scholarly journals Advances in the classification of pediatric brain tumors through DNA methylation profiling: From research tool to frontline diagnostic

Cancer ◽  
2018 ◽  
Vol 124 (21) ◽  
pp. 4168-4180 ◽  
Author(s):  
Rahul Kumar ◽  
Anthony P. Y. Liu ◽  
Brent A. Orr ◽  
Paul A. Northcott ◽  
Giles W. Robinson
Keyword(s):  
Dna Methylation ◽  
Brain Tumors ◽  
Pediatric Brain Tumors ◽  
Research Tool ◽  
Dna Methylation Profiling ◽  
Pediatric Brain ◽  
Methylation Profiling

scholarly journals Advances in the molecular classification of pediatric brain tumors: a guide to the galaxy

2020 ◽  
Vol 251 (3) ◽  
pp. 249-261 ◽  
Author(s):  
Chantel Cacciotti ◽  
Adam Fleming ◽  
Vijay Ramaswamy
Keyword(s):  
Brain Tumors ◽  
Molecular Classification ◽  
Pediatric Brain Tumors ◽  
The Galaxy ◽  
Pediatric Brain

scholarly journals PATH-21. CLINICAL UTILITY OF DNA METHYLATION PROFILING FOR DIAGNOSIS OF CHALLENGING CENTRAL NERVOUS SYSTEM TUMORS: THE TORONTO EXPERIENCE

2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi147-vi147
Author(s):  
Shirin Karimi ◽  
Jeffrey Zuccato ◽  
Yasin Mamatjan ◽  
Sheila Mansouri ◽  
Suganth Suppiah ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Central Nervous System ◽  
Nervous System ◽  
Clinical Utility ◽  
Cns Tumors ◽  
Cns Tumor ◽  
Dna Methylation Profiling ◽  
Diffuse Gliomas ◽  
Methylation Profiling

Abstract The update on the WHO classification of central nervous system (CNS) tumors incorporated molecular signatures for a more accurate diagnosis. Recently, DKFZ has demonstrated the utility of DNA methylation profiling(MP) for molecular classification of CNS tumors. We performed a prospective clinical study over the last three years to evaluate the clinical utility ofDNA MP on FFPE samples of 66 challenging CNS tumor cases using online DKFZ classifier. Eleven samples were excluded due to low tumor DNA content or low calibration(predictive) scores(CS)< 0.3.DNA MP confirmed the original pathology diagnoses in 15(27%)cases. The integrated molecular diagnoses were changed in 38/55(70%) including establishment of a new diagnostic entity, change in molecular signature and subtyping. TheWHO grades were changed in 16(27%) of the tumors; about two-thirds resulted in upgrading. We detected non-canonical IDH mutations in 9 diffuse gliomas and the CNV plots revealed false positive FISH results for 1p/19q co-deletion in two diffuse gliomas. The CNV plots contributed to the final diagnosis in 40(72%) patients. The molecular subtypes of medulloblastoma, ependymoma and glioblastoma subclasses were determined in 36(65%) cases. Seventy-five percent of cases with confirmation of initial diagnosis or change in molecular diagnosis had CS > 0.5, among which 51% had a CS >0.9. The median and range CS of cases with new diagnostic entity and confirmed cases were 0.86(0.37–0.99) and 0.98(0.42–0.99), respectably. Furthermore, we detected higher CS in IDH-mutant gliomas in comparison to glioblastoma IDH-wild type(P=0.04). We also observed lower CS in mesenchymal glioblastoma in comparison to other subclasses. The MGMT promoter methylation was determined in 17/20(85%) glioblastoma cases. While the DKFZ group established CS of 0.9 as a cut-off for matching to methylation classes, our findings suggest lower threshold values in challenging CNS tumor cases. Our experience indicates clinical utility of MP of challenging CNS tumors as a reliable ancillary diagnostic tool in routine neuropathology practice.

