gliomas is of paramount importance for diagnostic, prognostic and predictive purposes. While targeted next generation sequencing (NGS) has been widely implemented for glioma molecular profiling, its role in detecting structural chromosomal variants is less well established, requiring supplementary informatic tools for robust detection. Herein, we evaluated a commercially available amplicon-based targeted NGS panel (Oncomine Comprehensive Assay v3) for the detection of 1p/19q losses in glioma tissues using an Ion Torrent platform and the standard built-in NGS data analysis pipeline solely. METHODS Using as little as 20 ng of DNA from formalin-fixed paraffin-embedded tissues, we analysed 25 previously characterised gliomas for multi-locus copy number losses (CNLs) on 1p and 19q, including 11 oligodendrogliomas (ODG) and 14 non-oligodendroglial (non-ODG) controls. Fluorescence in-situ hybridisation (FISH) was used as a reference standard. RESULTS The software confidently detected combined contiguous 1p/19q CNLs in 11/11 ODGs (100% sensitivity), using a copy number cut-off of ≤1.5 and a minimum of 10 amplicons covering the regions. Only partial non-specific losses were identified in non-ODGs (100% specificity). Copy number averages of ODG and non-ODG groups were significantly different (p<0.001). NGS was concordant with FISH and was superior to it in distinguishing partial from contiguous losses indicative of whole-arm chromosomal deletion. CONCLUSIONS This commercial NGS panel, along with the standard Ion Torrent algorithm, accurately detected 1p/19q losses in ODG samples, obviating the need for specialised custom-made informatic analyses. This can easily be incorporated into routine glioma workflow as an alternative to FISH.
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Affiliation(s)
- Rola H Ali
- Department of Pathology, Kuwait University, Jabriya, Kuwait .,Cytogenetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Kuwait
| | - Mona Alateeqi
- Molecular Genetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Kuwait
| | - Hiba Jama
- Molecular Genetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Kuwait
| | - Noor Alrumaidhi
- Molecular Genetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Kuwait
| | - Ali Alqallaf
- Cytogenetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Kuwait
| | | | | | - Shakir Bahzad
- Molecular Genetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Kuwait
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Brandner S, McAleenan A, Jones HE, Kernohan A, Robinson T, Schmidt L, Dawson S, Kelly C, Leal ES, Faulkner CL, Palmer A, Wragg C, Jefferies S, Vale L, Higgins JPT, Kurian KM. Diagnostic accuracy of 1p/19q codeletion tests in oligodendroglioma: A comprehensive meta-analysis based on a Cochrane systematic review. Neuropathol Appl Neurobiol 2022; 48:e12790. [PMID: 34958131 PMCID: PMC9208578 DOI: 10.1111/nan.12790] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/23/2021] [Accepted: 11/27/2021] [Indexed: 11/29/2022]
Abstract
Codeletion of chromosomal arms 1p and 19q, in conjunction with a mutation in the isocitrate dehydrogenase 1 or 2 gene, is the molecular diagnostic criterion for oligodendroglioma, IDH mutant and 1p/19q codeleted. 1p/19q codeletion is a diagnostic marker and allows prognostication and prediction of the best drug response within IDH-mutant tumours. We performed a Cochrane review and simple economic analysis to establish the most sensitive, specific and cost-effective techniques for determining 1p/19q codeletion status. Fluorescent in situ hybridisation (FISH) and polymerase chain reaction (PCR)-based loss of heterozygosity (LOH) test methods were considered as reference standard. Most techniques (FISH, chromogenic in situ hybridisation [CISH], PCR, real-time PCR, multiplex ligation-dependent probe amplification [MLPA], single nucleotide polymorphism [SNP] array, comparative genomic hybridisation [CGH], array CGH, next-generation sequencing [NGS], mass spectrometry and NanoString) showed good sensitivity (few false negatives) for detection of 1p/19q codeletions in glioma, irrespective of whether FISH or PCR-based LOH was used as the reference standard. Both NGS and SNP array had a high specificity (fewer false positives) for 1p/19q codeletion when considered against FISH as the reference standard. Our findings suggest that G banding is not a suitable test for 1p/19q analysis. Within these limits, considering cost per diagnosis and using FISH as a reference, MLPA was marginally more cost-effective than other tests, although these economic analyses were limited by the range of available parameters, time horizon and data from multiple healthcare organisations.
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Affiliation(s)
- Sebastian Brandner
- Division of Neuropathology, The National Hospital for Neurology and NeurosurgeryUniversity College London Hospitals NHS Foundation TrustLondonUK
- Department of Neurodegenerative Disease, Queen Square Instituite of NeurologyUniversity College LondonLondonUK
| | - Alexandra McAleenan
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Hayley E. Jones
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Ashleigh Kernohan
- Population Health Sciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Tomos Robinson
- Population Health Sciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Lena Schmidt
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Sarah Dawson
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Claire Kelly
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | | | - Claire L. Faulkner
- Bristol Genetics Laboratory, Pathology SciencesSouthmead HospitalBristolUK
| | - Abigail Palmer
- Bristol Genetics Laboratory, Pathology SciencesSouthmead HospitalBristolUK
| | - Christopher Wragg
- Bristol Genetics Laboratory, Pathology SciencesSouthmead HospitalBristolUK
| | | | - Luke Vale
- Population Health Sciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Julian P. T. Higgins
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Kathreena M. Kurian
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
- Bristol Medical School: Brain Tumour Research Centre, Public Health SciencesUniversity of BristolBristolUK
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9
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McAleenan A, Jones HE, Kernohan A, Robinson T, Schmidt L, Dawson S, Kelly C, Spencer Leal E, Faulkner CL, Palmer A, Wragg C, Jefferies S, Brandner S, Vale L, Higgins JP, Kurian KM. Diagnostic test accuracy and cost-effectiveness of tests for codeletion of chromosomal arms 1p and 19q in people with glioma. Cochrane Database Syst Rev 2022; 3:CD013387. [PMID: 35233774 PMCID: PMC8889390 DOI: 10.1002/14651858.cd013387.pub2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Complete deletion of both the short arm of chromosome 1 (1p) and the long arm of chromosome 19 (19q), known as 1p/19q codeletion, is a mutation that can occur in gliomas. It occurs in a type of glioma known as oligodendroglioma and its higher grade counterpart known as anaplastic oligodendroglioma. Detection of 1p/19q codeletion in gliomas is important because, together with another mutation in an enzyme known as isocitrate dehydrogenase, it is needed to make the diagnosis of an oligodendroglioma. Presence of 1p/19q codeletion also informs patient prognosis and prediction of the best drug treatment. The main two tests in use are fluorescent in situ hybridisation (FISH) and polymerase chain reaction (PCR)-based loss of heterozygosity (LOH) assays (also known as PCR-based short tandem repeat or microsatellite analysis). Many other tests are available. None of the tests is perfect, although PCR-based LOH is expected to have very high sensitivity. OBJECTIVES To estimate the sensitivity and specificity and cost-effectiveness of different deoxyribonucleic acid (DNA)-based techniques for determining 1p/19q codeletion status in glioma. SEARCH METHODS We searched MEDLINE, Embase and BIOSIS up to July 2019. There were no restrictions based on language or date of publication. We sought economic evaluation studies from the results of this search and using the National Health Service Economic Evaluation Database. SELECTION CRITERIA We included cross-sectional studies in adults with glioma or any subtype of glioma, presenting raw data or cross-tabulations