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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Kalaroopan D, Lasocki A. MRI-based deep learning techniques for the prediction of isocitrate dehydrogenase and 1p/19q status in grade 2-4 adult gliomas. J Med Imaging Radiat Oncol 2023; 67:492-498. [PMID: 36919468 DOI: 10.1111/1754-9485.13522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/16/2023] [Indexed: 03/16/2023]
Abstract
Molecular biomarkers are becoming increasingly important in the classification of intracranial gliomas. While tissue sampling remains the gold standard, there is growing interest in the use of deep learning (DL) techniques to predict these markers. This narrative review with a systematic approach identifies and synthesises the current published data on DL techniques using conventional MRI sequences for predicting isocitrate dehydrogenase (IDH) and 1p/19q-codeletion status in World Health Organisation grade 2-4 gliomas. Three databases were searched for relevant studies. In all, 13 studies met the inclusion criteria after exclusions. Key results, limitations and discrepancies between studies were synthesised. High accuracy has been reported in some studies, but the existing literature has several limitations, including generally small cohort sizes, a paucity of studies with independent testing cohorts and a lack of studies assessing IDH and 1p/19q together. While DL shows promise as a non-invasive means of predicting glioma genotype, addressing these limitations in future research will be important for facilitating clinical translation.
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Affiliation(s)
- Dinusha Kalaroopan
- Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia
| | - Arian Lasocki
- Department of Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Radiology, The University of Melbourne, Melbourne, Victoria, Australia
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Brown J, Byatt S, Khan T, St Heaps L, Dexter M, Nahar N, Wong M, Tan K, Varikatt W. FISH analysis of brain smears obtained at intraoperative diagnosis - An accurate and fast method to detect 1p/19q-codeletion in gliomas. J Clin Neurosci 2021; 92:115-9. [PMID: 34509237 DOI: 10.1016/j.jocn.2021.07.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 06/22/2021] [Accepted: 07/25/2021] [Indexed: 11/24/2022]
Abstract
The importance of molecular testing of gliomas is highlighted in the 2016 revised 4th edition of the WHO Classification of Tumours of the Central Nervous System, which applies an integrated diagnosis of histological and molecular features. In this classification system, oligodendrogliomas (ODG) are defined as IDH-mutant and 1p/19q-codeleted. Fluorescence in situ hybridization (FISH) analysis of formalin-fixed paraffin-embedded (FFPE) tissue is a standard method of determining 1p/19q-codeletion. However, it has several disadvantages, including requiring lengthy pretreatment, truncation artefact and lack of on-site access in many centers. In an effort to address these issues, we analysed FISH performed on smears obtained at intraoperative frozen section on 51 gliomas and compared this to FISH performed on subsequent FFPE sections. Four cases were excluded due to uninterpretable FISH results. Of the remaining 47 cases, 17 were concordant for 1p/19q-codeletion, 29 were concordant for lack of 1p/19q-codeletion, and 1 was discordant with 1p/19q-codeletion found on FFPE tissue but not on intraoperative smears. The discordant case was most likely due to sampling error, as the frozen section had not shown definite tumor. The FISH results on intraoperative smears were received within 24-48 h after the sample was collected, compared with 3-4 days for FFPE tissue. FISH on smears obtained at intraoperative frozen section is an accurate and fast method for determining 1p/19q-codeletion.
