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Nakashima T, Yamamoto R, Ohno M, Sugino H, Takahashi M, Funakoshi Y, Nambu S, Uneda A, Yanagisawa S, Uzuka T, Arakawa Y, Hanaya R, Ishida J, Yoshimoto K, Saito R, Narita Y, Suzuki H. Development of a rapid and comprehensive genomic profiling test supporting diagnosis and research for gliomas. Brain Tumor Pathol 2024; 41:50-60. [PMID: 38332448 DOI: 10.1007/s10014-023-00476-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/25/2023] [Indexed: 02/10/2024]
Abstract
A prompt and reliable molecular diagnosis for brain tumors has become crucial in precision medicine. While Comprehensive Genomic Profiling (CGP) has become feasible, there remains room for enhancement in brain tumor diagnosis due to the partial lack of essential genes and limitations in broad copy number analysis. In addition, the long turnaround time of commercially available CGPs poses an additional obstacle to the timely implementation of results in clinics. To address these challenges, we developed a CGP encompassing 113 genes, genome-wide copy number changes, and MGMT promoter methylation. Our CGP incorporates not only diagnostic genes but also supplementary genes valuable for research. Our CGP enables us to simultaneous identification of mutations, gene fusions, focal and broad copy number alterations, and MGMT promoter methylation status, with results delivered within a minimum of 4 days. Validation of our CGP, through comparisons with whole-genome sequencing, RNA sequencing, and pyrosequencing, has certified its accuracy and reliability. We applied our CGP for 23 consecutive cases of intracranial mass lesions, which demonstrated its efficacy in aiding diagnosis and prognostication. Our CGP offers a comprehensive and rapid molecular profiling for gliomas, which could potentially apply to clinical practices and research primarily in the field of brain tumors.
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Affiliation(s)
- Takuma Nakashima
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
- Department of Neurosurgery, Nagoya University School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Ryo Yamamoto
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
- Department of Neurosurgery, Nagoya University School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Makoto Ohno
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Hirokazu Sugino
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Masamichi Takahashi
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Yusuke Funakoshi
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Shohei Nambu
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Atsuhito Uneda
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Shunsuke Yanagisawa
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Takeo Uzuka
- Department of Neurosurgery, Dokkyo Medical University, 880 Kitakobaya-Shi, Mibu, Shimotsuga-Gun, Tochigi, 321-0293, Japan
| | - Yoshiki Arakawa
- Department of Neurosurgery, Kyoto University Graduate School of Medicine, 54 Kawahara-Cho Shogoin Sakyo-Ku, Kyoto, 606-8507, Japan
| | - Ryosuke Hanaya
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1, Sakuragaoka, Kagoshima, 890-8544, Japan
| | - Joji Ishida
- Department of Neurosurgery, Okayama University Graduate School of Medicine, 2-5-1 Shikata-Cho, Kita-Ku, Okayama, 700-8558, Japan
| | - Koji Yoshimoto
- Department of Neurosurgery, Graduate School of Medical Science, Kyushu University, 3-1-1, Maidashi, Higashi-Ku, Fukuoka City, 812-8582, Japan
| | - Ryuta Saito
- Department of Neurosurgery, Nagoya University School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Yoshitaka Narita
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan
| | - Hiromichi Suzuki
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045, Japan.
