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Links from GEO DataSets

Items: 20

1.

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
2.

Clinical associations of ESR2 (estrogen receptor beta; ERβ) expression across thousands of primary breast tumors 

(Submitter supplied) PURPOSE: Estrogen receptor alpha (ERα, encoded by ESR1) is a well-characterized transcription factor expressed in more than 75% of breast tumors and is the key biomarker to direct endocrine therapies. On the other hand, much less is known about estrogen receptor beta (ERβ, encoded by ESR2) and its importance in cancer. Previous studies had some disagreement, however most reports suggested a more favorable prognosis for patients with high ESR2 expression. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL11154 GPL18573
3207 Samples
Download data: GTF, TSV
Series
Accession:
GSE202203
ID:
200202203
3.

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
4.

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
5.

Discovery of naturally occurring ESR1 mutations during acquisition of resistance to endocrine therapy in widely used estrogen receptor positive breast cancer cell lines

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL16791 GPL18573
27 Samples
Download data: XLS
Series
Accession:
GSE100076
ID:
200100076
6.

Discovery of naturally occurring ESR1 mutations during acquisition of resistance to endocrine therapy in widely used estrogen receptor positive breast cancer cell lines [RNA-Seq]

(Submitter supplied) We report the first discovery of naturally occurring ESR1Y537C and ESR1Y537S mutations in MCF7 and SUM44 ESR1-positive cell-lines after acquisition of resistance to long-term-estrogen-deprivation (LTED) and subsequent resistance to fulvestrant (ICIR).
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL18573 GPL16791
15 Samples
Download data: TXT
7.

Discovery of naturally occurring ESR1 mutations during acquisition of resistance to endocrine therapy in widely used estrogen receptor positive breast cancer cell lines [ChIP-Seq]

(Submitter supplied) We report the first discovery of naturally occurring ESR1Y537C and ESR1Y537S mutations in MCF7 and MCF7 ESR1-positive cell-lines after acquisition of resistance to long-term-estrogen-deprivation (LTED) and subsequent resistance to fulvestrant (ICIR).
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
12 Samples
Download data: XLS
Series
Accession:
GSE100074
ID:
200100074
8.

ESR1 mutations affect anti-proliferative responses to tamoxifen through enhanced cross-talk with IGF signaling

(Submitter supplied) The rediscovery of estrogen receptor (ESR1) mutations in metastatic breast cancer is current clinical scenario. We have modeled the three most frequent ESR1 mutations using stable lentiviral vectors in human breast cancer cell lines, and determined that they confer relative resistance to tamoxifen (Tam) in a cell-type specific manner due to distinct epigenetic changes. Resistance was only observed with concomitant engagement and activation of the insulin growth factor signaling pathway (IGF1R). more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL570
23 Samples
Download data: CEL
Series
Accession:
GSE95529
ID:
200095529
9.

Transcriptional profiling of estrogen receptor fusion genes in breast cancer cell lines

(Submitter supplied) Genomic analysis has recently identified multiple ESR1 gene translocations in estrogen receptor-alpha positive (ERα+) metastatic breast cancer (MBC) that encode chimeric proteins whereby the ESR1 ligand binding domain (LBD) is replaced by C-terminal sequences from many different gene partners. Here we functionally screened 15 ESR1 fusions and identified 10 that promoted estradiol-independent cell growth, motility, invasion, EMT and resistance to fulvestrant. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
42 Samples
Download data: RESULTS
Series
Accession:
GSE191158
ID:
200191158
10.

Analysis of breast cancer cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL20301 GPL18573
149 Samples
Download data: CSV, TXT
Series
Accession:
GSE241944
ID:
200241944
11.

PRO-seq analysis of estradiol, OP-1250, fulvestrant and 4OH-tamoxifen treatments at multiple timepoints in breast cancer cells

(Submitter supplied) The estrogen receptor (ER) is a well-established target for the treatment of breast cancer, with the majority of patients presenting as ER-positive (ER+). Endocrine therapy is a mainstay of breast cancer treatment but the development of resistance mutations in response to aromatase inhibitors, poor pharmacokinetic properties of fulvestrant, agonist activity of tamoxifen, and limited benefit for elacestrant leave unmet needs for patients with or without resistance mutations in ESR1, the gene that encodes the ER protein. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
96 Samples
Download data: TXT
Series
Accession:
GSE241764
ID:
200241764
12.

RNA-seq analysis of ESR1 mutations in T47D and MCF7 cell lines

(Submitter supplied) Purpose: Transcriptome analysis of ESR1 mutant cells was performed via sequencing total RNA in T47D and MCF7 cell lines containing Y537S and D538G mutations.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
48 Samples
Download data: CSV
13.

Targeting ESR1 mutation-induced transcriptional addiction with BET inhibition

(Submitter supplied) We investigated the therapeutic potential of BET inhibition to target ESR1 mutation-induced “transcriptional addiction” in ER-positive breast cancer. Our studies show that ESR1 mutant (Y537S and D538G) cells activate unique transcriptional programs that are targeted by OTX015, a BET inhibitor
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
18 Samples
Download data: XLSX
Series
Accession:
GSE206185
ID:
200206185
14.

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
15.

DNA methylation of estrogen regulated enhancers defines endocrine sensitivity in breast cancer

(Submitter supplied) Expression of estrogen receptor (ESR1) determines whether a breast cancer patient receives endocrine therapy as part of their adjuvant care, but does not guarantee patient response. However, the molecular factors that define endocrine response in ESR1-positive breast cancer patients remain poorly understood. Here, we characterize the DNA methylome of endocrine sensitivity and demonstrate the potential impact of differential DNA methylation on endocrine response in breast cancer. more...
Organism:
Homo sapiens
Type:
Methylation profiling by array
Platform:
GPL13534
8 Samples
Download data: IDAT
Series
Accession:
GSE69118
ID:
200069118
16.

Modeling the ESR1 tyrosine 537 mutation with CRISPR-Cas9 for mechanistic studies and evaluation of therapeutic approaches for metastatic breast cancer

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL11154 GPL16791
17 Samples
Download data: WIG
Series
Accession:
GSE78286
ID:
200078286
17.

Modeling the ESR1 tyrosine 537 mutation with CRISPR-Cas9 for mechanistic studies and evaluation of therapeutic approaches for metastatic breast cancer [RNA-Seq]

(Submitter supplied) Estrogen receptor-α (ERα) is an important driver of breast cancer and is the target for hormonal therapies, anti-estrogens and drugs that limit estrogen biosynthesis (aromatase inhibitors). Mutations in the ESR1 gene identified in metastatic breast cancer provide a potential mechanism for acquired resistance to hormone therapies. We have used CRISPR-Cas9 mediated genome editing in the MCF-7 breast cancer cell line, generating MCF-7-Y537S. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16791
11 Samples
Download data: XLSX
18.

Modeling the ESR1 tyrosine 537 mutation with CRISPR-Cas9 for mechanistic studies and evaluation of therapeutic approaches for metastatic breast cancer [ChIP-Seq]

(Submitter supplied) Estrogen receptor-α (ERα) is an important driver of breast cancer and is the target for hormonal therapies, anti-estrogens and drugs that limit estrogen biosynthesis (aromatase inhibitors). Mutations in the ESR1 gene identified in metastatic breast cancer provide a potential mechanism for acquired resistance to hormone therapies. We have used CRISPR-Cas9 mediated genome editing in the MCF-7 breast cancer cell line, generating MCF-7-Y537S. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL11154
6 Samples
Download data: WIG
Series
Accession:
GSE78284
ID:
200078284
19.

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
20.

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