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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: 7] [Impact Index Per Article: 3.5] [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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3
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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: 8] [Impact Index Per Article: 4.0] [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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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: 7] [Impact Index Per Article: 2.3] [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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Higa N, Akahane T, Yokoyama S, Yonezawa H, Uchida H, Takajo T, Kirishima M, Hamada T, Matsuo K, Fujio S, Hanada T, Hosoyama H, Yonenaga M, Sakamoto A, Hiraki T, Tanimoto A, Yoshimoto K. A tailored next-generation sequencing panel identified distinct subtypes of wildtype IDH and TERT promoter glioblastomas. Cancer Sci 2020; 111:3902-3911. [PMID: 32748499 PMCID: PMC7541004 DOI: 10.1111/cas.14597] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/27/2020] [Accepted: 07/29/2020] [Indexed: 12/14/2022] Open
Abstract
Central nervous system tumors are classified based on an integrated diagnosis combining histology and molecular characteristics, including IDH1/2 and H3-K27M mutations, as well as 1p/19q codeletion. Here, we aimed to develop and assess the feasibility of a glioma-tailored 48-gene next-generation sequencing (NGS) panel for integrated glioma diagnosis. We designed a glioma-tailored 48-gene NGS panel for detecting 1p/19q codeletion and mutations in IDH1/2, TP53, PTEN, PDGFRA, NF1, RB1, CDKN2A/B, CDK4, and the TERT promoter (TERTp). We analyzed 106 glioma patients (grade II: 19 cases, grade III: 23 cases, grade IV: 64 cases) using this system. The 1p/19q codeletion was detected precisely in oligodendroglial tumors using our NGS panel. In a cohort of 64 grade Ⅳ gliomas, we identified 56 IDH-wildtype glioblastomas. Within these IDH-wildtype glioblastomas, 33 samples (58.9%) showed a mutation in TERTp. Notably, PDGFRA mutations and their amplification were more commonly seen in TERTp-wildtype glioblastomas (43%) than in TERTp-mutant glioblastomas (6%) (P = .001). Hierarchical molecular classification of IDH-wildtype glioblastomas revealed 3 distinct groups of IDH-wildtype glioblastomas. One major cluster was characterized by mutations in PDGFRA, amplification of CDK4 and PDGFRA, homozygous deletion of CDKN2A/B, and absence of TERTp mutations. This cluster was significantly associated with older age (P = .021), higher Ki-67 score (P = .007), poor prognosis (P = .012), and a periventricular tumor location. We report the development of a glioma-tailored NGS panel for detecting 1p/19q codeletion and driver gene mutations on a single platform. Our panel identified distinct subtypes of IDH- and TERTp-wildtype glioblastomas with frequent PDGFRA alterations.
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Affiliation(s)
- Nayuta Higa
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Toshiaki Akahane
- Department of Pathology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.,Center for Human Genome and Gene Analysis, Kagoshima University Hospital, Kagoshima, Japan
| | - Seiya Yokoyama
- Department of Pathology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Hajime Yonezawa
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Hiroyuki Uchida
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Tomoko Takajo
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Mari Kirishima
- Department of Pathology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Taiji Hamada
- Department of Pathology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Kei Matsuo
- Department of Pathology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Shingo Fujio
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Tomoko Hanada
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Hiroshi Hosoyama
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Masanori Yonenaga
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Akihisa Sakamoto
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Tsubasa Hiraki
- Department of Pathology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Akihide Tanimoto
- Department of Pathology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.,Center for Human Genome and Gene Analysis, Kagoshima University Hospital, Kagoshima, Japan
| | - Koji Yoshimoto
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
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6
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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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7
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Ballester LY, Huse JT, Tang G, Fuller GN. Molecular classification of adult diffuse gliomas: conflicting IDH1/IDH2, ATRX, and 1p/19q results. Hum Pathol 2017; 69:15-22. [DOI: 10.1016/j.humpath.2017.05.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 05/05/2017] [Accepted: 05/10/2017] [Indexed: 11/29/2022]
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9
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Woehrer A, Hainfellner JA. Molecular diagnostics: techniques and recommendations for 1p/19q assessment. CNS Oncol 2015; 4:295-306. [PMID: 26545171 DOI: 10.2217/cns.15.28] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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] [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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11
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Nauen DW, Guajardo A, Haley L, Powell K, Burger PC, Gocke CD. Chromosomal defects track tumor subpopulations and change in progression in oligodendroglioma. CONVERGENT SCIENCE PHYSICAL ONCOLOGY 2015; 1. [PMID: 31602317 DOI: 10.1088/2057-1739/1/1/015001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
To assess karyotypic changes and tumor subpopulations in progression of oligodendroglioma (ODG) we analyzed histologically diagnosed 1p/19q codeleted cases using single nucleotide polymorphism (SNP) microarray data. We separated cases according to grade, which was assigned blind to karyotype information beyond 1p/19q status. The 51 WHO grade II (O2) and 18 WHO grade III (O3) specimens showed frequent chromosomal locations and patterns of change including loss of heterozygosity (LOH), often copy-neutral, on 9p and LOH on 4p and 4q together. Analysis of co-occurrence indicated that most defects were independent but also suggested increased likelihood of defects on 11q, 13q, and 14q in the presence of defects on 18, 4, and 9, respectively. We used the relative degree of change in B-allele frequency as an indicator of an abnormality's extent, and we present simulated data to clarify how information on subpopulations was thus inferred. Among 9p defects, 89.3% involved the whole tumor, whereas only 47.6% of 4q defects did so. We modeled extent through the tumor as due to a karyotypic change's likelihood of occurring and the fitness it confers on its subpopulation, and used group data to estimate these values. To assess progression directly, we evaluated specimens from six patients who underwent multiple resections since 1996. Four of these patients had received no chemotherapy or radiation, permitting assessment of the natural history of the tumor karyotype in situ. Defects present throughout a tumor at first resection remained so, whereas among subpopulations, some expanded, some remained constant, and some disappeared. The rate of expansion among subpopulations that did so was not uniform, and estimates of fitness predicted subpopulation composition at recurrence. These results extend prior studies of increased karyotypic abnormality in progression of oligodendroglioma and reveal the complex dynamics of subpopulations in the tumor over time.
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Affiliation(s)
- David W Nauen
- Department of Pathology, Johns Hopkins Hospital, Ross 558, 720 Rutland Avenue, Baltimore MD 21205, USA
| | - Andrew Guajardo
- Department of Pathology, Johns Hopkins Hospital, Ross 558, 720 Rutland Avenue, Baltimore MD 21205, USA
| | - Lisa Haley
- Department of Pathology, Johns Hopkins Hospital, Ross 558, 720 Rutland Avenue, Baltimore MD 21205, USA
| | - Kerry Powell
- Department of Pathology, Johns Hopkins Hospital, Ross 558, 720 Rutland Avenue, Baltimore MD 21205, USA
| | - Peter C Burger
- Department of Pathology, Johns Hopkins Hospital, Ross 558, 720 Rutland Avenue, Baltimore MD 21205, USA
| | - Christopher D Gocke
- Department of Pathology, Johns Hopkins Hospital, Ross 558, 720 Rutland Avenue, Baltimore MD 21205, USA
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12
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1p/19q-driven prognostic molecular classification for high-grade oligodendroglial tumors. J Neurooncol 2014; 120:607-14. [DOI: 10.1007/s11060-014-1593-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 08/17/2014] [Indexed: 10/24/2022]
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13
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Sonabend AM, Lesniak MS. Oligodendrogliomas: clinical significance of 1p and 19q chromosomal deletions. Expert Rev Neurother 2014; 5:S25-32. [PMID: 16274268 DOI: 10.1586/14737175.5.6.s25] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Oligodendrogliomas are a distinct subgroup of brain tumors with a fairly favorable clinical prognosis. However, these tumor exhibit varying degrees of heterogeneity and their clinical behavior is therefore not always the same. For this reason, genetic markers have been developed to further guide the clinical treatment. One such marker, the 1p and 19q chromosomal deletions, has been well documented in a subset of patients with oligodendrogliomas. Most importantly, patients who exhibit these chromosomal deletions respond favorably to chemotherapy. This article reviews the evidence describing the association of such deletions with a favorable response to chemotherapy and improved prognosis of patients with oligodendrogliomas. In addition, attempts to elucidate the molecular mechanisms behind the biologic behavior of these tumors are further explored.
