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Journal articles on the topic 'NA methylation profiling'

Author: Grafiati

Published: 2 June 2025

Last updated: 31 July 2025

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1

Lobon-Iglesias, María-Jesús, Arnault Tauziede-Espariat, Mamy Andrianteranagna, Zhiyan Han, Julien Masliah-Planchon, and Franck Bourdeaut. "ATRT-27. COST-EFFECTIVE ASSAYS TO SUBGROUP ATRT IN THE DAILY ROUTINE." Neuro-Oncology 22, Supplement_3 (2020): iii281. http://dx.doi.org/10.1093/neuonc/noaa222.026.

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Abstract Three atypical teratoid rhabdoid tumors (ATRT) molecular subgroups with different bio-clinical characteristics have been reported (TYR, SHH and MYC). Molecular subgrouping relies on either methylation profiling (reference methods), or expression profiling. However, the cost-effectiveness of such pangenomic screening is questionable. This work aims to study the reliability of alternative techniques for subgroup classification in the daily routine. Illumina EPIC-arrays were performed on 46 samples. Among those cases, expression profiling were analysed by RNAseq (n=30). We designed a 26-

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Toyota, Minoru, Kenneth J. Kopecky, Mutsumi-Ohe Toyota, Kam-Wing Jair, Cheryl L. Willman, and Jean-Pierre J. Issa. "Methylation profiling in acute myeloid leukemia." Blood 97, no. 9 (2001): 2823–29. http://dx.doi.org/10.1182/blood.v97.9.2823.

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Abstract Aberrant methylation of multiple CpG islands has been described in acute myeloid leukemia (AML), but it is not known whether these are independent events or whether they reflect specific methylation defects in a subset of cases. To study this issue, the methylation status of 14 promoter-associated CpG islands was analyzed in 36 cases of AML previously characterized for estrogen-receptor methylation (ERM). Cases with methylation density of 10% or greater were considered positive. Seventeen cases (47%) were ERM+ while 19 cases were ERM−. Hypermethylation of any of the following,p15, p16

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Rukova, B., R. Staneva, S. Hadjidekova, G. Stamenov, V. Milanova, and D. Toncheva. "Genome-Wide Methylation Profiling of Schizophrenia." Balkan Journal of Medical Genetics 17, no. 2 (2014): 15–23. http://dx.doi.org/10.2478/bjmg-2014-0070.

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Abstract Schizophrenia is one of the major psychiatric disorders. It is a disorder of complex inheritance, involving both heritable and environmental factors. DNA methylation is an inheritable epigenetic modification that stably alters gene expression. We reasoned that genetic modifications that are a result of environmental stimuli could also make a contribution. We have performed 26 high-resolution genomewide methylation array analyses to determine the methylation status of 27,627 CpG islands and compared the data between patients and healthy controls. Methylation profiles of DNAs were analy

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Jamshidi, Pouya, Kristyn Galbraith, Matthew Mccord, et al. "PATH-44. VARIANT ALLELIC FREQUENCY OF DRIVER MUTATIONS PREDICTS SUCCESS OF GENOMIC METHYLATION CLASSIFICATION IN CNS TUMORS." Neuro-Oncology 24, Supplement_7 (2022): vii160. http://dx.doi.org/10.1093/neuonc/noac209.617.

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Abstract Whole genome CpG DNA methylation profiling is an extremely valuable tool in the workup of central nervous system (CNS) tumors. Reliability of such profiling depends on sufficient tumor cellularity. Many neoplastic entities have well-known driver mutations that occur in virtually 100% of tumor cells, and next-generation sequencing (NGS) assays can detect those mutations and report their relative amounts in the form of Variant Allelic Frequency (VAF). Since NGS and methylation profiling are often done on the same tumor block, we sought to determine whether driver mutation VAF affects th

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Zuo, Tao, Benjamin Tycko, Ta-Ming Liu, Huey-Jen L. Lin, and Tim H.-M. Huang. "Methods in DNA methylation profiling." Epigenomics 1, no. 2 (2009): 331–45. http://dx.doi.org/10.2217/epi.09.31.

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Fang Lim, Shuang, Alena Karpusenko, John J. Sakon, Joseph A. Hook, Tyra A. Lamar, and Robert Riehn. "DNA methylation profiling in nanochannels." Biomicrofluidics 5, no. 3 (2011): 034106. http://dx.doi.org/10.1063/1.3613671.

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Chim, C. S., Y. L. Kwong, T. K. Fung, and R. Liang. "Methylation profiling in multiple myeloma." Leukemia Research 28, no. 4 (2004): 379–85. http://dx.doi.org/10.1016/j.leukres.2003.08.008.

