GEO DataSets

(Submitter supplied) Genome-wide screening for regions of genetic gains and losses on nine prostate cancer cell lines (PC3, DU145, LNCaP, CWR22, and derived sublines) was carried out using comparative genomic hybridization on a 35 K longmer oligonucleotide microarray (arrayCGH). Compared to conventional chromosomal CGH more deletions and small regions of gains, particularly in pericentromeric regions and regions next to the telomers, were detected. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL5046

11 Samples

Download data: TXT

(Submitter supplied) Circulating (CTCs) and disseminated (DTCs) tumor cells are of great interest to the field of cancer research as they provide a minimally-invasive window for assessing aspects of cancer biology including tumor heterogeneity, a means to discover biomarkers of disease behavior, and a way to identify and prioritize therapeutic targets in the emerging era of precision oncology. However, the rarity of CTC/DTC poses a significant challenge to the consistent success in analyzing the molecular features of these cells including genomic aberrations. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL13829

8 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:

GPL4012 GPL2641 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) Genomic changes in chromosome 8 are commonly observed in breast cancer cell lines and tumors. Fine mapping of such genomic changes, and evaluation of associated expression changes, are expected to provide reagents for diagnosis, insights into understanding the disease, and open up avenues for novel therapeutic intervention. We made an effort to search for genes on chromosome 8 with altered copy number and expression. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL4615 GPL4611

42 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL6947 GPL4723

150 Samples

Download data: GPR

(Submitter supplied) Lung cancer is the worldwide leading cause of death from cancer. This GEO series correspond to one of the BAC aCGH data sets used as validation cohort for the study: Landscape of somatic allelic imbalances and copy number alterations in human lung cancer, Int J Cancer 2013.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4723

78 Samples

Download data: GPR, XLS

(Submitter supplied) We demonstrate that comparative genomic hybridisation (CGH) onto cDNA microarrays may be used to carry out genome-wide screens for regions of genetic loss, including homozygous (complete) deletions that may represent the possible location of tumour suppressor genes in human cancer. Screening of the prostate cancer cell lines LNCaP, PC3 and DU145 allowed the mapping of specific regions where genome copy number appeared altered and led to the identification of two novel regions of complete loss at 17q21.31 (500 kb spanning STAT3) and at 10q23.1 (50-350 kb spanning SFTPA2) in the PC3 cell line. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL3898

8 Samples

Download data

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL10558 GPL10123

32 Samples

Download data: TXT

(Submitter supplied) The imbalances scored by arrayCGH mapped to different chromosomes with losses being more common than gains. Frequent losses of large chromosomal segments were scored from 3p and 8p whereas same-sized gains were frequent from 3q and 8q. This is the first study of vulvar tumors using arrayCGH, and some frequent imbalances could be defined precisely.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10123

14 Samples

Download data: TXT

(Submitter supplied) The genome of 14 vulvar SCC was analyzed by aCGH and microarray to identify common imbalances present in the tumors as well as which genes were deregulated. Overall there was a good concordance between the imbalances scored by aCGH and the level of gene expression found by microarray, i.e., the genes located in gained regions were overexpressed while those located in lost regions were found down-regulated.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

18 Samples

Download data: TXT

(Submitter supplied) Whole-genome BAC-array. Isolated BAC-DNA was amplified by two-step DOP-PCR. PCR products were dissolved in 3xSSC, 1.5M betaine and spotted as triplicates on epoxysilane-coated slides. Keywords = Matrix-CGH Keywords = array-CGH

Organism:

Homo sapiens

1 Series

94 Samples

Download data

(Submitter supplied) We analyzed the 10q22 amplification in advanced prostate cancer and subjected the genes located in the common amplified region to an RNAi screen. We found vinculin as the most promising candidate gene and analyzed its protein expression on more than 400 prostate cancers by using the tissue micrarray (TMA) technology. We discovered a strong correlation between amplification of the vinculin gene and increased protein expression. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4091

4 Samples

Download data: TXT

(Submitter supplied) To evaluate the mechanisms and consequences of chromosomal aberrations in colorectal cancer (CRC), we used a combination of spectral karyotyping, array comparative genomic hybridization (aCGH), and array-based global gene expression profiling on 31 primary carcinomas and 15 established cell lines. Importantly, aCGH showed that the genomic profiles of primary tumors are recapitulated in the cell lines. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL6848 GPL6480

50 Samples

Download data: TXT

(Submitter supplied) Detection of genomic rearrangements from a single cell instead of a population of cells is an emerging research technique with important applications in the study of human fertility, constitutional chromosomal disorders, and tumor progression. Here, we develop a method to improve the detection of single-cell genome-wide copy number variation. Additional information about the blastomeres can be found in GSE11663.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL9128

21 Samples

Download data: TXT

(Submitter supplied) Detection of genomic rearrangements from a single cell instead of a population of cells is an emerging research technique with important applications in the study of human fertility, constitutional chromosomal disorders, and tumor progression. Here, we develop a method to improve the detection of single-cell genome-wide copy number variation.

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL9128

7 Samples

Download data: TXT

(Submitter supplied) Embryonic chromosome aberrations cause birth defects and reduce human fertility. However, neither their nature nor incidence are known. Here, we develop a method to assess genome-wide copy number variation and loss of heterozygosity in single cells and apply it to screen blastomeres from in vitro fertilized preimplantation embryos. Complex patterns of chromosome-arm imbalances or segmental deletions, duplications or amplifications that were reciprocal in sister blastomeres were detected in a large proportion of the embryos. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL6929 GPL3718 GPL6928

290 Samples

Download data: CEL, CHP, GPR

(Submitter supplied) K14Cre; Brca2F/F; p53F/F tumor analysis Keywords: Comparative Genomic Hybridization, aCGH

Organism:

Mus musculus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL2851

4 Samples

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