biostudies-arrayexpressUnknownTranscriptomicsGenomicsProteomicsBeatriz Martins Wolffmethylation profiling by arrayHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15074This study aimed to validate the use of DNA methylation profiling in the classification of pediatric central nervous system (CNS) tumors within the Brazilian public healthcare system. A total of 16 tumor samples from pediatric patients previously diagnosed with medulloblastoma or ependymoma—the two most common CNS tumors in children—were analyzed. DNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue and processed using the Infinium MethylationEPIC BeadChip array (Illumina). Methylation data were interpreted using two versions of the DKFZ brain tumor classifier (v11b4 and v12.5) and compared to reference diagnoses established through routine histopathological and molecular analyses. The study was conducted at the largest public hospital complex in Latin America and reflects practical challenges and opportunities for implementing precision diagnostics in real-world, resource-limited healthcare settings.biostudies-arrayexpressSample Collection - Tumor samples were obtained from the archives of the Pathology Department of Hospital das Clínicas, University of São Paulo Medical School (HC-FMUSP), following diagnostic procedures. Formalin-fixed paraffin-embedded (FFPE) tissue blocks were used. The study was approved by the local Research Ethics Committee (CAAE: 61103822.2.0000.0068).Scaning - After hybridization, the arrays were washed and scanned using the iScan System (Illumina). Raw intensity data were extracted using Illumina GenomeStudio software. The resulting .idat files were used for downstream methylation analysis.Nucleic Acid Extraction - Genomic DNA was extracted from FFPE tissue sections using the QIAamp DNA FFPE Tissue Kit (Qiagen), following the manufacturer’s instructions. DNA quality and concentration were assessed using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific).Labeling - Genomic DNA was extracted from FFPE tissue sections using the QIAamp DNA FFPE Tissue Kit (Qiagen), following the manufacturer’s instructions. DNA quality and concentration were assessed using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific).Hybridization - Labeled and fragmented DNA samples were hybridized to the Infinium MethylationEPIC BeadChip arrays (Illumina) according to the manufacturer’s instructions in the Infinium HD Assay Methylation Protocol Guide.MIAME ScoreRaw DataOrganizationAssays and DataProcessed DataMAGE-TAB FilesArray DesignsBeatriz Martins WolffData Transformation - Raw IDAT files were processed using the minfi R package. Signal intensities were normalized using the Noob (normal-exponential out-of-band) background correction method. Quality control and probe filtering steps were performed prior to downstream analyses. Beta-values were calculated for each probe to represent DNA methylation levels.falseDNA methylation profiling of pediatric central nervous system tumors in a Brazilian public healthcare settingThis study aimed to validate the use of DNA methylation profiling in the classification of pediatric central nervous system (CNS) tumors within the Brazilian public healthcare system. A total of 16 tumor samples from pediatric patients previously diagnosed with medulloblastoma or ependymoma—the two most common CNS tumors in children—were analyzed. DNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue and processed using the Infinium MethylationEPIC BeadChip array (Illumina). Methylation data were interpreted using two versions of the DKFZ brain tumor classifier (v11b4 and v12.5) and compared to reference diagnoses established through routine histopathological and molecular analyses. The study was conducted at the largest public hospital complex in Latin America and reflects practical challenges and opportunities for implementing precision diagnostics in real-world, resource-limited healthcare settings.2026-03-31T00:00:00Z2026-03-31T01:03:46.905Z2025-04-17T12:05:59.463ZE-MTAB-15074EFO_0002944EFO_0003814EFO_0003813EFO_0002759EFO_0005518EFO_0003816EFO_0003815