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Bibikova, Marina, and Jian‐Bing Fan. "Genome‐wide DNA methylation profiling." Wiley Interdisciplinary Reviews: Systems Biology and Medicine 2, no. 2 (2010): 210–23. http://dx.doi.org/10.1002/wsbm.35.

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Rondinone, Ornella, Alessio Murgia, Jole Costanza, et al. "Extensive Placental Methylation Profiling in Normal Pregnancies." International Journal of Molecular Sciences 22, no. 4 (2021): 2136. http://dx.doi.org/10.3390/ijms22042136.

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The placental methylation pattern is crucial for the regulation of genes involved in trophoblast invasion and placental development, both key events for fetal growth. We investigated LINE-1 methylation and methylome profiling using a methylation EPIC array and the targeted methylation sequencing of 154 normal, full-term pregnancies, stratified by birth weight percentiles. LINE-1 methylation showed evidence of a more pronounced hypomethylation in small neonates compared with normal and large for gestational age. Genome-wide methylation, performed in two subsets of pregnancies, showed very simil

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Inoue, Yohei, Otani Yoshihiro, Joji Ishida, et al. "10150- MPC-14 THE COMPARISON BETWEEN HISTOLOGICAL DIAGNOSIS, GENOME-WIDE DNA METHYLATION PROFILING AND INTEGRATED DIAGNOSIS FOR PEDIATRIC LOW-GRADE GLIOMA." Neuro-Oncology Advances 6, Supplement_4 (2024): iv14—iv15. http://dx.doi.org/10.1093/noajnl/vdae173.055.

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Abstract INTRODUCTION Genome-wide DNA methylation profiling is performed for pediatric low-grade glioma (pLGG) with diagnostic challenge. We compared histological diagnosis, DNA methylation profiling and integrated diagnosis for pLGG. METHODS We analyzed histology, molecular findings, DNA methylation profiling and integrated diagnosis of pLGG that were registered to the central diagnosis of Japan Children’s Cancer Group from March 2018 to June 2024 and underwent genome-wide DNA methylation profiling. RESULTS Fifty-eight cases were enrolled. Thirty-seven cases (64%) had calibrated scores of 0.8

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Wright, Kyla, Kristyn Galbraith, Matija Snuderl, and Nidhi Agrawal. "DNA Methylation Profiling in Rare Sellar Tumors." Biomedicines 10, no. 9 (2022): 2225. http://dx.doi.org/10.3390/biomedicines10092225.

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The histologic diagnosis of sellar masses can be challenging, particularly in rare neoplasms and tumors without definitive biomarkers. Moreover, there is significant inter-observer variability in the histopathological diagnosis of many tumors of the CNS, and some rare tumors risk being misclassified. DNA methylation has recently emerged as a useful diagnostic tool. To illustrate the clinical utility of machine-learning-based DNA methylation classifiers, we report a rare case of primary sellar esthesioneuroblastoma histologically mimicking a non-functioning pituitary adenoma. The patient had mu

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Hillary, Robert F., and Riccardo E. Marioni. "MethylDetectR: a software for methylation-based health profiling." Wellcome Open Research 5 (April 13, 2021): 283. http://dx.doi.org/10.12688/wellcomeopenres.16458.2.

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DNA methylation is an important biological process that involves the reversible addition of chemical tags called methyl groups to DNA and affects whether genes are active or inactive. Individual methylation profiles are determined by both genetic and environmental influences. Inter-individual variation in DNA methylation profiles can be exploited to estimate or predict a wide variety of human characteristics and disease risk profiles. Indeed, a number of methylation-based predictors of human traits have been developed and linked to important health outcomes. However, there is an unmet need to

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Hillary, Robert F., and Riccardo E. Marioni. "MethylDetectR: a software for methylation-based health profiling." Wellcome Open Research 5 (December 7, 2020): 283. http://dx.doi.org/10.12688/wellcomeopenres.16458.1.

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DNA methylation is an important biological process which involves the reversible addition of chemical tags called methyl groups to DNA and affects whether genes are active or inactive. Individual methylation profiles are determined by both genetic and environmental influences. Inter-individual variation in DNA methylation profiles can be exploited to estimate or predict a wide variety of human characteristics and disease risk profiles. Indeed, a number of methylation-based predictors of human traits have been developed and linked to important health outcomes. However, there is an unmet need to

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Wang, Rui, Emily G. Hamilton, Diego Almanza, Angela Hui, Maximilian Diehn, and Ash A. Alizadeh. "Abstract 960: Improved cfDNA methylation profiling through correction of misrepaired jagged-ends." Cancer Research 84, no. 6_Supplement (2024): 960. http://dx.doi.org/10.1158/1538-7445.am2024-960.

