GEO DataSets

(Submitter supplied) Fallopian tube carcinoma (FTC) is a rare, poorly studied and aggressive cancer, associated with poor survival. Since tumorigenesis is related to acquisition of genetic changes, we used genome-wide array CGH to analyze copy number aberrations occurring in FTC in order to obtain a better understanding of FTC carcinogenesis and to identify prognostic events and targets for therapy. We used arrays of 2464 genomic clones, providing ~1.4 Mb resolution across the genome to quantitatively map genomic DNA copy number aberrations from fourteen FTC onto the human genome sequence. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4896

14 Samples

Download data: TXT

(Submitter supplied) Primary serous ovarian carcinoma (OVCA) and serous Fallopian tube carcinoma (FTC), both belonging to the BRCA-linked tumour spectrum, share many properties and are treated similarly. However, a detailed molecular comparison has been lacking. We hypothesized that comparative genomic studies of serous OVCAs and FTCs should point to gene regions critically involved in their tumorigenesis. Array comparative genomic hybridization (array CGH) analysis indicated that serous OVCAs and serous FTCs displayed common but also more distinctive patterns of recurrent changes. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4896

28 Samples

Download data: TXT

(Submitter supplied) BACKGROUND: Cervical carcinoma develops as a result of multiple genetic alterations. Different studies investigated genomic alterations in cervical cancer mainly by means of metaphase comparative genomic hybridization (mCGH) and microsatellite marker analysis for the detection of loss of heterozygosity (LOH). Currently, high throughput methods such as array comparative genomic hybridization (array CGH), single nucleotide polymorphism array (SNP array) and gene expression arrays are available to study genome-wide alterations. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by genome tiling array; Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL2641 GPL4012 GPL201

40 Samples

Download data: CEL, GPR

(Submitter supplied) A BAC-array platform for comparative genomic hybridization was constructed from a library of 32,433 clones providing complete genome coverage, and evaluated by screening for DNA copy number changes in 11 breast cell lines (BT474, MCF7, HCC1937, SK-BR-3, L56Br-C1, ZR-75-1, MCF10A, JIMT1, MDA-MB-231, MDA-MB-361 and HCC2218). These were also characterized by gene expression analysis and found to represent all five recently described breast cancer subtypes using the ‘intrinsic gene set’ and centroid correlation. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4723

11 Samples

Download data: TXT

(Submitter supplied) RNA expression analysis was performed to compare patterns to DNA copy number changes and sensitivity to BCL2 inhibitors. Keywords: cell line comparison

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3029

Platform:

GPL571

34 Samples

Download data: CEL

Analysis of small-cell lung carcinoma cell (SCLC) lines. Expression profiles compared to the cell lines' sensitivity to the Bcl-2 antagonist ABT-737 and chromosomal gains that include changes in Bcl-2 gene copy number. ABT-737 induces the regression of a fraction of SCLC solid tumors.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 cell type, 4 genotype/variation sets

Platform:

GPL571

Series:

GSE7097

34 Samples

Download data: CEL

(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 GPL5477 GPL7394

28 Samples

Download data

(Submitter supplied) Glioblastoma multiforme shows multiple chromosomal aberrations, the impact of which on gene expression remains unclear. To investigate this relationship and to identify putative initiating genomic events, we integrated a paired copy number and gene expression survey in glioblastoma using whole human genome arrays. Loci of recurrent copy number alterations were combined with gene expression profiles obtained on the same tumor samples. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array; Expression profiling by genome tiling array

Platforms:

GPL2879 GPL6480

60 Samples

Download data: TXT

(Submitter supplied) Background/Aims: Microarray-based comparative genomic hybridisation (CGH) has allowed high-resolution analysis of DNA copy number alterations across the entire cancer genome. Recent advances in bioinformatics tools enable us to perform a robust and highly sensitive analysis of array CGH data and facilitate the discovery of novel cancer-related genes. Methods: We analysed a total of 29 pancreatic ductal adenocarcinoma (PDAC) samples (six cell lines and 23 microdissected tissue specimens) using 1 Mb-spaced CGH arrays. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL6181

52 Samples

Download data: TXT

(Submitter supplied) We analyzed DNA copy number alterations in 64 human gastric cancer samples and 8 gastric cancer cell lines using bacterial artificial chromosome (BAC) arrays based comparative genomic hybridisation (aCGH).

