GEO DataSets

(Submitter supplied) DNA methylation analysis was perfomed using Infinium 450K Methylation BeadChip platform on 140 PFA ependymoma patient samples. Resulting .idat files were then uploaded to the molecularneuropathology.org classifier to obtain molecular subgroup and copy number variance. Idat files were batch normalized and background corrected using default settings of the R package ChAMP to obtain GpG methylation beta values for analysis of differentially methylated GpG regions.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

140 Samples

Download data: IDAT, TXT

(Submitter supplied) Ependymoma (EPN) posterior fossa group A (PFA) has the highest rate of recurrence and the worst prognosis of all EPN types. At relapse, it is typically incurable even with re-resection and re-irradiation. The biology of recurrent PFA EPN remains largely unknown, which hinders clinical advances. In this large longitudinal multicenter study, we examined matched samples of primary and recurrent disease from PFA EPN patients (n=95) to investigate the biology of recurrence. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

14 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Methylation profiling by array

4 related Platforms

291 Samples

Download data: IDAT

(Submitter supplied) Posterior fossa subgroup A (PFA) ependymoma is a brain tumor of childhood with a high rate of recurrence. Here we have performed RNAseq on a longitudinal cohort of patient samples obtained at presentation and at recurrence(s), in order to identify the biological correlates of treatment failure and tumor evolution.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL24676

72 Samples

Download data: XLSX

(Submitter supplied) DNA methylation analysis was perfomed using Infinium EPIC Methylation BeadChip platform on 65 PFA ependymoma patient samples. Resulting .idat files were then uploaded to the molecularneuropathology.org classifier to obtain molecular subgroup and copy number variance. Idat files were batch normalized and background corrected using default settings of the R package ChAMP to obtain GpG methylation beta values for analysis of differentially methylated GpG regions.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

65 Samples

Download data: IDAT, TXT

(Submitter supplied) Combined EPIC and 450k analysis across 212 posterior fossa ependymoma's classified as PFB using the Heidelberg Brain Tumour Classifier Methylation profiling across 212 posterior fossa PFB ependymoma's to discern molecular heterogeneity

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platforms:

GPL21145 GPL16304

212 Samples

Download data: IDAT, TXT

(Submitter supplied) Normal brain RNAseq data provides a critical comparitor for evaluation of gene expression changes in childhood brain tumors.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

16 Samples

Download data: XLSX

(Submitter supplied) Posterior fossa type A (PF-EPN-A, PFA) ependymoma are aggressive tumors that mainly affect children and have a poor prognosis. Histopathology shows significant intratumoral heterogeneity, ranging from loose tissue to often sharply demarcated, extremely cell dense tumor areas. Spatial transcriptomics of six cases allow for a comparison of the transcriptome of high and low cell density areas.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

37 Samples

Download data: DCC, XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Methylation profiling by array; Other

Platforms:

GPL13534 GPL21145 GPL24676

128 Samples

Download data: DCC, IDAT

(Submitter supplied) Posterior fossa type A (PF-EPN-A, PFA) ependymoma are aggressive tumors that mainly affect children and have a poor prognosis. Histopathology shows significant intratumoral heterogeneity, ranging from loose tissue to often sharply demarcated, extremely cell dense tumor areas. To determine molecular differences between these morphologically different areas and to understand their clinical significance, we analyzed 113 PF-EPN-A samples, including 40 corresponding relapse samples. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platforms:

GPL13534 GPL21145

79 Samples

Download data: CSV, IDAT, RDS

(Submitter supplied) Posterior fossa type A (PF-EPN-A, PFA) ependymoma are aggressive tumors that mainly affect children and have a poor prognosis. Histopathology shows significant intratumoral heterogeneity, ranging from loose tissue to often sharply demarcated, extremely cell dense tumor areas. To determine molecular differences in morphologically different areas and to understand their clinical significance, we analyzed 113 PF-EPN-A samples, including 40 corresponding relapse samples. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