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Abstract Background: Profiling cfDNA methylation enables early cancer detection and classification, but challenges arise from "jagged ends" (JEs) for ~90% of cfDNA molecules, as well as for FFPE samples and partially degraded genomic DNA. Repair of these jagged ends introduces erroneous methylation signals, especially in shorter cfDNA fragments enriched for tumor derived molecules. Separately, DNA conversions during 5mC profiling hamper accurate simultaneous ctDNA genotyping of somatic mutations. To meet these needs, we developed a method preserving double-stranded cfDNA molecules without erro

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Papanicolau-Sengos, Antonios, and Kenneth Aldape. "DNA Methylation Profiling: An Emerging Paradigm for Cancer Diagnosis." Annual Review of Pathology: Mechanisms of Disease 17, no. 1 (2022): 295–321. http://dx.doi.org/10.1146/annurev-pathol-042220-022304.

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Histomorphology has been a mainstay of cancer diagnosis in anatomic pathology for many years. DNA methylation profiling is an additional emerging tool that will serve as an adjunct to increase accuracy of pathological diagnosis. Genome-wide interrogation of DNA methylation signatures, in conjunction with machine learning methods, has allowed for the creation of clinical-grade classifiers, most prominently in central nervous system and soft tissue tumors. Tumor DNA methylation profiling has led to the identification of new entities and the consolidation of morphologically disparate cancers into

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Macrae, Cassie, Bradley Gampel, Kee Kiat Yeo, et al. "RARE-26. Evaluating the clinical utility of DNA methylation profiling for choroid plexus tumors." Neuro-Oncology 24, Supplement_1 (2022): i15. http://dx.doi.org/10.1093/neuonc/noac079.051.

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Abstract INTRODUCTION: Choroid plexus tumors (CPT) are rare, potentially aggressive CNS tumors with defined histologic criteria for grading. In recent years, several patients within our practice have demonstrated discordance between histological diagnosis and clinical behavior. DNA methylation profiling has emerged as a potential diagnostic adjunct for aiding clinical planning and treatment approach. In this study, we sought to retrospectively evaluate the clinical utility of DNA methylation profiling within our cohort of patients with CPT. METHODS: We performed a retrospective chart review of

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Tran, Robert K., Jorja G. Henikoff, Daniel Zilberman, Renata F. Ditt, Steven E. Jacobsen, and Steven Henikoff. "DNA Methylation Profiling Identifies CG Methylation Clusters in Arabidopsis Genes." Current Biology 15, no. 2 (2005): 154–59. http://dx.doi.org/10.1016/j.cub.2005.01.008.

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Gebhard, Claudia, Mohammed Sadeh, Dagmar Glatz, et al. "Profiling of Aberrant DNA Methylation In AML Reveals Subclasses of CpG Islands with Epigenetic or Genetic Association." Blood 116, no. 21 (2010): 2498. http://dx.doi.org/10.1182/blood.v116.21.2498.2498.

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Abstract Abstract 2498 CpG islands show frequent and often disease-specific epigenetic alterations during malignant transformation, however, the underlying mechanisms are poorly understood. We used methyl-CpG immunoprecipitation (MCIp) to generate comparative DNA methylation profiles of 30 patients with acute myeloid leukemia for human CpG islands across the genome. DNA methylation profiles across 23.000 CpG islands revealed highly heterogeneous methylation patterns in AML with over 6000 CpG islands showing aberrant de novo methylation in AML. Based on these profiles we selected a subset of 38

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Reinders, Jon, and Jerzy Paszkowski. "Bisulfite methylation profiling of large genomes." Epigenomics 2, no. 2 (2010): 209–20. http://dx.doi.org/10.2217/epi.10.6.

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Marx, Vivien. "Genetics: profiling DNA methylation and beyond." Nature Methods 13, no. 2 (2016): 119–22. http://dx.doi.org/10.1038/nmeth.3736.

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Pi, Li, Zhaofeng Zhang, Yan Gu, et al. "DNA methylation profiling in recurrent miscarriage." PeerJ 8 (January 7, 2020): e8196. http://dx.doi.org/10.7717/peerj.8196.