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Yogananda CGB, Shah BR, Yu FF, Pinho MC, Nalawade SS, Murugesan GK, Wagner BC, Mickey B, Patel TR, Fei B, Madhuranthakam AJ, Maldjian JA. A novel fully automated MRI-based deep-learning method for classification of 1p/19q co-deletion status in brain gliomas. Neurooncol Adv 2021; 2:vdaa066. [PMID: 32705083 PMCID: PMC7367418 DOI: 10.1093/noajnl/vdaa066] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND One of the most important recent discoveries in brain glioma biology has been the identification of the isocitrate dehydrogenase (IDH) mutation and 1p/19q co-deletion status as markers for therapy and prognosis. 1p/19q co-deletion is the defining genomic marker for oligodendrogliomas and confers a better prognosis and treatment response than gliomas without it. Our group has previously developed a highly accurate deep-learning network for determining IDH mutation status using T2-weighted (T2w) MRI only. The purpose of this study was to develop a similar 1p/19q deep-learning classification network. METHODS Multiparametric brain MRI and corresponding genomic information were obtained for 368 subjects from The Cancer Imaging Archive and The Cancer Genome Atlas. 1p/19 co-deletions were present in 130 subjects. Two-hundred and thirty-eight subjects were non-co-deleted. A T2w image-only network (1p/19q-net) was developed to perform 1p/19q co-deletion status classification and simultaneous single-label tumor segmentation using 3D-Dense-UNets. Three-fold cross-validation was performed to generalize the network performance. Receiver operating characteristic analysis was also performed. Dice scores were computed to determine tumor segmentation accuracy. RESULTS 1p/19q-net demonstrated a mean cross-validation accuracy of 93.46% across the 3 folds (93.4%, 94.35%, and 92.62%, SD = 0.8) in predicting 1p/19q co-deletion status with a sensitivity and specificity of 0.90 ± 0.003 and 0.95 ± 0.01, respectively and a mean area under the curve of 0.95 ± 0.01. The whole tumor segmentation mean Dice score was 0.80 ± 0.007. CONCLUSION We demonstrate high 1p/19q co-deletion classification accuracy using only T2w MR images. This represents an important milestone toward using MRI to predict glioma histology, prognosis, and response to treatment.
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Affiliation(s)
| | - Bhavya R Shah
- Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Frank F Yu
- Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Marco C Pinho
- Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Sahil S Nalawade
- Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Gowtham K Murugesan
- Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Benjamin C Wagner
- Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Bruce Mickey
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Toral R Patel
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Baowei Fei
- Department of Bioengineering, University of Texas at Dallas, Richardson, Texas, USA
| | - Ananth J Madhuranthakam
- Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Joseph A Maldjian
- Corresponding Author: Joseph A. Maldjian, MD, Department of Radiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390-9178, USA ()
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Michaud K, de Tayrac M, D'Astous M, Duval C, Paquet C, Samassekou O, Gould PV, Saikali S. Contribution of 1p, 19q, 9p and 10q Automated Analysis by FISH to the Diagnosis and Prognosis of Oligodendroglial Tumors According to WHO 2016 Guidelines. PLoS One 2016; 11:e0168728. [PMID: 28030632 DOI: 10.1371/journal.pone.0168728] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 12/05/2016] [Indexed: 01/19/2023] Open
Abstract
Objective To study the feasibility and the diagnostic and prognostic interest of automated analysis of 1p, 19q, 9p and 10q status by FISH technique in oligodendroglial tumors. Methods We analyzed a retrospective series of 33 consecutive gliomas with oligodendroglial histology (originally diagnosed as 24 oligodendrogliomas and 9 oligoastrocytomas). For all cases, automated FISH analysis of 1p, 19q, 9p and 10q status were performed and compared to clinical and histological data, ATRX, IDH1R132H and alpha-internexin status (studied by immunohistochemistry) and overall survival (OS). Manual analysis of 9p and 10q status were also performed and compared to automated analysis to verify the concordance of the two methods. Results The 33 gliomas were reclassified into 13 low-grade oligodendrogliomas (OII), 10 anaplastic oligodendrogliomas (OIII), 3 diffuse astrocytomas (AII), 3 anaplastic astrocytomas (AIII) and 4 glioblastomas (GBM) according to the WHO 2016 histological criteria. The 1p and/or 19q imbalanced status were restricted to astrocytomas with no correlation to their grade or their OS. Chromosome 9p deletion was restricted to OIII (70%) and GBM (100%) and was correlated with a shorter OS in the total cohort (p = 0.0007), the oligodendroglioma cohort (p = 0.03) and the astrocytoma cohort (p = 0.001). Concordance between 9p manual and automated analysis was satisfactory (81%, κ = 0.69). Chromosome 10q deletion was restricted to GBMs (50%) and was correlated with a poor OS in both the total cohort (p = 0.003) and the astrocytoma (AS) cohort (p = 0.04). Concordance between manual and automated analysis was satisfactory (79%, κ = 0.62). Conclusion Automated analysis of 1p, 19q, 9p and 10q status by FISH is a reliable technique which allows for refined classification of oligodendroglial tumors. 1p and/or 19q imbalanced status is evidence of astrocytic differentiation. 9p deletion is found in high grade oligodendrogliomas and astrocytomas with a poor OS. 10q is related to GBM status and a poor OS.
