GEO DataSets

(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) A 36-gene classifier was constructed through expression profiling of 132 tumors from tamoxifen-treated patients using 70-mer oligonucleotide microarrays. The robustness of the signature was demonstrated using expression data from 83 independent tumors. The 36-gene signature was (i) more efficient to predict disease-free survival than the traditional histo-pathological prognostic factors, (ii) as effective as the Nottingham Prognostic Index or the "Adjuvant!" software, and (iii) the only independent prognostic factor. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5049

155 Samples

Download data: GPR, TXT

(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) Tamoxifen is the most widely administered adjuvant first-line hormone therapy for Estrogen receptor α (ERα) positive breast cancer patients. However, one from three patients will develop resistance, while the underlying molecular mechanisms are currently unclear. Recent studies reported that abnormal expression of miRNAs played a role in cancer progress. To study the potential function of miRNAs in tamoxifen resistance, Affymetrix GeneChip® miRNA 3.0 microarray was employed to identify differentially expressed miRNAs between tamoxifen sensitive MCF7 parent (MCF7-Pa) cells and induced resistant (MCF7-Re) cells.

Organism:

synthetic construct; Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL16384

2 Samples

Download data: CEL

(Submitter supplied) Therapies targeting estrogenic stimulation in estrogen receptor positive (ER+) breast cancer (BC) reduce mortality, but resistance remains a major clinical problem. Molecular studies have shown few high frequency mutations to be associated with endocrine resistance. In contrast, expression profiling of primary ER+ BC samples has identified several promising signatures/networks for targeting. In this study, the cholesterol biosynthesis pathway was the common upregulated pathway in the ER+ LTED but not ER- LTED cell lines, suggesting a potential mechanism dependent on continued ER expression. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

54 Samples

Download data: TXT

(Submitter supplied) Approximately 30% of women diagnosed with ERα breast cancer relapse with metastatic disease following adjuvant treatment with endocrine therapies. The connection between acquisition of drug resistance and invasive potential is poorly understood. In this study, we demonstrate that the type II keratin topological associating domain (TAD) undergoes epigenetic reprogramming in cells that develop resistance to aromatase inhibitors (AI), leading to keratin 80 (KRT80) upregulation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: TSV

(Submitter supplied) We profiled primary breast cancer, nodal and liver metastatic tumours from three patients. At the time of initial diagnosis, all three patients presented with luminal breast cancer with adjacent nodal metastasis. They all received 5 years of enodrine therapy and all subsequently developed liver metastasis.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: TXT

(Submitter supplied) To assess the global effects of HOXC11 in endocrine resistant breast cancer cells we performed RNA-seq on LY2 cells which were transfected with either siRNA targeting HOXC11 (siHOXC11) or a scrambled negative control siRNA (scrHOXC11) in the presence of 4-OH-tamoxifen (10-8M). Knockdown was verified by Taq-man qRT-PCR prior to library preparation. RNA (10µg) was extracted using an Oligotex mRNA kit (Qiagen) as per manufacturer’s instructions (n=4). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9115

8 Samples

Download data: XLSX

(Submitter supplied) To investigate response or resistance to endocrine therapy, mice with targeted over-expression of Esr1 or CYP19A1 to mammary epithelial cells were employed, representing two direct pathophysiological interventions in estrogen pathway signaling. Both Esr1 and CYP19A1 over-expressing mice responded to letrozole with reduced HAN prevalence and decreased mammary epithelial cell proliferation. CYP19A1 over-expressing mice were tamoxifen-sensitive but Esr1 over-expressing mice were tamoxifen-resistant. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

17 Samples

Download data: TXT

(Submitter supplied) Fresh-frozen primary cancer specimens of 107 breast cancer patients whose metastases were treated with first-line aromatase inhibitors were evaluated for their whole genome mRNA expression profiles.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16233

107 Samples

Download data: TXT

(Submitter supplied) ChIP-seq on primary breast cancer tumor samples for Era, H3K4me3, H3K27me3. Patients had a poor or good outcome after aromatase inhibitor treatment. Differential binding patterns between good and poor outcome patients were identified for each marker, predicting response to treatment

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

36 Samples

Download data: BED

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

Organism:

Homo sapiens

Type:

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

4 related Platforms

72 Samples

Download data: IDAT, TXT

(Submitter supplied) Relapse neuroblastoma were characterized by sequencing, gene expression, arrayCGH and genome-wide methylation. This data set contains genome-wide methylation data.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

32 Samples

Download data: CSV, IDAT

(Submitter supplied) Relapse neuroblastoma were characterized by sequencing, gene expression, arrayCGH and genome-wide methylation. This data set contains the aCGH data.

Organism:

Homo sapiens

Type:

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

Platforms:

GPL4093 GPL10123

22 Samples

Download data: TXT

(Submitter supplied) Relapse neuroblastoma were characterized by sequencing, gene expression, arrayCGH and genome-wide methylation. Here we describe the expression data.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16876

18 Samples

Download data: TXT