Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Array-based comparative genomic hybridisation analysis at 1Mb resolution of 44 pilocytic astrocytomas

ABSTRACT: Pilocytic astrocytomas (PAs), WHO Grade I, are one of the most frequently occurring childhood brain tumors. We have used microarray comparative genomic hybridization (aCGH) at 1Mb resolution to study copy number changes in a series of PAs (n=44). Single hybridization per case. 44 pilocytic astrocytomas WHO grade I were analyzed. Target (tumor) labelled with Cy5 and reference with Cy3. Mixture of 20 normal male or female genomic DNA was used in sex-mismatched hybridization.

ORGANISM(S): Homo sapiens

SUBMITTER: David Jones

PROVIDER: E-GEOD-11263 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Genomic analysis of pilocytic astrocytomas at 0.97 Mb resolution shows an increasing tendency toward chromosomal copy number change with age.

Jones David T W DT Ichimura Koichi K Liu Lu L Pearson Danita M DM Plant Karen K Collins V Peter VP

Journal of neuropathology and experimental neurology 20061101 11

Brain tumors are the most common solid tumors of childhood, accounting for over 20% of cancers in children under 15 years of age. Pilocytic astrocytomas (PAs), World Health Organization grade I, are one of the most frequently occurring childhood brain tumors, yet little is known about genetic changes characterizing this entity. We have used microarray comparative genomic hybridization at 0.97 Mb resolution to study a series of PAs (n = 44). No copy number abnormality was seen in 64% of cases at ...[more]

PMID: 17086101

Similar Datasets

Tandem duplication producing a novel oncogenic BRAF fusion gene defines the majority of pilocytic astrocytomas

Project description:Pilocytic astrocytomas (PAs), WHO Grade I, are one of the most frequently occurring childhood brain tumors. We have used microarray comparative genomic hybridization (aCGH) to study copy number changes on chromosome 7 in a series of PAs (n=44). Keywords: Comparative Genomic Hybridization Single hybridization per case. 44 pilocytic astrocytomas WHO grade I were analyzed. Target (tumor) labelled with Cy5 and reference with Cy3. Mixture of 20 normal male or female genomic DNA was used in sex-mismatched hybridization.

2009-04-15 | E-GEOD-11265 | biostudies-arrayexpress

Adult grade II astrocytomas are genetically distinct from their pediatric counterparts, and display a more stem cell-like expression pattern linked with more aggressive behaviour

Project description:We have used microarray comparative genomic hybridization (aCGH) at 1Mb resolution to study copy number changes in a series of WHO Grade II Astrocytomas (n=21). We have used Illumina arrays to study genome-wide expression patterns in a series of WHO Grade II Astrocytomas (n=10). Keywords: Array Comparative Genomic Hybridization (aCGH), Expression microarray [aCGH]: Single hybridization per case. 21 astrocytomas WHO grade II were analyzed. Target (tumor) labelled with Cy5 and reference with Cy3. Mixture of 20 normal male or female genomic DNA was used in sex-mismatched hybridization. [mRNA]: Single hybridization per case. 10 astrocytomas WHO grade II were analyzed (5 adult, 5 pediatric)

2010-08-30 | E-GEOD-23869 | biostudies-arrayexpress

Tandem duplication producing a novel oncogenic BRAF fusion gene defines the majority of pilocytic astrocytomas

2009-04-15 | GSE11265 | GEO

Array-based comparative genomic hybridisation analysis at 1Mb resolution of 44 pilocytic astrocytomas

2008-04-28 | GSE11263 | GEO

Transcription profiling of human pilocytic astrocytoma to develop molecular signatures

Project description:Pilocytic astrocytomas (PAs) are the most common glioma in children. While many PAs; are slow growing or clinically indolent, others exhibit more aggressive features with tumor; recurrence and death. In order to identify genetic signatures that might predict PA clinical; behavior, we performed gene expression profiling on 41 primary PAs arising sporadically and in; patients with neurofibromatosis type 1 (NF1). While no expression signature was found that; could discriminate clinically-aggressive or recurrent tumors from more indolent cases, PAs; arising in patients with NF1 did exhibit a unique gene expression pattern. In addition, we; identified a gene expression signature that stratified PAs by location (supratentorial versus; infratentorial). Experiment Overall Design: 41 pilocytic astrocytoma samples were analyzed.

