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

Array-based karyotyping for prognostic assessment in chronic lymphocytic leukemia: performance comparison of Affymetrix 10K2.0, 250K Nsp, and SNP6.0 arrays.

Project description:Specific chromosomal alterations are recognized as important prognostic factors in chronic lymphocytic leukemia (CLL). Array-based karyotyping is gaining acceptance as an alternative to the standard fluorescence in situ hybridization (FISH) panel for detecting these aberrations. This study explores the optimum single nucleotide polymorphism (SNP) array probe density for routine clinical use, presents clinical validation results for the 250K Nsp Affymetrix SNP array, and highlights clinically actionable genetic lesions missed by FISH and conventional cytogenetics. CLL samples were processed on low (10K2.0), medium (250K Nsp), and high (SNP6.0) probe density Affymetrix SNP arrays. Break point definition and detection rates for clinically relevant genetic lesions were compared. The 250K Nsp array was subsequently validated for routine clinical use and demonstrated 98.5% concordance with the standard CLL FISH panel. SNP array karyotyping detected genomic complexity and/or acquired uniparental disomy not detected by the FISH panel. In particular, a region of acquired uniparental disomy on 17p was shown to harbor two mutated copies of TP53 that would have gone undetected by FISH, conventional cytogenetics, or array comparative genomic hybridization. SNP array karyotyping allows genome-wide, high resolution detection of copy number and uniparental disomy at genomic regions with established prognostic significance in CLL, detects lesions missed by FISH, and provides insight into gene dosage at these loci.

| S-EPMC2871725 | biostudies-literature

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