of two or more DNA-based tests for 1p/19q codeletion. We also sought economic evaluations of these tests. DATA COLLECTION AND ANALYSIS We followed procedures outlined in the Cochrane Handbook for Diagnostic Test Accuracy Reviews. Two review authors independently screened titles/abstracts/full texts, performed data extraction, and undertook applicability and risk of bias assessments using QUADAS-2. Meta-analyses used the hierarchical summary ROC model to estimate and compare test accuracy. We used FISH and PCR-based LOH as alternate reference standards to examine how tests compared with those in common use, and conducted a latent class analysis comparing FISH and PCR-based LOH. We constructed an economic model to evaluate cost-effectiveness. MAIN RESULTS We included 53 studies examining: PCR-based LOH, FISH, single nucleotide polymorphism (SNP) array, next-generation sequencing (NGS), comparative genomic hybridisation (CGH), array comparative genomic hybridisation (aCGH), multiplex-ligation-dependent probe amplification (MLPA), real-time PCR, chromogenic in situ hybridisation (CISH), mass spectrometry (MS), restriction fragment length polymorphism (RFLP) analysis, G-banding, methylation array and NanoString. Risk of bias was low for only one study; most gave us concerns about how patients were selected or about missing data. We had applicability concerns about many of the studies because only patients with specific subtypes of glioma were included. 1520 participants contributed to analyses using FISH as the reference, 1304 participants to analyses involving PCR-based LOH as the reference and 262 participants to analyses of comparisons between methods from studies not including FISH or PCR-based LOH. Most evidence was available for comparison of FISH with PCR-based LOH (15 studies, 915 participants): PCR-based LOH detected 94% of FISH-determined codeletions (95% credible interval (CrI) 83% to 98%) and FISH detected 91% of codeletions determined by PCR-based LOH (CrI 78% to 97%). Of tumours determined not to have a deletion by FISH, 94% (CrI 87% to 98%) had a deletion detected by PCR-based LOH, and of those determined not to have a deletion by PCR-based LOH, 96% (CrI 90% to 99%) had a deletion detected by FISH. The latent class analysis suggested that PCR-based LOH may be slightly more accurate than FISH. Most other techniques appeared to have high sensitivity (i.e. produced few false-negative results) for detection of 1p/19q codeletion when either FISH or PCR-based LOH was considered as the reference standard, although there was limited evidence. There was some indication of differences in specificity (false-positive rate) with some techniques. Both NGS and SNP array had high specificity when considered against FISH as the reference standard (NGS: 6 studies, 243 participants; SNP: 6 studies, 111 participants), although we rated certainty in the evidence as low or very low. NGS and SNP array also had high specificity when PCR-based LOH was considered the reference standard, although with much more uncertainty as these results were based on fewer studies (just one study with 49 participants for NGS and two studies with 33 participants for SNP array). G-banding had low sensitivity and specificity when PCR-based LOH was the reference standard. Although MS had very high sensitivity and specificity when both FISH and PCR-based LOH were considered the reference standard, these results were based on only one study with a small number of participants. Real-time PCR also showed high specificity with FISH as a reference standard, although there were only two studies including 40 participants. We found no relevant economic evaluations. Our economic model using FISH as the reference standard suggested that the resource-optimising test depends on which measure of diagnostic accuracy is most important. With FISH as the reference standard, MLPA is likely to be cost-effective if society was willing to pay GBP 1000 or less for a true positive detected. However, as the value placed on a true positive increased, CISH was most cost-effective. Findings differed when the outcome measure changed to either true negative detected or correct diagnosis. When PCR-based LOH was used as the reference standard, MLPA was likely to be cost-effective for all measures of diagnostic accuracy at lower threshold values for willingness to pay. However, as the threshold values increased, none of the tests were clearly more likely to be considered cost-effective. AUTHORS' CONCLUSIONS In our review, most techniques (except G-banding) appeared to have good sensitivity (few false negatives) for detection of 1p/19q codeletions in glioma against both FISH and PCR-based LOH as a reference standard. However, we judged the certainty of the evidence low or very low for all the tests. There are possible differences in specificity, with both NGS and SNP array having high specificity (fewer false positives) for 1p/19q codeletion when considered against FISH as the reference standard. The economic analysis should be interpreted with caution due to the small number of studies.
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Affiliation(s)
- Alexandra McAleenan
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Hayley E Jones
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ashleigh Kernohan
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Tomos Robinson
- Institute of Health & Society, Newcastle University, Newcastle upon Tyne , UK
| | - Lena Schmidt
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Sarah Dawson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Claire Kelly
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Emmelyn Spencer Leal
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Claire L Faulkner
- Bristol Genetics Laboratory, Pathology Sciences, Southmead Hospital, Bristol, UK
| | - Abigail Palmer
- Bristol Genetics Laboratory, Pathology Sciences, Southmead Hospital, Bristol, UK
| | - Christopher Wragg
- Bristol Genetics Laboratory, Pathology Sciences, Southmead Hospital, Bristol, UK
| | - Sarah Jefferies
- Department of Oncology, Addenbrooke's Hospital, Cambridge, UK
| | - Sebastian Brandner
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
| | - Luke Vale
- Institute of Health & Society, Newcastle University, Newcastle upon Tyne, UK
| | - Julian Pt Higgins
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kathreena M Kurian
- Bristol Medical School: Brain Tumour Research Centre, Public Health Sciences, University of Bristol, Bristol, UK
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10
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Sporikova Z, Slavkovsky R, Tuckova L, Kalita O, Megova Houdova M, Ehrmann J, Hajduch M, Hrabalek L, Vaverka M. IDH1/2 Mutations in Patients With Diffuse Gliomas: A Single Centre Retrospective Massively Parallel Sequencing Analysis. Appl Immunohistochem Mol Morphol 2022; 30:178-183. [PMID: 35262523 PMCID: PMC8920008 DOI: 10.1097/pai.0000000000000997] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 10/26/2021] [Indexed: 12/05/2022]
Abstract
Patients below 55 years were genetically studied because the prevalence of isocitrate dehydrogenase 1 (IDH1) decreases in older patients and on grounds of cost-effectiveness, as suggested by the World Health Organization (WHO) in 2016. The aim of our study was to use novel massively parallel sequencing (MPS) approaches to examine rare variants of IDH1/2 in Czech diffuse astrocytic and oligodendroglial tumors (gliomas) patients below 55 years of age who had been immunohistochemically (IHC) diagnosed as IDH1 R132H negative. The IHC IDH1 status (wild type or mutant) of 275 tissue samples was analyzed using antibodies against the IDH1 R132H protein. Sixty-three samples of 55 years old patients with IHC IDH1 WT status were genotyped using two different MPS technologies to detect rare IDH1 and IDH2 variants. The tiered IHC (60 positive) and molecular (10 positive) approach thus revealed that 70 of the 275 samples (25%) bore IDH1/IDH2 mutations. The combined molecular and IHC approach thus revealed that 70 of the 275 samples (25%) considered in the study bore IDH1/IDH2 mutations. IHC detection of the IDH1 R132H variant should be routinely complemented with MPS to detect rare IDH1/2 variants in glioma patients below 55 years of age with negative IHC result of IDH R132H variant.
