Gene expression profiles for paediatric brain tumours
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE42656 | GEO | 2013/07/29
SECONDARY ACCESSION(S): PRJNA182519
REPOSITORIES: GEO
Similar Datasets
Project description:In this study, we screened a cohort of 57 paediatric brain tumours, with a wide range of pathologies to identify microRNA profiles
2015-12-10 | GSE42657 | GEO
Project description:In this study, we screened a cohort of 57 paediatric brain tumours, with a wide range of pathologies to identify microRNA profiles We analysed the microRNA profiles in paediatric brain tumours as compared to normal adult brain. Our cohort included 14 pilocytic astrocytomas, 3 diffuse astrocytomas, 2 anaplastic astrocytomas, 5 glioblastomas, 14 ependymomas, 9 medulloblastomas, 5 atypical teratoid/rhabdoid tumours, 4 choroid plexus papillomas, 1 papillary glioneuronal, and 7 adult brain controls.
2015-12-10 | E-GEOD-42657 | biostudies-arrayexpress
Project description:In this study, we screened a cohort of 57 paediatric brain tumours, with a wide range of pathologies to identify gene expression profiles We analysed gene expression in paediatric brain tumours as compared to normal adult brain in order to understand the molecular profiles. Our cohort included 15 pilocytic astrocytomas, 3 diffuse astrocytomas, 2 anaplastic astrocytomas, 5 glioblastomas, 14 ependymomas, 9 medulloblastomas, 5 atypical teratoid/rhabdoid tumours, 4 choroid plexus papillomas, 8 adult brain and 8 foetal brain controls.
2013-07-29 | E-GEOD-42656 | biostudies-arrayexpress
Project description:DNA methylation is increasingly used for tumour classification and has expanded upon the > 100 currently known brain tumour entities. A correct diagnosis is the basis for suitable treatment for patients with brain tumours, which is the leading cause of cancer-related death in children. DNA methylation profiling is required for diagnosis of certain tumours, and used clinically for paediatric brain tumours in several countries. We therefore evaluated if the methylation-based classification is robust in different locations of the same tumour, and determined how the methylation pattern changed over time to relapse.
2024-03-21 | GSE247880 | GEO
Project description:The pathogenesis of paediatric central nervous system tumours is still poorly understood. In an attempt to increase the knowledge of the genetic mechanisms underlying these tumours, we performed genome-wide screening of 17 paediatric gliomas and embryonal tumours using a combination of G-band karyotyping and array comparative genomic hybridisation (aCGH). G-banding revealed abnormal karyotypes in 56% of tumour samples (9 of 16; one failed in culture), whereas aCGH analysis found copy number aberrations in all 13 tumours that could be examined. Pilocytic astrocytomas (n=3) showed normal karyotypes or simple non-recurrent translocations by karyotyping, but revealed the now well-established recurrent gain of 7q34 by aCGH. Our series included one anaplastic oligoastrocytoma, tumours that have not previously been characterised genomically in children, and an anaplastic neuroepithelial tumour (probably an oligoastrocytoma); both tumours showed losses of chromosomes 14 by G-banding as well as structural aberrations of the long arm of chromosome 6, and loss of 14q, 17p, and 22q by aCGH. Three supratentorial primitive neuroectodermal tumours (n=5) showed aberrant karyotypes; two near-diploid with mainly structural changes and one near-triploid with several trisomies including gains of one copy of chromosomes 1, 2, and 7. aCGH confirmed these findings and revealed additional recurrent gains of 1q21-44, 3p21, and 3q29. We also describe cytogenetically for the first time a cribriform neuroepithelial tumour, a recently identified variant of atypical teratoid/rhabdoid tumour with a favourable prognosis, which showed loss of 1p33, 4q13.2, 10p12.31, 10q11.22, and 22q by aCGH.
