GEO DataSets

(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) 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) 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) 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) Determination of recurrent chromosomal aberrations in Luninal A, Luminal B, HER2-positve, and triple negative breast cancers

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10152

131 Samples

Download data: TXT

(Submitter supplied) PURPOSE: Preclinically, cisplatin is synergistic with vinorelbine and the poly(ADP-ribose) polymerase (PARP) inhibitor veliparib, and has anti-neoplastic activity in TNBC and BRCA mutation-associated breast cancer. This phase I study assessed veliparib with cisplatin and vinorelbine. PATIENTS AND METHODS: A 3+3 dose escalation design evaluated veliparib administered BID for 14 days with cisplatin (75 mg/m2 day 1) and vinorelbine (25 mg/m2 days 1,8) every 21 days, for six to ten cycles, followed by veliparib monotherapy. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13938

39 Samples

Download data: IDAT, TXT

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

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL15520

3386 Samples

Download data: TSV

(Submitter supplied) Background: Normal cell BRCA1 epimutations have been associated with increased risk of triple-negative breast cancer (TNBC). However, the fraction of TNBCs that may have BRCA1 epimutations as their underlying cause is unknown. Neither are the time of occurrence and the potential inheritance patterns of BRCA1 epimutations established. Methods: To address these questions, we analyzed BRCA1 methylation status in breast cancer tissue and matched white blood cells (WBC) from 408 patients with 411 primary breast cancers, including 66 TNBCs, applying a highly sensitive sequencing assay, allowing allele-resolved methylation assessment. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL15520

2567 Samples

Download data: TSV, TXT

(Submitter supplied) Background: Normal cell BRCA1 epimutations have been associated with increased risk of triple-negative breast cancer (TNBC). However, the fraction of TNBCs that may have BRCA1 epimutations as their underlying cause is unknown. Neither are the time of occurrence and the potential inheritance patterns of BRCA1 epimutations established. Methods: To address these questions, we analyzed BRCA1 methylation status in breast cancer tissue and matched white blood cells (WBC) from 408 patients with 411 primary breast cancers, including 66 TNBCs, applying a highly sensitive sequencing assay, allowing allele-resolved methylation assessment. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL15520

819 Samples

Download data: TSV, TXT

(Submitter supplied) The Illumina Infinium Epic Human DNA methylation Beadchip was used to obtain DNA methylation profiles across more than 850,000 CpGs.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

18 Samples

Download data: CSV

(Submitter supplied) Breast cancer is a leading cause of death in premenopausal women. Progesterone drives expansion of luminal progenitor cells, leading to the development of poor-prognostic breast cancers. However, it is not known if antagonising progesterone can prevent breast cancers in humans. We suggest that targeting progesterone signalling could be a means of reducing features which are known to promote breast cancer formation.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

32 Samples

Download data: TXT

(Submitter supplied) Current clinical guidelines suggest that breast cancers with low hormone receptor expression (LowHR) in 1% to 10% of tumor cells should be regarded as hormone receptor positive tumors. However, clinical data shows that patients with such tumors have a worse outcome compared to patients with hormone receptor expression above 10 %. Further, gene expression studies suggest that these tumors have a TNBC-like signature similar to triple negative breast cancers (TNBC). more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

36 Samples

Download data: IDAT

(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

(Submitter supplied) Despite recent consensus on eligibility of adjuvant systemic therapy in lymph-node negative breast cancer (NNBC) patients based on clinico-pathological criteria, specific biological markers are needed to predict sensitivity to the different therapeutic options. We examined the feasibility of developing a genomic predictor of chemotherapy response and recurrence risk in 185 patients with NNBC using assembled arrays containing 2,460 BAC clones for scanning the genome for DNA copy number changes. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL3632

185 Samples

Download data: PDF, TXT

(Submitter supplied) Transcriptional profiling of human breast cancer cell line LM2, a subline of MDA-MB-231 highly metastatic to lung when injected to nude mice, to identify the genes that are regulated after the metastasis gene metadherin is knocked down. Keywords: Genetic modification

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3179

Platform:

GPL4133

12 Samples

Download data: TXT