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Affiliation(s)
- Adam M Sonabend
- Division of Neurosurgery, The University of Chicago, 5841 S. Maryland Ave., MC 3026, Chicago, IL 60637, USA.
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14
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The importance of 10q status in an outcomes-based comparison between 1p/19q fluorescence in situ hybridization and polymerase chain reaction-based microsatellite loss of heterozygosity analysis of oligodendrogliomas. J Neuropathol Exp Neurol 2012; 71:73-82. [PMID: 22157622 DOI: 10.1097/nen.0b013e318240fa65] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
1p/19q codeletion is a favorable prognostic marker of oligodendrogliomas. Although fluorescence in situ hybridization (FISH) and microsatellite-based polymerase chain reaction (PCR) for loss of heterozygosity (LOH) are common methods to test for 1p/19q codeletion, it is unclear which test is better at prognostic stratification. This study analyzed outcomes of 111 oligodendrogliomas with both 1p/19q FISH and LOH done at the time of diagnosis. Overall concordance between the 2 assays was 81.1%. In grade III oligodendrogliomas, LOH was better than FISH at survival stratification (p < 0.0001 for LOH vs p = 0.02 for FISH), although increasing the stringency of FISH interpretation criteria improved concordance and prognostic power. Oligodendrogliomas that were 1p/19q-codeleted by FISH but also had 10q LOH were negative for 1p/19q codeletion by PCR analysis in more than 70% of cases, with very poor survival in the grade III subset. Thus, although PCR-based LOH is a better stratifier of 1p/19q status, FISH still has clinical and prognostic utility, especially if 10q data can be incorporated.
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15
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Abstract
In recent years, advances in the understanding of low-grade glioma (LGG) biology have driven new paradigms in molecular markers, diagnostic imaging, operative techniques and technologies, and adjuvant therapies. Taken together, these developments are collectively pushing the envelope toward improved quality of life and survival. In this article, the authors evaluate the recent literature to synthesize a comprehensive review of LGGs in the modern neurosurgical era.
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Affiliation(s)
- Nader Sanai
- Barrow Brain Tumor Research Center, Department of Neurological Surgery, Barrow Neurological Institute, Phoenix, Arizona, USA
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16
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Abstract
In recent years, advances in the understanding of low-grade glioma (LGG) biology have driven new paradigms in molecular markers, diagnostic imaging, operative techniques and technologies, and adjuvant therapies. Taken together, these developments are collectively pushing the envelope toward improved quality of life and survival. In this article, the authors evaluate the recent literature to synthesize a comprehensive review of LGGs in the modern neurosurgical era.
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Affiliation(s)
- Nader Sanai
- 1Barrow Brain Tumor Research Center, Department of Neurological Surgery, Barrow Neurological Institute, Phoenix, Arizona; and
| | - Susan Chang
- 2Brain Tumor Research Center, Department of Neurological Surgery, University of California at San Francisco, California
| | - Mitchel S. Berger
- 2Brain Tumor Research Center, Department of Neurological Surgery, University of California at San Francisco, California
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17
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Genomic aberrations associated with outcome in anaplastic oligodendroglial tumors treated within the EORTC phase III trial 26951. J Neurooncol 2010; 103:221-30. [PMID: 20820870 PMCID: PMC3097344 DOI: 10.1007/s11060-010-0380-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Accepted: 08/20/2010] [Indexed: 11/19/2022]
Abstract
Despite similar morphological aspects, anaplastic oligodendroglial tumors (AOTs) form a heterogeneous clinical subgroup of gliomas. The chromosome arms 1p/19q codeletion has been shown to be a relevant biomarker in AOTs and to be perfectly exclusive from EGFR amplification in gliomas. To identify new genomic regions associated with prognosis, 60 AOTs from the EORTC trial 26951 were analyzed retrospectively using BAC-array-based comparative genomic hybridization. The data were processed using a binary tree method. Thirty-three BACs with prognostic value were identified distinguishing four genomic subgroups of AOTs with different prognosis (p < 0.0001). Type I tumors (25%) were characterized by: (1) an EGFR amplification, (2) a poor prognosis, (3) a higher rate of necrosis, and (4) an older age of patients. Type II tumors (21.7%) had: (1) loss of prognostic BACs located on 1p tightly associated with 19q deletion, (2) a longer survival, (3) an oligodendroglioma phenotype, and (4) a frontal location in brain. Type III AOTs (11.7%) exhibited: (1) a deletion of prognostic BACs located on 21q, and (2) a short survival. Finally, type IV tumors (41.7%) had different genomic patterns and prognosis than type I, II and III AOTs. Multivariate analysis showed that genomic type provides additional prognostic data to clinical, imaging and pathological features. Similar results were obtained in the cohort of 45 centrally reviewed–validated cases of AOTs. Whole genome analysis appears useful to screen the numerous genomic abnormalities observed in AOTs and to propose new biomarkers particularly in the non-1p/19q codeleted AOTs.
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Drucker KL, Kitange GJ, Kollmeyer TM, Law ME, Passe S, Rynearson AL, Blair H, Soderberg CL, Morlan BW, Ballman KV, Giannini C, Jenkins RB. Characterization and gene expression profiling in glioma cell lines with deletion of chromosome 19 before and after microcell-mediated restoration of normal human chromosome 19. Genes Chromosomes Cancer 2009; 48:854-64. [PMID: 19544381 DOI: 10.1002/gcc.20688] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Nearly 10% of human gliomas are oligodendrogliomas. Deletion of chromosome arm 19q, often in conjunction with deletion of 1p, has been observed in 65-80% of these tumors. This has suggested the presence of a tumor suppressor gene located on the 19q arm. Chromosome 19 deletion is also of interest due to the better prognosis of patients with deletion, including longer survival and better response to chemotherapy, compared with patients without deletion. Two glioma cell lines with deletion of 19q were used for chromosome 19 microcell-mediated transfer, to assess the effect of replacing the deleted segment. Complementation with chromosome 19 significantly reduced the growth rate of the hybrid cells compared with the parental cell lines. Affymetrix U133 Plus 2.0 Gene Chip analysis was performed to measure and compare the expression of the chromosome 19 genes in the chromosome 19 hybrid cell lines to the parental cell line. Probes were considered significantly different when a P value <0.01 was seen in all of the cell line comparisons. Of 345 probes within the commonly deleted 19q region, seven genes (APOE, RCN3, FLJ10781, SAE1, STRN4, CCDC8, and BCL2L12) were identified as potential candidate genes. RT-PCR analysis of primary tumor specimens showed that several genes had significant differences when stratified by tumor morphology or deletion status. This suggests that one or more of these candidates may play a role in glioma formation or progression.
