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Nourmohammadi Abadchi S, Sena LA, Antonarakis ES, Pritchard CC, Eshleman JR, Konnick EQ, Salipante SJ, Shenderov E, Lotan TL. MLH1 Loss in Primary Prostate Cancer. JCO Precis Oncol 2023; 7:e2200611. [PMID: 37196219 PMCID: PMC10309570 DOI: 10.1200/po.22.00611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/25/2023] [Accepted: 03/17/2023] [Indexed: 05/19/2023] Open
Abstract
PURPOSE Among mismatch repair-deficient (MMRd) prostate cancers, loss of MLH1 is relatively uncommon and few cases have been reported in detail. METHODS Here, we describe the molecular features of two cases of primary prostate cancer with MLH1 loss detected by immunohistochemistry, and in one case, confirmed via transcriptomic profiling. RESULTS Both cases were microsatellite stable on standard polymerase chain reaction (PCR)-based microsatellite instability (MSI) testing, but showed evidence of MSI on a newer PCR-based long mononucleotide repeat (LMR) assay and by next-generation sequencing. Germline testing was negative for Lynch syndrome-associated mutations in both cases. Targeted or whole-exome tumor sequencing using multiple commercial/academic platforms (Foundation, Tempus, JHU, and UW-OncoPlex) showed modestly elevated, though variable, tumor mutation burden estimates (2.3-10 mutations/Mb) consistent with MMRd, but without identifiable pathogenic single-nucleotide or indel mutations in MLH1. Copy-number analysis confirmed biallelic MLH1 loss in one case and monoallelic MLH1 loss in the second case, without evidence of MLH1 promoter hypermethylation in either. The second patient was treated with single-agent pembrolizumab and demonstrated a short-lived prostate-specific antigen response. CONCLUSION These cases highlight the challenges in identifying MLH1-deficient prostate cancers using standard MSI testing and commercial sequencing panels, and support the utility of immunohistochemical assays and LMR- or sequencing-based MSI testing for detection of MMRd prostate cancers.
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Affiliation(s)
| | - Laura A. Sena
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Emmanuel S. Antonarakis
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD
- University of Minnesota Masonic Cancer Center, Minneapolis, MN
| | - Colin C. Pritchard
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - James R. Eshleman
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Eric Q. Konnick
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Stephen J. Salipante
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Eugene Shenderov
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD
| | - Tamara L. Lotan
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD
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Kravitz A, Tyler R, Manohar BM, Ronald BSM, Collins MT, Sriranganathan N. Successful restoration of archived ovine formalin fixed paraffin-embedded tissue DNA and single nucleotide polymorphism analysis. Vet Res Commun 2023; 47:131-139. [PMID: 35618986 PMCID: PMC9873697 DOI: 10.1007/s11259-022-09937-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/09/2022] [Indexed: 01/28/2023]
Abstract
Archived formalin fixed paraffin-embedded (FFPE) tissues are powerful tools in medicine, capable of harboring diagnostic and genetic answers to challenging clinical questions. Successful utilization of DNA derived from FFPE samples is dependent upon repairing DNA damage generated from the fixation process. Methods to repair FFPE DNA have been successful in human medicine for a variety of research and clinical applications, yet remain underutilized in veterinary medicine. Despite the available technology, our study is the first to evaluate the repair of FFPE derived DNA from veterinary species for single-nucleotide polymorphism (SNP) analysis using the Illumina OvineSNP50 BeadChip and Illumina FFPE QC and DNA Restore kit. To accomplish this, 48 ovine FFPE samples were run using the Illumina OvineSNP50 BeadChip with and without restoration. Compared to pre-restore data, we found increased sample call rates, SNP call frequency, and assay metrics for all samples post-restoration. Further, we utilized four sheep with available parallel fresh DNA and FFPE DNA to compare assay metrics and genotype calls between the two starting sample types. Although fresh samples generated increased call rates, we found 99% concordance in allele calls between restored FFPE and fresh DNA for all four samples. Our results indicate successful restoration and genotyping of ovine FFPE samples using this technology, with potential for utilization in other veterinary species.
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Affiliation(s)
- Amanda Kravitz
- Center for One Health Research, Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA USA
| | - Ron Tyler
- Center for One Health Research, Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA USA
| | - B. Murali Manohar
- Tamilnadu Veterinary and Animal Sciences University, Madhavaram Milk Colony, Chennai, 600051 Tamil Nadu India
| | - B. Samuel Masilamoni Ronald
- Tamilnadu Veterinary and Animal Sciences University, Madhavaram Milk Colony, Chennai, 600051 Tamil Nadu India
| | - Michael T. Collins
- Department of Pathobiological Sciences, University of Wisconsin-Madison School of Veterinary Medicine, Madison, WI USA
| | - Nammalwar Sriranganathan
- Center for One Health Research, Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA USA
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3
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Brandner S, McAleenan A, Jones HE, Kernohan A, Robinson T, Schmidt L, Dawson S, Kelly C, Leal ES, Faulkner CL, Palmer A, Wragg C, Jefferies S, Vale L, Higgins JPT, Kurian KM. Diagnostic accuracy of 1p/19q codeletion tests in oligodendroglioma: A comprehensive meta-analysis based on a Cochrane systematic review. Neuropathol Appl Neurobiol 2022; 48:e12790. [PMID: 34958131 PMCID: PMC9208578 DOI: 10.1111/nan.12790] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/23/2021] [Accepted: 11/27/2021] [Indexed: 11/29/2022]
Abstract
Codeletion of chromosomal arms 1p and 19q, in conjunction with a mutation in the isocitrate dehydrogenase 1 or 2 gene, is the molecular diagnostic criterion for oligodendroglioma, IDH mutant and 1p/19q codeleted. 1p/19q codeletion is a diagnostic marker and allows prognostication and prediction of the best drug response within IDH-mutant tumours. We performed a Cochrane review and simple economic analysis to establish the most sensitive, specific and cost-effective techniques for determining 1p/19q codeletion status. Fluorescent in situ hybridisation (FISH) and polymerase chain reaction (PCR)-based loss of heterozygosity (LOH) test methods were considered as reference standard. Most techniques (FISH, chromogenic in situ hybridisation [CISH], PCR, real-time PCR, multiplex ligation-dependent probe amplification [MLPA], single nucleotide polymorphism [SNP] array, comparative genomic hybridisation [CGH], array CGH, next-generation sequencing [NGS], mass spectrometry and NanoString) showed good sensitivity (few false negatives) for detection of 1p/19q codeletions in glioma, irrespective of whether FISH or PCR-based LOH was used as the reference standard. Both NGS and SNP array had a high specificity (fewer false positives) for 1p/19q codeletion when considered against FISH as the reference standard. Our findings suggest that G banding is not a suitable test for 1p/19q analysis. Within these limits, considering cost per diagnosis and using FISH as a reference, MLPA was marginally more cost-effective than other tests, although these economic analyses were limited by the range of available parameters, time horizon and data from multiple healthcare organisations.