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Recurrent miscarriage (RM) is a complex clinical problem. However, specific diagnostic biomarkers and candidate regulatory targets have not yet been identified. To explore RM-related biological markers and processes, we performed a genome-wide DNA methylation analysis using the Illumina Infinium HumanMethylation450 array platform. Methylation variable positions and differentially methylated regions (DMRs) were selected using the Limma package in R language. Thereafter, gene ontology (GO) enrichment analysis and pathway enrichment analysis were performed on these DMRs. A total of 1,799 DMRs wer

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Guldberg, Per, Jesper Worm, and Kirsten Grønbæk. "Profiling DNA methylation by melting analysis." Methods 27, no. 2 (2002): 121–27. http://dx.doi.org/10.1016/s1046-2023(02)00063-4.

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Samarakoon, PS. "Epigenomics and Genome Wide Methylation Profiling." Sri Lanka Journal of Bio-Medical Informatics 1, no. 1 (2010): 53. http://dx.doi.org/10.4038/sljbmi.v1i1.1486.

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Salhia, Bodour, Angela Baker, Jonathan J. Keats, et al. "CpG Methylation Profiling in Multiple Myeloma." Blood 114, no. 22 (2009): 604. http://dx.doi.org/10.1182/blood.v114.22.604.604.

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Abstract Abstract 604 We have conducted a pilot study to interrogate both CpG hyper- and hypomethylation in Multiple Myeloma (MM) using the Illumina GoldenGate (GG) BeadArrayTM high-throughput assay. Specifically, we utilized the Illumina Methylation Cancer Panel I, which spans 1,505 CpG loci selected from 807 genes including known tumor suppressor genes and oncogenes. To date we have profiled 50 CD138+ MM specimens, 4 MM cell lines and 6 normal CD138+ plasma cell samples (each representing a pool of 3-5 individuals) obtained from the bone marrow of patients who have undergone hip or knee repl

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Kreitmaier, Peter, Diane Swift, Mark Wilkinson, and Eleftheria Zeggini. "PROFILING METHYLATION IN PRIMARY OSTEOARTHRITIS CARTILAGE." Osteoarthritis and Cartilage 32 (April 2024): S484. http://dx.doi.org/10.1016/j.joca.2024.02.718.

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Møller, Morten Winkler, Marianne Skovsager Andersen, Bo Halle, et al. "Genome-Wide DNA Methylation Profiling as a Prognostic Marker in Pituitary Adenomas—A Pilot Study." Cancers 16, no. 12 (2024): 2210. http://dx.doi.org/10.3390/cancers16122210.

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Background: The prediction of the regrowth potential of pituitary adenomas after surgery is challenging. The genome-wide DNA methylation profiling of pituitary adenomas may separate adenomas into distinct methylation classes corresponding to histology-based subtypes. Specific genes and differentially methylated probes involving regrowth have been proposed, but no study has linked this epigenetic variance with regrowth potential and the clinical heterogeneity of nonfunctioning pituitary adenomas. This study aimed to investigate whether DNA methylation profiling can be useful as a clinical progn

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Huang and Wang. "Cell-Free DNA Methylation Profiling Analysis—Technologies and Bioinformatics." Cancers 11, no. 11 (2019): 1741. http://dx.doi.org/10.3390/cancers11111741.

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Analysis of circulating nucleic acids in bodily fluids, referred to as “liquid biopsies”, is rapidly gaining prominence. Studies have shown that cell-free DNA (cfDNA) has great potential in characterizing tumor status and heterogeneity, as well as the response to therapy and tumor recurrence. DNA methylation is an epigenetic modification that plays an important role in a broad range of biological processes and diseases. It is well known that aberrant DNA methylation is generalizable across various samples and occurs early during the pathogenesis of cancer. Methylation patterns of cfDNA are als

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Littrell, Mary Elizabeth, Parth Patel, Megan Blue, et al. "MDB-98. HISTOPATHOLOGY IS A ROBUST TOOL TO DIFFERENTIATE BETWEEN SHH AND WNT MEDULLOBLASTOMA VERSUS NON-SHH/NON-WNT MEDULLOBLASTOMA: COMPARATIVE ANALYSIS OF HISTOPATHOLOGY, CHROMOSOMAL MICROARRAY, NANOSTRING BASED 22-GENE ASSAY, AND DNA METHYLATION FOR MEDULLOBLASTOMA SUBGROUP ASSIGNMENT ON “HEAD START” 4 CLINICAL TRIAL." Neuro-Oncology 26, Supplement_4 (2024): 0. http://dx.doi.org/10.1093/neuonc/noae064.546.

