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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE26075 | GEO | 2010/12/16

SECONDARY ACCESSION(S): PRJNA135205

REPOSITORIES: GEO

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

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

Genome-wide molecular characterisation of CNS PNET and Pineoblastoma

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Homo sapiens

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Genome-wide copy number profiling of 18 gastric cancer cell lines using 500K SNP arrays

Project description:The genomic loci with copy number alterations are known to harbor cancer genes. We investigated a comprehensive panel of gastric cancer cell lines for their genome-wide copy number alterations. Eighteen gastric cancer cell lines were profiled using Affymetrix 500K SNP arrays. For copy number calculation, seven independent normal blood samples were profiled together. The copy numbers were calculated genome-wide, in these cell lines with high resolution and reveal the cell line specific amplification and copy number changes.

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Genome-wide molecular characterisation of CNS PNET and Pineoblastoma

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

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2010-04-13 | E-GEOD-15730 | biostudies-arrayexpress

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Project description:Genome-wide profiling of Copy Number Alterations (CNA) and Loss of Heterozygosity (LOH), gene expression and resequencing of pediatric AML. This study characterizes the CNA and LOH in a representative cross-section through subtypes of pediatric AML. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved diagnostic bone marrow or peripheral blood samples. 111 pediatric AML samples were studied using either Affymetrix 100K + 500K 5.0 SNP arrays, 65 of the samples had paired germ line material. The supplemental files 'GSE15731_AML_175_SNP_Sty_signal.txt' and 'GSE15731_AML_176_SNP_Sty_signal.txt' contain the raw signals generated by dChip without normalization. The CNA and LOH data can be found in the Supplemental Information of the associated manuscript.

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