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Affiliation(s)
- Kristen L Drucker
- Department of Laboratory Medicine and Pathology, Mayo Clinic and Foundation, Rochester, MN 55905, USA
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19
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Gadji M, Fortin D, Tsanaclis AM, Drouin R. Is the 1p/19q deletion a diagnostic marker of oligodendrogliomas? ACTA ACUST UNITED AC 2009; 194:12-22. [PMID: 19737649 DOI: 10.1016/j.cancergencyto.2009.05.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Revised: 04/22/2009] [Accepted: 05/04/2009] [Indexed: 02/06/2023]
Abstract
The diagnosis and classification of diffusely infiltrative gliomas are based on their histopathological appearance; however, histopathological delineation of diffuse gliomas can be difficult because of vague and subjective histopathological criteria. Combined loss of chromosome arms 1p and 19q (denoted as 1p-/19q-) has proven to be a powerful predictor of chemotherapeutic response and survival in oligodendrogliomas. We undertook retrospective and prospective studies of brain tumor patients originally diagnosed as oligodendrogliomas or oligoastrocytomas patients followed at our institution using molecular genetic techniques. Fluorescence in situ hybridization using probes specific for chromosomes 1 and 19 was performed on 22 paraffin-embedded tissues retrospectively; 15 touch-preparation smear samples were studied prospectively; and loss of heterozygosity (LOH) screening was performed on 11 samples with microsatellite markers specific to chromosome 1 and chromosome 19. Of the 37 cases, 24 had 1p-/19q-, 1 case had 1p- only, 2 cases had 19q- only, and 10 cases had no deletion. The length of the largest deletion was mapped between markers D1S2795 (1p36.31 locus) and D1S2722 (1p34.2 locus) and between markers D19S416 (19q13.11 locus) and D19S397 (19q13.14 locus), using LOH. All of the pure oligodendrogliomas (n=7) harbored 1p-/19q-. In light of previous findings, the 1p-/19q- combination appears to be an objective diagnosis marker of classic oligodendrogliomas, one that can be used, in combination with histological examination, to improve the diagnosis of oligodendroglioma. Fluorescence in situ hybridization on touch preparations is a simple way to obtain information on 1p-/19q- in 24 hours.
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Affiliation(s)
- Macoura Gadji
- Division of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, University of Sherbrooke, 3001 12th Avenue North, Quebec, Canada
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20
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Idbaih A, Crinière E, Ligon KL, Delattre O, Delattre JY. Array-based genomics in glioma research. Brain Pathol 2009; 20:28-38. [PMID: 19298630 DOI: 10.1111/j.1750-3639.2009.00274.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Over the years, several relevant biomarkers with a potential clinical interest have been identified in gliomas using various techniques, such as karyotype, microsatellite analysis, fluorescent in situ hybridization and chromosome comparative genomic hybridization. Despite their pivotal contribution to our understanding of gliomas biology, clinical application of these approaches has been limited by technological and clinical complexities. In contrast, genomic arrays (array-based comparative genomic hybridization and single nucleotide polymorphisms array) have emerged as promising technologies for clinical use in the setting of gliomas. Indeed, their feasibility and reliability have been rigorously assessed in gliomas and are discussed in this review. The well-known genomic biomarkers in gliomas are in fact readily and reliably identified using genomic arrays. Moreover, it detects a multitude of new cryptic genomic markers, with potential biological and/or clinical significances. The main studies dedicated to genomic characterization of gliomas using genomic arrays are reviewed here. Interestingly, several recurrent genomic signatures have been reported by different teams, suggesting the validity of these genomic patterns. In light of this, genomic arrays are relatively simple and cost-effective techniques whose implementation in molecular diagnostic laboratories should be encouraged as a valuable clinical tool for management of glioma patients.
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21
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Novel Genomic Alterations and Mechanisms Associated With Tumor Progression in Oligodendroglioma and Mixed Oligoastrocytoma. J Neuropathol Exp Neurol 2009; 68:274-85. [DOI: 10.1097/nen.0b013e31819a3e8c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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22
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Cowell JK, Lo KC. Application of oligonucleotides arrays for coincident comparative genomic hybridization, ploidy status and loss of heterozygosity studies in human cancers. Methods Mol Biol 2009; 556:47-65. [PMID: 19488871 DOI: 10.1007/978-1-60327-192-9_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Many oligonucleotide arrays comprise of spotted short oligonucleotides from throughout the genome under study. Hybridization of tumor DNA samples to these arrays will provide copy number estimates at each reference point with varying degrees of accuracy. In addition to copy number changes, however, tumors often undergo loss of heterozygosity for specific regions of the genome without copy number changes and these genetic changes can only be identified using arrays that identify polymorphic alleles at each reference point. In addition, because the hybridization intensity can be measured at each of the allelic variants, allelic ratios can be established which give indications of ploidy status in the tumor which is not generally possible using most other oligonucleotide array designs. The only arrays currently available that simultaneously report copy number, ploidy, and loss of heterozygosity are the Affymetrix SNP mapping arrays. In this review, the features of the SNP mapping arrays are described and computational tools explored which allow the maximum genetic information to be extracted from the experiment. Although the methodologies to generate the SNP data are now well established, approaches to interpret the data are only just being developed. From our experience using these arrays, we provide insights into how to evaluate the SNP data to report copy number changes, loss of heterozygosity, and ploidy in the same tumor samples using a single array.
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Affiliation(s)
- John K Cowell
- School of Medicine, Medical College of Georgia Cancer Center, Augusta, GA, USA
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23
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Idbaih A, Crinière E, Marie Y, Rousseau A, Mokhtari K, Kujas M, El Houfi Y, Carpentier C, Paris S, Boisselier B, Laigle-Donadey F, Thillet J, Sanson M, Hoang-Xuan K, Delattre JY. Gene amplification is a poor prognostic factor in anaplastic oligodendrogliomas. Neuro Oncol 2008; 10:540-7. [PMID: 18544654 DOI: 10.1215/15228517-2008-022] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Various gene amplifications have been observed in gliomas. Prognostic-genomic correlations testing simultaneously all these amplified genes have never been conducted in anaplastic oligodendrogliomas. A set of 38 genes that have been reported to be amplified in gliomas and investigated as the main targets of amplicons were studied in a series of 52 anaplastic oligodendrogliomas using bacterial artificial chromosome-array based comparative genomic hybridization and quantitative polymerase chain reaction. Among the 38 target genes, 15 were found to be amplified in at least one tumor. Overall, 27% of anaplastic oligodendrogliomas exhibited at least one gene amplification. The most frequently amplified genes were epidermal growth factor receptor (EGFR) and cyclin-dependent kinase 4/sarcoma amplified sequence (CDK4/SAS) in 17% and 8% of anaplastic oligodendrogliomas, respectively. Gene amplification and codeletion of chromosome arms 1p/19q were perfectly exclusive (p = 0.005). In uni- and multivariate analyses, gene amplification was a negative prognostic factor for progression-free survival and overall survival in anaplastic oligodendrogliomas, providing complementary information to the classic prognostic factors identified in anaplastic oligodendrogliomas (extent of surgery, KPS, and chromosome arms 1p/19q status).
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Affiliation(s)
- Ahmed Idbaih
- Institut National de la Santé et de la Recherche Médicale, U711, Université Pierre et Marie Curie, Hôpital Pitié-Salpêtrière, Paris, France.
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24
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Idbaih A, Marie Y, Lucchesi C, Pierron G, Manié E, Raynal V, Mosseri V, Hoang-Xuan K, Kujas M, Brito I, Mokhtari K, Sanson M, Barillot E, Aurias A, Delattre JY, Delattre O. BAC array CGH distinguishes mutually exclusive alterations that define clinicogenetic subtypes of gliomas. Int J Cancer 2008; 122:1778-86. [PMID: 18076069 DOI: 10.1002/ijc.23270] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The pathological classification of gliomas constitutes a critical step of the clinical management of patients, yet it is frequently challenging. To assess the relationship between genetic abnormalities and clinicopathological characteristics, we have performed a genetic and clinical analysis of a series of gliomas. A total of 112 gliomas were analyzed by comparative genomic hybridization on a BAC array with a 1 megabase resolution. Altered regions were identified and correlation analysis enabled to retrieve significant associations and exclusions. Whole chromosomes (chrs) 1p and 19q losses with centromeric breakpoints and EGFR high level amplification were found to be mutually exclusive, permitting identification of 3 distinct, nonoverlapping groups of tumors with striking clinicopathological differences. Type A tumors with chrs 1p and 19q co-deletion exhibited an oligodendroglial phenotype and a longer patient survival. Type B tumors were characterized by EGFR amplification. They harbored a WHO high grade of malignancy and a short patient survival. Finally, type C tumors displayed none of the previous patterns but the presence of chr 7 gain, chr 9p deletion and/or chr 10 loss. It included astrocytic tumors in patients younger than in type B and whose prognosis was highly dependent upon the number of alterations. A multivariate analysis based on a Cox model shows that age, WHO grade and genomic type provide complementary prognostic informations. Finally, our results highlight the potential of a whole-genome analysis as an additional diagnostic in cases of unclear conventional genetic findings.