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Srebotnik-Kirbiš I, Limbäck-Stokin C. Application of brush cytology for FISH-based detection of 1p/19q codeletion in oligodendroglial tumors. J Neurooncol 2016; 129:415-422. [DOI: 10.1007/s11060-016-2211-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/06/2016] [Indexed: 12/19/2022]
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Abstract
Several morphology- and polymerase chain reaction (PCR)-based methods for chromosome 1p 19q deletion status assessment are available. Important prerequisites for all molecular techniques concern tissue quality and selection of regions of interest. The most common methods for diagnostic 1p 19q assessment are fluorescence in situ hybridization and PCR-based microsatellite analysis. While the latter requires the use of autologous blood samples, more advanced techniques such as array comparative genomic hybridization, multiplex ligation-dependent probe amplification or real-time PCR are independent from autologous DNA samples. However, due to high technical demand and experience required their applicability as diagnostic tests remains to be shown. On the other hand, chromogenic in situ hybridization evolves as attractive alternative to FISH. Herein, the available test methods are reviewed and outlined, their advantages and drawbacks being discussed in detail.
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Affiliation(s)
- Adelheid Woehrer
- Institute of Neurology, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria
| | - Johannes A Hainfellner
- Institute of Neurology, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria
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Pinkham M, Telford N, Whitfield G, Colaco R, O'Neill F, McBain C. FISHing Tips: What Every Clinician Should Know About 1p19q Analysis in Gliomas Using Fluorescence in situ Hybridisation. Clin Oncol (R Coll Radiol) 2015; 27:445-53. [DOI: 10.1016/j.clon.2015.04.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 04/01/2015] [Accepted: 04/07/2015] [Indexed: 11/25/2022]
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Duval C, de Tayrac M, Michaud K, Cabillic F, Paquet C, Gould PV, Saikali S. Automated Analysis of 1p/19q Status by FISH in Oligodendroglial Tumors: Rationale and Proposal of an Algorithm. PLoS One 2015; 10:e0132125. [PMID: 26135922 PMCID: PMC4489714 DOI: 10.1371/journal.pone.0132125] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 06/10/2015] [Indexed: 11/28/2022] Open
Abstract
Objective To propose a new algorithm facilitating automated analysis of 1p and 19q status by FISH technique in oligodendroglial tumors with software packages available in the majority of institutions using this technique. Methods We documented all green/red (G/R) probe signal combinations in a retrospective series of 53 oligodendroglial tumors according to literature guidelines (Algorithm 1) and selected only the most significant combinations for a new algorithm (Algorithm 2). This second algorithm was then validated on a prospective internal series of 45 oligodendroglial tumors and on an external series of 36 gliomas. Results Algorithm 2 utilizes 24 G/R combinations which represent less than 40% of combinations observed with Algorithm 1. The new algorithm excludes some common G/R combinations (1/1, 3/2) and redefines the place of others (defining 1/2 as compatible with normal and 3/3, 4/4 and 5/5 as compatible with imbalanced chromosomal status). The new algorithm uses the combination + ratio method of signal probe analysis to give the best concordance between manual and automated analysis on samples of 100 tumor cells (91% concordance for 1p and 89% concordance for 19q) and full concordance on samples of 200 tumor cells. This highlights the value of automated analysis as a means to identify cases in which a larger number of tumor cells should be studied by manual analysis. Validation of this algorithm on a second series from another institution showed a satisfactory concordance (89%, κ = 0.8). Conclusion Our algorithm can be easily implemented on all existing FISH analysis software platforms and should facilitate multicentric evaluation and standardization of 1p/19q assessment in gliomas with reduction of the professional and technical time required.
