GEO DataSets

(Submitter supplied) Comparison of concordance in single and multi-gene genomic indices from data generated by two different laboratories (MD Anderson Cancer Center (MDA) and Jules Bordet Institute (JBI)) and on two different Affymetrix platforms (U113A and U133_Plus2). We used a 2x2 factorial study in which 16 clinical breast cancer samples were profiled by both laboratories on both platforms (64 arrays total).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL570 GPL96

64 Samples

Download data: CEL

(Submitter supplied) Validation dataset of 298 ER-positive patients treated with tamoxifen for 5 years. All patients in this dataset have ER+ breast cancer and were uniformly treated with tamoxifen for 5 years. The objective of the study was to correlate levels of genomic markers to outcomes (relapse free survival) in this cohort of uniformly treated patients.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

298 Samples

Download data: CEL

(Submitter supplied) Endocrine therapy is the most used treatment for hormone receptor positive breast cancers. Despite the clear benefit of endocrine therapy for patients with ER+ breast cancer, resistance to treatment is a critical clinical issue affecting a large number of patients. While many studies have shown that genetics is an important factor in therapy resistance, recent publications have also reported that epigenetics might play a major role in the acquisition of resistance to endocrine therapies. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

40 Samples

Download data: TXT

(Submitter supplied) Hyperactivation of phosphatidylinositol-3 kinase (PI3K) promotes escape from hormone dependence in estrogen receptor-positive breast cancer. A significant fraction of breast cancers exhibit de novo or acquired resistance to estrogen deprivation. We used gene expression microarrays to identify genes and pathways that are commonly dysregulated in ER+ cell lines with acquired hormone-independent growth. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

24 Samples

Download data: CEL, CHP

(Submitter supplied) Gene expression profiling of invasive breast cancer events from the tamoxifen prevention trial validates low estrogen receptor mRNA level as the main determinant of tamoxifen resistance in estrogen receptor positive breast cancer. In NSABP Breast Cancer Prevention Trial (BCPT), tamoxifen reduced the incidence of estrogen receptor (ER) positive tumors but not estrogen receptor negative breast cancer. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

108 Samples

Download data: TXT

(Submitter supplied) Adjuvant tamoxifen is a valid treatment option for women with estrogen receptor (ER)-positive breast cancer. However, up to 40% of patients experience distant or local recurrence or die. MicroRNAs have been suggested to be important prognosticators in breast cancer. This study aims to identify microRNAs with the potential to predict tamoxifen response. We performed a global microRNA screen in primary tumours of six matched pairs of postmenopausal, ER-positive breast cancer patients treated with tamoxifen, who were either recurrence free or had developed a recurrence. more...

Organism:

Homo sapiens; synthetic construct

Type:

Non-coding RNA profiling by array

Platform:

GPL14613

12 Samples

Download data: CEL

(Submitter supplied) Paired FNA and CBX specimens were prospectively collected from 37 breast cancers before any systemic therapy during a biomarker discovery study at The University of Texas M. D. Anderson Cancer Center. We identified 293 probe sets overexpressed in core biopsies; these included five highly coexpressed gene clusters (metagenes) corresponding to immune functions and extracellular matrix components. We compared gene expression profiles of pairs of fine-needle (stroma-poor) and core-needle (stroma-rich) biopsies from 37 cancers to identify stroma-associated genes

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

74 Samples

Download data: CEL, TXT

(Submitter supplied) Purpose Aromatase inhibitors (AIs) have an established role in breast cancer treatment. Response rates are only 50-70% in the neoadjuvant setting and lower in advanced disease. Accurate biomarkers are urgently needed to predict response in these settings and to determine which individuals will benefit from adjuvant AI therapy. Participants and Methods Pre- and on-treatment (after 2 weeks and 3 months) biopsies were obtained from 89 post-menopausal women with ER+ breast cancer receiving neoadjuvant letrozole for transcript profiling. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

75 Samples

Download data: TXT

(Submitter supplied) Invasive lobular cancer (ILC) accounts for approximately 10-15% of breast carcinomas and although it responds poorly to neoadjuvant chemotherapy, it appears to respond well to endocrine therapy. Pre- and on-treatment (after 2 weeks and 3 months) biopsies and surgical samples were obtained from 14 post-menopausal women with ER+ histologically confirmed ILC who responded to 3 months of neoadjuvant letrozole and were compared with a cohort of 14 responding infiltrating ductal carcinomas (IDCs) matched on clinicopathological features by gene expression profiling. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