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2
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Rogers JL, Wall T, Acquaye-Mallory AA, Boris L, Kim Y, Aldape K, Quezado MM, Butman JA, Smirniotopoulos JG, Chaudhry H, Tsien CI, Chittiboina P, Zaghloul K, Aboud O, Avgeropoulos NG, Burton EC, Cachia DM, Dixit KS, Drappatz J, Dunbar EM, Forsyth P, Komlodi-Pasztor E, Mandel J, Ozer BH, Lee EQ, Ranjan S, Lukas RV, Raygada M, Salacz ME, Smith-Cohn MA, Snyder J, Soldatos A, Theeler BJ, Widemann BC, Camphausen KA, Heiss JD, Armstrong TS, Gilbert MR, Penas-Prado M. Virtual multi-institutional tumor board: a strategy for personalized diagnoses and management of rare CNS tumors. J Neurooncol 2024; 167:349-359. [PMID: 38427131 PMCID: PMC11023967 DOI: 10.1007/s11060-024-04613-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/17/2024] [Indexed: 03/02/2024]
Abstract
PURPOSE Multidisciplinary tumor boards (MTBs) integrate clinical, molecular, and radiological information and facilitate coordination of neuro-oncology care. During the COVID-19 pandemic, our MTB transitioned to a virtual and multi-institutional format. We hypothesized that this expansion would allow expert review of challenging neuro-oncology cases and contribute to the care of patients with limited access to specialized centers. METHODS We retrospectively reviewed records from virtual MTBs held between 04/2020-03/2021. Data collected included measures of potential clinical impact, including referrals to observational or therapeutic studies, referrals for specialized neuropathology analysis, and whether molecular findings led to a change in diagnosis and/or guided management suggestions. RESULTS During 25 meetings, 32 presenters discussed 44 cases. Approximately half (n = 20; 48%) involved a rare central nervous system (CNS) tumor. In 21% (n = 9) the diagnosis was changed or refined based on molecular profiling obtained at the NIH and in 36% (n = 15) molecular findings guided management. Clinical trial suggestions were offered to 31% (n = 13), enrollment in the observational NCI Natural History Study to 21% (n = 9), neuropathology review and molecular testing at the NIH to 17% (n = 7), and all received management suggestions. CONCLUSION Virtual multi-institutional MTBs enable remote expert review of CNS tumors. We propose them as a strategy to facilitate expert opinions from specialized centers, especially for rare CNS tumors, helping mitigate geographic barriers to patient care and serving as a pre-screening tool for studies. Advanced molecular testing is key to obtaining a precise diagnosis, discovering potentially actionable targets, and guiding management.
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Affiliation(s)
- James L Rogers
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
| | - Thomas Wall
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
| | - Alvina A Acquaye-Mallory
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
| | - Lisa Boris
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
| | - Yeonju Kim
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
- Wayne State University School of Medicine, 540 E Canfield St, Detroit, MI, 48201, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr, Bethesda, MD, 20892, USA
| | - Martha M Quezado
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr, Bethesda, MD, 20892, USA
| | - John A Butman
- Radiology and Imaging Sciences, Clinical Center, National Institutes of Health, 10 Center Dr, Bethesda, MD, 20892, USA
| | - James G Smirniotopoulos
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
| | - Huma Chaudhry
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr, Bethesda, MD, 20892, USA
| | - Christina I Tsien
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
- Proton Therapy Center, Sibley Memorial Hospital, Johns Hopkins Medicine, 5255 Loughboro Rd NW, Washington, DC, 20016, USA
| | - Prashant Chittiboina
- Surgical Neurology Branch,, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 10 Center Dr, Bethesda, MD, 20892, USA
| | - Kareem Zaghloul
- Surgical Neurology Branch,, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 10 Center Dr, Bethesda, MD, 20892, USA
| | - Orwa Aboud
- Department of Neurology and Neurological Surgery, UC Davis Comprehensive Cancer Center, 4860 Y Street, Sacramento, CA, 95817, USA
| | - Nicholas G Avgeropoulos
- Brain and Spine Tumor Program, Orlando Health Cancer Institute, 1400 S. Orange Ave, Orlando, FL, 32806, USA
- Global Medical Affairs, Novocure GmbH, D4 Pk. 6, 6039, Root, Switzerland
| | - Eric C Burton
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
| | - David M Cachia