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25
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Nowak NJ, Miecznikowski J, Moore SR, Gaile D, Bobadilla D, Smith DD, Kernstine K, Forman SJ, Mhawech-Fauceglia P, Reid M, Stoler D, Loree T, Rigual N, Sullivan M, Weiss LM, Hicks D, Slovak ML. Challenges in array comparative genomic hybridization for the analysis of cancer samples. Genet Med 2007; 9:585-95. [PMID: 17873646 DOI: 10.1097/gim.0b013e3181461c4a] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
PURPOSE To address some of the challenges facing the incorporation of array comparative genomic hybridization technology as a clinical tool, including archived tumor tissue, tumor heterogeneity, DNA quality and quantity, and array comparative genomic hybridization platform selection and performance. METHODS Experiments were designed to assess the impact of DNA source (e.g., archival material), quantity, and amplification on array comparative genomic hybridization results. Two microdissection methods were used to isolate tumor cells to minimize heterogeneity. These data and other data sets were used in a further performance comparison of two commonly used array comparative genomic hybridization platforms: bacterial artificial chromosome (Roswell Park Cancer Institute) and oligonucleotide (Agilent Technologies, Santa Clara, CA). RESULTS Array comparative genomic hybridization data from as few as 100 formalin-fixed, paraffin-embedded cells isolated by laser capture microdissection and amplified were remarkably similar to array comparative genomic hybridization copy number alterations detected in the bulk (unamplified) population. Manual microdissection from frozen sections provided a rapid and inexpensive means to isolate tumor from adjacent DNA for amplification and array comparative genomic hybridization. Whole genome amplification introduced no appreciable allele bias on array comparative genomic hybridization. The array comparative genomic hybridization results provided by the bacterial artificial chromosome and Agilent platforms were concordant in general, but bacterial artificial chromosome array comparative genomic hybridization showed far fewer outliers and overall less technical noise, which could adversely affect the statistical interpretation of the data. CONCLUSIONS This study demonstrates that copy number alterations can be robustly and reproducibly detected by array comparative genomic hybridization in DNA isolated from challenging tumor types and sources, including archival materials, low DNA yield, and heterogeneous tissues. Furthermore, bacterial artificial chromosome array comparative genomic hybridization offers the advantage over the Agilent oligonucleotide platform of presenting fewer outliers, which could affect data interpretation.
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MESH Headings
- Azure Stains
- Cell Line, Tumor
- Chromosome Banding
- Chromosomes, Artificial, Bacterial
- Chromosomes, Human, Pair 2
- Chromosomes, Human, Pair 7
- Chromosomes, Human, Pair 9
- Cohort Studies
- DNA, Neoplasm/analysis
- DNA, Neoplasm/genetics
- Female
- Fluorescent Antibody Technique, Direct
- Gene Dosage
- Hodgkin Disease/genetics
- Hodgkin Disease/pathology
- Humans
- Lasers
- Microdissection
- Neoplasms/genetics
- Neoplasms/pathology
- Nucleic Acid Amplification Techniques
- Nucleic Acid Hybridization/methods
- Oligonucleotide Array Sequence Analysis/methods
- Reed-Sternberg Cells/pathology
- Reproducibility of Results
- Spectral Karyotyping
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Affiliation(s)
- Norma J Nowak
- New York State Center of Excellence in Bioinformatics and Life Sciences and Department of Biochemistry, University at Buffalo, Buffalo, New York 14203, USA.
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26
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Aldape K, Burger PC, Perry A. Clinicopathologic aspects of 1p/19q loss and the diagnosis of oligodendroglioma. Arch Pathol Lab Med 2007; 131:242-51. [PMID: 17284109 DOI: 10.5858/2007-131-242-caoqla] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2006] [Indexed: 11/06/2022]
Abstract
CONTEXT Significant interobserver variability exists with respect to the diagnosis of oligodendroglial neoplasms, especially their distinction from astrocytoma and mixed oligoastrocytoma. Combined loss of the short arm of chromosome 1 and the long arm of chromosome 19 has been shown to be both relatively specific to oligodendroglioma and, when present, a marker of improved prognosis in patients with these tumors. In addition, 1p/19q loss has been shown to be a marker of "classic" oligodendroglial histology. These findings raise questions as to the role of 1p/19q testing in clinical practice, both as a prognostic marker and as a potential diagnostic marker among infiltrating glial neoplasms. OBJECTIVE This review discusses the issues raised above and tries to clarify the current status of 1p/19q evaluation in the diagnosis of oligodendroglioma. DATA SOURCES Sources for this review include recent literature as well as the experience of 3 practicing neuropathologists. CONCLUSIONS 1p/19q status is an important marker in oligodendroglioma. Loss of 1p/19q is associated with classic oligodendroglioma histology as well as improved prognosis. The combined 1p/19q marker will continue to be a clinically useful marker of prognosis and could potentially be incorporated into diagnostic criteria in the future.
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Affiliation(s)
- Kenneth Aldape
- M. D. Anderson Cancer Center, Department of Pathology and Brain Tumor Center, 1515 Holcombe Blvd, Houston, TX 60153, USA.
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27
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Tubbs RR, Swain E, Pettay JD, Hicks DG. An approach to the validation of novel molecular markers of breast cancer via TMA-based FISH scanning. J Mol Histol 2007; 38:141-50. [PMID: 17211577 DOI: 10.1007/s10735-006-9076-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Accepted: 12/13/2006] [Indexed: 12/12/2022]
Abstract
Tissue microarrays (TMA) are valuable tools for validating results of array-based comparative genomic hybridization (ACGH) and other translational research applications requiring independent verification of genomic gains and losses by fluorescence in situ hybridization (FISH). However, spatial orientation and accurate manual tracking of the TMA cores is challenging and prone to error. Image analysis combined with core tracking software, implemented via an automated FISH scanning workstation, represents a new approach to FISH and TMA-based validation of novel genomic changes discovered by ACGH in breast and other cancers. Automated large-scale tissue microarray validation FISH studies of genomic gains and losses identified by ACGH for breast cancer are feasible using an automated imaging scanner and tracking/classifying software. Furthermore, by leveraging the bifunctional fluorescent and chromogenic properties of the alkaline phosphatase chromogen fast red K and combining the technology with FISH, correlative and simultaneous phenotype/genotype studies may be enabled.
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Affiliation(s)
- Raymond R Tubbs
- Departments of Anatomical and Clinical Pathology, The Cleveland Clinic Foundation, The Lerner College of Medicine, Cleveland, OH 44195, USA.
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28
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Miliaras D, Conroy J, Pervana S, Meditskou S, McQuaid D, Nowak N. Karyotypic changes detected by comparative genomic hybridization in a stillborn infant with chorioangioma and liver hemangioma. ACTA ACUST UNITED AC 2007; 79:236-41. [PMID: 17203486 DOI: 10.1002/bdra.20332] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND Placental hemangioma (chorioangioma) and congenital hemangioma are relatively common tumors, which on rare occasions may occur together. Very little is known about the pathogenetic mechanisms underlying these lesions. CASE Herein we describe a rare case of a stillborn infant with chorioangioma, placental mesenchymal dysplasia, and liver cavernous hemangioma. In addition, we present the findings of the karyotype analysis of these lesions, which was done with the bacterial artificial chromosome arrays using the comparative genomic hybridization method. The chromosomal abnormalities that we found were deletions at 2q13 and 7p21.1 and were common to both placental and liver lesions. CONCLUSIONS None of the identified chromosomal aberrations have been previously associated with chorioangiomas or hemangiomas. Important genes that lie in these DNA regions may be implicated in the pathogenesis of congenital hemangiomas and mesenchymal dysplasia.