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL14846

72 Samples

Download data: TXT

(Submitter supplied) We carried out a cross species cattle-sheep array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the sheep genome analysing animals of Italian dairy breeds (Sarda, Bagnolese, Laticauda, Massese and Valle del Belice) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. We identified 135 CNV regions (CNVRs) covering about 10.5 Mb of the virtual sheep genome referred to the bovine genome (0.398%) with a mean and median equal to 77.6 kb and 55.9 kb, respectively. more...

Organism:

Bos taurus; Ovis aries

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10990

11 Samples

Download data: PAIR

(Submitter supplied) Chromosomal changes in human aggressive breast cancer samples with basal-like features were detected using 44K oligo array CGH Keywords: DNA copy number change

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL2879

16 Samples

Download data: TXT

(Submitter supplied) Array-CGH profiles of Merkel cell carcinoma tumors Keywords: fresh frozen and formalin fixed paraffin embedded primary tumor, nodal and metastasis merkel cell carcinoma tumor samples

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL2879

25 Samples

Download data: TXT

(Submitter supplied) Genomic DNA copy number alterations are key genetic events in the development and progression of human cancers. Here we report a genome-wide microarray comparative genomic hybridization (array CGH) analysis of DNA copy number variation in a series of primary human breast tumors. We have profiled DNA copy number alteration across 6,691 mapped human genes, in 44 predominantly advanced, primary breast tumors and 10 breast cancer cell lines. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by array

Platforms:

GPL180 GPL2830

100 Samples

Download data

(Submitter supplied) Fifty-one breast tumors were profiled for copy-number alterations with the high-resolution Affymetrix 500K Mapping Array. Combined analysis of the prevalence and amplitude of copy-number alterations defined regions of recurrent gain or loss. Gains were most frequently observed on chromosomes 1, 8, 10, 11, 13, 15, 17, and 20. Losses were most frequent on chromosomes 3, 6, 11, 13, 14, 16, and 17. Compared with previous lower-resolution data, our analysis provided significantly more precise boundaries for frequently altered regions, greatly reducing the number of potential alteration-driving genes. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platforms:

GPL3718 GPL3720

102 Samples

Download data: CEL, EXP

(Submitter supplied) Genome-wide copy number variation was measured in primary tumours of the ovary, Fallopian tube and peritoneum. A well-defined subset of advanced-stage serous tumors was then used to relate CNV to primary resistance to treatment. Analysis is described in: Etemadmoghadam, D., et al. (2009). "Integrated genome-wide DNA copy number and expression analysis identifies distinct mechanisms of primary chemoresistance in ovarian carcinomas." Clin Cancer Res 15(4): 1417-27.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL2005

118 Samples

Download data: CEL, TXT

(Submitter supplied) Tumor recurrence represents a significant clinical challenge in the treatment and management of breast cancer. To investigate whether copy number aberrations (CNAs) facilitate the re-emergence of tumor growth from residual disease we performed array comparative genomic hybridization (aCGH) on primary and recurrent mammary tumors from an inducible mouse model of type-I insulin-like growth factor receptor (IGF-IR) driven breast cancer. more...

Organism:

Mus musculus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL15076

19 Samples

Download data: TXT

(Submitter supplied) Molecular profiling was used to classify mammary tumors that develop in MTB-IGFIR transgenic mice. It was determined that the primary mammary tumors (PMT), which develop due to elevated expression of the type I insulin-like growth factor receptor (IGF-IR) in mammary epithelial cells, most closely resemble murine tumors with basal-like or mixed gene expression profiles and with human basal-like breast cancers. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

28 Samples

Download data: TXT

(Submitter supplied) Prostate cancer-associated stroma (CAS) plays an active role in malignant transformation, tumor progression, and metastasis. Molecular analyses of CAS have demonstrated significant changes in gene expression; however, conflicting evidence exists on whether genomic alterations in benign cells comprising the tumor microenvironment (TME) underlie gene expression changes and oncogenic phenotypes. This study evaluates the nuclear and mitochondrial DNA integrity of prostate carcinoma cells, CAS, matched benign epithelium and benign epithelium-associated stroma by whole genome copy number analyses, targeted sequencing of TP53, and fluorescence in situ hybridization. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platforms:

GPL16333 GPL21289

89 Samples

Download data: TXT

(Submitter supplied) genomic analysis using arrayCGH to gain insight into chromosomal copy number in mucoepidermoid carcinoma (MEC). Results suggest that two types of MECs can be distinguished: (i) a group of MECs without t(11;19)(q21;p13) translocation with many copy number aberrations (> 6), independent of histological grade, and (ii) a group of MECs with the t(11;19)(q21;p13) translocation with no or a few copy number aberrations (<6 ) with two exceptions classified as low and intermediate grade. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL8687

27 Samples

Download data: TXT