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Affiliation(s)
| | | | | | - Ondrej Kalita
- Neurosurgery, Faculty of Medicine and Dentistry, Palacky University and University Hospital, Olomouc
- Department of Health Care Science, Faculty of Humanities, T. Bata University in Zlin, the Czech Republic
| | | | | | | | - Lumir Hrabalek
- Neurosurgery, Faculty of Medicine and Dentistry, Palacky University and University Hospital, Olomouc
| | - Miroslav Vaverka
- Neurosurgery, Faculty of Medicine and Dentistry, Palacky University and University Hospital, Olomouc
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11
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Barresi V, Mafficini A, Calicchia M, Piredda ML, Musumeci A, Ghimenton C, Scarpa A. Recurrent oligodendroglioma with changed 1p/19q status. Neuropathology 2022; 42:160-166. [PMID: 35144313 PMCID: PMC9546156 DOI: 10.1111/neup.12789] [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: 08/26/2021] [Revised: 10/15/2021] [Accepted: 10/15/2021] [Indexed: 11/28/2022]
Abstract
We report a case of oligodendroglioma that had consistent histopathological features as well as a distinct change in 1p/19q status in the second recurrence, after temozolomide chemotherapy and radiotherapy. The first tumor recurrence had oligodendroglial morphology, IDH1 R132H and TERT promoter mutations, and 1p/19q codeletion detected by fluorescent in situ hybridization (FISH). Copy number analysis, assessed by next‐generation sequencing, confirmed 1p/19q codeletion, and disclosed loss of heterozygosity (LOH) of chromosomes 4 and 9 and chromosome 11 gain. The second recurrence featured not only oligodendroglial morphology but also the appearance of admixed multinucleated giant cells or neoplastic cells having oval nuclei and mitoses and showing microvascular proliferation; it maintained IDH1 R132H and TERT promoter mutations, acquired TP53 mutation, and showed 19q LOH, but disomic 1p, detected by FISH. Copy number analysis depicted LOH of chromosomes 3p, 13, and 19q, 1p partial deletion (1p chr1p34.2‐p11), and gain of chromosomes 2p25.3‐p24.1, 8q12.2‐q24.3, and 11q13.3‐q25. B‐allele frequency analysis of polymorphic sites disclosed copy‐neutral LOH at 1p36.33‐p34.2, supporting the initial deletion of 1p, followed by reduplication of 1p36.33‐p34.2 alone. These findings suggest that the two tumor recurrences might have originated from an initial neoplastic clone, featuring 1p/19q codeletion and IDH1 and TERT promoter mutations, and have independently acquired other copy number alterations. The reduplication of chromosome 1p might be the result of temozolomide treatment, and gave rise to false negative 1p deletion detected by FISH. The possibility of 1p copy‐neutral LOH should be considered in recurrent oligodendrogliomas with altered 1p/19q status detected by FISH.
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Affiliation(s)
- Valeria Barresi
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy.,ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Martina Calicchia
- ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Maria Liliana Piredda
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy
| | - Angelo Musumeci
- Department of Neurosciences, Unit of Neurosurgery, Hospital Trust of Verona, Verona, Italy
| | - Claudio Ghimenton
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Verona, Italy.,ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
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12
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Van der Eecken K, Van der Linden M, Raman L, Creytens D, Dedeurwaerdere F, De Winne K, Ferdinande L, Lammens M, Menten B, Rottiers I, Van Gaever B, Van den Broecke C, Van de Vijver K, Van Roy N, Verbeke S, Van Dorpe J. Shallow whole-genome sequencing: a useful, easy to apply molecular technique for CNA detection on FFPE tumor tissue-a glioma-driven study. Virchows Arch 2022; 480:677-686. [PMID: 35034191 DOI: 10.1007/s00428-022-03268-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/10/2021] [Accepted: 01/03/2022] [Indexed: 11/27/2022]
Abstract
Copy number alterations (CNAs) have increasingly become part of the diagnostic algorithm of glial tumors. Alterations such as homozygous deletion of CDKN2A/B, 7 +/ 10 - chromosome copy number changes or EGFR amplification are predictive of a poor prognosis. The codeletion of chromosome arms 1p and 19q, typically associated with oligodendroglioma, implies a more favorable prognosis. Detection of this codeletion by the current diagnostic standard, being fluorescence in situ hybridization (FISH), is sometimes however subject to technical and interpretation problems. In this study, we evaluated CNA detection by shallow whole-genome sequencing (sWGS) as an inexpensive, complementary molecular technique. A cohort of 36 glioma tissue samples, enriched with "difficult" and "ambiguous" cases, was analyzed by sWGS. sWGS results were compared with FISH assays of chromosomes 1p and 19q. In addition, CNAs relevant to glioblastoma diagnosis were explored. In 4/36 samples, EGFR (7p11.2) amplifications and homozygous loss of CDKN2A/B were identified by sWGS. Six out of 8 IDH-wild-type glioblastomas demonstrated a prognostic chromosome 7/chromosome 10 signature. In 11/36 samples, local interstitial and terminal 1p/19q alterations were detected by sWGS, implying that FISH's targeted nature might promote false arm-level extrapolations. In this cohort, differences in overall survival between patients with and without codeletion were better pronounced by the sequencing-based distinction (likelihood ratio of 7.48) in comparison to FISH groupings (likelihood ratio of 0.97 at diagnosis and 1.79 ± 0.62 at reobservation), suggesting sWGS is more accurate than FISH. We recognized adverse effects of tissue block age on FISH signals. In addition, we show how sWGS reveals relevant aberrations beyond the 1p/19q state, such as EGFR amplification, combined gain of chromosome 7 and loss of chromosome 10, and homozygous loss of CDKN2A/B. The findings presented by this study might stimulate implementation of sWGS as a complementary, easy to apply technique for copy number detection.
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Affiliation(s)
- Kim Van der Eecken
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium
- Cancer Research Institute (CRIG), Ghent, Belgium
| | - Malaïka Van der Linden
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium
- Cancer Research Institute (CRIG), Ghent, Belgium
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Lennart Raman
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - David Creytens
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium
- Cancer Research Institute (CRIG), Ghent, Belgium
| | | | - Koen De Winne
- Department of Pathology, Antwerp University Hospital, Antwerp, Belgium
| | - Liesbeth Ferdinande
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium
- Cancer Research Institute (CRIG), Ghent, Belgium
| | - Martin Lammens
- Department of Pathology, Antwerp University Hospital, Antwerp, Belgium
| | - Björn Menten
- Cancer Research Institute (CRIG), Ghent, Belgium
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Isabelle Rottiers
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium
- Cancer Research Institute (CRIG), Ghent, Belgium
| | - Bram Van Gaever
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium
| | | | - Koen Van de Vijver
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium
- Cancer Research Institute (CRIG), Ghent, Belgium
| | - Nadine Van Roy
- Cancer Research Institute (CRIG), Ghent, Belgium
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Sofie Verbeke
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium
- Cancer Research Institute (CRIG), Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium.