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Affiliation(s)
- Sebastian Brandner
- Division of Neuropathology, The National Hospital for Neurology and NeurosurgeryUniversity College London Hospitals NHS Foundation TrustLondonUK
- Department of Neurodegenerative Disease, Queen Square Instituite of NeurologyUniversity College LondonLondonUK
| | - Alexandra McAleenan
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Hayley E. Jones
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Ashleigh Kernohan
- Population Health Sciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Tomos Robinson
- Population Health Sciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Lena Schmidt
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Sarah Dawson
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Claire Kelly
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | | | - Claire L. Faulkner
- Bristol Genetics Laboratory, Pathology SciencesSouthmead HospitalBristolUK
| | - Abigail Palmer
- Bristol Genetics Laboratory, Pathology SciencesSouthmead HospitalBristolUK
| | - Christopher Wragg
- Bristol Genetics Laboratory, Pathology SciencesSouthmead HospitalBristolUK
| | | | - Luke Vale
- Population Health Sciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Julian P. T. Higgins
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Kathreena M. Kurian
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
- Bristol Medical School: Brain Tumour Research Centre, Public Health SciencesUniversity of BristolBristolUK
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4
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Utility of Targeted Next-Generation Sequencing Assay to Detect 1p/19q Co-Deletion in Formalin-fixed Paraffin-embedded Glioma Specimens. Hum Pathol 2022; 126:63-76. [PMID: 35561840 DOI: 10.1016/j.humpath.2022.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/03/2022] [Indexed: 12/12/2022]
Abstract
Molecular classification of brain neoplasms is important for diagnosis, prognosis, and treatment outcome of histologically similar tumors. Oligodendroglioma is a glioma subtype characterized by 1p/19q co-deletion and IDH1/IDH2 mutations, which predicts a good prognosis, responsiveness to therapy and an improved overall survival compared to other adult gliomas. In a routine clinical setting, 1p/19q co-deletion is detected by interphase-FISH and SNP microarray, and somatic mutations are detected by targeted next generation sequencing (NGS). The aim of this proof-of-principle study was to investigate the feasibility of using targeted NGS to simultaneously detect both 1p/19q co-deletion and somatic mutations. Among two hundred forty-seven consecutive patients with formalin-fixed paraffin-embedded brain tumors with various subtypes, NGS revealed 1p/19q co-deletion in twenty-six oligodendrogliomas and an IDH-wildtype astrocytoma, and partial loss across chromosomes 1p and 19q/whole-arm loss of 1p or 19q/copy neutral loss of heterozygosity in eleven non-oligodendrogliomas. For this 247 brain-tumor cohort, the overall sensitivity, specificity, and accuracy of detecting 1p/19q co-deletion by NGS in oligodendrogliomas were 96.2%, 99.6%, and 99.2%, respectively. The oligodendroglioma cohort had more mutations in IDH1/IDH2, CIC, FUBP1, and TERT, and fewer mutations in ATRX and TP53 than the non-oligodendroglioma cohort. This proof-of-concept study demonstrated that targeted NGS can simultaneously detect both 1p/19q co-deletion and somatic mutations, which can provide a more comprehensive genetic profiling for patients with gliomas using a single assay in a clinical setting.
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5
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McAleenan A, Jones HE, Kernohan A, Robinson T, Schmidt L, Dawson S, Kelly C, Spencer Leal E, Faulkner CL, Palmer A, Wragg C, Jefferies S, Brandner S, Vale L, Higgins JP, Kurian KM. Diagnostic test accuracy and cost-effectiveness of tests for codeletion of chromosomal arms 1p and 19q in people with glioma. Cochrane Database Syst Rev 2022; 3:CD013387. [PMID: 35233774 PMCID: PMC8889390 DOI: 10.1002/14651858.cd013387.pub2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Complete deletion of both the short arm of chromosome 1 (1p) and the long arm of chromosome 19 (19q), known as 1p/19q codeletion, is a mutation that can occur in gliomas. It occurs in a type of glioma known as oligodendroglioma and its higher grade counterpart known as anaplastic oligodendroglioma. Detection of 1p/19q codeletion in gliomas is important because, together with another mutation in an enzyme known as isocitrate dehydrogenase, it is needed to make the diagnosis of an oligodendroglioma. Presence of 1p/19q codeletion also informs patient prognosis and prediction of the best drug treatment. The main two tests in use are fluorescent in situ hybridisation (FISH) and polymerase chain reaction (PCR)-based loss of heterozygosity (LOH) assays (also known as PCR-based short tandem repeat or microsatellite analysis). Many other tests are available. None of the tests is perfect, although PCR-based LOH is expected to have very high sensitivity. OBJECTIVES To estimate the sensitivity and specificity and cost-effectiveness of different deoxyribonucleic acid (DNA)-based techniques for determining 1p/19q codeletion status in glioma. SEARCH METHODS We searched MEDLINE, Embase and BIOSIS up to July 2019. There were no restrictions based on language or date of publication. We sought economic evaluation studies from the results of this search and using the National Health Service Economic Evaluation Database. SELECTION CRITERIA We included cross-sectional studies in adults with glioma or any subtype of glioma, presenting raw data or cross-tabulations of two or more DNA-based tests for 1p/19q codeletion. We also sought economic evaluations of these tests. DATA COLLECTION AND ANALYSIS We followed procedures outlined in the Cochrane Handbook for Diagnostic Test Accuracy Reviews. Two review authors independently screened titles/abstracts/full texts, performed data extraction, and undertook applicability and risk of bias assessments using QUADAS-2. Meta-analyses used the hierarchical summary ROC model to estimate and compare test accuracy. We used FISH and PCR-based LOH as alternate reference standards to examine how tests compared with those in common use, and conducted a latent class analysis comparing FISH and PCR-based LOH. We constructed an economic model to evaluate cost-effectiveness. MAIN RESULTS We included 53 studies examining: PCR-based LOH, FISH, single nucleotide polymorphism (SNP) array, next-generation sequencing (NGS), comparative genomic hybridisation (CGH), array comparative genomic hybridisation (aCGH), multiplex-ligation-dependent probe amplification (MLPA), real-time PCR, chromogenic in situ hybridisation (CISH), mass spectrometry (MS), restriction fragment length polymorphism (RFLP) analysis, G-banding, methylation array and NanoString. Risk of bias was low for only one study; most gave us concerns about how patients were selected or about missing data. We had applicability concerns about many of the studies because only patients with specific subtypes of glioma were included. 