2008-06-14 | E-GEOD-5675 | biostudies-arrayexpress

Pilocytic astrocytoma

Project description:Pilocytic astrocytomas (PAs) are the most common glioma in children. While many PAs are slow growing or clinically indolent, others exhibit more aggressive features with tumor recurrence and death. In order to identify genetic signatures that might predict PA clinical behavior, we performed gene expression profiling on 41 primary PAs arising sporadically and in patients with neurofibromatosis type 1 (NF1). While no expression signature was found that could discriminate clinically-aggressive or recurrent tumors from more indolent cases, PAs arising in patients with NF1 did exhibit a unique gene expression pattern. In addition, we identified a gene expression signature that stratified PAs by location (supratentorial versus infratentorial). Keywords: Human, WHO grade I, Brain tumor, Pilocytic astrocytoma, NF1

2007-03-14 | GSE5675 | GEO

Array based comparative genomic hybridisation analysis of 1 Mb resolution of 21 follicular lymphomas (FL), 31 transformed diffuse large B-cells lymphomas (DLBCL), 29 de novo DLBCL (10 of GC and 19 non-GC related immunophenotype).

Project description:Follicular lymphoma (FL) is one of the most common types of indolent B-cell lymphoma in Western countries. FL commonly transforms to more aggressive diffuse large B-cell lymphoma (DLBCL) at reported frequencies between 15 - 60%. We have used microarray comparative genomic hybridisation (aCGH) at 1 Mb resolution to study copy number changes in paired tumor samples (primary FL and a subsequent tDLBCL) as well as de novo DLBCL cases to outline genetic mechanisms of transformation from follicular lymphoma to diffuse large B-cell lymphoma. Single hybridization per case. 21 FL, 31 transformed DLBCL, 29 de novo DLBCL (10 GC and 19 non-GC DLBCL). Tumor labelled with Cy5 and reference with Cy3. Mixture of 20 normal male or female genomic DNA was used in sex-mismatched hybridization.

2014-04-18 | E-GEOD-56884 | biostudies-arrayexpress

DNA methylation analysis of paediatric pilocytic and diffuse astrocytomas

Project description:Paediatric low-grade gliomas (LGGs) account for about a third of all brain tumours in children. We conducted a detailed study of DNA methylation to improve our understanding of the biology of pilocytic and diffuse astrocytomas. Comparisons were performed between tumours and normal brain controls from matching location, and between pilocytic and diffuse astrocytomas. Pilocytic astrocytomas were found to have a distinctive signature involving 315 CpG sites, with the majority of the sites (312 CpG sites) hypomethylated in pilocytic astrocytomas. Additionally many of the sites were located within annotated enhancers. The distinct signature in pilocytic astrocytomas was not present in diffuse astrocytomas or in published profiles of other brain tumours and normal brain tissue. On further analysis of the 315 CpG sites, the AP-1 transcription factor complex was predicted to bind within 200bp of a subset of teh 315 differentially methylated CpG sites. We also observed up-regulation of the AP-1 factors, FOS and FOSL1 in pilocytic astrocytomas. Our findings highlight novel epigenetic differences between pilocytic and diffuse astrocytomas, in addition to well-described alterations involving BRAF, MYB and FGFR1.

2016-05-10 | GSE77241 | GEO

Affymetrix SNP array data for low-grade astrocytoma samples

Project description:Copy number analysis of 21 paediatric low-grade astrocytomas identified a discrete copy number gain of 1.9Mb in chromosome band 7q34. The gain was present in 12/14 cerebellar pilocytic astrocytomas. Subsequent analysis of tumour cDNA indentified a novel gene fusion between KIAA1549 and BRAF in these tumours. Copy number analysis of 21 paediatric low-grade astrocytomas using the Affymetrix GeneChip Human Mapping 250K Nsp Array. This study comprised 14 pilocytic astrocytomas, 4 diffuse astrocytomas, one pilomyxoid astrocytoma, one pilomyxoid glioma and one pleomorphic xanthoastrocytoma. Tumours were compared to the mean of two normal male DNA controls.

2010-04-09 | E-GEOD-14960 | biostudies-arrayexpress

Homo sapiens

Project description:Array-based comparative genomic hybridisation analysis at 1Mb resolution of 44 pilocytic astrocytomas

| PRJNA106777 | ENA