- Cancer Research Institute (CRIG), Ghent, Belgium.
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13
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de Biase D, Acquaviva G, Visani M, Marucci G, De Leo A, Maloberti T, Sanza V, Di Oto E, Franceschi E, Mura A, Ragazzi M, Serra S, Froio E, Bisagni A, Brandes AA, Pession A, Tallini G. Next-Generation Sequencing Panel for 1p/19q Codeletion and IDH1-IDH2 Mutational Analysis Uncovers Mistaken Overdiagnoses of 1p/19q Codeletion by FISH. J Mol Diagn 2021; 23:1185-1194. [PMID: 34186176 DOI: 10.1016/j.jmoldx.2021.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/15/2021] [Accepted: 06/08/2021] [Indexed: 02/08/2023] Open
Abstract
The 1p/19q codeletion is the result of a translocation between chromosome 1 (Chr1p) and chromosome 19 (Chr19q) with the loss of derivative (1;19)(p10;q10) chromosome. The 1p/19q codeletion has predictive and prognostic significance, and it is essential for the classification of gliomas. In routine practice, the fluorescence in situ hybridization (FISH) diagnosis of 1p/19q codeletion is sometimes unexpected. This study aimed to develop a next-generation sequencing panel for the concurrent definition of the 1p/19q codeletion and IDH1/IDH2 mutation status to resolve these equivocal cases. A total of 65 glioma samples were investigated using a 1p/19q-single-nucleotide polymorphism (SNP)-IDH panel. The panel consists of 192 amplicons, including SNPs mapping to Chr1 and Chr19 and amplicons for IDH1/IDH2 analysis. The 1p/19q SNP-IDH panel consistently identified IDH1/IDH2 mutations. In 49 of 60 cases (81.7%), it provided the same 1p/19q results obtained by FISH. In the remaining 11 cases, the 1p/19q SNP-IDH panel uncovered partial chromosome imbalances as a result of interstitial amplification or deletion of the regions where the FISH probes map, leading to a mistaken overdiagnosis of 1p/19q codeletion by FISH. The 1p/19q SNP-IDH next-generation sequencing panel allows reliable analysis of the 1p/19q codeletion and IDH1/IDH2 mutation at the same time. The panel not only allows resolution of difficult cases but also represents a cost-effective alternative to standard molecular diagnostics procedures.
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Affiliation(s)
- Dario de Biase
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy; Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Giorgia Acquaviva
- Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy; Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), University of Bologna, Bologna, Italy
| | - Michela Visani
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), University of Bologna, Bologna, Italy
| | - Gianluca Marucci
- Neuropathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Antonio De Leo
- Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy; Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), University of Bologna, Bologna, Italy
| | - Thais Maloberti
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), University of Bologna, Bologna, Italy
| | - Viviana Sanza
- Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy; Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), University of Bologna, Bologna, Italy
| | - Enrico Di Oto
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), University of Bologna, Bologna, Italy
| | - Enrico Franceschi
- Department of Oncology, Azienda Unitá Sanitaria Locale (AUSL) Bologna, Bologna, Italy
| | - Antonella Mura
- Department of Oncology, Azienda Unitá Sanitaria Locale (AUSL) Bologna, Bologna, Italy
| | - Moira Ragazzi
- Anatomic Pathology Unit, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Silvia Serra
- Anatomic Pathology Unit, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Elisabetta Froio
- Anatomic Pathology Unit, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Alessandra Bisagni
- Anatomic Pathology Unit, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Alba A Brandes
- Neuropathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Annalisa Pession
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy; Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Giovanni Tallini
- Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy; Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), University of Bologna, Bologna, Italy.
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14
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Ammendola S, Caldonazzi N, Simbolo M, Piredda ML, Brunelli M, Poliani PL, Pinna G, Sala F, Ghimenton C, Scarpa A, Barresi V. H3K27me3 immunostaining is diagnostic and prognostic in diffuse gliomas with oligodendroglial or mixed oligoastrocytic morphology. Virchows Arch 2021; 479:987-996. [PMID: 34165590 PMCID: PMC8572829 DOI: 10.1007/s00428-021-03134-1] [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: 05/07/2021] [Revised: 05/27/2021] [Accepted: 05/30/2021] [Indexed: 12/14/2022]
Abstract
Oligodendroglioma is defined by IDH mutation and 1p/19q codeletion. The latter is mutually exclusive to ATRX immunohistochemical loss and has been recently associated with the loss of H3K27me3 immunostaining. We aimed to assess the diagnostic and prognostic value of H3K27me3 immuno-expression in diffuse gliomas with oligodendroglial or mixed oligoastrocytic morphology. H3K27me3 immunostaining was performed in 69 diffuse gliomas with oligodendroglial (n = 62) or oligoastrocytic (n = 7) morphology. The integration with routinely assessed IDH mutations, ATRX immunostaining, and 1p/19q codeletion classified these cases as 60 oligodendroglial and 9 astrocytic. H3K27me3 was lost in 58/60 oligodendrogliomas with retained (n = 47) or non-conclusive (n = 11) ATRX staining, 3/6 IDH-mutant astrocytomas with ATRX loss, and 3/3 IDH-wt astrocytomas. H3K27me3 was retained in 2/60 oligodendrogliomas with retained ATRX, and in 3/6 IDH-mutant astrocytomas, two of which had lost and one retained ATRX. The combination of H3K27me3 and ATRX immunostainings with IDH mutational status correctly classified 55/69 (80%) cases. In IDH-mutant gliomas, ATRX loss indicates astrocytic phenotype, while ATRX retention and H3K27me3 loss identify oligodendroglial phenotype. Only 14 (20%) IDH-mutant cases with retained ATRX and H3K27me3 or inconclusive ATRX immunostaining would have requested 1p/19q codeletion testing to be classified. Furthermore, H3K27me3 retention was associated with significantly shorter relapse-free survival (P < 0.0001), independently from IDH mutation or 1p/19q codeletion (P < 0.005). Our data suggest that adding H3K27me3 immunostaining to the diagnostic workflow of diffuse gliomas with oligodendroglial or mixed morphology is useful for drastically reducing the number of cases requiring 1p/19q codeletion testing and providing relevant prognostic information.