1520 participants contributed to analyses using FISH as the reference, 1304 participants to analyses involving PCR-based LOH as the reference and 262 participants to analyses of comparisons between methods from studies not including FISH or PCR-based LOH. Most evidence was available for comparison of FISH with PCR-based LOH (15 studies, 915 participants): PCR-based LOH detected 94% of FISH-determined codeletions (95% credible interval (CrI) 83% to 98%) and FISH detected 91% of codeletions determined by PCR-based LOH (CrI 78% to 97%). Of tumours determined not to have a deletion by FISH, 94% (CrI 87% to 98%) had a deletion detected by PCR-based LOH, and of those determined not to have a deletion by PCR-based LOH, 96% (CrI 90% to 99%) had a deletion detected by FISH. The latent class analysis suggested that PCR-based LOH may be slightly more accurate than FISH. Most other techniques appeared to have high sensitivity (i.e. produced few false-negative results) for detection of 1p/19q codeletion when either FISH or PCR-based LOH was considered as the reference standard, although there was limited evidence. There was some indication of differences in specificity (false-positive rate) with some techniques. Both NGS and SNP array had high specificity when considered against FISH as the reference standard (NGS: 6 studies, 243 participants; SNP: 6 studies, 111 participants), although we rated certainty in the evidence as low or very low. NGS and SNP array also had high specificity when PCR-based LOH was considered the reference standard, although with much more uncertainty as these results were based on fewer studies (just one study with 49 participants for NGS and two studies with 33 participants for SNP array). G-banding had low sensitivity and specificity when PCR-based LOH was the reference standard. Although MS had very high sensitivity and specificity when both FISH and PCR-based LOH were considered the reference standard, these results were based on only one study with a small number of participants. Real-time PCR also showed high specificity with FISH as a reference standard, although there were only two studies including 40 participants. We found no relevant economic evaluations. Our economic model using FISH as the reference standard suggested that the resource-optimising test depends on which measure of diagnostic accuracy is most important. With FISH as the reference standard, MLPA is likely to be cost-effective if society was willing to pay GBP 1000 or less for a true positive detected. However, as the value placed on a true positive increased, CISH was most cost-effective. Findings differed when the outcome measure changed to either true negative detected or correct diagnosis. When PCR-based LOH was used as the reference standard, MLPA was likely to be cost-effective for all measures of diagnostic accuracy at lower threshold values for willingness to pay. However, as the threshold values increased, none of the tests were clearly more likely to be considered cost-effective. AUTHORS' CONCLUSIONS In our review, most techniques (except G-banding) appeared to have good sensitivity (few false negatives) for detection of 1p/19q codeletions in glioma against both FISH and PCR-based LOH as a reference standard. However, we judged the certainty of the evidence low or very low for all the tests. There are possible differences in specificity, with both NGS and SNP array having high specificity (fewer false positives) for 1p/19q codeletion when considered against FISH as the reference standard. The economic analysis should be interpreted with caution due to the small number of studies.
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Affiliation(s)
- Alexandra McAleenan
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Hayley E Jones
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ashleigh Kernohan
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Tomos Robinson
- Institute of Health & Society, Newcastle University, Newcastle upon Tyne , UK
| | - Lena Schmidt
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Sarah Dawson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Claire Kelly
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Emmelyn Spencer Leal
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Claire L Faulkner
- Bristol Genetics Laboratory, Pathology Sciences, Southmead Hospital, Bristol, UK
| | - Abigail Palmer
- Bristol Genetics Laboratory, Pathology Sciences, Southmead Hospital, Bristol, UK
| | - Christopher Wragg
- Bristol Genetics Laboratory, Pathology Sciences, Southmead Hospital, Bristol, UK
| | - Sarah Jefferies
- Department of Oncology, Addenbrooke's Hospital, Cambridge, UK
| | - Sebastian Brandner
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
| | - Luke Vale
- Institute of Health & Society, Newcastle University, Newcastle upon Tyne, UK
| | - Julian Pt Higgins
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kathreena M Kurian
- Bristol Medical School: Brain Tumour Research Centre, Public Health Sciences, University of Bristol, Bristol, UK
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6
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McAleenan A, Jones HE, Kernohan A, Faulkner CL, Palmer A, Dawson S, Wragg C, Jefferies S, Brandner S, Vale L, Higgins JPT, Kurian KM. Diagnostic test accuracy and cost-effectiveness of tests for codeletion of chromosomal arms 1p and 19q in people with glioma. Hippokratia 2019. [DOI: 10.1002/14651858.cd013387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Alexandra McAleenan
- University of Bristol; Population Health Sciences, Bristol Medical School; 39 Whatley Road Bristol UK BS8 2PS
| | - Hayley E Jones
- University of Bristol; Population Health Sciences, Bristol Medical School; 39 Whatley Road Bristol UK BS8 2PS
| | - Ashleigh Kernohan
- Newcastle University; Institute of Health & Society; Baddiley-Clark Building, Richardson Road Newcastle upon Tyne UK NE2 4AA
| | - Claire L Faulkner