MicroRNA expression profiling for Molecular Classification of pediatric brain tumors

2011 ◽  
Vol 57 (1) ◽  
pp. 183-184 ◽  
Author(s):  
Simone Treiger Sredni ◽  
Chiang-Ching Huang ◽  
Maria de Fátima Bonaldo ◽  
Tadanori Tomita
Keyword(s):  
Brain Tumors ◽  
Expression Profiling ◽  
Molecular Classification ◽  
Pediatric Brain Tumors ◽  
Microrna Expression ◽  
Pediatric Brain

scholarly journals Application of pattern recognition techniques for classification of pediatric brain tumors by in vivo 3T 1 H‐MR spectroscopy—A multi‐center study

2017 ◽  
Vol 79 (4) ◽  
pp. 2359-2366 ◽  
Author(s):  
Niloufar Zarinabad ◽  
Laurence J. Abernethy ◽  
Shivaram Avula ◽  
Nigel P. Davies ◽  
Daniel Rodriguez Gutierrez ◽  
...  
Keyword(s):  
Pattern Recognition ◽  
Brain Tumors ◽  
Mr Spectroscopy ◽  
Pediatric Brain Tumors ◽  
Pattern Recognition Techniques ◽  
Multi Center Study ◽  
Pediatric Brain ◽  
Center Study

scholarly journals LINC-03. MOLECULAR CLASSIFICATION OF PAEDIATRIC MEDULLOBLASTOMA FROM FOUR TERTIARY CENTRES IN MALAYSIA: DIAGNOSTIC DILEMMA WITH CONVENTIONAL METHODS

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii378-iii378
Author(s):  
Revathi Rajagopal ◽  
Vida Jawin ◽  
Ay Jiuan Teng ◽  
Oy Leng Wong ◽  
Kein Seong Mun ◽  
...  
Keyword(s):  
Dna Methylation ◽  
High Risk ◽  
General Hospital ◽  
Prognostic Significance ◽  
Molecular Classification ◽  
Diagnostic Dilemma ◽  
Dna Methylation Profiling ◽  
Treatment Abandonment ◽  
Methylation Profiling

Abstract OBJECTIVE To determine the prognostic significance of the four molecular subgroups of medulloblastoma (MB) among children in Malaysia. METHODS We assembled MB samples of children &lt; 18 years between January 1999 and July 2017 in University Malaya Medical Centre, Penang General Hospital, Sarawak General Hospital and Sabah Woman and Children’s Hospital. MB was sub-grouped using 850k DNA methylation profiling. RESULTS Fifty-one tumour samples were retrieved. Histopathological subtypes were classic (n=12), MB extensive nodularity/desmoplastic (n=9) and 30 MB results without subtypes. Thirteen patients were M1-M4. Fourteen patients were stratified as standard-risk (SR,27.4%), 22 as high-risk (HR,43.2%) and 15 as high-risk children ≤ 3 years old (iHR,29.4%). Molecular subgrouping revealed 16 Group4, 11 SHH, 10 Group3 and 4 Wnt. In 8 patients, DNA methylation profiling identified a diagnosis other than MB and in 2 samples the DNA was inadequate. For patients &gt;3 years old, the 5-year event-free survival (EFS) was 35.7%±13% in HR and 39.7%±20% in SR. The 5-year overall survival (OS) in these two groups was 43.4%±14% and 41.7±30% respectively. iHR had 5-year EFS and OS of 48.0%±16% and 60.0%±16% respectively. WNT tumours had the best 5y-OS of 66.7±22% of the cohort, albeit significantly lower than other reports, followed by SHH (56.8±17%), Group4 (44.3±17.6%) and Group3 (41.7±18%). Treatment abandonment rate was 20%. CONCLUSION The discrepancy in the histological diagnoses highlights the importance of DNA methylation profiling technique for accurate diagnosis. We observed poor OS across all the subgroups, in part due to treatment abandonment.