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Affiliation(s)
- Serena Ammendola
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Policlinico G.B. Rossi. P.le L.A. Scuro 10, 37134, Verona, Italy
| | - Nicolò Caldonazzi
- Department of Translational and Molecular Medicine, Pathology Unit, University of Brescia, Brescia, Italy
| | - Michele Simbolo
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Policlinico G.B. Rossi. P.le L.A. Scuro 10, 37134, Verona, Italy
| | - Maria Liliana Piredda
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Policlinico G.B. Rossi. P.le L.A. Scuro 10, 37134, Verona, Italy
| | - Matteo Brunelli
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Policlinico G.B. Rossi. P.le L.A. Scuro 10, 37134, Verona, Italy
| | - Pietro Luigi Poliani
- Department of Translational and Molecular Medicine, Pathology Unit, University of Brescia, Brescia, Italy
| | - Giampietro Pinna
- Department of Neurosciences, Unit of Neurosurgery, Hospital Trust of Verona, Verona, Italy
| | - Francesco Sala
- Department of Neurosciences, Biomedicines and Movement Sciences, Institute of Neurosurgery, University of Verona, Verona, Italy
| | - Claudio Ghimenton
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Policlinico G.B. Rossi. P.le L.A. Scuro 10, 37134, Verona, Italy.,ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Valeria Barresi
- Department of Diagnostics and Public Health, Section of Anatomic Pathology, University of Verona, Policlinico G.B. Rossi. P.le L.A. Scuro 10, 37134, Verona, Italy.
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15
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Sharaf R, Pavlick DC, Frampton GM, Cooper M, Jenkins J, Danziger N, Haberberger J, Alexander BM, Cloughesy T, Yong WH, Liau LM, Nghiemphu PL, Ji M, Lai A, Ramkissoon SH, Albacker LA. FoundationOne CDx testing accurately determines whole arm 1p19q codeletion status in gliomas. Neurooncol Adv 2021; 3:vdab017. [PMID: 33778493 PMCID: PMC7986056 DOI: 10.1093/noajnl/vdab017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Molecular profiling of gliomas is vital to ensure diagnostic accuracy, inform prognosis, and identify clinical trial options for primary and recurrent tumors. This study aimed to determine the accuracy of reporting the whole arm 1p19q codeletion status from the FoundationOne platform. METHODS Testing was performed on glioma samples as part of clinical care and analyzed up to 395 cancer-associated genes (including IDH1/2). The whole arm 1p19q codeletion status was predicted from the same assay using a custom research-use only algorithm, which was validated using 463 glioma samples with available fluorescence in-situ hybridization (FISH) data. For 519 patients with available outcomes data, progression-free and overall survival were assessed based on whole arm 1p19q codeletion status derived from sequencing data. RESULTS Concordance between 1p19q status based on FISH and our algorithm was 96.7% (449/463) with a positive predictive value (PPV) of 100% and a positive percent agreement (PPA) of 91.0%. All discordant samples were positive for codeletion by FISH and harbored genomic alterations inconsistent with oligodendrogliomas. Median overall survival was 168 months for the IDH1/2 mutant, codeleted group, and 122 months for IDH1/2 mutant-only (hazard ratio (HR): 0.42; P < .05). CONCLUSIONS 1p19q codeletion status derived from FoundationOne testing is highly concordant with FISH results. Genomic profiling may be a reliable substitute for traditional FISH testing while also providing IDH1/2 status.
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Affiliation(s)
- Radwa Sharaf
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Dean C Pavlick
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Garrett M Frampton
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Maureen Cooper
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Jacqueline Jenkins
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Natalie Danziger
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - James Haberberger
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Brian M Alexander
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Timothy Cloughesy
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - William H Yong
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Linda M Liau
- Department of Neurosurgery, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Phioanh L Nghiemphu
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Matthew Ji
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Albert Lai
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Shakti H Ramkissoon
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
- Wake Forest Comprehensive Cancer Center and Department of Pathology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Lee A Albacker
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
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Abstract
BACKGROUND The revised fourth edition of the World Health Organization Classification of Tumors of the Central Nervous System-published in 2016-established 1p19q codeletion as the molecular hallmark for the diagnosis of oligodendrogliomas. Fluorescence in situ hybridization (FISH) is currently the most commonly used modality for 1p19q testing. However, as with most laboratory testing, 1p19q FISH testing has a false-positive rate, potentially resulting in an erroneous diagnosis of oligodendroglioma with significant implications for the choice of therapy and prognosis. METHODS The authors describe a case series of 5 patients treated at the Ohio State University James Cancer Center to illustrate the problem of false-positive 1p19q FISH results. RESULTS In our case series, the authors present a spectrum of possibilities for conflicting 1p19q testing results and the clinical consequences. The authors present 4 cases that, in retrospect, are believed to have had a false 1p19q FISH results. One other case may represent a true transformation of oligodendroglioma to glioblastoma or a second malignancy. Neuro-oncologists should pay attention to additional molecular markers, namely ATRX, TP53, and MGMT methylation status, before discussing the pathology with the patient and formulating a treatment plan. CONCLUSIONS Pathologists and neuro-oncologists should be aware of false-positive 1p19q FISH results as they can significantly change treatment and prognosis for glioma patients. Moreover, this issue should be taken into account when designing clinical trials specific to this disease cohort.
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17
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Ball MK, Kollmeyer TM, Praska CE, McKenna ML, Giannini C, Raghunathan A, Jentoft ME, Lachance DH, Kipp BR, Jenkins RB, Ida CM. Frequency of false-positive FISH 1p/19q codeletion in adult diffuse astrocytic gliomas. Neurooncol Adv 2020; 2:vdaa109. [PMID: 33205043 PMCID: PMC7654379 DOI: 10.1093/noajnl/vdaa109] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Background Oligodendroglioma is genetically defined by concomitant IDH (IDH1/IDH2) mutation and whole-arm 1p/19q codeletion. Codeletion of 1p/19q traditionally evaluated by fluorescence in situ hybridization (FISH) cannot distinguish partial from whole-arm 1p/19q codeletion. Partial 1p/19q codeletion called positive by FISH is diagnostically a "false-positive" result. Chromosomal microarray (CMA) discriminates partial from whole-arm 1p/19q codeletion. Herein, we aimed to estimate the frequency of partial 1p/19q codeletion that would lead to a false-positive FISH result. Methods FISH 1p/19q codeletion test probe coordinates were mapped onto Oncoscan CMA data to determine the rate of partial 1p/19q codeletion predicted to be positive by FISH. Diffuse astrocytic gliomas with available CMA data (2015-2018) were evaluated and classified based on IDH1-R132H/ATRX/p53 immunohistochemistry, IDH/TERT promoter targeted sequencing, and/or CMA according to classification updates. Predicted false-positive cases were verified by FISH whenever possible. Results The overall estimated false-positive FISH 1p/19q codeletion rate was 3.6% (8/223). Predicted false positives were verified by FISH in 6 (of 8) cases. False-positive rates did not differ significantly (P = .49) between IDH-mutant (4.6%; 4/86) and IDH-wildtype (2.9%; 4/137) tumors. IDH-wildtype false positives were all WHO grade IV, whereas IDH-mutant false positives spanned WHO grades II-IV. Testing for 1p/19q codeletion would not have been indicated for most false positives based on current classification recommendations. Conclusion Selective 1p/19q codeletion testing and cautious interpretation for conflicting FISH and histopathological findings are recommended to avoid potential misdiagnosis.