12 Samples

Download data: CSV, IDAT, RDS

(Submitter supplied) Introduction: Ependymoma (EPN) studies have revealed certain genetic markers, such as gain of chromosome 1q (1q+), as indicators of poor survival and high rate of recurrence. Development of novel therapeutics for EPN has been hampered by a lack of in vivo and in vivo models. We describe two unique 1q+ cell lines (811 and 928) derived from two children with metastatic, recurrent EPN. Both cell lines were characterized using histological, karyotypic and transcriptomic methods Transcriptomic analysis revealed that both lines, when cultured in 3D format, clustered closer to primary EPN tumors than monolayer format and with better fidelity of EPN-specific transcripts, namely those related to cilia function. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

110 Samples

Download data: CEL

(Submitter supplied) Ependymomas are neuroepithelial tumors of the central nervous system (CNS), presenting in both adults and children but accounting for almost 10% of all pediatric CNS tumors and up to 30% of CNS tumors in children under 3 years (Bouffet et al., 2009; McGuire et al., 2009; Rodriguez et al., 2009). In children, most ependymomas arise in the posterior fossa, while most adult ependymomas present around the lower spinal cord and spinal nerve roots. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platforms:

GPL13534 GPL21145

675 Samples

Download data: IDAT

(Submitter supplied) We have discovered two major molecular subgroups of PFA molecular group posterior fossa ependymomas by DNA methylation profiling. These are also distinguished by gene expression profiling using Affymetrix U133v2 arrays with correspondence to data generated by DNA methylation profiling.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

39 Samples

Download data: CEL

(Submitter supplied) Ependymal tumors across age groups have been classified and graded solely by histopathology. It is, however, commonly accepted that this classification scheme has limited clinical utility based on its lack of reproducibility in predicting patient outcome. We aimed at establishing a reliable molecular classification using DNA methylation fingerprints and gene expression data of the tumors on a large cohort of 500 tumors. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

209 Samples

Download data: CEL

(Submitter supplied) The diagnosis of ependymoma has moved from a purely histopathological review with limited prognostic value to an integrated diagnosis, relying heavily on molecular information. However, as the integrated approach is still novel and some molecular ependymoma subtypes are quite rare, few studies have correlated integrated pathology and clinical outcome, often focusing on small series of single molecular types. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array; Third-party reanalysis

Platforms:

GPL21145 GPL13534

287 Samples

Download data: IDAT, TXT, XLS

(Submitter supplied) Methylation analysis of subepndymoma of the posterior fossa

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platforms:

GPL21145 GPL13534

54 Samples

Download data: CSV, IDAT

(Submitter supplied) We compared molecular characteristics of primary and recurrent pediatric ependymoma to identify sub-group specific differences. Gene expression profiles were used to identify unique immunobiologic sub-types of posterior fossa pediatric ependymoma.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

65 Samples

Download data: CEL

(Submitter supplied) Background: The high incidence of recurrence and unpredictable clinical outcome for paediatric ependymoma reflect the imprecision of current therapeutic staging and need for novel risk stratification markers. Gain of chromosome 1q has been reported as a frequent aberration and correlate of adverse outcome in ependymoma. We therefore evaluated a prognostic role for 1q25 gain across three age-defined European clinical trial cohorts of paediatric intracranial ependymoma. more...

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array

Platforms:

GPL3720 GPL3718

182 Samples

Download data: CEL, CHP, TXT

(Submitter supplied) PFA (posterior fossa group A) ependymomas are a lethal glial malignancy of the hindbrain found in infants and toddlers. Lacking any highly recurrent somatic mutations, PFAs have been proposed as a largely epigenetically driven tumor type. An almost complete lack of model systems has inhibited discovery of novel PFA therapies. Both in vitro and in vivo, the PFA hypoxic microenvironment controls the availability of specific metabolites to diminish histone methylation, and to increase both histone demethylation and acetylation at H3K27. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: BW