Project description:Copy number profiling of 36 ovarian tumors on Affymetrix 100K SNP arrays Thirty-six ovarian tumors were profiled for copy-number alterations with the Affymetrix 100K Mapping Array. Copy number profiling of 36 ovarian tumors on Affymetrix 500K SNP arrays Sixteen ovary tumors were profiled for copy-number alterations with the high-resolution Affymetrix 500K Mapping Array. Affymetrix 100K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization. Each probe set was mapped to the genome, NCBI assembly version 36, using annotation provided by the Affymetrix web site. The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment. Copy number was calculated as power(2,log2ratio + 1). Affymetrix 500K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization. Forty-eight normal samples were downloaded from the Affymetrix website (http://www.affymetrix.com/support/technical/byproduct.affx?product=500k) and analyzed at the same time. One CEL file for each set (Sty and Nsp) with the median signal intensity across the set was selected as the reference array. The dChip-normalized signal intensities were converted to log2 ratios and segmented as follows. For each autosomal probe set, the log2 tumor/normal ratio of each tumor sample was calculated using the average intensity for each probe set in the normal set. For Chromosome X, the average of the 20 normal female samples was used. Each probe set was mapped to the genome, NCBI assembly version 36, using annotation provided by the Affymetrix web site. The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment. Copy number was calculated as power(2,log2ratio + 1).

2010-12-16 | E-GEOD-26075 | biostudies-arrayexpress

Affymetrix 500K Mapping Array data from ovary tumors

Project description:Fifty-seven ovary tumors were profiled for copy-number alterations with the high-resolution Affymetrix 500K Mapping Array. Keywords: Mapping Array

2009-05-18 | GSE11960 | GEO

Genome-wide molecular characterisation of CNS PNET and Pineoblastoma

Project description:sPNETs are highly malignant embryonal brain tumours of poor prognosis. The underlying biology is poorly understood. To address this we therefore performed high resolution genetic analysis. 36 CNS PNETs and 8 PBs were analysed using the Affymetrix 100K and 500K Mapping Set to identify copy number imbalance at both the chromosome and gene level. Keywords: Affymetrix 100K SNP array, Affymetrix 500K SNP arrays 36 CNS PNETs and 8 PBs with constitutional controls

2011-08-21 | E-GEOD-12370 | biostudies-arrayexpress

Affymetrix 500K SNP array data for Primary Effusion Lymphoma samples

Project description:Affymetrix 500K array was used to determine gross genomic aberrations in a panel of Primary Effusion Lymphoma (PEL) cell lines, specifically focusing on chromosome 10, which includes the Phosphatase and Tensin Homolog (PTEN) locus.

2011-06-23 | GSE28684 | GEO

A gene expression signature associated with K-Ras addiction reveals regulators of EMT and tumor cell survival

Project description:K-Ras mutations occur frequently in epithelial cancers. Using shRNAs to deplete K-Ras in lung and pancreatic cancer cell lines harboring K-Ras mutations, two classes were identified—lines that do or do not require K-Ras to maintain viability. Comparing these two classes of cancer cells revealed a gene expression signature in K-Ras-dependent cells, associated with a well-differentiated epithelial phenotype, which was also seen in primary tumors. Several of these genes encode pharmacologically tractable proteins, such as Syk and Ron kinases and integrin beta6, depletion of which induces epithelial-mesenchymal transformation (EMT) and apoptosis specifically in K-Ras-dependent cells. These findings indicate that epithelial differentiation and tumor cell viability are associated, and that EMT regulators in “K-Ras-addicted” cancers represent candidate therapeutic targets. Expression analysis: 40 Samples representing K-Ras mutant cancer cell lines derived from various tissue types were hybridized to the Affymetrix GeneChip Human X3P Array. Copy number analysis: 10 samples representing K-Ras mutant cancer cell lines were hybridized to the Affymetrix Mapping 500K Set Arrays (250K_Nsp_SNP and 250K_Sty2_SNP). Reference data included 63 randomly chosen female samples (supplementary file Sing_etal_CopyNumber_NormalSamples.txt) from the HapMap project Affy 500K SNP data (http://www.hapmap.org/downloads/raw_data/affy500k).

2009-03-06 | E-GEOD-15126 | biostudies-arrayexpress

Copy number profiling of 36 ovarian tumors on Affymetrix 100K SNP arrays and 16 ovarian tumors on 500K SNP arrays

2010-12-16 | GSE26075 | GEO