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MESH Headings
- Chromosome Aberrations
- Chromosomes, Artificial, Bacterial
- Chromosomes, Human, Pair 2
- Chromosomes, Human, Pair 7
- Female
- Hemangioma/complications
- Hemangioma/genetics
- Hemangioma/pathology
- Hemangioma, Cavernous/complications
- Hemangioma, Cavernous/genetics
- Hemangioma, Cavernous/pathology
- Humans
- Infant, Newborn
- Karyotyping
- Liver Neoplasms/complications
- Liver Neoplasms/genetics
- Liver Neoplasms/pathology
- Nucleic Acid Hybridization
- Placenta Diseases/genetics
- Placenta Diseases/pathology
- Pregnancy
- Stillbirth/genetics
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Affiliation(s)
- Dimosthenis Miliaras
- Laboratory of Histology, Embryology & Anthropology, Medical School, Aristotle University of Thessaloniki, Greece.
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Griffin CA, Burger P, Morsberger L, Yonescu R, Swierczynski S, Weingart JD, Murphy KM. Identification of der(1;19)(q10;p10) in five oligodendrogliomas suggests mechanism of concurrent 1p and 19q loss. J Neuropathol Exp Neurol 2006; 65:988-94. [PMID: 17021403 DOI: 10.1097/01.jnen.0000235122.98052.8f] [Citation(s) in RCA: 197] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Deletions of portions of chromosomes 1p and 19q are closely associated with the oligodendroglioma histologic phenotype. In most cases, 1p and 19q are codeleted, yet the mechanism of dual loss is unexplained. We report 5 cases (World Health Organization grade III) in which metaphase cytogenetics identified a derivative chromosome consisting of what appears to be the whole arms of 1q and 19p forming a der(1;19)(q10;p10). Metaphase fluorescent in situ hybridization (FISH) confirmed the derivative chromosome was composed of 1q and 19p material in 3 cases; in 2 cases with few metaphases, FISH confirmed 19p material on the derivative chromosome. In all cases, interphase FISH showed net loss of 1p and 19q in 77% to 92% of cells, and microsatellite studies were consistent with 1p and 19q loss. We hypothesize the following: occurrence of a balanced whole-arm translocation between chromosomes 1 and 19 forming 2 derivative chromosomes, one composed of 1q and 19p, the other of 1p and 19q. Subsequent loss of the der(1;19)(p10;q10) then results in the simultaneous 1p and 19q loss observed in oligodendroglioma with retention of the der(1;19)(q10;p10) seen in these cases.
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Affiliation(s)
- Constance A Griffin
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21287, USA.
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30
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Jeuken J, Cornelissen S, Boots-Sprenger S, Gijsen S, Wesseling P. Multiplex ligation-dependent probe amplification: a diagnostic tool for simultaneous identification of different genetic markers in glial tumors. J Mol Diagn 2006; 8:433-43. [PMID: 16931583 PMCID: PMC1867615 DOI: 10.2353/jmoldx.2006.060012] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genetic aberrations in tumors are predictive for chemosensitivity and survival. A test is needed that allows simultaneous detection of multiple changes and that is widely applicable in a routine diagnostic setting. Multiplex ligation-dependent probe amplification (MLPA) allows detection of DNA copy number changes of up to 45 loci in one relatively simple, semiquantitative polymerase chain reaction-based assay. To assess the applicability of MLPA, we performed MLPA analysis to detect relevant genetic markers in a spectrum of 88 gliomas. The vast majority of these tumors (n = 79) were previously characterized by comparative genomic hybridization. With MLPA kit P088 (78 cases), complete and partial loss of 1p and 19q were reliably identified, even in samples containing only 50% tumor DNA. Distinct 1p deletions exist with different clinically prognostic consequences, and in contrast to the commonly used diagnostic strategies (loss of heterozygosity or fluorescent in situ hybridization 1p36), P088 allows detection of such distinct 1p losses. Combining P088 with P105 will further increase the accurate prediction of clinical behavior because this kit identified markers (EGFR, PTEN, and CDKN2A) of high-grade malignancy in 41 cases analyzed. We conclude that MLPA is a reliable diagnostic tool for simultaneous identification of different region-specific genetic aberrations of tumors.
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Affiliation(s)
- Judith Jeuken
- Department of Pathology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands.
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31
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Skacel M, Siva A, Xu B, Tubbs RR. From array to array: Confirmation of genomic gains and losses discovered by array-based comparative genomic hybridization utilizing fluorescence in situ hybridization on tissue microarrays. J Mol Histol 2006; 38:135-40. [PMID: 17043918 DOI: 10.1007/s10735-006-9051-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2005] [Accepted: 07/28/2006] [Indexed: 01/08/2023]
Abstract
The combination of array-based comparative genomic hybridization (CGH) with fluorescence in situ hybridization utilizing custom-designed bacterial artificial chromosome (BAC) probes applied to tissue microarrays represents a powerful compendium of techniques-greatly enhancing the throughput of genomic analysis and subsequent target validation. Such approach can be automated at various levels and allows managing large volume of targets and samples in a few experiments. As such, this approach facilitates discovery, validation and implementation of findings in the process of identification of new diagnostic, prognostic and potentially therapeutic molecular markers.
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Affiliation(s)
- Marek Skacel
- Department of Anatomic Pathology, The Cleveland Clinic Foundation, L-25, Cleveland, OH 44191, USA.
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32
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Pan CC, Jong YJ, Chai CY, Huang SH, Chen YJ. Comparative genomic hybridization study of perivascular epithelioid cell tumor: molecular genetic evidence of perivascular epithelioid cell tumor as a distinctive neoplasm. Hum Pathol 2006; 37:606-12. [PMID: 16647959 DOI: 10.1016/j.humpath.2006.01.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2005] [Revised: 01/02/2006] [Accepted: 01/10/2006] [Indexed: 12/31/2022]
Abstract
Perivascular epithelioid cell tumor (PEComa) is a neoplasm composed chiefly of HMB-45-positive epithelioid cells with clear to granular cytoplasm and a perivascular distribution. Such tumors have been reported in different organs under a variety of designations. The cytogenetic features of these neoplasms have not been well studied. We collected 9 tumors (5 of kidney, 1 of prostate, 1 of urinary bladder, 1 of the pelvic cavity soft tissue, and 1 of uterus) from 8 patients, including one patient with tuberous sclerosis complex. The paraffin blocks of tumor tissue were submitted for comparative genomic hybridization analyses. Gross chromosomal aberrances were observed in all cases. The frequent imbalances were losses on chromosome 19 (8 cases), 16p (6 cases), 17p (6 cases), 1p (5 cases), and 18p (4 cases) and gains on chromosome X (6 cases), 12q (6 cases), 3q (5 cases), 5 (4 cases), and 2q (4 cases). The frequent deletion of 16p in which TSC2 gene is located indicates the oncogenetic relationship of PEComas with angiomyolipoma as a TSC2-linked neoplasm. From a molecular genetic perspective, the recurrent chromosomal alterations in both renal and extrarenal tumors further support the concept of PEComa as a distinctive tumor entity regardless of anatomic location.
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Affiliation(s)
- Chin-Chen Pan
- Department of Pathology, National Yang-Ming University, Taipei, Taiwan; Department of Pathology, Taipei Veterans General Hospital, Taipei, Taiwan.