scholarly journals Pediatric Brain Tumors: From Modern Classification System to Current Principles of Management

2021 ◽  
Author(s):  
Ahmad Ozair ◽  
Erum Khan ◽  
Vivek Bhat ◽  
Arjumand Faruqi ◽  
Anil Nanda
Keyword(s):  
Brain Tumors ◽  
Pediatric Brain Tumors ◽  
Solid Organ ◽  
Therapeutic Decision ◽  
Modern Classification ◽  
Therapeutic Decision Making ◽  
Pediatric Brain ◽  
Cns Malignancies

Central nervous system (CNS) malignancies contribute significantly to the global burden of cancer. Brain tumors constitute the most common solid organ tumors in children and the second most common malignancies of childhood overall. Accounting for nearly 20% of all pediatric malignancies, these are the foremost cause of cancer-related deaths in children 0–14 years of age. This book chapter provides a state-of-the-art overview of pediatric brain tumors. It discusses their morbidity and mortality and introduces the WHO 2021 classification of CNS tumors, which is critical to therapeutic decision-making. It then describes the modern understanding of tumor grading and its clinical implications, followed by the general principles of diagnosis and management. The chapter then discusses, in detail, those brain tumors which have the highest disease burden in children, including medulloblastoma, astrocytoma, ependymoma, schwannoma, meningioma, amongst others. The landscape of treatment of pediatric brain tumors has been rapidly evolving, with several effective therapies on the horizon.

scholarly journals Multiclass imbalance learning: Improving classification of pediatric brain tumors from magnetic resonance spectroscopy

2016 ◽  
Vol 77 (6) ◽  
pp. 2114-2124 ◽  
Author(s):  
Niloufar Zarinabad ◽  
Martin Wilson ◽  
Simrandip K Gill ◽  
Karen A Manias ◽  
Nigel P Davies ◽  
...  
Keyword(s):  
Magnetic Resonance ◽  
Magnetic Resonance Spectroscopy ◽  
Brain Tumors ◽  
Pediatric Brain Tumors ◽  
Resonance Spectroscopy ◽  
Imbalance Learning ◽  
Pediatric Brain

scholarly journals DNA methylation profiling for molecular classification of adult diffuse lower-grade gliomas

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Sandra Ferreyra Vega ◽  
Thomas Olsson Bontell ◽  
Alba Corell ◽  
Anja Smits ◽  
Asgeir Store Jakola ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Molecular Classification ◽  
Lower Grade ◽  
Who Grade ◽  
Class Prediction ◽  
Mutation Status ◽  
Molecular Features ◽  
Dna Methylation Profiling ◽  
Methylation Profiling

Abstract Background DNA methylation profiling has facilitated and improved the classification of a wide variety of tumors of the central nervous system. In this study, we investigated the potential utility of DNA methylation profiling to achieve molecular diagnosis in adult primary diffuse lower-grade glioma (dLGG) according to WHO 2016 classification system. We also evaluated whether methylation profiling could provide improved molecular characterization and identify prognostic differences beyond the classical histological WHO grade together with IDH mutation status and 1p/19q codeletion status. All patients diagnosed with dLGG in the period 2007–2016 from the Västra Götaland region in Sweden were assessed for inclusion in the study. Results A total of 166 dLGG cases were subjected for genome-wide DNA methylation analysis. Of these, 126 (76%) were assigned a defined diagnostic methylation class with a class prediction score ≥ 0.84 and subclass score ≥ 0.50. The assigned methylation classes were highly associated with their IDH mutation status and 1p/19q codeletion status. IDH-wildtype gliomas were further divided into subgroups with distinct molecular features. Conclusion The stratification of the patients by methylation profiling was as effective as the integrated WHO 2016 molecular reclassification at predicting the clinical outcome of the patients. Our study shows that DNA methylation profiling is a reliable and robust approach for the classification of dLGG into molecular defined subgroups, providing accurate detection of molecular markers according to WHO 2016 classification.

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