GEO DataSets

(Submitter supplied) To evaluate the effect of tissue type (cytology vs. surgical tissue) on gene expression measurements. Information was used to select probesets with a high spatial reproducibility for the development of gene signatures.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

232 Samples

Download data: CEL

(Submitter supplied) 63 samples were profiled in replicates on Affymetrix microarrays and using a custom RNASeq panel. The samples were randomly split in a training and validation cohort. SET ER/PR was calculated and a linear model was trained and validated to reproduce values obtained by microarray using RNASeq. In addition, the microarray replicates were used to validate the technical reproducibility of SET ER/PR.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

128 Samples

Download data: CEL

(Submitter supplied) To evaluate the effect of technical repetition on gene expression measurements, we repeated the laboratory protocol at 6 different steps. Information was used to select probesets with a high technical reproducibility for the development of gene signatures.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

120 Samples

Download data: CEL

(Submitter supplied) To evaluate the effect of intratumorally heterogeneity on gene expression measurements, we profiled and compared samples from different macroscopic tumor areas. Information was used to select probe sets with a high spatial reproducibility for the development of gene signatures.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

153 Samples

Download data: CEL

(Submitter supplied) 88 breast cancer samples were profiled on Affymetrix U133A and Plus2 microarrays.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL96 GPL570

176 Samples

Download data: CEL

(Submitter supplied) Samples from hormone-receptor positive breast cancer to identify transcripts related to ESR1 and PGR expression.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

147 Samples

Download data: CEL

(Submitter supplied) There is clinical need to predict sensitivity of metastatic hormone receptor-positive and HER2-negative (HR+/HER2-) breast cancer to endocrine therapy, and targeted RNA sequencing (RNAseq) offers diagnostic potential to measure both transcriptional activity and functional mutation. We developed the SETER/PR index to measure gene expression microarray probe sets that were correlated with hormone receptors (ESR1 and PGR) and robust to pre-analytical and analytical influences. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL96 GPL570

1196 Samples

Download data: CEL

(Submitter supplied) There is clinical need to predict sensitivity of metastatic hormone receptor-positive and HER2-negative (HR+/HER2-) breast cancer to endocrine therapy, and targeted RNA sequencing (RNAseq) offers diagnostic potential to measure both transcriptional activity and functional mutation. We developed the SET ER/PR index to measure gene expression microarray probe sets that were correlated with hormone receptors (ESR1 and PGR) and robust to pre-analytical and analytical influences. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

140 Samples

Download data: CEL

(Submitter supplied) PURPOSE: To estimate the effect of contamination with normal breast tissue for the development of gene signatures robust to pre-analytical conditions. METHODS: We evaluated the effect of contamination with normal breast tissue on gene signatures by comparing microarray profiles of breast cancer samples contaminated with increasing amounts of normal breast tissue.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

100 Samples

Download data: CEL

(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) How breast cancers respond to endocrine therapy strongly depends on the expression of the estrogen and progesterone receptors (ER and PR, respectively), with doublenegative ER-/PR- breast cancers having worse clinical outcome than ER+/PR+ breast cancers. Although much is known about ERα gene (ESR1) regulation after hormonal stimulation, how it is regulated in the absence of hormones is not fully understood. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

1 Sample

Download data: BW

(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

(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) 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