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Abstract BACKGROUND “Head Start-4” (HS-4) is a prospective, randomized clinic trial that tailors treatment based on medulloblastoma molecular subgroups (WNT, SHH, Group 3, and Group 4) and response to induction chemotherapy, and compares the efficacy of one versus three (tandem) cycles of myeloablative therapy. Here we compare different methodologies used to distinguish between WNT/SHH medulloblastoma (low-risk arm) and non-SHH/non-WNT medulloblastoma (high-risk arm) during the course of the trial. METHODS When HS-4 trial began enrolling patients in 2015, in the absence of a CAP-CLIA certified

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Ahn, Jongseong, Sunghoon Heo, Jihyun Lee, and Duhee Bang. "Introduction to Single-Cell DNA Methylation Profiling Methods." Biomolecules 11, no. 7 (2021): 1013. http://dx.doi.org/10.3390/biom11071013.

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DNA methylation is an epigenetic mechanism that is related to mammalian cellular differentiation, gene expression regulation, and disease. In several studies, DNA methylation has been identified as an effective marker to identify differences between cells. In this review, we introduce single-cell DNA-methylation profiling methods, including experimental strategies and approaches to computational data analysis. Furthermore, the blind spots of the basic analysis and recent alternatives are briefly described. In addition, we introduce well-known applications and discuss future development.

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Wenger, Anna, and Helena Carén. "Methylation Profiling in Diffuse Gliomas: Diagnostic Value and Considerations." Cancers 14, no. 22 (2022): 5679. http://dx.doi.org/10.3390/cancers14225679.

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Diffuse gliomas cause significant morbidity across all age groups, despite decades of intensive research efforts. Here, we review the differences in diffuse gliomas in adults and children, as well as the World Health Organisation (WHO) 2021 classification of these tumours. We explain how DNA methylation-based classification works and list the methylation-based tumour types and subclasses for adult and paediatric diffuse gliomas. The benefits and utility of methylation-based classification in diffuse gliomas demonstrated to date are described. This entails the identification of novel tumour typ

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Ricklefs, Franz, Cecile Maire, Katharina Kolbe, et al. "GENE-22. GENOME-WIDE METHYLATION PROFILING OF GLIOBLASTOMA EXTRACELLULAR VESICLE DNA ALLOWS TUMOR CLASSIFICATION." Neuro-Oncology 21, Supplement_6 (2019): vi102. http://dx.doi.org/10.1093/neuonc/noz175.424.

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Abstract BACKGROUND Genome-wide methylation profiling has recently been developed into a tool that allows subtype tumor classification in central nervous system (CNS) tumors. Extracellular vesicles (EVs) are released by CNS tumor cells and contain high molecular weight tumor DNA, rendering EVs a potential biomarker source to identify tumor subgroups, stratify patients and monitor therapy by liquid biopsy. We investigated whether the DNA in glioma-derived EVs reflects genome-wide tumor methylation profiles and allows tumor subtype classification. METHODS DNA was isolated from EVs secreted by cu

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Wu, Songlin, Yuqiu Wang, Jiayin Wang, Xilong Li, Jiayang Li, and Keqiong Ye. "Profiling of RNA ribose methylation in Arabidopsis thaliana." Nucleic Acids Research 49, no. 7 (2021): 4104–19. http://dx.doi.org/10.1093/nar/gkab196.

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Abstract Eukaryotic rRNAs and snRNAs are decorated with abundant 2′-O-methylated nucleotides (Nm) that are predominantly synthesized by box C/D snoRNA-guided enzymes. In the model plant Arabidopsis thaliana, C/D snoRNAs have been well categorized, but there is a lack of systematic mapping of Nm. Here, we applied RiboMeth-seq to profile Nm in cytoplasmic, chloroplast and mitochondrial rRNAs and snRNAs. We identified 111 Nm in cytoplasmic rRNAs and 19 Nm in snRNAs and assigned guide for majority of the detected sites using an updated snoRNA list. At least four sites are directed by guides with m

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Brodwater, William, Yelena Wilson, Alexis Judd, Sarah Rush, and Erin Wright. "PATH-02. Using DNA methylation profiling to define tumor type and appropriate treatment: a case report and review of the literature of a rare CNS CIC altered sarcoma." Neuro-Oncology 24, Supplement_1 (2022): i158. http://dx.doi.org/10.1093/neuonc/noac079.586.