- Southmead Hospital; Bristol Genetics Laboratory, Pathology Sciences; North Bristol NHS Trust Bristol UK BS10 5NB
| | - Abigail Palmer
- Southmead Hospital; Bristol Genetics Laboratory, Pathology Sciences; North Bristol NHS Trust Bristol UK BS10 5NB
| | - Sarah Dawson
- University of Bristol; Population Health Sciences, Bristol Medical School; 39 Whatley Road Bristol UK BS8 2PS
| | - Christopher Wragg
- Southmead Hospital; Bristol Genetics Laboratory, Pathology Sciences; North Bristol NHS Trust Bristol UK BS10 5NB
| | - Sarah Jefferies
- Addenbrooke's Hospital; Department of Oncology; Hills Road Cambridge UK CB2 0QQ
| | - Sebastian Brandner
- The National Hospital for Neurology and Neurosurgery; Division of Neuropathology and Department of Neurodegeneration; University College Hospital NHS Foundation Trust and UCL Institute of Neurology Queen Square London UK WC1N 3BG
| | - Luke Vale
- Newcastle University; Institute of Health & Society; Baddiley-Clark Building, Richardson Road Newcastle upon Tyne UK NE2 4AA
| | - Julian P T Higgins
- University of Bristol; Population Health Sciences, Bristol Medical School; 39 Whatley Road Bristol UK BS8 2PS
| | - Kathreena M Kurian
- University of Bristol; Bristol Medical School: Brain Tumour Research Centre, Public Health Sciences; Oakfield House, Oakfield Grove Bristol UK BS8 2BN
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Central Nervous System-type Neuroepithelial Tumors and Tumor-like Proliferations Developing in the Gynecologic Tract and Pelvis. Am J Surg Pathol 2018; 42:1429-1444. [DOI: 10.1097/pas.0000000000001131] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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8
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Vizcaino MA, Palsgrove DN, Yuan M, Giannini C, Cabrera-Aldana EE, Pallavajjala A, Burger PC, Rodriguez FJ. Granular cell astrocytoma: an aggressive IDH-wildtype diffuse glioma with molecular genetic features of primary glioblastoma. Brain Pathol 2018; 29:193-204. [PMID: 30222900 DOI: 10.1111/bpa.12657] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 09/10/2018] [Indexed: 12/30/2022] Open
Abstract
Granular cell astrocytoma (GCA) is a rare adult infiltrating glioma subtype. We studied a series of 39 GCAs. Median age of presentation was 57.8 years and most cases developed in the frontal or temporal lobes. Tumors included grade II (n = 14), grade III (n = 11), and grade IV (n = 14) by WHO criteria. Granular cell morphology was diffuse in 31 (79%) cases and partial in eight (21%). Immunohistochemistry showed frequent positivity for GFAP (28 of 31), OLIG2 (16 of 16), and CD68 (27 of 30), but HAM56, CD163, and IBA-1 histiocytic markers were all negative (22 of 22). IDH1(R132H) was negative in all the cases tested (16 of 16), while ATRX expression was retained (12 of 12). Cytogenetics demonstrated monosomy 10 (6 of 6) cases, +7 in 4 (of 6), -13q in 4 of 6, and -14 in 4 of 6. Next-generation sequencing demonstrated mutations in PTEN/PIK3 genes in 6/13 (46%), NF1 in 3 of 10 (30%), TP53 in 3 of 13 (23%), PALB2 in 3 of 10 (30%), STAG2 in 3 of 10 (30%), EGFR mutation/amplification in 3 of 13 (23%), and AR in 2 of 10 (20%). CDKN2A/B deletion was identified in 5 of 13 (30%) cases (homozygous deletion in 4). The TERT C228T mutation was identified in 9 of 13 (69%). No mutations were encountered in IDH1, IDH2, CIC, FUBP1, H3F3A, BRAF or ATRX genes. The mean overall survival was 11.3 months. Patients >60 years old at diagnosis had a worse survival than patients <60 years (P = 0.001). There were no statistically significant differences in survival by WHO grade, extent of granular cell change, sex or MIB-1 (P > 0.05). GCA is a variant of IDH-wildtype diffuse glioma with aggressive behavior irrespective of grade and extent of granular cell morphology, and with molecular genetic features corresponding to primary glioblastoma.
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Affiliation(s)
- M Adelita Vizcaino
- Department of Pathology, Johns Hopkins University, Baltimore, MD.,Faculty of Medicine, Department of Cellular and Tissue Biology, UNAM, Mexico City, Mexico
| | - Doreen N Palsgrove
- Department of Pathology, Johns Hopkins University, Baltimore, MD.,Sydney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Ming Yuan
- Department of Pathology, Johns Hopkins University, Baltimore, MD
| | - Caterina Giannini
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | | | - Peter C Burger
- Department of Pathology, Johns Hopkins University, Baltimore, MD.,Sydney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Fausto J Rodriguez
- Department of Pathology, Johns Hopkins University, Baltimore, MD.,Sydney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
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9
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Pesenti C, Paganini L, Fontana L, Veniani E, Runza L, Ferrero S, Bosari S, Menghi M, Marfia G, Caroli M, Silipigni R, Guerneri S, Tabano S, Miozzo M. Mass spectrometry-based assay for the molecular diagnosis of glioma: concomitant detection of chromosome 1p/19q codeletion, and IDH1, IDH2, and TERT mutation status. Oncotarget 2017; 8:57134-57148. [PMID: 28915660 PMCID: PMC5593631 DOI: 10.18632/oncotarget.19103] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/19/2017] [Indexed: 02/06/2023] Open
Abstract
The World Health Organization recently revised the diagnosis of glioma, to integrate molecular parameters, including IDH mutations and codeletion (loss of heterozygosity; LOH) of chromosome arms 1p/19q, into the definitions of adult glioma histological subtypes. Mutations in the TERT promoter may also be useful for glioma diagnosis and prognosis. The integration of molecular markers into routine diagnosis requires their rapid and reliable assessment. We propose a MassARRAY (MS)-based test that can identify 1p/19q codeletion using quantitative SNP genotyping and, simultaneously, characterize hotspot mutations in the IDH1, IDH2, and TERT genes in tumor DNA. We determined the reliability of the MS approach testing 50 gliomas and comparing the MS results with those obtained by standard methods, such as short tandem repeat genotyping, array comparative genomic hybridization (array-CGH) and Fluorescence In Situ Hybridization (FISH) for 1p/19q codeletion and Sanger sequencing for hotspots mutations. The results indicate that MS is suitable for the accurate, rapid, and cost-effective evaluation of chromosome deletions combined with hotspot mutation detection. This MS approach could be similarly exploited in evaluation of LOH in other situations of clinical and/or research importance.
