GEO DataSets

(Submitter supplied) Comparison of copy number changes in MPNST samples against benign neurofibromas in NF1 patients

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL6088

27 Samples

Download data: GPR

(Submitter supplied) Somatic copy number changes in cNFs samples in NF1 patients

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL9777

18 Samples

Download data: TXT

(Submitter supplied) Salivary gland myoepithelial tumors are relatively uncommon tumors with an unpredictable clinical course. More knowledge about their genetic profiles is necessary to identify novel predictors of disease. In this study, we subjected 27 primary tumors (15 myoepitheliomas and 12 myoepithelial carcinomas) to genome-wide microarray-based comparative genomic hybridization (array CGH). We set out to delineate known chromosomal aberrations in more detail and to unravel chromosomal differences between benign myoepitheliomas and myoepithelial carcinomas. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL2843 GPL7394 GPL5477

28 Samples

Download data

(Submitter supplied) Patients with neurofibromatosis type 1 (NF1) develop benign plexiform neurofibromas that frequently progress to become malignant peripheral nerve sheath tumors (MPNSTs). A genetically engineered mouse model that accurately models plexiform neurofibroma-MPNST progression would facilitate the identification of somatic mutations driving this process. We have previously reported that transgenic mice overexpressing the growth factor neuregulin-1 in Schwann cells (P0-GGFβ3 mice) develop MPNSTs. more...

Organism:

Mus musculus

Type:

Genome variation profiling by array

Platform:

GPL11288

12 Samples

Download data: TXT

(Submitter supplied) Allele call files from on 250K StyI SNP array using DNA from 60 human cell lines from metastasized melanoma and from 44 corresponding peripheral blood mononuclear cells (CEL and CHP files provided).

Organism:

Homo sapiens

Type:

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

Platform:

GPL3720

104 Samples

Download data: CEL, CHP

(Submitter supplied) 7 MPNSTs from 7 neurofibromatosis-type 1 patients were screened with a high resolution array-CGH. Each MPNST DNA (somatic tumor DNA) was individually hybridized on Agilent whole human genome 244K microarrays (Platform GPL4091) using the pooled genomic constitutional DNA (lymphocytes DNA) from the normal control patients as reference, in order to detect tumor-specific aberrations.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4091

7 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by RT-PCR

Platform:

GPL27487

28 Samples

Download data

(Submitter supplied) Malignant peripheral nerve sheath tumors (MPNST) are aggressive cancers that occur spontaneously (sporadic MPNST) or from pre-existing, benign plexiform neurofibromas in neurofibromatosis type 1 (NF1) patients. MPNSTs metastasize easily, are resistant to therapeutic intervention and are frequently fatal. The molecular changes underlying the transition to malignancy in the NF1 setting are incompletely understood. more...

Organism:

Homo sapiens

Type:

Expression profiling by RT-PCR

Platform:

GPL27487

10 Samples

Download data: XLSX

(Submitter supplied) Malignant peripheral nerve sheath tumors (MPNST) are aggressive cancers that occur spontaneously (sporadic MPNST) or from pre-existing, benign plexiform neurofibromas in neurofibromatosis type 1 (NF1) patients. MPNSTs metastasize easily, are resistant to therapeutic intervention and are frequently fatal. The molecular changes underlying the transition to malignancy in the NF1 setting are incompletely understood. more...

Organism:

Homo sapiens

Type:

Expression profiling by RT-PCR

Platform:

GPL27487

18 Samples

Download data: XLSX

(Submitter supplied) The diagnosis of Malignant peripheral nerve sheath tumors (MPNSTs) can be challenging, but is aided by their characteristic DNA methylation profile (DMP). An MPNST-like group, characterized by retained H3K27me3 expression, was recently recognized. To evaluate the diagnostic usefulness of DMP in pediatric/juvenile MPNSTs, we selected pediatric/juvenile malignancies from the Bambino Gesù Children's Hospital DMP database. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

