GEO DataSets

(Submitter supplied) PURPOSE: Validated biomarkers predictive of response/resistance to anthracyclines in breast cancer are currently lacking. The neoadjuvant TOP trial, in which patients with estrogen receptor (ER)-negative tumors were treated with anthracycline (epirubicin) monotherapy, was specifically designed to evaluate the predictive value of topoisomerase IIα (TOP2A) and to develop a gene expression signature to identify those patients who do not benefit from anthracyclines. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

120 Samples

Download data: CEL, TXT

(Submitter supplied) Integrated DNA and expression array analysis in primary human breast tumors identified chromosome 8q22 copy number gain and a suite of over-expressed genes in this region highly relevant to subsequent recurrence. 8q copy gain is associated with increased risk of distant metastasis despite adjuvant chemotherapy and multiple genes from 8q22 are overexpressed and have pleiotropic effects, contributing to tumor growth, survival, and reduced killing of tumor cell by chemotherapy.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

115 Samples

Download data: CEL

(Submitter supplied) Genome-wide study of LOH and copy number changes associated with breast cancer, their subtypes and their clinical outcome including response to chemotherapy in women sufferred from breast cancinomas. Mapping chromosome 8q22 copy gain associated with poor clinical outcome of breast cancer and discovery of 8q22 genes relevant to specific drug resistance.

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array

Platform:

GPL1266

88 Samples

Download data: CEL, TXT

(Submitter supplied) Evidence suggests that BRCA1 mutation associated tumors have increased sensitivity to DNA damaging agents like cisplatin. Sporadic triple negative breast cancers (TNBC) have many phenotypic similarities to BRCA1 tumors and may have a similar sensitivity to cisplatin. We tested the efficacy of cisplatin monotherapy in 28 TNBC patients in a single arm neoadjuvant trial with outcome measured by pathologic treatment response quantified using the Miller-Payne scale. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

84 Samples

Download data: CEL

(Submitter supplied) Gene expression profiling of surgical biopsies from 74 breast cancer patients of different subtypes from Hamburg dataset.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

74 Samples

Download data: CEL

(Submitter supplied) EORTC 10994 phase III breast cancer clinical trial comparing FEC (5-fluorouracil, cyclophosphamide, epirubicin) with ET (epirubicin, docetaxel). 161 needle biopsies of locally advanced or large operable breast tumours were hybridised to Affymetrix X3P chips. The array data from the ER negative tumours (28/65 pathological CR in the FEC arm, 27/59 pathological CR in the ET arm) were used to validate the cell line-based chemotherapy response predictors developed by the Potti/Nevins group at Duke University (doi:10.1038/nm1491). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1352

161 Samples

Download data: CEL

(Submitter supplied) Low topo2a expression and ER-negative status were predictors of response to doxorubicin, while small tumor size and ER-negative status predicted response to docetaxel. Docetaxel was superior to doxorubicin in triple-negative/basal-like tumors, while no significant differences between these drugs were seen in the remaining intrinsic subtypes Keywords: reference x sample

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL5325 GPL1390 GPL7504

98 Samples

Download data

(Submitter supplied) The FinHER trial is a multicentre phase 3 randomised adjuvant breast cancer trial that enrolled 1010 patients. The women were randomly assigned to receive three cycles of docetaxel or vinorelbine, followed by three cycles of fluorouracil, epirubicin, and cyclophosphamide.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13667

203 Samples

Download data: CEL

(Submitter supplied) BrighTNess was a phase III, multicenter, randomized, double-blind, placebo-controlled study that enrolled stage II/III TNBC patients to receive neoadjuvant chemotherapy with paclitaxel followed by doxorubicin/cyclophosphamid (AC), or the same plus carboplatin or carboplatin plus the PARP inhibitor veliparib concurrent with paclitaxel. Whole transcriptome RNA sequencing (RNAseq) was performed on pre-treatment research biopsies.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21290

482 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) Transcriptional profiling was conducted on RNA from 23 breast cancer cell lines to identify genes whose expression level correlates with sensitivity of particular drug Keywords: comparison of sensitive group versus resistant group of cell lines to particular drug

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL97 GPL96

46 Samples

Download data

(Submitter supplied) The behavior of breast cancers and their response to different chemotherapy treatments depend on their phenotype which is to a large extent determined by gene expression programs within the cancer cell. We used gene expression values from 30 probes on affymetrix U133A chips to calculate a score that would predict if a breast cancer is likely to achieve pathological complete response to chemotherapy consisting of T/FAC.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

178 Samples

Download data: CEL

(Submitter supplied) Tumor samples were obtained from patients with stage II-III breast cancer before starting neoadjuvant chemotherapy with four cycles of 5-fluorouracil/epirubicin/cyclophosphamide (FEC) followed by four cycles of docetaxel/capecitabine (TX) on US Oncology clinical trial 02-103. Most patients with HER-2-positive cancer also received trastuzumab (H).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

91 Samples

Download data: CEL

(Submitter supplied) Abstract Introduction Response rates to chemotherapy remain highly variable in breast cancer patients. We set out to identify genes associated with chemotherapy resistance. We analyzed what is currently the largest single-institute set of gene expression profiles derived from breast cancers prior to a single neoadjuvant chemotherapy regimen (dose-dense doxorubicine and cyclophophamide). Methods We collected, gene expression-profiled and analyzed 178 HER2-negative breast tumor biopsies (‘NKI dataset’). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6884

178 Samples

Download data: TXT

(Submitter supplied) Drug resistance in breast cancer is the major obstacle to a successful outcome following chemotherapy treatment. While upregulation of multidrug resistance (MDR) genes is a key component of drug resistance in multiple cancers, the complexity and hierarchy of non-MDR driven drug resistance pathways are still largely unknown. The aim of this study was to identify pathways contributing to anthracycline resistance using isogenic drug resistant breast cancer cell lines. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

24 Samples

Download data: TXT

(Submitter supplied) The goal of the study was to identify a gene expression signature capable of predicting a pathological complete response following neoadjuvant anthracycline-based chemotherapy of breast cancer. The samples were taken from the FEC arm (5-fluorouracil, epirubicin, cyclophosphamide) of the EORTC 10994 trial. EORTC 10994 is a phase III clinical trial comparing FEC with ET (epirubicin, docetaxel) in patients with large operable, locally advanced or inflammatory breast cancer (www.eortc.be). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1352

102 Samples

Download data: CEL

(Submitter supplied) Prospective, non-comparative Phase II multicenter trial (EXPRESSION EudraCT: 2008-006381-29) where the patients received three 3-week cycles of docetaxel (100 mg/m2) followed by three 3-week cycles of 5-fluorouracil (500 mg/m2), epirubicin (100 mg/m2), and cyclophosphamide (500 mg/m2) (FEC). The primary end point was the identification of a gene expression signature predictive of pathological complete response (pCR). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

91 Samples

Download data: CEL

(Submitter supplied) To investigate genes regulated by miR-489, gene expression analysis was carried out between control siRNA and miR-489 mimic transfected cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

6 Samples

Download data: TXT