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Affiliation(s)
- Chiara Pesenti
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Leda Paganini
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Laura Fontana
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Emanuela Veniani
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Letterio Runza
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Ferrero
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Milan, Italy
| | - Silvano Bosari
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Giovanni Marfia
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, Milan, Italy
- Neurosurgery Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Manuela Caroli
- Neurosurgery Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Rosamaria Silipigni
- Laboratory of Medical Genetics, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Silvana Guerneri
- Laboratory of Medical Genetics, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Silvia Tabano
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Monica Miozzo
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
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10
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Carter JH, McNulty SN, Cimino PJ, Cottrell CE, Heusel JW, Vigh-Conrad KA, Duncavage EJ. Targeted Next-Generation Sequencing in Molecular Subtyping of Lower-Grade Diffuse Gliomas. J Mol Diagn 2017; 19:328-337. [DOI: 10.1016/j.jmoldx.2016.10.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 10/16/2016] [Accepted: 10/27/2016] [Indexed: 10/20/2022] Open
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11
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Rodriguez FJ, Vizcaino MA, Lin MT. Recent Advances on the Molecular Pathology of Glial Neoplasms in Children and Adults. J Mol Diagn 2016; 18:620-634. [PMID: 27444975 PMCID: PMC5397677 DOI: 10.1016/j.jmoldx.2016.05.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 05/06/2016] [Accepted: 05/11/2016] [Indexed: 02/02/2023] Open
Abstract
Gliomas represent the most common primary intraparenchymal tumors of the central nervous system in adults and children and are a genetic and phenotypic heterogeneous group. Large multi-institutional studies and The Cancer Genome Atlas have provided firm insights into the basic genetic drivers in gliomas. The main molecular biomarkers routinely applied to evaluate diffuse gliomas include MGMT promoter methylation, EGFR alterations (eg, EGFRvIII), IDH1 or IDH2 mutations, and 1p19q co-deletion. Many of these markers have become standard of care for molecular testing and prerequisites for clinical trial enrollment. Other recent biomarkers include TERT promoter and ATRX mutations, alterations that identify specific molecular subgroups of diffuse gliomas with biological and clinical relevance. It has also become apparent that distinctive patterns of molecular genetic evolution develop in the context of current therapeutic regimens. Important insights have also been uncovered in the field of pediatric glioma, including the identification of recurrent mutation, fusion, and/or duplication events of the BRAF, FGFR1, MYB, and MYBL1 genes in pediatric low-grade gliomas, mutations affecting histone components (H3F3A p.K27M or p.G34) in pediatric high-grade gliomas, and aggressive subsets developing in midline central nervous system structures. Here, we summarize current concepts in molecular testing for glial tumors, including recent findings by large-scale discovery efforts and technologic advances that are affecting routine diagnostic work.
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Affiliation(s)
- Fausto J Rodriguez
- Division of Neuropathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - M Adelita Vizcaino
- Division of Neuropathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Cellular and Tissue Biology, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Ming-Tseh Lin
- Division of Molecular Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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12
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Dubbink HJ, Atmodimedjo PN, van Marion R, Krol NMG, Riegman PHJ, Kros JM, van den Bent MJ, Dinjens WNM. Diagnostic Detection of Allelic Losses and Imbalances by Next-Generation Sequencing: 1p/19q Co-Deletion Analysis of Gliomas. J Mol Diagn 2016; 18:775-786. [PMID: 27461031 DOI: 10.1016/j.jmoldx.2016.06.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 05/06/2016] [Accepted: 06/01/2016] [Indexed: 02/05/2023] Open
Abstract
Cancer cells are genomically unstable and accumulate tumor type-specific molecular aberrations, which may represent hallmarks for predicting prognosis and targets for therapy. Co-deletion of chromosomes 1p and 19q marks gliomas with an oligodendroglioma component and predicts a better prognosis and response to chemotherapy. In the current study, we present a novel method to detect chromosome 1p/19q co-deletion or loss of heterozygosity (LOH) in a diagnostic setting, based on single-nucleotide polymorphism (SNP) analysis and next-generation sequencing (NGS). We selected highly polymorphic SNPs distributed evenly over both chromosome arms. To experimentally determine the sensitivity and specificity of targeted SNP analysis, we used DNAs extracted from 49 routine formalin-fixed, paraffin-embedded glioma tissues and compared the outcome with diagnostic microsatellite-based LOH analysis and calculated estimates. We show that targeted SNP analysis by NGS allows reliable detection of 1p and/or 19q deletion in a background of 70% of normal cells according to calculated outcomes, is more sensitive than microsatellite-based LOH analysis, and requires much less DNA. This specific and sensitive SNP assay is broadly applicable for simultaneous allelic imbalance analysis of multiple genomic regions and can be incorporated easily into NGS mutation analyses. The combined mutation and chromosomal imbalance analysis in a single NGS assay is suited perfectly for routine glioma diagnostics and other diagnostic molecular pathology applications.