36 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

508 Samples

Download data: CEL, TXT

(Submitter supplied) PURPOSE: To develop a predictive test for response and survival following neoadjuvant taxane-anthracycline chemotherapy for HER2-negative invasive breast cancer. METHODS: We developed a microarray-based gene expression test from pre-treatment tumor biopsies (310 patients) to predict favorable outcome based on estrogen receptor (ER) status,pathologic response to chemotherapy, 3-year disease outcomes, and sensitivity to endocrine therapy. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

198 Samples

Download data: CEL

(Submitter supplied) PURPOSE: To develop a predictive test for response and survival following neoadjuvant taxane-anthracycline chemotherapy for HER2-negative invasive breast cancer. METHODS: We developed a microarray-based gene expression test from pre-treatment tumor biopsies (310 patients) to predict favorable outcome based on estrogen receptor (ER) status,pathologic response to chemotherapy, 3-year disease outcomes, and sensitivity to endocrine therapy. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

310 Samples

Download data: CEL

(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) Classification of tamixifen-treated breast cancer patients into high and low risk groups using the 76-gene signature

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

136 Samples

Download data: CEL

(Submitter supplied) To identify in clinical breast cancer those genes and pathways most associated with resistance to aromatase inhibitors by examining the global transcriptional effects of aromatase inhibitor (AI) treatment. Analysis of gene-expression measured in core-cut biopsies at baseline and surgery from patients received 2-week’s presurgical AI revealed: i) the molecular response to AI treatment varies greatly between patients, consistent with the variable clinical benefit from AI treatment; ii) higher baseline expression of an inflammatory signature is associated with poor antiproliferative response, and should be assessed further as a novel biomarker and potential target for AI-treated patients.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13376

162 Samples

Download data: TXT

(Submitter supplied) Purpose: Despite the benefits of estrogen receptor (ER)-targeted endocrine therapies in breast cancer, many tumors develop resistance. MicroRNAs (miRNAs) have been suggested as promising biomarkers and we here evaluated whether a miRNA profile could be identified, sub-grouping ER+ breast cancer patients treated with adjuvant Tamoxifen with regards to probability of recurrence. Experimental design: Global miRNA analysis was performed on 152 ER+ primary tumors from high-risk breast cancer patients with an initial discovery set of 52 patients, followed by 2 independent test sets (N=60 and N=40). more...

Organism:

human gammaherpesvirus 4; JC polyomavirus; Human gammaherpesvirus 8; Betapolyomavirus macacae; Homo sapiens; Human alphaherpesvirus 1; Human betaherpesvirus 5; Murid betaherpesvirus 1; Human immunodeficiency virus 1; Murid gammaherpesvirus 4; Betapolyomavirus hominis

Type:

Non-coding RNA profiling by array

Platforms:

GPL15462 GPL14149 GPL13703

153 Samples

Download data: TXT

(Submitter supplied) PURPOSE In early breast cancer (BC), five conventional biomarkers—estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor 2 (HER2), Ki67, and Nottingham histologic grade (NHG)—are used to determine prognosis and treatment. We aimed to develop classifiers for these biomarkers that were based on tumor mRNA sequencing (RNA-seq), compare classification performance, and test whether such predictors could add value for risk stratification. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL18573

3409 Samples

Download data: CSV, GTF

(Submitter supplied) This SuperSeries is composed of the SubSeries GSE81538 [cohort 405] and GSE96058 [cohort 3273] linked to below. PURPOSE In early breast cancer (BC), five conventional biomarkers—estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor 2 (HER2), Ki67, and Nottingham histologic grade (NHG)—are used to determine prognosis and treatment. We aimed to develop classifiers for these biomarkers that were based on tumor mRNA sequencing (RNA-seq), compare classification performance, and test whether such predictors could add value for risk stratification. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL11154

3814 Samples

Download data

(Submitter supplied) PURPOSE In early breast cancer (BC), five conventional biomarkers—estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor 2 (HER2), Ki67, and Nottingham histologic grade (NHG)—are used to determine prognosis and treatment. We aimed to develop classifiers for these biomarkers that were based on tumor mRNA sequencing (RNA-seq), compare classification performance, and test whether such predictors could add value for risk stratification. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

405 Samples

Download data: CSV, GTF, XLSX

(Submitter supplied) Most of the breast cancer samples used in clinical research contain multiple cell types other than epithelial cells alone. The non-epithelial cell types have have a substantial effect on the gene expression-profile, which is used to define molecular subtypes of the tumours. The purpose of this data set is to retrieve gene-expression profile within tumour epithelial cells. We collected 9 breast cancer epithelial cell lines and 5 tumour sampes from which epithelial cells were sorted and enriched using BerEp4 antibody coated beads. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

14 Samples

Download data: CEL