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Abstract The utilization of methylation profiling is increasingly becoming part of the standard evaluation for high-grade malignancies. CNS primary tumors with CIC alteration are a recently recognized CNS tumor entity identified via DNA methylation profiling of primitive neuroectodermal tumors (PNET). PNETs have historically carried a poor overall prognosis; however, CNS tumors with CIC alteration have rarely been described in the literature and much remains to be discovered regarding the presentation, tumor characteristics, outcomes, and ideal treatment strategy to optimize survival in these

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Gupta, Sumit, Xiangjun Tian, Jing Wang, et al. "EPEN-10. SPINAL MYXOPAPILLARY EPENDYMOMA AND METHYLATION-PROFILING: THE MD ANDERSON CANCER CENTER (MDACC) EXPERIENCE." Neuro-Oncology 22, Supplement_3 (2020): iii309—iii310. http://dx.doi.org/10.1093/neuonc/noaa222.150.

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Abstract INTRODUCTION Spinal myxopapillary ependymoma (MPE) is a rare histological variant of ependymoma, classified as WHO grade I tumor. Further interrogation of the molecular and clinical profile is warranted, to better understand the biology and clinical phenotype. We summarize our institutional experience with spinal MPE including methylation-profiling. METHODS A retrospective analysis of charts during the period of 2001 to 2019 of histologically proven MPE was done. We performed methylation profiling for 12 patients by Infinium MethylationEPIC Kit. RESULTS 26 patients with spinal MPE wer

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Skvortsova, Ksenia, Clare Stirzaker, and Phillippa Taberlay. "The DNA methylation landscape in cancer." Essays in Biochemistry 63, no. 6 (2019): 797–811. http://dx.doi.org/10.1042/ebc20190037.

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Abstract As one of the most abundant and well-studied epigenetic modifications, DNA methylation plays an essential role in normal development and cellular biology. Global alterations to the DNA methylation landscape contribute to alterations in the transcriptome and deregulation of cellular pathways. Indeed, improved methods to study DNA methylation patterning and dynamics at base pair resolution and across individual DNA molecules on a genome-wide scale has highlighted the scope of change to the DNA methylation landscape in disease states, particularly during tumorigenesis. More recently has

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Suri, Vaishali, Jyotsna Singh, Ashish Suri, and M. C. Sharma. "PATH-50. GENETIC AND EPIGENETIC PROFILING OF MENINGIOMAS TO GAIN INSIGHTS INTO MOLECULAR HETEROGENEITY AND RISK STRATIFICATION." Neuro-Oncology 25, Supplement_5 (2023): v179—v180. http://dx.doi.org/10.1093/neuonc/noad179.0680.

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Abstract BACKGROUND Meningiomas are slow-growing CNS tumors, with most being benign (WHO grade 1) and having indolent behavior. Limited data on molecular profiling of meningiomas and its clinical implications have hindered the implementation of effective therapies and new treatments. Aims & Objectives: Perform DNA methylation profiling, copy number analysis, and targeted sequencing in meningiomas. MATERIALS & METHODS 208 meningiomas, grade 1 (n=109), grade 2 (n=83), and grade 3 (n=16)were assessed for pTERT mutation, CDKN2A homozygous deletion, and H3K27me3 expression. Additionally, 35

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Ruiz, F., L. D'Antona, M. Dutt, et al. "P18.10.B WHICH MENINGIOMAS BENEFIT MOST FROM METHYLATION PROFILING?" Neuro-Oncology 25, Supplement_2 (2023): ii124. http://dx.doi.org/10.1093/neuonc/noad137.418.

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Abstract BACKGROUND methylation profiling combined with copy number assay provide a better prognostication than WHO grade alone. Profiling all meningiomas is financially unsustainable in most centres, therefore pathologists and clinicians ask for guidance which meningiomas to analyse. Here, we analysed how the WHO grades resolve into methylation classes and risk strata, to provide guidance on which meningiomas to profile MATERIAL AND METHODS From 2018-2023 a subset of meningiomas diagnosed within our institution, and all referred meningiomas underwent methylation profiling with copy number ass

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Onken, J. S. "P07.05.B DNA-METHYLATION PROFILING IS AN EFFECTIVE ASSET FOR IDENTIFICATION OF TUMORS IN SUSPECTED, YET IMMUNOHISTOCHEMICALLY UNSPECIFIABLE, NEURO-ONCOLOGICAL CASES." Neuro-Oncology 25, Supplement_2 (2023): ii51—ii52. http://dx.doi.org/10.1093/neuonc/noad137.165.

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Abstract BACKGROUND Patients with a suspected neurooncological disease on radiographic images and no histopathological evidence of a tumor on the surgically retrieved tissue, pose a great challenge for clinicians and neuropathologists. DNA methylation-based classifications and copy number variation (CNV) analysis allow robust brain tumor classification. Here, we aim to evaluate their diagnostic properties in histopathologically unspecifiable or negative cases. MATERIAL AND METHODS We screened all neurosurgical cases, which underwent surgery at our institution between 2009 and 2021, with suspec

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Yamazawa, Erika, Shota Tanaka, Genta Nagae, et al. "EPCO-01. MOLECULAR PROFILING OF SPINAL CORD EPENDYMOMA." Neuro-Oncology 23, Supplement_6 (2021): vi1. http://dx.doi.org/10.1093/neuonc/noab196.000.