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Affiliation(s)
- Hendrikus J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Peggy N Atmodimedjo
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ronald van Marion
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Niels M G Krol
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Peter H J Riegman
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Johan M Kros
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Martin J van den Bent
- Department of Neuro-Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
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13
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Dickinson PJ, York D, Higgins RJ, LeCouteur RA, Joshi N, Bannasch D. Chromosomal Aberrations in Canine Gliomas Define Candidate Genes and Common Pathways in Dogs and Humans. J Neuropathol Exp Neurol 2016; 75:700-10. [PMID: 27251041 DOI: 10.1093/jnen/nlw042] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Indexed: 12/16/2022] Open
Abstract
Spontaneous gliomas in dogs occur at a frequency similar to that in humans and may provide a translational model for therapeutic development and comparative biological investigations. Copy number alterations in 38 canine gliomas, including diffuse astrocytomas, glioblastomas, oligodendrogliomas, and mixed oligoastrocytomas, were defined using an Illumina 170K single nucleotide polymorphism array. Highly recurrent alterations were seen in up to 85% of some tumor types, most notably involving chromosomes 13, 22, and 38, and gliomas clustered into 2 major groups consisting of high-grade IV astrocytomas, or oligodendrogliomas and other tumors. Tumor types were characterized by specific broad and focal chromosomal events including focal loss of the INK4A/B locus in glioblastoma and loss of the RB1 gene and amplification of the PDGFRA gene in oligodendrogliomas. Genes associated with the 3 critical pathways in human high-grade gliomas (TP53, RB1, and RTK/RAS/PI3K) were frequently associated with canine aberrations. Analysis of oligodendrogliomas revealed regions of chromosomal losses syntenic to human 1p involving tumor suppressor genes, such as CDKN2C, as well as genes associated with apoptosis, autophagy, and response to chemotherapy and radiation. Analysis of high frequency chromosomal aberrations with respect to human orthologues may provide insight into both novel and common pathways in gliomagenesis and response to therapy.
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Affiliation(s)
- Peter J Dickinson
- From the Departments of Surgical and Radiological Sciences (PJD, DY, RAL), Pathology, Microbiology and Immunology (RJH), and Population Health & Reproduction (DB), School of Veterinary Medicine, University of California, Davis, and Bioinformatics Core, UC Davis Genome Center (NJ) University of California, Davis, California.
| | - Dan York
- From the Departments of Surgical and Radiological Sciences (PJD, DY, RAL), Pathology, Microbiology and Immunology (RJH), and Population Health & Reproduction (DB), School of Veterinary Medicine, University of California, Davis, and Bioinformatics Core, UC Davis Genome Center (NJ) University of California, Davis, California
| | - Robert J Higgins
- From the Departments of Surgical and Radiological Sciences (PJD, DY, RAL), Pathology, Microbiology and Immunology (RJH), and Population Health & Reproduction (DB), School of Veterinary Medicine, University of California, Davis, and Bioinformatics Core, UC Davis Genome Center (NJ) University of California, Davis, California
| | - Richard A LeCouteur
- From the Departments of Surgical and Radiological Sciences (PJD, DY, RAL), Pathology, Microbiology and Immunology (RJH), and Population Health & Reproduction (DB), School of Veterinary Medicine, University of California, Davis, and Bioinformatics Core, UC Davis Genome Center (NJ) University of California, Davis, California
| | - Nikhil Joshi
- From the Departments of Surgical and Radiological Sciences (PJD, DY, RAL), Pathology, Microbiology and Immunology (RJH), and Population Health & Reproduction (DB), School of Veterinary Medicine, University of California, Davis, and Bioinformatics Core, UC Davis Genome Center (NJ) University of California, Davis, California
| | - Danika Bannasch
- From the Departments of Surgical and Radiological Sciences (PJD, DY, RAL), Pathology, Microbiology and Immunology (RJH), and Population Health & Reproduction (DB), School of Veterinary Medicine, University of California, Davis, and Bioinformatics Core, UC Davis Genome Center (NJ) University of California, Davis, California
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14
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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: 28] [Impact Index Per Article: 3.1] [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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Nauen D, Haley L, Lin MT, Perry A, Giannini C, Burger PC, Rodriguez FJ. Molecular Analysis of Pediatric Oligodendrogliomas Highlights Genetic Differences with Adult Counterparts and Other Pediatric Gliomas. Brain Pathol 2015. [PMID: 26206478 DOI: 10.1111/bpa.12291] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Oligodendroglioma represents a distinctive neoplasm in adults but similar neoplasms occur rarely in children. We studied 20 cases of pediatric oligodendroglioma by SNP array (median age 9 years, range 1-19; 15 grade II and 5 grade III). Cytogenetic abnormalities were present in 8 (53%) grade II and all five anaplastic oligodendrogliomas. Most changes were in the form of deletion and copy neutral loss of heterozygosity (LOH). The most common abnormality was 1p deletion (n = 5). Whole arm 1p19q co-deletion was present in three cases from adolescent patients and 9p loss in 3, including one low-grade oligodendroglioma with CDKN2A homozygous deletion. Common losses were largely limited to the anaplastic subset (n = 5) and included 3q29 (n = 3), 11p (n = 3), 17q (n = 3), 4q (n = 2), 6p (n = 2), 13q (n = 2), 14q (n = 2), 17p (n = 2) and whole Ch 18 loss (n = 2). Gains were non-recurrent except for whole Ch 7 (n = 2) and gain on 12q (n = 2) including the MDM2 locus. Possible germ line LOH (or uniparental disomy) was present in seven cases (35%), with one focal abnormality (22q13.1-13.2) in two. BRAF-KIAA1549 fusions and BRAF p.V600E mutations were absent (n = 13 and 8). In summary, cytogenetic alterations in pediatric oligodendrogliomas are characterized mostly by genomic losses, particularly in anaplastic tumors.