- Department of Hematology/Oncology, University of Massachusetts, 55 Lake Ave, Worcester, MA, 01655, USA
| | - Karan S Dixit
- Lou and Jean Malnati Brain Tumor Institute, Northwestern University Feinberg School of Medicine, 675 N St Clair St, Chicago, IL, 60611, USA
| | - Jan Drappatz
- Department of Neurology, University of Pittsburgh Medical Center, 5115 Centre Ave, Pittsburgh, PA, 15232, USA
| | - Erin M Dunbar
- Piedmont Brain Tumor Center, Piedmont Atlanta Hospital, Atlanta, GA, 2001 Peachtree St30309, USA
| | - Peter Forsyth
- Department of Neuro-Oncology, Moffitt Cancer Center, 12902 USF Magnolia Drive, Tampa, FL, 33612, USA
| | - Edina Komlodi-Pasztor
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
- Department of Neurology, MedStar Georgetown University Hospital, 3800 Reservoir Road Washington, Washington DC, 20007, USA
| | - Jacob Mandel
- Department of Neurology, Baylor College of Medicine, 7200 Cambridge St, Houston, TX, 77030, USA
| | - Byram H Ozer
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
| | - Eudocia Q Lee
- Center for Neuro-Oncology, Dana Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Surabhi Ranjan
- Department of Neurology, Cleveland Clinic Florida, Weston Hospital, 2950 Cleveland Clinic Boulevard, Weston, FL, 33331, US
| | - Rimas V Lukas
- Lou and Jean Malnati Brain Tumor Institute, Northwestern University Feinberg School of Medicine, 675 N St Clair St, Chicago, IL, 60611, USA
| | - Margarita Raygada
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 1 Center Dr, Bethesda, MD, 20892, USA
| | - Michael E Salacz
- Department of Hematology and Medical Oncology, MD Anderson Cancer Center at Cooper, Cooper University Health Care, Two Cooper Plaza, Camden, NJ, 08103, USA
| | - Matthew A Smith-Cohn
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
- Benefis Sletten Cancer Institute, 1117 29Th St. S, Great Falls, MT, 59405, USA
| | - James Snyder
- Hermelin Brain Tumor Center, Henry Ford Cancer Institute, 2800 W Grand Blvd, Detroit, MI, 48202, USA
| | - Ariane Soldatos
- National Institute of Neurological Disorders and Stroke,, National Institutes of Health, 10 Center Dr, Bethesda, MD, 20892, USA
| | - Brett J Theeler
- School of Medicine, Uniformed Services University, 4301 Jones Bridge Rd, Bethesda, MD, 20814, USA
| | - Brigitte C Widemann
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr, Bethesda, MD, 20892, USA
| | - Kevin A Camphausen
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr, Bethesda, MD, 20892, USA
| | - John D Heiss
- Surgical Neurology Branch,, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 10 Center Dr, Bethesda, MD, 20892, USA
| | - Terri S Armstrong
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA
| | - Marta Penas-Prado
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9030 Old Georgetown Rd, Bethesda, MD, 20892, USA.
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Pitcher JL, Alexander N, Miranda PJ, Johns TG. ErbB4 in the brain: Focus on high grade glioma. Front Oncol 2022; 12:983514. [PMID: 36119496 PMCID: PMC9471956 DOI: 10.3389/fonc.2022.983514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) family of receptor tyrosine kinases (RTKs) consists of EGFR, ErbB2, ErbB3, and ErbB4. These receptors play key roles in cell proliferation, angiogenesis, cell migration, and in some cases, tumor promotion. ErbB4 is a unique member of the EGFR family, implicated not only in pro-tumorigenic mechanisms, such as cell proliferation and migration, but also in anti-tumorigenic activities, including cell differentiation and apoptosis. ErbB4 is differentially expressed in a wide variety of tissues, and interestingly, as different isoforms that result in vastly different signalling outcomes. Most studies have either ignored the presence of these isoforms or used overexpression models that may mask the true function of ErbB4. ErbB4 is widely expressed throughout the body with significant expression in skeletal tissue, mammary glands, heart, and brain. Knockout models have demonstrated embryonic lethality due to disrupted heart and brain development. Despite high expression in the brain and a critical role in brain development, remarkably little is known about the potential signalling activity of ErbB4 in brain cancer.This review focuses on the unique biology of ErbB4 in the brain, and in particular, highlights brain cancer research findings. We end the review with a focus on high grade gliomas, primarily glioblastoma, a disease that has been shown to involve EGFR and its mutant forms. The role of the different ErbB4 isotypes in high grade gliomas is still unclear and future research will hopefully shed some light on this question.