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33
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Roversi G, Pfundt R, Moroni RF, Magnani I, van Reijmersdal S, Pollo B, Straatman H, Larizza L, Schoenmakers EFPM. Identification of novel genomic markers related to progression to glioblastoma through genomic profiling of 25 primary glioma cell lines. Oncogene 2006; 25:1571-83. [PMID: 16247447 DOI: 10.1038/sj.onc.1209177] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Identification of genetic copy number changes in glial tumors is of importance in the context of improved/refined diagnostic, prognostic procedures and therapeutic decision-making. In order to detect recurrent genomic copy number changes that might play a role in glioma pathogenesis and/or progression, we characterized 25 primary glioma cell lines including 15 non glioblastoma (non GBM) (I-III WHO grade) and 10 GBM (IV WHO grade), by array comparative genomic hybridization, using a DNA microarray comprising approx. 3500 BACs covering the entire genome with a 1 Mb resolution and additional 800 BACs covering chromosome 19 at tiling path resolution. Combined evaluation by single clone and whole chromosome analysis plus 'moving average (MA) approach' enabled us to confirm most of the genetic abnormalities previously identified to be associated with glioma progression, including +1q32, +7, -10, -22q, PTEN and p16 loss, and to disclose new small genomic regions, some correlating with grade malignancy. Grade I-III gliomas exclusively showed losses at 3p26 (53%), 4q13-21 (33%) and 7p15-p21 (26%), whereas only GBMs exhibited 4p16.1 losses (40%). Other recurrent imbalances, such as losses at 4p15, 5q22-q23, 6p23-25, 12p13 and gains at 11p11-q13, were shared by different glioma grades. Three intervals with peak of loss could be further refined for chromosome 10 by our MA approach. Data analysis of full-coverage chromosome 19 highlighted two main regions of copy number gain, never described before in gliomas, at 19p13.11 and 19q13.13-13.2. The well-known 19q13.3 loss of heterozygosity area in gliomas was not frequently affected in our cell lines. Genomic hotspot detection facilitated the identification of small intervals resulting in positional candidate genes such as PRDM2 (1p36.21), LRP1B (2q22.3), ADARB2 (10p15.3), BCCIP (10q26.2) and ING1 (13q34) for losses and ECT2 (3q26.3), MDK, DDB2, IG20 (11p11.2) for gains. These data increase our current knowledge about cryptic genetic changes in gliomas and may facilitate the further identification of novel genetic elements, which may provide us with molecular tools for the improved diagnostics and therapeutic decision-making in these tumors.
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Affiliation(s)
- G Roversi
- Department of Biology and Genetics, University of Milan, Milan, Italy
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34
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French PJ, Swagemakers SMA, Nagel JHA, Kouwenhoven MCM, Brouwer E, van der Spek P, Luider TM, Kros JM, van den Bent MJ, Sillevis Smitt PA. Gene expression profiles associated with treatment response in oligodendrogliomas. Cancer Res 2006; 65:11335-44. [PMID: 16357140 DOI: 10.1158/0008-5472.can-05-1886] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Oligodendrogliomas are a specific subtype of brain tumor of which the majority responds favorably to chemotherapy. In this study, we made use of expression profiling to identify chemosensitive oligodendroglial tumors. Correlation of expression profiles to loss of heterozygosity on 1p and 19q, common chromosomal aberrations associated with response to treatment, identified 376, 64, and 60 differentially expressed probe sets associated with loss of 1p, 19q or 1p, and 19q, respectively. Correlation of expression profiles to the tumors' response to treatment identified 16 differentially expressed probe sets. Because transcripts associated with chemotherapeutic response were identified independent of common chromosomal aberrations, expression profiling may be used as an alternative approach to the tumors' 1p status to identify chemosensitive oligodendroglial tumors. Finally, we correlated expression profiles to survival of the patient after diagnosis and identified 103 differentially expressed probe sets. The observation that many genes are differentially expressed between long and short survivors indicates that the genetic background of the tumor is an important factor in determining the prognosis of the patient. Furthermore, these transcripts can help identify patient subgroups that are associated with favorable prognosis. Our study is the first to correlate gene expression with chromosomal aberrations and clinical performance (response to treatment and survival) in oligodendrogliomas. The differentially expressed transcripts can help identify patient subgroups with good prognosis and those that will benefit from chemotherapeutic treatments.
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Affiliation(s)
- Pim J French
- Department of Neurology, Cancer Genomics Center, Erasmus Medical Center, Rotterdam, the Netherlands.
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35
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Jeuken JWM, Boots-Sprenger SHE, Wesseling P. Re: multiplex ligation dependent probe amplification for the detection of 1p and 19q loss in oligodendroglial tumors. Brain Pathol 2006; 15:364; author reply 365. [PMID: 16389947 PMCID: PMC8095997 DOI: 10.1111/j.1750-3639.2005.tb00120.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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36
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Larralde M, Happle R. Cutis tricolor parvimaculata: a distinct neurocutaneous syndrome? Dermatology 2005; 211:149-51. [PMID: 16088163 DOI: 10.1159/000086446] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2004] [Accepted: 11/05/2004] [Indexed: 11/19/2022] Open
Abstract
An 11-year-old girl had multiple, disseminated, rather small café-au-lait macules and hypochromic spots involving the neck, the trunk and the legs. In part, the two types of macules showed a spatial proximity, suggesting didymosis (twin spotting). The term cutis tricolor has been proposed to describe congenital paired hyperchromic and hypochromic macules on a background of intermediate skin. Because the spots present in this case were much smaller than those described in previous cases of cutis tricolor, we here propose the distinguishing term 'cutis tricolor parvimaculata'. The underlying gene locus may be a hot spot for postzygotic recombinations, giving rise to multiple twin spots. Moreover, the girl had developed seizures from the age of 10 years, and a large oligodendroglioma involving the left frontal lobe was found. A causal relationship between the cutaneous phenotype and the cerebral tumor is unproven but likely. The skin lesions were reminiscent of a disorder described by Westerhof et al. in 1978 under the term 'hereditary congenital hypopigmented and hyperpigmented macules'. So far, however, it is not clear whether cutis tricolor parvimaculata is identical with or different from this disorder.
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Affiliation(s)
- Margarita Larralde
- Pediatric Dermatology Division, Ramos Mejía Hospital, Buenos Aires, Argentina
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37
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Rossi MR, La Duca J, Matsui SI, Nowak NJ, Hawthorn L, Cowell JK. Novel amplicons on the short arm of chromosome 7 identified using high resolution array CGH contain over expressed genes in addition to EGFR in glioblastoma multiforme. Genes Chromosomes Cancer 2005; 44:392-404. [PMID: 16110500 DOI: 10.1002/gcc.20256] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Amplification of a defined chromosome segment on the short arm of chromosome 7 has frequently been reported in glioblastoma multiforme (GBM), where it is generally assumed that it is the result of over expression of the epidermal growth factor receptor (EGFR) gene that provides the selective pressure to maintain the amplification event. We have used high resolution array comparative genomic hybridization (aCGH) to analyze amplification events on chromosome 7p in GBM, which demonstrates that, in fact, several other regions distinct from EGFR can be amplified. To determine the changes in gene expression levels associated with these amplification events, we used oligonucleotide expression arrays to investigate which of the genes in the amplified regions were also over expressed. These analyses demonstrated that not all genes in the amplicons showed increased expression, and we have defined a series of over expressed genes on 7p that could potentially contribute to the development of the malignant phenotype in these tumors. The global analysis of amplification afforded by aCGH analysis has improved our ability to define numerical chromosome abnormalities in cancer cells and has raised the possibility that genes other than EGFR may be important.
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Affiliation(s)
- Michael R Rossi
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
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38
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Mason DX, Keppler D, Zhang J, Jackson TJ, Seger YR, Matsui S, Abreo F, Cowell JK, Hannon GJ, Lowe SW, Lin AW. Defined genetic events associated with the spontaneous in vitro transformation of ElA/Ras-expressing human IMR90 fibroblasts. Carcinogenesis 2005; 27:350-9. [PMID: 16280331 PMCID: PMC4590994 DOI: 10.1093/carcin/bgi264] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In contrast to rodent cells, normal human fibroblasts are generally resistant to neoplastic transformation in vitro. Here, we report the derivation and characterization of a spontaneously transformed cell line from normal human IMR90 fibroblasts transduced with E1A and Ras oncogenes. Unlike the parental, non-tumorigenic E1A/Ras-expressing IMR90 cells, these spontaneously transformed cells displayed aberrant growth potential in vitro and were capable of tumorigenesis in vivo. In contrast to the parental E1A/Ras-expressing cells, both the spontaneously transformed cells and cells derived from resultant tumors displayed specific t(7q;8q) and t(5q;17) structural chromosomal changes. Chromosome 8q contains c-Myc, which is capable of activating the telomerase catalytic subunit hTERT. Notably, upregulation of c-Myc, hTERT and telomerase activity were detected only in the tumorigenic cells. Transduction of Myc siRNA into the tumorigenic cells led to a concomitant downregulation of hTERT. Furthermore, transduction of Myc or hTERT into the non-tumorigenic E1A/Ras-expressing IMR90 cells was able to confer tumorigenesis on these cells. These studies suggest that the t(7;8) translocation may result in Myc overexpression and its subsequent activation of hTERT, which may contribute to the tumorigenicity of the IMR90 cells. Furthermore, this report describes additional successful neoplastic transformation of human IMR90 fibroblasts by defined genetic elements. The spontaneously transformed cells we have derived provide a valuable model system for the study of neoplastic transformation.
