GEO DataSets

(Submitter supplied) Background: The amplification event occurring at chromosome locus 11q13, reported in several different cancers, includes a number of potential oncogenes. We have previously reported amplification of one such oncogene, CCND1, to be correlated with an adverse effect of tamoxifen in premenopausal breast cancer patients. Overexpression of cyclin D1 protein however, confers tamoxifen resistance but not a tamoxifen induced adverse effect. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL4723 GPL7247

56 Samples

Download data: GPR

(Submitter supplied) Amplification of chromosomal region 11q13, containing the cell cycle regulatory gene CCND1, is frequently found in breast cancer and other malignancies. It is associated with the favourable oestrogen receptor (ER) positive breast tumour phenotype, but also with poor prognosis and treatment failure. 11q13 spans almost 14 Mb and contains more than 200 genes and is affected by various patterns of copy number gains, suggesting complex mechanisms and selective pressure during tumour progression. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL7247 GPL4723

94 Samples

Download data: GPR

(Submitter supplied) Breast cancer is a profoundly heterogeneous disease with respect to biological and clinical behavior. Gene expression profiling has been used to dissect this complexity and stratify tumors into intrinsic gene expression subtypes associated with distinct biology, patient outcome and different genomic alterations. Additionally, breast tumors occurring in individuals with germline BRCA1 or BRCA2 mutations typically fall into distinct subtypes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by array

Platforms:

GPL4723 GPL5345 GPL7247

718 Samples

Download data: GPR, TXT

(Submitter supplied) OBJECTIVES: Amplification of the 11q13 locus is commonly observed in a number of human cancers including both breast and ovarian cancer. Cyclin D1 and EMS1 have been implicated as candidate oncogenes involved in the emergence of amplification at this locus. Detailed analysis of the 11q13 amplicon in breast cancer led to the discovery of four regions of amplification suggesting the involvement of other genes. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL8641

51 Samples

Download data

(Submitter supplied) Co-amplification at chromosomes 8p11-8p12 and 11q12-11q14 occurs often in breast tumors, suggesting possible cooperation between genes in these regions in oncogenesis. We used high resolution array comparative genomic hybridization (array CGH) to map the minimal amplified regions. The 8p and 11q amplicons are complex and consist of at least four amplicon cores at each site. Candidate genes mapping to these regions were identified by combining copy number and RNA and protein expression analyses. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL7298

42 Samples

Download data: TXT

(Submitter supplied) Despite recent consensus on eligibility of adjuvant systemic therapy in lymph-node negative breast cancer (NNBC) patients based on clinico-pathological criteria, specific biological markers are needed to predict sensitivity to the different therapeutic options. We examined the feasibility of developing a genomic predictor of chemotherapy response and recurrence risk in 185 patients with NNBC using assembled arrays containing 2,460 BAC clones for scanning the genome for DNA copy number changes. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL3632

185 Samples

Download data: PDF, TXT

(Submitter supplied) The molecular mechanisms of endocrine resistance in breast cancer remain poorly understood. Here we used PRO-seq to map the location of hundreds of genes and thousands of distal enhancers whose activities differ between endocrine sensitive and resistant MCF-7 cells. Our genome-wide screen identified a 16-fold transcriptional increase in glial-cell line derived neurotrophic factor (GDNF), a RET tyrosine kinase receptor ligand, which is both necessary and sufficient for resistance in MCF-7 cells. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

22 Samples

Download data: BED, BW

(Submitter supplied) We sought to identify genetic variants associated with disease relapse and failure to hormonal treatment in hormone-receptor positive breast cancer (HRPBC). We analyzed a series of HRPBC with distant relapse, by sequencing pairs (n=11) of tumors (primary and metastases) at >800X. Comparative genomic hybridization was performed as well. Top hits, based on the frequency of alteration and severity of the changes, were tested in the TCGA series. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL21613

16 Samples

Download data: TXT

(Submitter supplied) The purpose of this study was to improve prediction of patients at high-risk for metastatic disease utilizing a nested case-control design that uniquely enables enrichment for relevant phenotypes. We identified all women diagnosed with primary breast cancer from January 1, 1997, to December 31, 2005, in the Stockholm health care region. Patients developing distant metastatic disease (cases) were selected and controls (free from distant disease) were randomly matched by adjuvant therapy, age and calendar period at diagnosis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10379

623 Samples

Download data: CEL

(Submitter supplied) Breast cancers can be classified using whole genome expression into distinct subtypes that show differences in patient prognosis. One of these groups, the basal-like carcinomas, are poorly differentiated, highly metastatic, and genomically unstable. These tumors also contain specific genetic alterations with one example being frequent p53 mutations. The loss of the tumor suppressor gene encoded by the retinoblastoma (RB1) locus is a well-characterized occurrence in many tumor types, however, its role in breast cancer is less clear with many reports demonstrating a Loss of Heterozygosity (LOH) that does not correlate with loss of RB1 protein expression. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

4 related Platforms

66 Samples

Download data

(Submitter supplied) Mice have been used as models for human breast cancers for many years, however, it is still unclear which murine models faithfully represent human tumor phenotypes. To address this question, we used DNA microarrays to characterize 10 different murine mammary models and compared these data to the expression patterns from primary human breast tumors. Hierarchical clustering analysis of the murine samples showed that the WAP-Myc, MMTV-Neu, MMTV-PyMT, WAP-Int3, and C3(1)-Tag tumors were highly correlated within each model. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by array

4 related Platforms

354 Samples

Download data

(Submitter supplied) To investigate the function of CCND1/CCND2/ORAOV1/miR548K in 11q13-amplified cancer cells or non cancerous keratinocytes, we established respective KO cells through CRISPR-Cas9. We performed gene expression profiling analysis using data obtained from RNA-seq upon target KO in either FaDu cells or TP53/CDKN2A k.o. oral keratinocytes

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

18 Samples

Download data: TSV

(Submitter supplied) Resistance to tamoxifen in breast cancer patients is a serious therapeutic problem and major efforts are underway to understand underlying mechanisms. Resistance can be either intrinsic or acquired. We derived a series of subcloned MCF7 cell lines that were either highly sensitive or naturally resistant to tamoxifen and studied the factors that lead to drug resistance. Gene-expression studies revealed a signature of 67 genes that differentially respond to tamoxifen in sensitive vs. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4051

Platform:

GPL570

24 Samples

Download data: CEL, EXP

Analysis of tamoxifen-sensitive and -resistant subclones of breast tumor MCF7 cells treated with estrogen (E), 4-hydroxy-tamoxifen (4-OHT), or E + 4-OHT. Success of 4-OHT therapy is limited by intrinsic and acquired drug resistance. Results provide insight into mechanisms leading to drug resistance.

Organism:

Homo sapiens

Type:

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

Platform:

GPL570

Series:

GSE26459

24 Samples

Download data: CEL, EXP

(Submitter supplied) DNA amplification, particularly of chromosomes 8 and 11, occurs frequently in breast cancer and is a key factor in tumorigenesis, often associated with poor prognosis. The mechanisms involved in the amplification of these regions are not fully understood. Studies from model systems have demonstrated that palindrome formation can be an early step in DNA amplification, most notably seen in the breakage-fusion-bridge (BFB) cycle. more...

Organism:

Homo sapiens

Type:

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

8 related Platforms

31 Samples

Download data: BAR, CEL, CNCHP