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Affiliation(s)
- Matthew K Ball
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Thomas M Kollmeyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Corinne E Praska
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Michelle L McKenna
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Caterina Giannini
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Aditya Raghunathan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Mark E Jentoft
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Jacksonville, Florida, USA
| | | | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Cristiane M Ida
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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18
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Garton ALA, Kinslow CJ, Rae AI, Mehta A, Pannullo SC, Magge RS, Ramakrishna R, McKhann GM, Sisti MB, Bruce JN, Canoll P, Cheng SK, Sonabend AM, Wang TJC. Extent of resection, molecular signature, and survival in 1p19q-codeleted gliomas. J Neurosurg 2020; 134:1357-1367. [PMID: 32384274 DOI: 10.3171/2020.2.jns192767] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/28/2020] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Genomic analysis in neurooncology has underscored the importance of understanding the patterns of survival in different molecular subtypes within gliomas and their responses to treatment. In particular, diffuse gliomas are now principally characterized by their mutation status (IDH1 and 1p/19q codeletion), yet there remains a paucity of information regarding the prognostic value of molecular markers and extent of resection (EOR) on survival. Furthermore, given the modern emphasis on molecular rather than histological diagnosis, it is important to examine the effect of maximal resection on survival in all gliomas with 1p/q19 codeletions, as these will now be classified as oligodendrogliomas under the new WHO guidelines. The objectives of the present study were twofold: 1) to assess the association between EOR and survival for patients with oligodendrogliomas in the National Cancer Database (NCDB), which includes information on mutation status, and 2) to demonstrate the same effect for all patients with 1p/19q codeleted gliomas in the NCDB. METHODS The NCDB was queried for all cases of oligodendroglioma between 2004 and 2014, with follow-up dates through 2016. The authors found 2514 cases of histologically confirmed oligodendrogliomas for the final analysis of the effect of EOR on survival. Upon further query, 1067 1p/19q-codeleted tumors were identified in the NCDB. Patients who received subtotal resection (STR) or gross-total resection (GTR) were compared to those who received no tumor debulking surgery. Univariable and multivariable analyses of both overall survival and cause-specific survival were performed. RESULTS EOR was associated with increased overall survival for both histologically confirmed oligodendrogliomas and all 1p/19q-codeleted-defined tumors (p < 0.001 and p = 0.002, respectively). Tumor grade, location, and size covaried predictably with EOR. When evaluating tumors by each classification system for predictors of overall survival, facility setting, age, comorbidity index, grade, location, chemotherapy, and radiation therapy were all shown to be significantly associated with overall survival. STR and GTR were independent predictors of improved survival in historically classified oligodendrogliomas (HR 0.83, p = 0.18; HR 0.69, p = 0.01, respectively) and in 1p/19q-codeleted tumors (HR 0.49, p < 0.01; HR 0.43, p < 0.01, respectively). CONCLUSIONS By using the NCDB, the authors have demonstrated a side-by-side comparison of the survival benefits of greater EOR in 1p/19q-codeleted gliomas.
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Affiliation(s)
- Andrew L A Garton
- 1Department of Neurological Surgery, NewYork-Presbyterian Hospital/Weill Cornell Medical Center
| | - Connor J Kinslow
- 2Department of Radiation Oncology, Vagelos College of Physicians and Surgeons, NewYork-Presbyterian Hospital/Columbia University Irving Medical Center, New York, New York
| | - Ali I Rae
- 3Department of Neurological Surgery, Oregon Health & Sciences University, Portland, Oregon
| | - Amol Mehta
- 4Department of Neurology, Vagelos College of Physicians and Surgeons, NewYork-Presbyterian Hospital/Columbia University Irving Medical Center
| | - Susan C Pannullo
- 1Department of Neurological Surgery, NewYork-Presbyterian Hospital/Weill Cornell Medical Center
| | - Rajiv S Magge
- 5Department of Radiation Oncology, NewYork-Presbyterian Hospital/Weill Cornell Medical Center
| | - Rohan Ramakrishna
- 1Department of Neurological Surgery, NewYork-Presbyterian Hospital/Weill Cornell Medical Center
| | - Guy M McKhann
- 6Department of Neurological Surgery, Vagelos College of Physicians and Surgeons, NewYork-Presbyterian Hospital/Columbia University Irving Medical Center
| | - Michael B Sisti
- 6Department of Neurological Surgery, Vagelos College of Physicians and Surgeons, NewYork-Presbyterian Hospital/Columbia University Irving Medical Center
| | - Jeffrey N Bruce
- 6Department of Neurological Surgery, Vagelos College of Physicians and Surgeons, NewYork-Presbyterian Hospital/Columbia University Irving Medical Center
| | - Peter Canoll
- 7Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, NewYork-Presbyterian Hospital/Columbia University Irving Medical Center.,8Departments of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, NewYork-Presbyterian Hospital/Columbia University Irving Medical Center
| | - Simon K Cheng
- 2Department of Radiation Oncology, Vagelos College of Physicians and Surgeons, NewYork-Presbyterian Hospital/Columbia University Irving Medical Center, New York, New York.,9Department of Epidemiology, Mailman School of Public Health, and Department of Medicine, Vagelos College of Physicians and Surgeons, NewYork-Presbyterian Hospital/Columbia University Irving Medical Center, New York, New York; and
| | - Adam M Sonabend
- 10Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Tony J C Wang
- 2Department of Radiation Oncology, Vagelos College of Physicians and Surgeons, NewYork-Presbyterian Hospital/Columbia University Irving Medical Center, New York, New York.,7Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, NewYork-Presbyterian Hospital/Columbia University Irving Medical Center
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19
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Van der Linden M, Raman L, Vander Trappen A, Dheedene A, De Smet M, Sante T, Creytens D, Lievens Y, Menten B, Van Dorpe J, Van Roy N. Detection of Copy Number Alterations by Shallow Whole-Genome Sequencing of Formalin-Fixed, Paraffin-Embedded Tumor Tissue. Arch Pathol Lab Med 2019; 144:974-981. [PMID: 31846367 DOI: 10.5858/arpa.2019-0010-oa] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— In routine clinical practice, tumor tissue is stored in formalin-fixed, paraffin-embedded blocks. However, the use of formalin-fixed, paraffin-embedded tissue for genome analysis is challenged by poorer DNA quality and quantity. Although several studies have reported genome-wide massive parallel sequencing applied on formalin-fixed, paraffin-embedded samples for mutation analysis, copy number analysis is not yet commonly performed. OBJECTIVE.— To evaluate the use of formalin-fixed, paraffin-embedded tissue for copy number alteration detection using shallow whole-genome sequencing, more generally referred to as copy number variation sequencing. DESIGN.— We selected samples from 21 patients, covering a range of different tumor entities. The performance of copy number detection was compared across 3 setups: array comparative genomic hybridization in combination with fresh material; copy number variation sequencing on fresh material; and copy number variation sequencing on formalin-fixed, paraffin-embedded material. RESULTS.— Very similar copy number profiles between paired samples were obtained. Although formalin-fixed, paraffin-embedded profiles often displayed more noise, detected copy numbers seemed equally reliable if the tumor fraction was at least 20%. CONCLUSIONS.— Copy number variation sequencing of formalin-fixed, paraffin-embedded material represents a trustworthy method. It is very likely that copy number variation sequencing of routinely obtained biopsy material will become important for individual patient care and research. Moreover, the basic technology needed for copy number variation sequencing is present in most molecular diagnostics laboratories.