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Affiliation(s)
- Douglas X. Mason
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Daniel Keppler
- Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
- Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
| | - Jun Zhang
- Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
| | - Tonya J. Jackson
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Yvette R. Seger
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Seiichi Matsui
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Fleurette Abreo
- Department of Pathology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
| | - John K. Cowell
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | | | - Scott W. Lowe
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Athena W. Lin
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
- To whom correspondence should be addressed. Tel: +1 716 845 1548; Fax: +1 716 845 8857;
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Nutt CL. Molecular genetics of oligodendrogliomas: a model for improved clinical management in the field of neurooncology. Neurosurg Focus 2005; 19:E2. [PMID: 16398466 DOI: 10.3171/foc.2005.19.5.3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Over the last several years, oligodendroglial tumors have become a model for the positive role of molecular genetics in improved treatment of patients with brain tumors. Oligodendrogliomas, in contrast to astrocytic gliomas, frequently respond to chemotherapy and have a better overall prognosis. Combined loss of chromosomes 1p and 19q has proven to be a powerful predictor of chemotherapeutic response and survival in oligodendrogliomas. In contrast, other genetic alterations, such as TP53 and PTEN mutations, EGFR amplification, and homozygous deletion of CDKN2A have been correlated with worse outcome in these tumors. Furthermore, 1p/19q loss has been shown to correlate with unequivocal oligodendroglial tumor histology, location and growth pattern of tumors within the brain, and magnetic resonance imaging characteristics. Although much is also known about the molecular pathological characteristics of astrocytic gliomas, the significance of this information to clinical management in patients with these tumors has not been as striking as has been the case for oligodendrogliomas; possible reasons for this are discussed. In this paper the author will summarize these advances, thus attempting to highlight the molecular genetic study of oligodendrogliomas as a model for improved clinical management in the field of neurooncology.
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Affiliation(s)
- Catherine L Nutt
- Department of Pathology, Neurosurgical Service and Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.
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40
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Cowell JK, LaDuca J, Rossi MR, Burkhardt T, Nowak NJ, Matsui SI. Molecular characterization of the t(3;9) associated with immortalization in the MCF10A cell line. ACTA ACUST UNITED AC 2005; 163:23-9. [PMID: 16271952 DOI: 10.1016/j.cancergencyto.2005.04.019] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2005] [Revised: 04/27/2005] [Accepted: 04/28/2005] [Indexed: 11/24/2022]
Abstract
The t(3;9)(p14;p21) in the MCF10A human mammary gland epithelial cell line was the single cytogenetic event that accompanied the transition from primary culture to immortalized cell line, suggesting that it is related to the development of the immortalization phenotype. To study the molecular consequences of the breakpoints in this rearrangement, we used a combination of fluorescence in situ hybridization (FISH) and array comparative genomic hybridization (CGH). The 3p14 translocation breakpoint occurs within BAC RP11-795e22, which accommodates only the TAFA1 gene, a novel cysteine-rich secreted protein thought to be involved in cytokine signaling. TAFA1 is expressed in normal breast tissue, not in MCF10A, and shows differential expression in a range of breast cancer cell lines. The 9p translocation breakpoint results in a deletion of approximately 4 megabases on the derivative chromosome 9, which includes the CDKN2A (p16) gene. Array CGH and FISH analysis demonstrated that BAC 149i22, which contains the CDKN2A/B genes, is also deleted specifically on the apparently normal copy of chromosome 9, making MCF10A null for the p16/p15 genes. The exact extent of gains and losses of chromosome regions resulting from rearrangements involving chromosomes 1q, 5q, and 8q have also been characterized using the BAC arrays.
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Affiliation(s)
- John K Cowell
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA.
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41
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Laigle-Donadey F, Benouaich-Amiel A, Hoang-Xuan K, Sanson M. Biologie moléculaire des tumeurs oligodendrogliales. Neurochirurgie 2005; 51:260-8. [PMID: 16292170 DOI: 10.1016/s0028-3770(05)83487-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Oligodendrogliomas have been the focus of considerable interest over the last decade, ever since they were recognized as chemosensitive tumors. However, the histological diagnosis remains highly controversial and unsatisfactory. Meanwhile, our understanding of glioma oncogenesis improved greatly. Gliomas are the consequence of specific genetic or epigenetic alterations - activations of oncogenes and inactivation of tumor suppressor genes - resulting in the disruption of critical cellular pathways and leading to phenotypic changes. Such genetic information complements the existing WHO morphological classification and, more importantly, provides additional prognostic markers. Indeed, 1p/19q deletion has been correlated with chemosensitivity in oligodendrogliomas, and is becoming more and more widely used in clinical practice. There is little doubt that emerging techniques, such as CGH-array and gene profiling will be very helpful in clinical practice for refining both classification and therapeutic indications of oligodendroglial tumors.
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Affiliation(s)
- F Laigle-Donadey
- Service de Neurologie Mazarin, Université P.-et M.-Curie, Groupe Hospitalier Pitié-Salpêtrière, Paris
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42
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Magnani I, Moroni RF, Ramona RF, Roversi G, Beghini A, Pfundt R, Schoenmakers EF, Larizza L. Identification of oligodendroglioma specific chromosomal copy number changes in the glioblastoma MI-4 cell line by array-CGH and FISH analyses. ACTA ACUST UNITED AC 2005; 161:140-5. [PMID: 16102584 DOI: 10.1016/j.cancergencyto.2005.02.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2004] [Revised: 02/02/2005] [Accepted: 02/08/2005] [Indexed: 01/03/2023]
Abstract
Glioblastomas, the most frequent and malignant glial tumors, are known to be phenotypically heterogeneous. A low fraction of glioblastomas is associated with specific chromosomal losses at 1p and 19q, which are commonly found in oligodendrogliomas and are generally considered to be a primary event in the development of these tumors. Subsequent progression of oligodendroglial tumors appears to be triggered by additional molecular features underlying the transition to anaplastic oligodendroglioma and glioblastoma multiforme (GBM) such as deletions of 9p and 10q, and alterations of CDKN2A (p16), which is located at 9p21. These findings strengthen the view that GBM on rare occasions may develop from oligodendroglial differentiated cells. In the present study, we evaluated the newly established MI-4 glioblastoma cell line, which displays 1p and 19q specific alterations targeting preferential regions of allelic loss in glial neoplasms, by array-CGH and fluorescence in situ hybridization (FISH) analyses that were combined to obtain a high resolution map of targeted chromosome rearrangements and copy number changes throughout the genome. Genome-wide and chromosome 19 full coverage array-CGH analysis of the MI-4 cell line revealed that in this particular cell line, 1p-specific loss, including the CDKN2 (p18) gene, is not accompanied by loss of the previously described 19q13.3 tumor suppressor candidate region. Interestingly, the array-CGH (CGHa) profile showed an increase in copy number along most of 19q including the AKT2 oncogene and the KLKs gene family, which have previously been shown to be amplified in pancreatic carcinomas and upregulated in several tumors, respectively. The concomitant 1p partial loss and chromosome 19 alterations, with the +7 and -10-specific GBM markers associated with homozygous deletion of 9p21.3 including CDKN2A (p16), are distinct features of the glioblastoma MI-4 cell line, illustrating its origin from an olidodendroglial tumor. Based on these results, we conclude that the MI-4 glioblastoma cell line might function as a model system for investigations into the behavior of a defined oligodendroglioma subtype.
