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Links from GEO DataSets

Items: 20

1.

Endocrine Sensitivity Index Validation Dataset

(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
Series
Accession:
GSE17705
ID:
200017705
2.

Factorial study for evaluating the effect of Affy platform and lab on gene expression measurements

(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:
GPL96 GPL570
64 Samples
Download data: CEL
Series
Accession:
GSE17700
ID:
200017700
3.

Time-resolved DNA methylation profiling of endocrine resistance in the T47D luminal A breast cancer cell line

(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
Series
Accession:
GSE154626
ID:
200154626
4.

Hyperactivation of PI3K promotes escape from hormone dependence in estrogen receptor-positive breast cancer

(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
Series
Accession:
GSE19639
ID:
200019639
5.

Gene expression profiling of invasive breast cancer events from the tamoxifen prevention trial

(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
Series
Accession:
GSE12665
ID:
200012665
6.

Genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer

(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
Series
Accession:
GSE25066
ID:
200025066
7.

Validation cohort for genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer

(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
Series
Accession:
GSE25065
ID:
200025065
8.

Discovery cohort for genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer

(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
Series
Accession:
GSE25055
ID:
200025055
9.

miRNA expression profiles of primary ER-positive breast tumors following Tamoxifen treatment

(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
Series
Accession:
GSE46823
ID:
200046823
10.

Expression data from paired matched breast cancer Fine needle aspiration (FNA) or Core needle biopsies (CBX)

(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
Series
Accession:
GSE32518
ID:
200032518
11.

Accurate prediction and validation of response to endocrine therapy in breast cancer

(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
Series
Accession:
GSE59515
ID:
200059515
12.

Molecular changes in lobular breast cancers in response to endocrine therapy

(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
Series
Accession:
GSE55374
ID:
200055374
13.

A gene expression signature predicting the recurrence of tamoxifen-treated primary breast cancer.

(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
Series
Accession:
GSE9893
ID:
200009893
14.

The 76-gene Signature Defines High-Risk Patients that Benefit from Adjuvant Tamoxifen Therapy

(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
Series
Accession:
GSE12093
ID:
200012093
15.

Molecular profiling of aromatase inhibitor-treated post-menopausal breast tumors identifies immunerelated correlates of resistance

(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
Series
Accession:
GSE153470
ID:
200153470
16.

Global microRNA expression profiling of high-risk ER+ breast cancers from patients receiving adjuvant Tamoxifen mono-therapy: a DBCG study

(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; Murid gammaherpesvirus 4; Betapolyomavirus hominis; Homo sapiens; Human alphaherpesvirus 1; Human betaherpesvirus 5; Murid betaherpesvirus 1; Human immunodeficiency virus 1
Type:
Non-coding RNA profiling by array
Platforms:
GPL15462 GPL14149 GPL13703
153 Samples
Download data: TXT
Series
Accession:
GSE37405
ID:
200037405
17.

Clinical Value of RNA Sequencing–Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network—Breast Initiative [cohort 3273]

(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
Series
Accession:
GSE96058
ID:
200096058
18.

Clinical Value of RNA Sequencing–Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network—Breast Initiative [superseries]

(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
Series
Accession:
GSE81540
ID:
200081540
19.

Clinical Value of RNA Sequencing–Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network—Breast Initiative [cohort 405]

(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
Series
Accession:
GSE81538
ID:
200081538
20.

Gene-expression profile of breast cancer cell lines and sorted breast cancer epithelial cells

(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
Series
Accession:
GSE23640
ID:
200023640
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