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Affiliation(s)
- David Nauen
- Department of Pathology, Division of Neuropathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Lisa Haley
- Department of Pathology, Division of Neuropathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Ming-Tseh Lin
- Department of Pathology, Division of Neuropathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Arie Perry
- Department of Pathology, Division of Neuropathology, University of California San Francisco School of Medicine, San Francisco, CA
| | - Caterina Giannini
- Laboratory of Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN
| | - Peter C Burger
- Department of Pathology, Division of Neuropathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Fausto J Rodriguez
- Department of Pathology, Division of Neuropathology, Johns Hopkins University School of Medicine, Baltimore, MD
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16
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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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17
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Dudley JC, Gurda GT, Tseng LH, Anderson DA, Chen G, Taube JM, Gocke CD, Eshleman JR, Lin MT. Tumor cellularity as a quality assurance measure for accurate clinical detection of BRAF mutations in melanoma. Mol Diagn Ther 2015; 18:409-18. [PMID: 24604154 DOI: 10.1007/s40291-014-0091-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
BACKGROUND Detection of BRAF mutations is an established standard of care to predict small-molecule inhibitor (vemurafenib) response in metastatic melanoma. Molecular assays should be designed to detect not only the most common p.V600E mutation, but also p.V600K and other non-p.V600E mutations. OBJECTIVE The purpose of this study was to assess if tumor cellularity can function as a quality assurance (QA) measure in molecular diagnostics. Potential causes of discrepancy between the observed and predicted mutant allele percentage were also explored. METHODS We correlated pathologist-generated estimates of tumor cellularity versus mutant allele percentage via pyrosequencing as a QA measure for BRAF mutation detection in formalin-fixed, paraffin-embedded melanoma specimens. RESULTS BRAF mutations were seen in 27/62 (44 %) specimens, with 93 % p.V600E and 7 % non-p.V600E. Correlation between p.V600E mutant percentage and tumor cellularity was poor-moderate (r = -0.02; p = 0.8), primarily because six samples showed a low p.V600E signal despite high tumor cellularity. A QA investigation revealed that our initial pyrosequencing assay showed a false positive, weak p.V600E signal in specimens with a p.V600K mutation. A redesigned assay detected BRAF mutations in 50/131 (38 %) specimens, including 30 % non-p.V600E. This revised assay showed strong correlation between p.V600E BRAF mutant percentage and tumor cellularity (r = 0.76; p ≤ 0.01). Re-evaluation of the previously discordant samples by the revised assay confirmed a high level of p.V600K mutation in five specimens. CONCLUSIONS Pathologists play important roles in molecular diagnostics, beyond identification of correct cells for testing. Accurate evaluation of tumor cellularity not only ensures sufficient material for required analytic sensitivity, but also provides an independent QA measure of the molecular assays.
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Affiliation(s)
- Jonathan C Dudley
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Park SB202, 600 North Wolfe St., Baltimore, MD, 21287, USA
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18
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Abstract
Oligodendrogliomas are an important adult form of diffuse gliomas with a distinctive clinical and genetic profile. Histologically similar tumors occurring rarely in children are incompletely characterized. We studied 50 patients with oligodendrogliomas (median age at diagnosis 8 y, range 7 mo to 20 y). Tumors resembling dysembryoplastic neuroepithelial tumors or pilocytic astrocytomas or those having a "mixed" histology were excluded. Tumors at first diagnosis were low grade (n=38) or anaplastic (n=12). Histologic features included uniform round cells with perinuclear halos (100%), secondary structures (predominantly perineuronal satellitosis) (90%), calcifications (46%), and microcysts (44%). Sequential surgical specimens were obtained in 8 low-grade oligodendroglioma patients, with only 1 progressing to anaplasia. Studies for 1p19q performed in 40 cases demonstrated intact 1p19q loci in 29 (73%), 1p19q codeletion in 10 (25%), and 1p deletion with intact 19q in 1 (2%). Except for 2 young patients (3 and 11 y of age), patients with 1p19q codeletion were older than 16 years at diagnosis. Mutant IDH1 (R132H) protein immunohistochemistry was positive in 4 (of 22) (18%) cases, 3 of which also had 1p19q codeletion, whereas 1p19q status was not available on the fourth case. There was a nonsignificant trend for worse overall survival in grade III tumors, but no significant association with age, extent of resection, or 1p19q status. In summary, oligodendrogliomas with classic histology occur in the pediatric population but lack 1p19q codeletion and IDH1 (R132H) mutations in most instances. They are predominantly low grade, recur/clinically progress in a subset, but demonstrate a relatively low frequency of histologic progression.
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19
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Ho CY, Mosier S, Safneck J, Salomao DR, Miller NR, Eberhart CG, Gocke CD, Batista DAS, Rodriguez FJ. Genetic profiling by single-nucleotide polymorphism-based array analysis defines three distinct subtypes of orbital meningioma. Brain Pathol 2014; 25:193-201. [PMID: 24773246 DOI: 10.1111/bpa.12150] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 04/23/2014] [Indexed: 12/12/2022] Open
Abstract
Orbital meningiomas can be classified as primary optic nerve sheath (ON) meningiomas, primary intraorbital ectopic (Ob) meningiomas and spheno-orbital (Sph-Ob) meningiomas based on anatomic site. Single-nucleotide polymorphism (SNP)-based array analysis with the Illumina 300K platform was performed on formalin-fixed, paraffin-embedded tissue from 19 orbital meningiomas (5 ON, 4 Ob and 10 Sph-Ob meningiomas). Tumors were World Health Organization (WHO) grade I except for two grade II meningiomas, and one was NF2-associated. We found genomic alterations in 68% (13 of 19) of orbital meningiomas. Sph-Ob tumors frequently exhibited monosomy 22/22q loss (70%; 7/10) and deletion of chromosome 1p, 6q and 19p (50% each; 5/10). Among genetic alterations, loss of chromosome 1p and 6q were more frequent in clinically progressive tumors. Chromosome 22q loss also was detected in the majority of Ob meningiomas (75%; 3/4) but was infrequent in ON meningiomas (20%; 1/5). In general, Ob tumors had fewer chromosome alterations than Sph-Ob and ON tumors. Unlike Sph-Ob meningiomas, most of the Ob and ON meningiomas did not progress even after incomplete excision, although follow-up was limited in some cases. Our study suggests that ON, Ob and Sph-Ob meningiomas are three molecularly distinct entities. Our results also suggest that molecular subclassification may have prognostic implications.