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Abstract BACKGROUND Ependymomas are currently classified into 9 subgroups by DNA methylation profiles. Although spinal cord ependymoma (SP-EPN) is distinct from other tumors, diversity within SP-EPN is still unclear. Here, we used transcriptomic and epigenomic profiles to investigate the diversity among Japanese SP-EPN cases. MATERIALS AND METHODS We analyzed 57 SP-EPN patients (32 males and 25 females, aged from 18 to 78 years, median: 52), including two cases of neurofibromatosis type 2, five cases of grade 3 (WHO grade). We obtained transcriptome (RNA-seq) and DNA methylation (Infinium Meth

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Algar, Elizabeth, White Christine, Kathryn Kinross, et al. "PATH-01. MOLECULAR PROFILING OF PAEDIATRIC CENTRAL NERVOUS SYSTEM TUMOURS IN AUSTRALASIA – AN UPDATE ON THE AIM BRAIN AND MNP2.0 PROJECTS." Neuro-Oncology 22, Supplement_3 (2020): iii424. http://dx.doi.org/10.1093/neuonc/noaa222.638.

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Abstract The Access to Innovative Molecular Profiling for Paediatric Brain Cancers (AIM BRAIN) project is a trial testing the feasibility of clinical implementation of diagnostic methylation and molecular profiling for central nervous system (CNS) tumours in Australia and New Zealand. AIM BRAIN builds on an existing study, MNP2.0, and allows cross-validation of results derived from identical samples in separate laboratories in Melbourne, Australia, and DKFZ, Heidelberg, Germany. Parallel methylation profiling (Illumina 850K EPIC array) from co-enrolled cases has revealed excellent concordance

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Ricklefs, Franz, Cecile Maire, Krys Fita, et al. "TBIO-07. Pediatric tumor classification through genome-wide methylation profiling of extracellular vesicle DNA." Neuro-Oncology 24, Supplement_1 (2022): i184. http://dx.doi.org/10.1093/neuonc/noac079.689.

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Abstract BACKGROUND: Genome-wide methylation profiling reliably classifies pediatric central nervous system (CNS) tumors. Extracellular vesicles (EVs) are released by pediatric CNS tumor cells (pCC) and contain high molecular weight tumor DNA, rendering EVs a potential biomarker source to identify tumor subgroups, stratify patients and monitor therapy by liquid biopsy. We investigated, whether the DNA in pCC-derived EVs reflects genome-wide tumor methylation profiles and allows tumor subtype classification. Currently, the tests are being expanded to include blood samples (n=80 patients). METHO

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Schoof, Melanie, Michael Spohn, Mario Dorostkar, et al. "PATH-04. Array-based global DNA Methylation profiling of mouse brain tumors allows comparison to human tumors." Neuro-Oncology 24, Supplement_1 (2022): i158—i159. http://dx.doi.org/10.1093/neuonc/noac079.588.

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Abstract The classification of human brain tumors by global DNA methylation profiling has become an essential part of modern integrated neuropathological diagnostics. It has proven to reliably identify known and novel brain tumor (sub-)types that are biologically and clinically distinct. Therefore, this technique has critically improved diagnostic accuracy and risk stratification of brain tumor patients. Although indispensable for the understanding of tumor biology and for preclinical drug trials, the comparison of genetically engineered mouse models to human brain tumors is still difficult. T

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Dell’Anna, Vito Andrea, Stefano Gabriele Vallero, Franca Fagioli, Paola Peretta, Paola Cassoni, and Luca Bertero. "ETMR-07. DNA methylation profiling of a series of rare CNS embryonal tumors in children: diagnostic and clinical impact." Neuro-Oncology 24, Supplement_1 (2022): i50—i51. http://dx.doi.org/10.1093/neuonc/noac079.185.