42 Samples

Download data: IDAT

(Submitter supplied) 22 plexiform neurofibromas from 18 unrelated neurofibromatosis-type 1 patients were screened with a high resolution array-CGH. Each PNF DNA (somatic tumor DNA) was individually hybridized on Agilent whole human genome 244K microarrays (Platform GPL4091) using the matched genomic constitutional DNA (lymphocytes DNA) from the corresponding patient as reference, in order to detect tumor-specific aberrations.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4091

22 Samples

Download data: TXT

(Submitter supplied) We aimed to characterize the genomic profiles of adenocarcinomas in the gastroesophageal junction in relation to cancers in the esophagus and the stomach. Profiles of gains/losses as well as gene expression profiles were obtained from 27 gastroesophageal adenocarcinomas using 32k high-resolution array-based comparative genomic hybridization (aCGH) and 27k oligo gene expression arrays and putative target genes were validated in an extended series. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4723

26 Samples

Download data: TXT

(Submitter supplied) We aimed to genetically characterize adenocarcinomas in the gastroesophagel junction in relation to cancers in the esophagus and the stomach. In total 27 tumors was genetically profiled using gene expression array. Adenocarcinomas located in the gastroesophageal junction showed strong similarites with tumors in the distal esophagus, whereas different profiles were generated for tumors in the proximal stomach.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10468

29 Samples

Download data: TXT

(Submitter supplied) Use existing public data, cell lines and patient tumors with a personalized medicine approach to predict effective therapies for treatment of Neurofibroma tumors.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

8 Samples

Download data: CEL

(Submitter supplied) We have performed gene expression analyses as part of a European multicentre study on MPNST. The data was used for transcriptomic subtyping, gene set enrichment analyses and integration with DNA copy number data.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

79 Samples

Download data: CEL, CHP

(Submitter supplied) Understanding biological pathways critical for common neurofibromatosis type 1 (NF1) peripheral nerve tumors is essential, as tumor biomarkers, prognostic factors and therapeutics are all lacking. We used gene expression profiling to define transcriptional changes between primary normal Schwann cells (n = 10), NF1-derived primary benign neurofibroma Schwann cells (n = 22), malignant peripheral nerve sheath tumor (MPNST) cell lines (n = 13), benign neurofibromas (n = 26) and MPNST (n = 6). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL7869

86 Samples

Download data: CEL

(Submitter supplied) NF1-associated malignant peripheral nerve sheath tumors (MPNST) are the major cause of mortality in neurofibromatosis. MPNST arise from benign peripheral nerve plexiform neurofibromas (PN) which originate in the embryonic neural crest cell lineage. Using reporter transgenes that label early neural crest lineage cells in multiple NF1 MPNST mouse models, we discovered and characterized a rare MPNST cell population with stem cell-like properties that is essential for tumor initiation and relapse. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

1 Sample

Download data: MTX, TSV

(Submitter supplied) BRD4 Inhibition of spindle cell malignant peripheral nerve sheath tumor (sMPNST) tumor cells

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

12 Samples

Download data: CEL, CHP

(Submitter supplied) SNP arrays allow for genome-wide profiling of copy-number alterations (CNAs) and copy-neutral runs of homozygosity (ROH) at high resolution. To identify novel genetic lesions in myeloproliferative neoplasms (MPN), a large series of 151 clinically well-characterized patients was analyzed in our study. CNAs were rare in essential thrombocythemia and polycythemia vera. In contrast, approximately one third of myelofibrosis patients exhibited small genomic losses (< 5 Mb). more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL3720 GPL3718

212 Samples

Download data: CEL, CHP

(Submitter supplied) Aberrant DNA methylation (DNAm) was first linked to cancer over 25 years ago. Since then, many studies have associated hypermethylation of tumour suppressor genes and hypomethylation of oncogenes to the tumourigenic process. However, most of these studies have been limited to the analysis of promoters and CpG islands (CGIs). Recently, new technologies for whole-genome DNAm (methylome) analysis have been developed, enabling unbiased analysis of cancer methylomes. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9052

3 Samples

Download data: BAM, GFF