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Affiliation(s)
- Ivana Magnani
- Department of Biology and Genetics, University of Milan, via Viotti3/5, 20133 Milan, Italy
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Hartmann C, Mueller W, Lass U, Kamel-Reid S, von Deimling A. Molecular genetic analysis of oligodendroglial tumors. J Neuropathol Exp Neurol 2005; 64:10-4. [PMID: 15715080 DOI: 10.1093/jnen/64.1.10] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Deletions on the short arm of chromosome 1 (1p) and the long arm of chromosome 19 (19q) are molecular hallmark lesions of oligodendroglial tumors. Ever since oligodendroglial tumors with 1p and 19q deletions were shown to respond to chemotherapy, neuropathologists have been facing increasing requests for such molecular analysis. Therefore, there is increasing demand for reliable and simple assays. This brief report compiles information on different technical approaches, including manual and automated loss of heterozygosity analysis, fluorescence in situ hybridization techniques, and quantitative polymerase chain reaction. Herein we present a detailed protocol describing loss of heterozygosity analysis with microsatellite markers currently in use for two multicenter studies.
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Affiliation(s)
- Christian Hartmann
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Humboldt University, Berlin, Germany
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Abstract
PURPOSE OF REVIEW Despite optimal clinical treatment, the prognosis for gliomas remains poor, and little progress has been observed during the last few years. Meanwhile, understanding of glioma oncogenesis has improved greatly. This review focuses on recent advances in molecular biology of glial tumors, with particular emphasis on lineage markers, genetic mechanisms underlying tumor progression, new diagnostic and prognostic markers, and potential therapeutic targets. RECENT FINDINGS The question of the cell of origin, illustrated by the evidence of tumor-derived multipotent progenitors, by the animal models of gliomas, and by lineage markers such as Olig1/2 markers, remains unsolved. Genotype/phenotype correlation studies have identified early and late genetic alterations related either to astrocytic or oligodendroglial phenotype. They complement the existing World Health Organization morphologic classification and provide additional prognostic markers such as 1p/19q deletion in oligodendrogliomas. Most of these genetic alterations result in the disruption of three main cellular systems: RB1, P53, and tyrosine kinase receptor pathways. New gene alterations have also been identified in glioma, promoting mitotic signal transduction, cell cycle regulation, apoptosis, angiogenesis, or invasion. Gene and protein profiling has been correlated with outcome. SUMMARY Management of gliomas, especially oligodendrogliomas with 1p19q deletion, benefits from advances in molecular genetics. A better understanding of the molecular pathogenesis and cellular lineage of gliomas will improve tumor classification and define more reliable prognostic markers. There is a hope that it will also lead to novel targets for therapy.
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Affiliation(s)
- Marc Sanson
- INSERM U495, Laboratoire de Biologie des Interactions Neurones-Glie, Paris, France.
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Miliaras D, Grimbizis G, Conroy J, Psarra N, Miliaras S, Nowak N, Bontis J. Novel karyotypic changes detected by comparative genomic hybridization in a case of congenital cervical immature teratoma. ACTA ACUST UNITED AC 2005; 73:572-6. [PMID: 16001440 DOI: 10.1002/bdra.20152] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
BACKGROUND Cervical immature teratoma is a rare congenital tumor, and very few cases have been studied cytogenetically. CASE In this article, we describe a case of this tumor type and present the findings of the karyotype of the lesion, which was performed with the bacterial artificial chromosome arrays using the comparative genomic hybridization method. The chromosomal abnormalities that we found included an amplification on 1p21.1, a 9p22 deletion, and a 1-copy gain of 17q21.33. CONCLUSIONS None of the identified chromosomal aberrations have been previously associated with congenital extragonadal teratomas. Important genes that lie in these DNA regions may be implicated in the pathogenesis of congenital teratomas.
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Affiliation(s)
- Dimosthenis Miliaras
- Laboratory of Histology, Embryology & Anthropology, Medical Faculty, Aristotle University of Thessaloniki, Greece.
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Rossi MR, Gaile D, Laduca J, Matsui SI, Conroy J, McQuaid D, Chervinsky D, Eddy R, Chen HS, Barnett GH, Nowak NJ, Cowell JK. Identification of consistent novel submegabase deletions in low-grade oligodendrogliomas using array-based comparative genomic hybridization. Genes Chromosomes Cancer 2005; 44:85-96. [PMID: 15940691 DOI: 10.1002/gcc.20218] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We have analyzed 18 low-grade gliomas using array comparative genomic hybridization (aCGH) with an average resolution of <500 kb. Because the majority of these tumors showed loss of chromosome arms 1p and 19q, we used custom statistical approaches to define submegabase hemizygous losses throughout the genome that correlated with 19q loss. As a result of this analysis, we have identified a approximately 550-kb region in 11q13 and a approximately 300-kb region in 13q12 that showed hemizygous deletion in virtually all the tumors analyzed regardless of their 1p/19q status. FISH analyses of interphase nuclei from the same tumors used for aCGH analysis confirmed the hemizygous loss. The identification of such specific changes provides a potentially very useful diagnostic marker for this subgroup of low-grade tumors. These regions of the genome define small numbers of candidate genes that are within the deletions. The aCGH analysis also defined the spectrum of gain and loss of genomic regions in low-grade oligodendrogliomas.
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Affiliation(s)
- Michael R Rossi
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York, USA
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Roerig P, Nessling M, Radlwimmer B, Joos S, Wrobel G, Schwaenen C, Reifenberger G, Lichter P. Molecular classification of human gliomas using matrix-based comparative genomic hybridization. Int J Cancer 2005; 117:95-103. [PMID: 15880582 DOI: 10.1002/ijc.21121] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Gliomas are the most frequent primary brain tumors and comprise a group of morphologically, biologically and clinically heterogeneous neoplasms. The different glioma types are associated with distinct genetic aberrations, which may provide useful information for tumor classification as well as prediction of prognosis and response to therapy. To facilitate the molecular classification of gliomas, we established a genomic microarray that consists of bacterial artificial chromosome (BAC) and P1-derived artificial chromosome (PAC) clones representing tumor suppressor genes, proto-oncogenes and chromosomal regions frequently gained or lost in gliomas. In addition, reference clones distributed evenly throughout the genome in approximately 15 Mbp intervals were spotted on the microarray. These customized microarrays were used for matrix-based comparative genomic hybridization (matrix CGH) analysis of 70 gliomas. Matrix CGH findings were validated by molecular genetic analyses of candidate genes, loss of heterozygosity studies and chromosomal CGH. Our results indicate that matrix CGH allows for the sensitive and specific detection of gene amplifications as well as low-level copy number gains and losses in clinical glioma samples. Furthermore, molecular classification based on matrix CGH data closely paralleled histological classification and was able to distinguish with few exceptions between diffuse astrocytomas and oligodendrogliomas, anaplastic astrocytomas and anaplastic oligodendrogliomas, anaplastic oligodendrogliomas and glioblastomas, as well as primary and secondary glioblastomas. Thus, matrix CGH is a powerful technique that allows for an automated genomic profiling of gliomas and represents a promising new tool for their molecular classification.
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Affiliation(s)
- Peter Roerig
- Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, Germany
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Cowell JK, Wang YD, Head K, Conroy J, McQuaid D, Nowak NJ. Identification and characterisation of constitutional chromosome abnormalities using arrays of bacterial artificial chromosomes. Br J Cancer 2004; 90:860-5. [PMID: 14970865 PMCID: PMC2410171 DOI: 10.1038/sj.bjc.6601588] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Constitutional chromosome deletions and duplications frequently predispose to the development of a wide variety of cancers. We have developed a microarray of 6000 bacterial artificial chromosomes for array-based comparative genomic hybridisation, which provides an average resolution of 750 kb across the human genome. Using these arrays, subtle gains and losses of chromosome regions can be detected in constitutional cells, following a single overnight hybridisation. In this report, we demonstrate the efficiency of this procedure in identifying constitutional deletions and duplications associated with predisposition to retinoblastoma, Wilms tumour and Beckwith–Wiedemann syndrome.
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Affiliation(s)
- J K Cowell
- Department of Cancer Genetics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA.
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