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Affiliation(s)
- Malaïka Van der Linden
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Lennart Raman
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Ansel Vander Trappen
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Annelies Dheedene
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Matthias De Smet
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Tom Sante
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - David Creytens
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Yolande Lievens
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Björn Menten
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Jo Van Dorpe
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Nadine Van Roy
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
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20
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Yang RR, Shi ZF, Zhang ZY, Chan AKY, Aibaidula A, Wang WW, Kwan JSH, Poon WS, Chen H, Li WC, Chung NYF, Punchhi G, Chu WCY, Chan ISH, Liu XZ, Mao Y, Li KKW, Ng HK. IDH mutant lower grade (WHO Grades II/III) astrocytomas can be stratified for risk by CDKN2A, CDK4 and PDGFRA copy number alterations. Brain Pathol 2019; 30:541-553. [PMID: 31733156 DOI: 10.1111/bpa.12801] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/29/2019] [Indexed: 12/31/2022] Open
Abstract
In the 2016, WHO classification of tumors of the central nervous system, isocitrate dehydrogenase (IDH) mutation is a main classifier for lower grade astrocytomas and IDH-mutated astrocytomas is now regarded as a single group with longer survival. However, the molecular and clinical heterogeneity among IDH mutant lower grade (WHO Grades II/III) astrocytomas have only rarely been investigated. In this study, we recruited 160 IDH mutant lower grade (WHO Grades II/III) astrocytomas, and examined PDGFRA amplification, CDKN2A deletion and CDK4 amplification by FISH analysis, TERT promoter mutation by Sanger sequencing and ATRX loss and p53 expression by immunohistochemistry. We identified PDGFRA amplification, CDKN2A homozygous deletion and CDK4 amplification in 18.8%, 15.0% and 18.1% of our cohort respectively, and these alterations occurred in a mutually exclusive fashion. PDGFRA amplification was associated with shorter PFS (P = 0.0003) and OS (P < 0.0001). In tumors without PDGFRA amplification, CDKN2A homozygous deletion or CDK4 amplification was associated with a shorter OS (P = 0.035). Tumors were divided into three risk groups based on the presence of molecular alterations: high risk (PDGFRA amplification), intermediate risk (CDKN2A deletion or CDK4 amplification) and low risk (neither CDKN2A deletion and CDK4 amplification nor PDGFRA amplification). These three risk groups were significantly different in overall survival with mean survivals of 40.5, 62.9 and 71.5 months. The high-risk group also demonstrated a shorter PFS compared to intermediate- (P = 0.036) and low-risk (P < 0.0001) groups. One limitation of this study is the relatively short follow-up period, a common confounding factor for studies on low-grade tumors. Our data illustrate that IDH mutant lower grade astrocytomas is not a homogeneous group and should be molecularly stratified for risk.
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Affiliation(s)
- Rui Ryan Yang
- Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China SAR
| | - Zhi-Feng Shi
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhen-Yu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Aden Ka-Yin Chan
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China SAR
| | | | - Wei-Wei Wang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Johnny Sheung Him Kwan
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China SAR
| | - Wai Sang Poon
- Department of Neurosurgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China SAR
| | - Hong Chen
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Wen-Cai Li
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Nellie Yuk-Fei Chung
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China SAR
| | - Gopika Punchhi
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China SAR
| | - William Ching-Yuen Chu
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China SAR
| | - Ivan Sik-Hei Chan
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China SAR
| | - Xian-Zhi Liu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Kay Ka-Wai Li
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China SAR
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China SAR
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21
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Ramírez-Ramírez R, Gutiérrez-Angulo M, Peregrina-Sandoval J, Moreno-Ortiz JM, Franco-Topete RA, Cerda-Camacho FDJ, Ayala-Madrigal MDLL. Somatic deletion of KDM1A/LSD1 gene is associated to advanced colorectal cancer stages. J Clin Pathol 2019; 73:107-111. [PMID: 31471467 PMCID: PMC7027028 DOI: 10.1136/jclinpath-2019-206128] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/20/2019] [Accepted: 08/20/2019] [Indexed: 01/08/2023]
Abstract
Aims KDM1A/LSD1 and ZNF217 are involved in a protein complex that participates in transcriptional regulation. ZNF217 has been analysed in numerous cancers and its amplification has been associated with advanced stages of disease; however, a similar role for KDM1A/LSD1 has not been uncovered. In this study, we estimated the number of KDM1A/LSD1 and ZNF217 gene copies in tissue samples from patients diagnosed with colorectal cancer (CRC), as well as its association with clinicopathological features in patients with CRC. Methods Paraffin-embedded tumour samples from 50 patients with CRC with a histopathological diagnosis of CRC were included. The number of copies of KDM1A/LSD1 and ZNF217 genes was determined by fluorescence in situ hybridisation (FISH). We also analysed the association between copy numbers of selected genes and clinicopathological data based on multivariate analysis. Results Deletion of the KDM1A/LSD1 gene occurred in 19 samples (38%), whereas ZNF217 gene amplification was identified in 11 samples (22%). We found a significant association between lymph node metastasis or advanced tumour stage and KDM1A/LSD1 gene deletion (p value=0.0003 and p value=0.011, respectively). Conclusions KDM1A/LSD1 gene deletion could be considered a novel prognostic biomarker of late-stage CRC.