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Abstract BACKGROUND: CNS embryonal tumors are a clinically and biologically heterogeneous group of tumors, more frequently arising in very young children. In the last few years, tumor classification through DNA methylation profiling has been demonstrated to be a powerful diagnostic tool which could be especially informative in this setting. METHODS: We reviewed original diagnosis and molecular profile of childhood CNS embryonal tumors other than medulloblastoma or AT/RT from a retrospective single-center cohort. Sixteen FFPE tissue samples from 14 unique patients (diagnosed from 1996 to 2017)

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Ricklefs, Franz, Cecile Maire, Krys Fita, et al. "BIOM-57. PEDIATRIC TUMOR CLASSIFICATION THROUGH GENOME-WIDE METHYLATION PROFILING OF EXTRACELLULAR VESICLE DNA." Neuro-Oncology 22, Supplement_2 (2020): ii14. http://dx.doi.org/10.1093/neuonc/noaa215.054.

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Abstract BACKGROUND Genome-wide methylation profiling reliably classifies pediatric central nervous system (CNS) tumors. Extracellular vesicles (EVs) are released by pediatric CNS tumor cells (pCC) and contain high molecular weight tumor DNA, rendering EVs a potential biomarker source to identify tumor subgroups, stratify patients and monitor therapy by liquid biopsy. We investigated whether the DNA in pCC-derived EVs reflects genome-wide tumor methylation profiles and allows tumor subtype classification. METHODS DNA was isolated from EVs secreted by pediatric CNS tumor cells (pCC) as well as

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Yuen, Carlen A., Silin Bao, Xiao-Tang Kong, et al. "A High-Grade Glioma, Not Elsewhere Classified in an Older Adult with Discordant Genetic and Epigenetic Analyses." Biomedicines 12, no. 9 (2024): 2042. http://dx.doi.org/10.3390/biomedicines12092042.

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The World Health Organization’s (WHO) classification of central nervous system (CNS) tumors is continually being refined to improve the existing diagnostic criteria for high-grade gliomas (HGGs), including glioblastoma. In 2021, advances in molecular analyses and DNA methylation profiling were incorporated to expand upon the diagnostic criteria for HGG, including the introduction of high-grade astrocytoma with piloid features (HGAP), a new tumor entity for which a match to the HGAP class in DNA methylation profiling is an essential criterion. We present an equivocal case of a 72-year-old male

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Tam, Otto C. H., Ronnie S. L. Ho, Shing Chan, et al. "Genome-Wide DNA Methylation Profiling as Frontline Diagnostics for Central Nervous System Embryonal Tumors in Hong Kong." Cancers 15, no. 19 (2023): 4880. http://dx.doi.org/10.3390/cancers15194880.

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This paper examines the link between CNS tumor biology and heterogeneity and the use of genome-wide DNA methylation profiling as a clinical diagnostic platform. CNS tumors are the most common solid tumors in children, and their prognosis remains poor. This study retrospectively analyzed pediatric patients with CNS embryonal tumors in Hong Kong between 1999 and 2017, using data from the territory-wide registry and available formalin-fixed paraffin-embedded tumor tissue. After processing archival tumor tissue via DNA extraction, quantification, and methylation profiling, the data were analyzed b

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Pages, Melanie, Emmanuelle Uro-Coste, Carole Colin, et al. "The Implementation of DNA Methylation Profiling into a Multistep Diagnostic Process in Pediatric Neuropathology: A 2-Year Real-World Experience by the French Neuropathology Network." Cancers 13, no. 6 (2021): 1377. http://dx.doi.org/10.3390/cancers13061377.

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DNA methylation profiling has recently emerged as a powerful tool to help establish diagnosis in neuro-oncology. Here we present our national diagnostic strategy as the French neuropathology network (RENOCLIP-LOC) and our current approach of integrating DNA methylation profiling into our multistep diagnostic process for challenging pediatric CNS tumors. The tumors with diagnostic uncertainty were prospectively selected for DNA methylation after two rounds of review by neuropathology experts. We first integrated the classifier score into the histopathological findings. Subsequent analyses using

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Shanmuganathan, Rajasree, Nazeema B. Basheer, Laxmi Amirthalingam, Harshiny Muthukumar, Rajendran Kaliaperumal, and Kumaran Shanmugam. "Conventional and Nanotechniques for DNA Methylation Profiling." Journal of Molecular Diagnostics 15, no. 1 (2013): 17–26. http://dx.doi.org/10.1016/j.jmoldx.2012.06.007.

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Ehrich, M., J. Turner, P. Gibbs, et al. "Cytosine methylation profiling of cancer cell lines." Proceedings of the National Academy of Sciences 105, no. 12 (2008): 4844–49. http://dx.doi.org/10.1073/pnas.0712251105.

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Yamagata, Kazuo. "DNA methylation profiling using live-cell imaging." Methods 52, no. 3 (2010): 259–66. http://dx.doi.org/10.1016/j.ymeth.2010.04.008.

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