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Affiliation(s)
- Jamie-Lee Pitcher
- Oncogenic Signalling Laboratory, Telethon Kids Institute, Nedlands, WA, Australia
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, Australia
- *Correspondence: Jamie-Lee Pitcher,
| | - Naomi Alexander
- Oncogenic Signalling Laboratory, Telethon Kids Institute, Nedlands, WA, Australia
| | - Panimaya Jeffreena Miranda
- Oncogenic Signalling Laboratory, Telethon Kids Institute, Nedlands, WA, Australia
- Division of Paediatrics/Centre for Child Health Research, University of Western Australia, Crawley, WA, Australia
| | - Terrance G. Johns
- Oncogenic Signalling Laboratory, Telethon Kids Institute, Nedlands, WA, Australia
- Division of Paediatrics/Centre for Child Health Research, University of Western Australia, Crawley, WA, Australia
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Chan AKY, Shi ZF, Li KKW, Wang WW, Chen H, Chung NYF, Chan DTM, Poon WS, Loong HHF, Liu XZ, Zhang ZY, Mao Y, Ng HK. Combinations of Single-Gene Biomarkers Can Precisely Stratify 1,028 Adult Gliomas for Prognostication. Front Oncol 2022; 12:839302. [PMID: 35558510 PMCID: PMC9090434 DOI: 10.3389/fonc.2022.839302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 03/04/2022] [Indexed: 11/23/2022] Open
Abstract
Advanced genomic techniques have now been incorporated into diagnostic practice in neuro-oncology in the literature. However, these assays are expensive and time-consuming and demand bioinformatics expertise for data interpretation. In contrast, single-gene tests can be run much more cheaply, with a short turnaround time, and are available in general pathology laboratories. The objective of this study was to establish a molecular grading scheme for adult gliomas using combinations of commonly available single-gene tests. We retrospectively evaluated molecular diagnostic data of 1,275 cases of adult diffuse gliomas from three institutions where we were testing for IDH1/2 mutation, TERTp mutation, 1p19q codeletion, EGFR amplification, 10q deletion, BRAF V600E, and H3 mutations liberally in our regular diagnostic workup. We found that a molecular grading scheme of Group 1 (1p19q codeleted, IDH mutant), Group 2 (IDH mutant, 1p19q non-deleted, TERT mutant), Group 3 (IDH mutant, 1p19q non-deleted, TERT wild type), Group 4 (IDH wild type, BRAF mutant), Group 5 (IDH wild type, BRAF wild type and not possessing the criteria of Group 6), and Group 6 (IDH wild type, and any one of TERT mutant, EGFR amplification, 10q deletion, or H3 mutant) could significantly stratify this large cohort of gliomas for risk. A total of 1,028 (80.6%) cases were thus classifiable with sufficient molecular data. There were 270 cases of molecular Group 1, 59 cases of molecular Group 2, 248 cases of molecular Group 3, 27 cases of molecular Group 4, 117 cases of molecular Group 5, and 307 cases of molecular Group 6. The molecular groups were independent prognosticators by multivariate analyses and in specific instances, superseded conventional histological grades. We were also able to validate the usefulness of the Groups with a cohort retrieved from The Cancer Genome Atlas (TCGA) where similar molecular tests were liberally available. We conclude that a single-gene molecular stratification system, useful for fine prognostication, is feasible and can be adopted by a general pathology laboratory.