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Affiliation(s)
- Ruth Ramírez-Ramírez
- Laboratorio de Inmunología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, México
| | - Melva Gutiérrez-Angulo
- Departamento de Clínicas, Centro Universitario de los Altos, Universidad de Guadalajara, Tepatitlán de Morelos, México.,Programa de Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México
| | - Jorge Peregrina-Sandoval
- Laboratorio de Inmunología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, México.,Laboratorio de Patología Clínica, Hospital Civil de Guadalajara "Fray Antonio Alcalde", Guadalajara, México
| | - José Miguel Moreno-Ortiz
- Programa de Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México.,Instituto de Genética Humana "Dr. Enrique Corona Rivera", Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México
| | - Ramon Antonio Franco-Topete
- Servicio de Anatomía Patológica, Hospital Civil de Guadalajara "Dr. Juan I Menchaca", Guadalajara, México.,Departamento de Microbiología y Patología, Universidad de Guadalajara, Guadalajara, México
| | | | - Maria de la Luz Ayala-Madrigal
- Programa de Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México .,Instituto de Genética Humana "Dr. Enrique Corona Rivera", Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, México
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McAleenan A, Jones HE, Kernohan A, Faulkner CL, Palmer A, Dawson S, Wragg C, Jefferies S, Brandner S, Vale L, Higgins JPT, Kurian KM. Diagnostic test accuracy and cost-effectiveness of tests for codeletion of chromosomal arms 1p and 19q in people with glioma. Hippokratia 2019. [DOI: 10.1002/14651858.cd013387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Alexandra McAleenan
- University of Bristol; Population Health Sciences, Bristol Medical School; 39 Whatley Road Bristol UK BS8 2PS
| | - Hayley E Jones
- University of Bristol; Population Health Sciences, Bristol Medical School; 39 Whatley Road Bristol UK BS8 2PS
| | - Ashleigh Kernohan
- Newcastle University; Institute of Health & Society; Baddiley-Clark Building, Richardson Road Newcastle upon Tyne UK NE2 4AA
| | - Claire L Faulkner
- Southmead Hospital; Bristol Genetics Laboratory, Pathology Sciences; North Bristol NHS Trust Bristol UK BS10 5NB
| | - Abigail Palmer
- Southmead Hospital; Bristol Genetics Laboratory, Pathology Sciences; North Bristol NHS Trust Bristol UK BS10 5NB
| | - Sarah Dawson
- University of Bristol; Population Health Sciences, Bristol Medical School; 39 Whatley Road Bristol UK BS8 2PS
| | - Christopher Wragg
- Southmead Hospital; Bristol Genetics Laboratory, Pathology Sciences; North Bristol NHS Trust Bristol UK BS10 5NB
| | - Sarah Jefferies
- Addenbrooke's Hospital; Department of Oncology; Hills Road Cambridge UK CB2 0QQ
| | - Sebastian Brandner
- The National Hospital for Neurology and Neurosurgery; Division of Neuropathology and Department of Neurodegeneration; University College Hospital NHS Foundation Trust and UCL Institute of Neurology Queen Square London UK WC1N 3BG
| | - Luke Vale
- Newcastle University; Institute of Health & Society; Baddiley-Clark Building, Richardson Road Newcastle upon Tyne UK NE2 4AA
| | - Julian P T Higgins
- University of Bristol; Population Health Sciences, Bristol Medical School; 39 Whatley Road Bristol UK BS8 2PS
| | - Kathreena M Kurian
- University of Bristol; Bristol Medical School: Brain Tumour Research Centre, Public Health Sciences; Oakfield House, Oakfield Grove Bristol UK BS8 2BN
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Conventional Magnetic Resonance Features for Predicting 1p19q Codeletion Status of World Health Organization Grade II and III Diffuse Gliomas. J Comput Assist Tomogr 2019; 43:269-276. [PMID: 30371623 DOI: 10.1097/rct.0000000000000816] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PURPOSE The conventional magnetic resonance features of World Health Organization (WHO) grade II and III diffuse gliomas in relation to chromosome 1p and 19q deletions (1p19q codeletion) were analyzed. METHODS We identified 147 cases of WHO grade II and III diffuse gliomas (1p/19q codeletion, 36 cases; no 1p/19q codeletion, 111 cases). χ Test and univariate and multivariate binary logistic regression analyses were conducted to evaluate the association between the imaging features and 1p19q codeletion status of WHO grade II and III diffuse gliomas in the discovery group, including the WHO grade II and III subgroups. RESULTS (1) In the entire population, multivariate regression demonstrated that proportion contrast-enhanced tumor (>5% vs ≤5%; odds ratio [OR], 0.169; P = 0.009), enhancing margin (poorly vs well defined; OR, 12.435; P = 0.002), and hemorrhage (yes vs no; OR, 21.082; P < 0.001) were associated with a higher incidence of 1p19q codeletion status. The nomogram showed good discrimination (area under the curve [AUC], 0.803) and calibration. (2) For grade II tumors, subgroup analysis found that enhancing margin (poorly vs well defined; OR, 0.308; P = 0.007) and subventricular zone (presence vs absence-; OR, 0.137; P < 0.001) were associated with a higher incidence of 1p19q codeletion status (AUC, 0.779). (3) For grade III tumors, subgroup analysis found that age (≥40 years vs <40 years; OR, 5.977; P = 0.03) and hemorrhage (yes vs no; OR, 18.051; P < 0.001) were associated with a higher incidence of 1p19q codeletion status (AUC, 0.816). CONCLUSIONS Conventional magnetic resonance features can be conveniently used to facilitate the preoperative prediction of 1p19q codeletion status of WHO grade II and III diffuse gliomas. Decision curve analysis demonstrated that the nomogram was clinically useful.
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Comparison of 1p and 19q status of glioblastoma by whole exome sequencing, array-comparative genomic hybridization, and fluorescence in situ hybridization. Med Oncol 2018; 35:60. [PMID: 29600313 DOI: 10.1007/s12032-018-1119-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/23/2018] [Indexed: 12/30/2022]
Abstract
According to the 2016 World Health Organization classification of tumors of the central nervous system, detecting 1p/19q co-deletion became essential in clinical neuropathology for gliomas with oligodendroglioma-like morphology. Here, we assessed genomic profiles of glioblastoma in 80 cases including 1p/19q status using fluorescent in situ hybridization (FISH), array-comparative genomic hybridization (aCGH), and/or whole exome sequencing (WES). Paraffin-embedded tumor tissues were subjected to FISH analysis, and the corresponding frozen tissues from the same tumors were evaluated for aCGH and/or WES for 1p/19q co-deletion and other genetic parameters, which included IDH1-R132H, ATRX, TP53, CIC, and NOTCH1 mutations and MGMT methylation status. We also evaluated correlations between 1p/19q co-deletion status and molecular markers or clinical outcomes. The FISH analyses revealed 1p/19q co-deletion in two cases, isolated deletion of 1p in six cases, and 19q in two cases, whereas the aCGH and WES results showed isolated deletion of 19q in four cases and 19 monosomy in only one case. Eleven cases showed discordant 1p/19q results between aCGH/WES and FISH analysis, and in most of them, 1p and/or 19q deletion on FISH analysis corresponded to the partial deletions at 1p36 and/or 19q13 on aCGH/WES. Our cohort exhibited IDH1-R132H mutations (5.4%), MGMT promotor methylation (34.6%), and mutations in ATRX (9.5%), TP53 (33.3%), and NOTCH1 (3.8%) but not in CIC (0%). In addition, MGMT methylation and ATRX mutation were significantly associated with clinical prognosis. In glioblastomas, partial deletions of 1p36 and/or 19q13 were uncommon, some of which appeared as 1p and/or 19q deletions on FISH analysis.
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Immunohistochemical ATRX expression is not a surrogate for 1p19q codeletion. Brain Tumor Pathol 2018; 35:106-113. [DOI: 10.1007/s10014-018-0312-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 03/07/2018] [Indexed: 10/17/2022]
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26
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Neuro-oncology Virtual Special Issue. Clin Oncol (R Coll Radiol) 2016; 28:540-1. [PMID: 27188782 DOI: 10.1016/j.clon.2016.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 05/04/2016] [Indexed: 11/24/2022]
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