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Affiliation(s)
- Céline Duval
- Department of pathology, Centre Hospitalier Universitaire de Québec, Québec, Canada
| | - Marie de Tayrac
- Department of genomic and molecular genetics, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Karine Michaud
- Department of Neurosurgery, Centre Hospitalier Universitaire de Québec, Québec, Canada
| | - Florian Cabillic
- Department of cytogenetics and cellular biology, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Claudie Paquet
- Department of pathology, Centre Hospitalier Universitaire de Québec, Québec, Canada
| | - Peter Vincent Gould
- Department of pathology, Centre Hospitalier Universitaire de Québec, Québec, Canada
| | - Stéphan Saikali
- Department of pathology, Centre Hospitalier Universitaire de Québec, Québec, Canada
- * E-mail:
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Massari F, Bria E, Ciccarese C, Munari E, Modena A, Zambonin V, Sperduti I, Artibani W, Cheng L, Martignoni G, Tortora G, Brunelli M. Prognostic Value of Beta-Tubulin-3 and c-Myc in Muscle Invasive Urothelial Carcinoma of the Bladder. PLoS One 2015; 10:e0127908. [PMID: 26046361 PMCID: PMC4457798 DOI: 10.1371/journal.pone.0127908] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 04/20/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND To date, putative prognostic biomarkers have shown limited utility from the clinical perspective for bladder urothelial carcinoma. Herein, the expression of beta-tubulin-3 and c-Myc was evaluated to determine their prognostic potential. METHODS In formalin fixed-paraffin embedded blocks, immunohistochemical expression of c-Myc and beta-tubulin-3 was evaluated. H score ranging from 0 to 300 was obtained by multiplying the percentage of positive cells by intensity (0-3); c-Myc and beta-tubulin-3 expression was defined: 0: negative, 1: weakly positive, 2: strongly positive. RESULTS beta-tubulin-3 and c-Myc immunoexpression was available for 46 cases. At the univariate analysis, node-involvement, beta-tubulin-3 and c-Myc overexpression discriminate shorter DFS (HR 2.19, p = 0.043; HR 3.10, p = 0.24 and HR 3.05, p = 0.011, respectively); 2-yrs DFS log-rank analysis according to low versus high level of immunoexpression were statistically significant; beta-tubulin-3, 53% low vs 12.7% high (p = value 0.02) and c-Myc 28 low vs 8 high (p-value 0.007). Patients displaying negative beta-tubulin-3/c-Myc had statistically significant better 2-yrs DFS than those with mixed expression or double positivity (54.5% versus 18.7% versus 0%, log-rank p = 0.006). CONCLUSIONS c-Myc and beta-tubulin-3 show improvement for prognostic risk stratification in patients with muscle invasive bladder urothelial carcinoma. These molecular pathways may also be candidate to improve predictiveness to targeted therapies.
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Affiliation(s)
- Francesco Massari
- Medical Oncology d.U., Azienda Ospedaliera Universitaria Integrata (AOUI) and University of Verona, Verona, Italy
| | - Emilio Bria
- Medical Oncology d.U., Azienda Ospedaliera Universitaria Integrata (AOUI) and University of Verona, Verona, Italy
| | - Chiara Ciccarese
- Medical Oncology d.U., Azienda Ospedaliera Universitaria Integrata (AOUI) and University of Verona, Verona, Italy
| | - Enrico Munari
- Department of Pathology and Diagnostic, Azienda Ospedaliera Universitaria Integrata (AOUI) and University of Verona, Verona, Italy
| | - Alessandra Modena
- Medical Oncology d.U., Azienda Ospedaliera Universitaria Integrata (AOUI) and University of Verona, Verona, Italy
| | - Valentina Zambonin
- Medical Oncology d.U., Azienda Ospedaliera Universitaria Integrata (AOUI) and University of Verona, Verona, Italy
| | | | - Walter Artibani
- Urologic Clinic, Department of Oncological and Surgical Sciences, Azienda Ospedaliera Universitaria Integrata (AOUI) and University of Verona, Verona, Italy
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Guido Martignoni
- Department of Pathology and Diagnostic, Azienda Ospedaliera Universitaria Integrata (AOUI) and University of Verona, Verona, Italy
| | - Giampaolo Tortora
- Medical Oncology d.U., Azienda Ospedaliera Universitaria Integrata (AOUI) and University of Verona, Verona, Italy
- * E-mail:
| | - Matteo Brunelli
- Department of Pathology and Diagnostic, Azienda Ospedaliera Universitaria Integrata (AOUI) and University of Verona, Verona, Italy
