GEO DataSets

(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) 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:

GPL5175 GPL9128

77 Samples

Download data: CEL, TXT

(Submitter supplied) Copy number variation profiling of gastric tissues comparing gastric cancer tissues with matched adjacent noncancerous tissues. Goal was to determine the effects of chromosomal imbalances on gene expression and carcinogenesis or progression.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL9128

27 Samples

Download data: TXT

(Submitter supplied) To elucidate gene expression associated with copy number changes, we performed a genome-wide copy number and expression microarray analysis of 25 pairs of gastric tissues.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

50 Samples

Download data: CEL

(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) Purpose: To improve clinical outcome of gastric cancer patients, most emphasis is on improving therapeutic regimens, including more extensive surgery as well as (neo)adjuvant chemotherapy. The present study set out to identify, based on DNA copy number profiling, subgroups of patients with different clinical outcomes who thus would qualify for different therapy intensities. Experimental Design: DNA of 206 gastric cancer patients was isolated and analyzed by genome wide array comparative genomic hybridization. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

4 related Platforms

183 Samples

Download data: TXT

(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) Objectives: Earlier studies involving a priori gene selection have identified promoter regions deregulated by DNA methylation changes in oral squamous cell cancers (OSCCs) and precancers. Interrogation of global DNA methylation patterns for such specimens has not been reported, though such analyses are needed to uncover novel molecular factors driving disease. Materials and Methods: We evaluated global DNA methylation patterns for 30 biopsies obtained from 10 patients undergoing surgical removal of an OSCC or carcinoma in situ (CIS). more...

Organism:

Homo sapiens

Type:

Methylation profiling by array; Expression profiling by array

Platforms:

GPL6480 GPL8490

60 Samples

Download data: TXT

(Submitter supplied) Analysis of DNA from 94 oral lesions by whole genome tiling-path array comparative genomic hybridization. Keywords: array comparative genomic hybridization

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL2043 GPL2616

94 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL8581 GPL96 GPL13248

139 Samples

Download data: CEL, FTR, GPR, TXT

(Submitter supplied) The identification of genetic and epigenetic alterations from primary tumor cells has become a common method to identify genes critical to the development and progression of cancer. We provide a bioinformatic analysis of copy number variation and DNA methylation covering the genetic landscape of ovarian cancer tumor cells. We individually examined the copy number variation and DNA methylation for 44 primary ovarian cancer samples and 7 ovarian normal samples using our MOMA-ROMA technology and Affymetrix expression data as well as 379 tumor samples analyzed by The Cancer Genome Atlas. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL8581

42 Samples

Download data: GPR, TXT

(Submitter supplied) The identification of genetic and epigenetic alterations from primary tumor cells has become a common method to identify genes critical to the development and progression of cancer. We provide a bioinformatic analysis of copy number variation and DNA methylation covering the genetic landscape of ovarian cancer tumor cells. We individually examined the copy number variation and DNA methylation for 44 primary ovarian cancer samples and 7 ovarian normal samples using our MOMA-ROMA technology and Affymetrix expression data as well as 379 tumor samples analyzed by The Cancer Genome Atlas. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

46 Samples

Download data: CEL

(Submitter supplied) The identification of genetic and epigenetic alterations from primary tumor cells has become a common method to identify genes critical to the development and progression of cancer. We provide a bioinformatic analysis of copy number variation and DNA methylation covering the genetic landscape of ovarian cancer tumor cells. We individually examined the copy number variation and DNA methylation for 44 primary ovarian cancer samples and 7 ovarian normal samples using our MOMA-ROMA technology and Affymetrix expression data as well as 379 tumor samples analyzed by The Cancer Genome Atlas. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13248

51 Samples

Download data: FTR, 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) Genome-wide association studies (GWAS) have identified 19 risk variants associated with colorectal cancer. As most of these risk variants reside outside the coding regions of genes, we conducted cis-expression quantitative trait loci (cis-eQTL) analyses to investigate possible regulatory functions on the expression of neighboring genes.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

80 Samples

Download data: CEL

(Submitter supplied) in 25% - 30% of all OS cases the chromosome region 17p11.2-p12 is aberrant. Using SNP array in conjunction with expression microarrays we try to identify genes which can be classified as oncogens or are in someway benificial to the survival of the tumor.

Organism:

Homo sapiens

Type:

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

Platforms:

GPL6947 GPL6985

68 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) Genome-wide expression profiling of NSCLC patients were done using Phalanx Human OneArray chip. The surgically resected tumor tissue and corresponding normal tissue were collected from 21 patients diagnosed with primary NSCLC admitted to Taipei Veterans General Hospital, Taiwan.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6254

42 Samples

Download data: GPR

(Submitter supplied) This study constructed a non-gapped bacterial artificial chromosomes (BAC) array containing 3604 BAC clones covering 18 lung cancer-related chromosome imbalance hotspot regions. Using this specialized array, DNA from tumor and normal tissues of 40 Asian and 20 Caucasian non-small cell lung cancer (NSLCL) patients was analyzed by array-comparative genomic hybridization (array-CGH). Block-wise normalization and a Bayes regression approach were used to refine the chromosomal imbalance regions identified by array-CGH. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10303

60 Samples

Download data: GPR