GEO DataSets

(Submitter supplied) A gene expression signature characterizes expression data from breast cancer samples of patients with pathological complete response (pCR) or residual disease (RD) following the neoadjuvant trial. Several gene expression profiles have been reported to predict breast cancer response to neoadjuvant chemotherapy. These studies often consider breast cancer as a homogeneous entity, although higher rates of pathologic complete response (pCR) are known to occur within the basal-like subclass. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

24 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) To elucidate candidate genes and pathways associated with poor response, we retrospectively analyzed gene expression profiles in serial biopsies from women with locally advanced breast cancer who failed to respond to anthracycline-based chemo followed by taxane in the I-SPY

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14668

248 Samples

Download data: GPR

(Submitter supplied) Breast cancer is a difficult disease to manage because it is comprised of a spectrum of tumor subtypes with different biological characteristics. Previous gene expression studies using breast tumor “intrinsic” gene lists identified five distinct subtypes of breast tumors: Luminal A, Luminal B, Normal Breast-like, HER2+/ER- and Basal-like. Using a training data set of 102 unique breast tumors, we derive a new “intrinsic” gene list based upon 26 paired samples. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL1390 GPL885 GPL887

170 Samples

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(Submitter supplied) In a prospective cohort study of 32 women with primary invasive breast cancer with a measurable lesion, we obtained a tumor specimen by high speed core biopsy before and after 4 cycles of NAC with epirubicine 90mg/m2 and cyclophosphamide 600mg/m2 every 3 weeks, followed by 4 cycles of docetaxel 100mg/m2. Total RNA was extracted from tumor specimens and the whole transcriptome was quantified with Agilent’s 44K single color microarray interrogating 41000 unique human genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

57 Samples

Download data: TXT

(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

(Submitter supplied) This is Phase II Trial of 4courses of 5-fluorouracil, doxorubicin and cyclophosphamide follwed by 4 additional courses of weekly docetaxel and capecitabine administered as Preoperative Therapy for Patients with Locally Advanced Breast Cancer, Stages II and III by US oncology (PROTOCOL 02-103) We performed gene set analysis (GSA) using functionally annotated gene sets corresponding to almost all known biological processes in ER-positive/HER2negative and ER-negative/HER2-negative breast cancer, respectively.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4056

Platform:

GPL96

61 Samples

Download data: CEL

(Submitter supplied) We assess if distinct biological processes might be associated with chemotherapy sensitivity in the different clinical subsets of breast cancers. We performed gene set analysis (GSA) using functionally annotated gene sets corresponding to almost all known biological processes in ER-positive/HER2negative and ER-negative/HER2-negative breast cancer, respectively.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4057

Platform:

GPL96

103 Samples

Download data: CEL

Analysis of pre-treatment biopsies from 103 HER2-normal breast cancer patients (ER-positive and ER-negative subtypes) from MD Anderson Cancer Center/Institut Goustave Russy. Results provide insight into molecular mechanisms associated with chemotherapy sensitivity in breast cancer subtypes.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 6 disease state, 3 genotype/variation, 3 other, 4 specimen sets

Platform:

GPL96

Series:

GSE22093

103 Samples

Download data: CEL

Analysis of pre-treatment biopsies from 62 HER2-normal breast cancer patients (ER-positive and ER-negative subtypes) from US Oncology clinical trial 02103. Results provide insight into molecular mechanisms associated with chemotherapy sensitivity in breast cancer subtypes.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 3 disease state, 2 genotype/variation, 2 other, 4 specimen sets

Platform:

GPL96

Series:

GSE23988

61 Samples

Download data: CEL

(Submitter supplied) Breast cancer is a heterogeneous disease with known tumor subtypes. In order to gain insight into the underlying etiologies of these disease subtypes, we first classified tumors according to gene expression intrinsic subtype, and second, identified subtype associated tumor genomic DNA copy number alterations (CNA) using a novel method called SWITCHdna. Most tumor subtypes showed specific CNA with Basal-like breast cancers being the most distinct and associated with loss of RB1, BRCA1, 5q11-35, and showed the greatest overall genomic instability. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by genome tiling array; Genome variation profiling by SNP array

7 related Platforms

504 Samples

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(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) Neoadjuvant chemotherapy has been shown to be equivalent to post-operative treatment for breast cancer, and allows for assessment of chemotherapy response. In a pilot trial of docetaxel (T) and capecitabine (X) neoadjuvant chemotherapy for Stage II/III BC, we assessed correlation between baseline gene expression and tumor response to treatment, and examined changes in gene expression associated with treatment. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

61 Samples

Download data: CEL

(Submitter supplied) Current prognostic gene expression profiles for breast cancer mainly reflect proliferation status and are most useful in ER-positive cancers. Triple-negative breast cancers (TNBCs) are clinically heterogeneous, and prognostic markers and biology-based therapies are needed to better treat this disease. We assembled Affymetrix gene expression data for 579 TNBCs and performed unsupervised analysis to define metagenes that distinguish molecular subsets within TNBC. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Third-party reanalysis

Platform:

GPL96

67 Samples

Download data: CEL, TXT

(Submitter supplied) INTRODUCTION: Basal-phenotype or basal-like breast cancers are characterized by basal epithelium cytokeratin (CK5/14/17) expression, negative estrogen receptor (ER) status and distinct gene expression signature. We studied the clinical and biological features of the basal-phenotype tumors determined by immunohistochemistry (IHC) and cDNA microarrays especially within the ER-negative subgroup. METHODS: IHC was used to evaluate the CK5/14 status of 445 stage II breast cancers. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL3883

100 Samples

Download data: GPR

(Submitter supplied) Genome-wide expression profiling was performed on 50 core needle biopsies from 18 breast cancer patients using Affymetrix GeneChip Human Genome Plus 2.0 Arrays.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

50 Samples

Download data: CEL

(Submitter supplied) Purpose:The identification of biomarkers predictive of neoadjuvant chemotherapy response in breast cancer patients would be an important advancement in personalized cancer therapy. We hypothesized that due to similarities between radiation and chemotherapy induced cellular response mechanisms, radiation responsive genes may be useful in predicting response to neoadjuvant chemotherapy. Materials and Methods: Murine p53 null breast cancer cell lines representative of the luminal, basal-like and claudin-low human breast cancer subtypes were irradiated to identify radiation responsive genes. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11383

18 Samples

Download data

(Submitter supplied) Assessment of tumor pathological and transcriptional biomarkers in pre- and on-treatment core biopsies predictive of response and outcome after neoadjuvant chemotherapy plus Bevacizumab in patients with HER2-negative breast cancer: Results from a multi-center, single-arm, phase 2 study (the PROMIX trial) Global gene expression profiling was performed on samples from 3 time points (baseline, after 2 cycles and surgery) from women with breast cancer receivcing neoadjuvant chemotherapy with bevacizumab in a phase 2 trial

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

275 Samples

Download data: TXT

(Submitter supplied) Functional genomics approach to metastatic colon cancer Mouse model translated to human colon cancer

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

6 Samples

Download data: CEL

(Submitter supplied) Analysis of Rab25 in human colon samples

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

6 Samples

Download data: CEL