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Duval C, de Tayrac M, Sanschagrin F, Michaud K, Gould PV, Saikali S. ImmunoFISH is a reliable technique for the assessment of 1p and 19q status in oligodendrogliomas. PLoS One 2014; 9:e100342. [PMID: 24949947 PMCID: PMC4065070 DOI: 10.1371/journal.pone.0100342] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 05/23/2014] [Indexed: 11/19/2022] Open
Abstract
Objective To develop a new ImmunoFISH technique for the study of oligodendrogliomas by combining a standard immunohistochemical stain using MIB-1 antibody with a standard FISH technique using commercial 1p36 and 19q13 chromosomal probes. Methods Validation was performed by two observers on a series of 36 pre-selected oligodendrogliomas and compared to the results previously determined by FISH alone. Results The ImFISH technique is easy to perform and to analyze and is no more time-consuming than the usual FISH technique. Our results show that the inter-observer reliability of ImFISH is high (κ = 0.86 and 0.95 respectively for 1p and 19q). Compared to FISH, the ImFISH exhibits a very high sensitivity (∼100%) and specificity (∼90%) for 1p and/or 19q deleted cases. The sensitivity is high for normal cases (∼85%) and imbalanced cases (∼90%) with a specificity ranging between 50 and 85%. Finally, there were no significant differences between FISH and ImFISH results calculated on 60, 40 or 20 cells. Conclusion Our study demonstrates the reliability of the ImFISH technique in oligodendrogliomas and emphasizes its advantage in poorly cellular tumoral specimen.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Antibodies, Antinuclear/metabolism
- Antibodies, Monoclonal/metabolism
- Brain Neoplasms/genetics
- Brain Neoplasms/metabolism
- Chromosomes, Human, Pair 1/genetics
- Chromosomes, Human, Pair 1/metabolism
- Chromosomes, Human, Pair 19/genetics
- Chromosomes, Human, Pair 19/metabolism
- Female
- Humans
- Immunohistochemistry
- In Situ Hybridization, Fluorescence/methods
- Male
- Middle Aged
- Observer Variation
- Oligodendroglioma/genetics
- Oligodendroglioma/metabolism
- Reproducibility of Results
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Affiliation(s)
- Céline Duval
- Department of Pathology, Centre Hospitalier Universitaire de Québec, Québec, Canada
| | - Marie de Tayrac
- Department of genomic and molecular genetics, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - François Sanschagrin
- Department of Pathology, Centre Hospitalier Universitaire de Québec, Québec, Canada
| | - Karine Michaud
- Department of Neurosurgery, Centre Hospitalier Universitaire de Québec, Québec, Canada
| | - Peter Vincent Gould
- Department of Pathology, Centre Hospitalier Universitaire de Québec, Québec, Canada
| | - Stéphan Saikali
- Department of Pathology, Centre Hospitalier Universitaire de Québec, Québec, Canada
- * E-mail:
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Komori T, Hirose T, Shibuya M, Suzuki H, Tanaka S, Sasaki A. Controversies over the diagnosis of oligodendroglioma: a report from the satellite workshop at the 4th international symposium of brain tumor pathology, Nagoya Congress Center, May 23, 2012. Brain Tumor Pathol 2014; 30:253-61. [PMID: 24100794 DOI: 10.1007/s10014-013-0165-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
With the goal of discussing how the neuropathology community should resolve the controversy over the diagnosis of oligodendroglioma, this Satellite Workshop reflects the collaboration between two invited keynote speakers: Dr. Johan M. Kros of the Erasmus Medical Center and Dr. Kenneth D. Aldape of the University of Texas MD Anderson Cancer Center and the Organizing Committee of the Japanese Society of Brain Tumor Pathology. In the first half of the workshop, the keynote speakers reviewed the current status of the pathology and genetics of oligodendroglioma. In the second half, six debatable cases that exemplify the current controversies over the diagnosis of oligodendroglioma were presented. The consensus diagnoses in these six cases, which have been reviewed by members of the Society, were opened to discussion and comments by the speakers. These cases highlight unresolved issues in the WHO 2007 classification of oligodendrogliomas, particularly the discordance between morphology and genetics. To achieve synchronization between phenotypes and genotypes, the neuropathology diagnosis should focus on the classic features of oligodendrogliomas that are highly correlated with the genetic background.
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Affiliation(s)
- Takashi Komori
- Department of Laboratory Medicine and Pathology (Neuropathology), Tokyo Metropolitan Neurological Hospital, 2-6-1 Musashidai, Fuchu, Tokyo, 183-0042, Japan,
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