2011-07-01 | GSE27671 | GEO
Project description:DNA methylation alterations across time and space in paediatric brain tumours
| PRJNA1040863 | ENA
Project description:The pathogenesis of paediatric central nervous system tumours is still poorly understood. In an attempt to increase the knowledge of the genetic mechanisms underlying these tumours, we performed genome-wide screening of 17 paediatric gliomas and embryonal tumours using a combination of G-band karyotyping and array comparative genomic hybridisation (aCGH). G-banding revealed abnormal karyotypes in 56% of tumour samples (9 of 16; one failed in culture), whereas aCGH analysis found copy number aberrations in all 13 tumours that could be examined. Pilocytic astrocytomas (n=3) showed normal karyotypes or simple non-recurrent translocations by karyotyping, but revealed the now well-established recurrent gain of 7q34 by aCGH. Our series included one anaplastic oligoastrocytoma, tumours that have not previously been characterised genomically in children, and an anaplastic neuroepithelial tumour (probably an oligoastrocytoma); both tumours showed losses of chromosomes 14 by G-banding as well as structural aberrations of the long arm of chromosome 6, and loss of 14q, 17p, and 22q by aCGH. Three supratentorial primitive neuroectodermal tumours (n=5) showed aberrant karyotypes; two near-diploid with mainly structural changes and one near-triploid with several trisomies including gains of one copy of chromosomes 1, 2, and 7. aCGH confirmed these findings and revealed additional recurrent gains of 1q21-44, 3p21, and 3q29. We also describe cytogenetically for the first time a cribriform neuroepithelial tumour, a recently identified variant of atypical teratoid/rhabdoid tumour with a favourable prognosis, which showed loss of 1p33, 4q13.2, 10p12.31, 10q11.22, and 22q by aCGH. Tumour sample analysed with control DNA (supplied by Agilent)
2011-07-01 | E-GEOD-27671 | biostudies-arrayexpress
Project description:Promoter hypermethylation and transcriptional silencing is a common epigenetic mechanism of tumour suppressor inactivation in cancer, including malignant brain tumours. To identify targets of epigenetic silencing mediated by CpG island methylation in paediatric ependymoma, we used a pharmacological unmasking approach through treatment with the demethylating agent 5-Aza-2’-deoxycytidine followed by global expression microarray analysis.
2013-12-02 | GSE45437 | GEO
Project description:Overall paediatric high grade glioma (pHGG) has a poor prognosis, in part due to the lack of understanding of the underlying biology. We therefore used high resolution 244k oligo array comparative genomic hybridisation (oligo aCGH) (Agilent Technologies) to analyse DNA from 38 formalin-fixed paraffin embedded pHGG samples, including 13 DIPG (ten pre-treatment samples and three post-mortem). The pattern of gains and losses were distinct from those seen in HGG arising in adults. In particular we found 1q gain in 22% of our cohort compared to 9% in adults. Homozygous loss at 8p12 was seen in 6/38 (15%) of pHGG. This deletion has not been previously reported in adult or paediatric high grade gliomas. The minimal deleted region is of the gene ADAM3A and homozygous deletion of ADAM3A was confirmed by quantitative real time PCR (qPCR). This novel homozygous deletion of ADAM3A in pHGG merits further study. Loss of CDKN2A/CDKN2B was seen in 4/38 (10%) samples by oligo a CGH, confirmed by FISH on TMAs and was restricted to supratentorial tumours. Amplification of the 4q11-13 region was detected in 8% of cases and included PDGFRA and KIT, subsequent qPCR analysis was consistent with amplification of PDGFRA. MYCN amplification was seen in 2/38 samples (5%) and was shown to be significantly associated with anaplastic astrocytomas (p=0.03). Overall DIPG shared similar spectrum of changes to supratentorial HGG with some notable differences including high frequency of 17p loss and 14q loss and lack of CDKN2A/CDKN2B deletion. To our knowledge, this study examines the largest DIPG cohort to date using high-throughput genetic techniques.
2010-12-01 | GSE21420 | GEO
Project description:Constitutive signalling pathway activation is a key feature of primary tumours and cancer cell lines. The regulation of gene expression changes may be via both genomic and epigenetic means, and understanding the mechanisms by which signal transduction may be activated can provide rational targets for therapeutic intervention. We have previously carried out DNA copy and expression profiling on a unique panel of five paediatric glioma cell lines, and have noted only a limited influence of gene amplification on gene expression. In the present study we have extended our work to include a measure of global methylation changes as well as micro RNA profiling in the same cell lines. We noted various instances of signalling pathway activation associated with specific hypermethylation or miRNA regulation of gene expression at various effectors also observed in primary paediatric tumours. These data provide evidence for the multifaceted nature of gene expression changes in paediatric high grade glioma, and identify novel targets for targeted therapy in this treatment refractory disease.
2010-12-03 | E-TABM-858 | biostudies-arrayexpress