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Affiliation(s)
- Aden Ka-Yin Chan
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Hong Kong and Shanghai Brain Consortium (HSBC), Hong Kong, Hong Kong SAR, China
| | - Zhi-Feng Shi
- Hong Kong and Shanghai Brain Consortium (HSBC), Hong Kong, Hong Kong SAR, China.,Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Kay Ka-Wai Li
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Hong Kong and Shanghai Brain Consortium (HSBC), Hong Kong, Hong Kong SAR, China
| | - Wei-Wei Wang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hong Chen
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Nellie Yuk-Fei Chung
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Danny Tat-Ming Chan
- Division of Neurosurgery, Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Wai-Sang Poon
- Division of Neurosurgery, Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Herbert Ho-Fung Loong
- Department of Clinical Oncology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Xian-Zhi Liu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhen-Yu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Mao
- Hong Kong and Shanghai Brain Consortium (HSBC), Hong Kong, Hong Kong SAR, China.,Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Hong Kong and Shanghai Brain Consortium (HSBC), Hong Kong, Hong Kong SAR, China
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5
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Lorenz J, Rothhammer-Hampl T, Zoubaa S, Bumes E, Pukrop T, Kölbl O, Corbacioglu S, Schmidt NO, Proescholdt M, Hau P, Riemenschneider MJ. A comprehensive DNA panel next generation sequencing approach supporting diagnostics and therapy prediction in neurooncology. Acta Neuropathol Commun 2020; 8:124. [PMID: 32758285 PMCID: PMC7405456 DOI: 10.1186/s40478-020-01000-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/17/2020] [Indexed: 11/30/2022] Open
Abstract
Recent updates in the classification of central nervous system (CNS) tumors have increased the need for molecular testing. Assessment of multiple alterations in parallel, complex combinations of gene sequence and chromosomal changes, as well as therapy prediction by identification of actionable mutations are the major challenges. We here report on a customized next generation sequencing (NGS)-based DNA panel assay that combines diagnostic and predictive testing and -as a comprehensive approach- allows for simultaneous single nucleotide variant (SNP) / small insertion/deletion (InDel), copy number variation (CNV) and loss of heterozygosity (LOH) detection. We analyzed formalin-fixed and paraffin-embedded (FFPE) DNA from a total of 104 patients with CNS tumors. After amplicon capture-based library preparation, sequencing was performed on the relatively cost-efficient Illiumina MiniSeq platform and evaluated with freely available bioinformatical tools. 57 genes for exonic SNP/InDel calling (19 of those in intronic regions for CNV analysis), 3 chromosomal arms and 4 entire chromosomes for CNV and LOH analysis were covered. Results were extensively validated. Our approach yielded high accuracy, sensitivity and specificity. It led to refined diagnoses in a relevant number of analyzed cases, reliably enabled complex subclassifications (e.g. for medulloblastomas) and identified actionable targets for clinical use. Thus, our single-platform approach is an efficient and powerful tool to comprehensively support molecular testing in neurooncology. Future functionality is guaranteed as novel upcoming biomarkers can be easily incorporated in a modular panel design.
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Affiliation(s)
- Julia Lorenz
- Department of Neuropathology, Regensburg University Hospital, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany
- Wilhelm Sander Neuro-Oncology Unit, Regensburg University Hospital, Regensburg, Germany
| | - Tanja Rothhammer-Hampl
- Department of Neuropathology, Regensburg University Hospital, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany
- Wilhelm Sander Neuro-Oncology Unit, Regensburg University Hospital, Regensburg, Germany
| | - Saida Zoubaa
- Department of Neuropathology, Regensburg University Hospital, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany
- Wilhelm Sander Neuro-Oncology Unit, Regensburg University Hospital, Regensburg, Germany
| | - Elisabeth Bumes
- Wilhelm Sander Neuro-Oncology Unit, Regensburg University Hospital, Regensburg, Germany
- Department of Neurology, Regensburg University Hospital, Regensburg, Germany
| | - Tobias Pukrop
- Department of Internal Medicine III, Regensburg University Hospital, Regensburg, Germany
| | - Oliver Kölbl
- Wilhelm Sander Neuro-Oncology Unit, Regensburg University Hospital, Regensburg, Germany
- Department of Radiotherapy, Regensburg University Hospital, Regensburg, Germany
| | - Selim Corbacioglu
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Regensburg University Hospital, Regensburg, Germany
| | - Nils O Schmidt
- Wilhelm Sander Neuro-Oncology Unit, Regensburg University Hospital, Regensburg, Germany
- Department of Neurosurgery, University Hospital Regensburg, Regensburg, Germany
| | - Martin Proescholdt
- Wilhelm Sander Neuro-Oncology Unit, Regensburg University Hospital, Regensburg, Germany
- Department of Neurosurgery, University Hospital Regensburg, Regensburg, Germany
| | - Peter Hau
- Wilhelm Sander Neuro-Oncology Unit, Regensburg University Hospital, Regensburg, Germany
- Department of Neurology, Regensburg University Hospital, Regensburg, Germany
| | - Markus J Riemenschneider
- Department of Neuropathology, Regensburg University Hospital, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany.
- Wilhelm Sander Neuro-Oncology Unit, Regensburg University Hospital, Regensburg, Germany.
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