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Affiliation(s)
- Cheng-Ying Ho
- Department of Pathology, Johns Hopkins University, Baltimore, MD; Division of Pathology, Children's National Medical Center, Washington, DC
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20
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Codispoti KET, Mosier S, Ramsey R, Lin MT, Rodriguez FJ. Genetic and pathologic evolution of early secondary gliosarcoma. Brain Tumor Pathol 2013; 31:40-6. [PMID: 23324827 DOI: 10.1007/s10014-012-0132-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Accepted: 12/23/2012] [Indexed: 12/18/2022]
Abstract
Gliosarcoma is a subset of glioblastoma with glial and mesenchymal components. True secondary gliosarcomas (i.e. progressing from lower-grade precursors) in the absence of radiation therapy are very rare. We report the unique case of a 61-year-old male who developed a fibrillary astrocytoma (WHO grade II). In the absence of adjuvant therapy the tumor recurred 3 years later as a gliosarcoma comprising an infiltrating glial component and a curious, early high-grade sarcomatous component surrounding intratumoral vessels. DNA was extracted from formalin fixed paraffin-embedded tissues from the precursor low-grade glioma and from the glioma and sarcomatous components at progression. Samples were hybridized separately to a 300 k Illumina SNP array. IDH1(R132H) mutant protein immunohistochemistry was positive in all tissue components. Alterations identified in all samples included dup(1)(q21q41), del(1)(q41qter), del(2)(q31.1), del(2)(q36.3qter), del(4)(q35.1qter), dup(7)(q22.2q36.3), del(7)(q36.3qter), del(9)(p21.3pter), dup(10)(p13pter), del(10)(q26.13q26.3), dup(17) (q12qter), and copy neutral LOH(20)(p11.23p11.21). The recurrent tumor had additional alterations, including del(3)(p21.31q13.31), del(18)(q21.2qter), and a homozygous del(9)(p21.3)(CDKN2A locus) and the sarcoma component had, in addition, del(4)(p14pter), del(6)(q12qter), del(11)(q24.3qter), and del(16)(p11.2pter). In conclusion, unique copy number alterations were identified during tumor progression from a low-grade glioma to gliosarcoma. A subset of alterations developed specifically in the sarcomatous component.
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Rodriguez FJ, Perry A, Rosenblum MK, Krawitz S, Cohen KJ, Lin D, Mosier S, Lin MT, Eberhart CG, Burger PC. Disseminated oligodendroglial-like leptomeningeal tumor of childhood: a distinctive clinicopathologic entity. Acta Neuropathol 2012; 124:627-41. [PMID: 22941225 DOI: 10.1007/s00401-012-1037-x] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Revised: 08/19/2012] [Accepted: 08/19/2012] [Indexed: 10/27/2022]
Abstract
Rare, generally pediatric oligodendroglioma-like neoplasms with extensive leptomeningeal dissemination have been interpreted variably as glial, oligodendroglial or glioneuronal. The clinicopathologic features have not been fully characterized. We studied 36 patients, 12 females and 24 males with a median age of 5 years (range 5 months-46 years). MRI demonstrated leptomeningeal enhancement, frequently with cystic or nodular T2 hyperintense lesions within the spinal cord/brain along the subpial surface. A discrete intraparenchymal lesion, usually in the spinal cord, was found in 25 (of 31) (81 %). Tumors contained oligodendroglioma-like cells with low-mitotic activity (median 0 per 10 high power fields, range 0-4), and rare ganglion/ganglioid cells in 6 cases (17 %). Tumors were mostly low-grade, with anaplastic progression in 8 (22 %). Immunohistochemistry demonstrated strong reactivity for OLIG2 (7 of 9) (78 %), and moderate/strong S100 (11 of 12) (92 %), GFAP (12 of 31) (39 %) and synaptophysin (19 of 27) (70 %). NeuN, EMA, and mutant IDH1 (R132H) protein were negative. Median MIB1 labeling index was 1.5 % (range <1-30 %). FISH (n = 13) or SNP array (n = 2) demonstrated 1p loss/intact 19q in 8 (53 %), 1p19q co-deletion in 3 (20 %), and no 1p or 19q loss in 4 (27 %). Clinical follow-up (n = 24) generally showed periods of stability or slow progression, but a subset of tumors progressed to anaplasia and behaved more aggressively. Nine patients (38 %) died 3 months-21 years after diagnosis (median total follow-up 5 years). We report a series of a neoplasm with distinct clinicopathologic and molecular features. Although most progress slowly, a significant fraction develop aggressive features.
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22
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DNA fragmentation simulation method (FSM) and fragment size matching improve aCGH performance of FFPE tissues. PLoS One 2012; 7:e38881. [PMID: 22719973 PMCID: PMC3376148 DOI: 10.1371/journal.pone.0038881] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Accepted: 05/14/2012] [Indexed: 11/30/2022] Open
Abstract
Whole-genome copy number analysis platforms, such as array comparative genomic hybridization (aCGH) and single nucleotide polymorphism (SNP) arrays, are transformative research discovery tools. In cancer, the identification of genomic aberrations with these approaches has generated important diagnostic and prognostic markers, and critical therapeutic targets. While robust for basic research studies, reliable whole-genome copy number analysis has been unsuccessful in routine clinical practice due to a number of technical limitations. Most important, aCGH results have been suboptimal because of the poor integrity of DNA derived from formalin-fixed paraffin-embedded (FFPE) tissues. Using self-hybridizations of a single DNA sample we observed that aCGH performance is significantly improved by accurate DNA size determination and the matching of test and reference DNA samples so that both possess similar fragment sizes. Based on this observation, we developed a novel DNA fragmentation simulation method (FSM) that allows customized tailoring of the fragment sizes of test and reference samples, thereby lowering array failure rates. To validate our methods, we combined FSM with Universal Linkage System (ULS) labeling to study a cohort of 200 tumor samples using Agilent 1 M feature arrays. Results from FFPE samples were equivalent to results from fresh samples and those available through the glioblastoma Cancer Genome Atlas (TCGA). This study demonstrates that rigorous control of DNA fragment size improves aCGH performance. This methodological advance will permit the routine analysis of FFPE tumor samples for clinical trials and in daily clinical practice.
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