GEO DataSets

(Submitter supplied) Introduction: In breast cancers, the basal-like subtype has high levels of genomic instability relative to other breast cancer subtypes with many basal-like-specific regions of aberration. There is evidence that this genomic instability extends to smaller scale genomic aberrations as well, as shown by a previously described micro-event in the PTEN gene in the Basal-like SUM149 breast cancer cell line. more...

Organism:

Homo sapiens

Type:

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

8 related Platforms

192 Samples

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(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) The ability to predict metastatic potential is of clinical and biological importance. Numerous metastasis/relapse predictors exist for breast cancer patients; however, what is less well established is whether predicting metastasis to specific organs sites is feasible. In this study we sought to determine: 1) the degree to which gene signatures vary across tumors and their metastases, 2) if genomic intrinsic subtypes associate with particular organs of relapse, and 3) if other genomic signatures can predict spread to specific organs. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

7 related Platforms

414 Samples

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(Submitter supplied) In breast cancer, gene expression analyses have defined five tumor subtypes, each of which has unique biologic and prognostic features. Here, we characterize the recently identified claudin-low tumor subtype as showing low to absent expression of luminal differentiation markers, high enrichment for epithelial-to-mesenchymal transition markers, immune response genes, and cancer stem cell–like features. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

7 related Platforms

372 Samples

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(Submitter supplied) Metaplastic breast cancers (MBC) are aggressive, chemoresistant tumors characterized by lineage plasticity. To advance understanding of their pathogenesis and relatedness to other breast cancer subtypes, 28 MBCs were compared with common breast cancers using comparative genomic hybridization, transcriptional profiling, and reverse-phase protein arrays and by sequencing for common breast cancer mutations. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

4 related Platforms

244 Samples

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(Submitter supplied) Results When compared with each other, primary tumors and regional metastases showed statistically indistinguishable gene expression patterns. Supervised analyses comparing patients with distant metastases versus primary tumors or regional metastases showed that the distant metastases were distinct and distinguished by the lack of expression of fibroblast/mesenchymal genes, and by the high expression of a 13-gene profile (that is, the ‘vascular endothelial growth factor (VEGF) profile’) that included VEGF, ANGPTL4, ADM and the monocarboxylic acid transporter SLC16A3. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL885 GPL1390 GPL887

195 Samples

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(Submitter supplied) Mice have been used as models for human breast cancers for many years, however, it is still unclear which murine models faithfully represent human tumor phenotypes. To address this question, we used DNA microarrays to characterize 10 different murine mammary models and compared these data to the expression patterns from primary human breast tumors. Hierarchical clustering analysis of the murine samples showed that the WAP-Myc, MMTV-Neu, MMTV-PyMT, WAP-Int3, and C3(1)-Tag tumors were highly correlated within each model. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by array

4 related Platforms

354 Samples

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(Submitter supplied) Determining agreement in classification between platforms and procurement methods requires a variety of methods. We have shown that centroid-based algorithms are robust classifiers for breast cancer subtype assignment across platforms (microarray and qRT-PCR data) and procurement conditions (fresh frozen and formalin-fixed, paraffin-embedded tissues). On a gene-by-gene basis, we found that the standard deviation, dynamic range, and concordance correlation coefficient are important parameters to assess individual primer set performance across procurement methods. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL885 GPL1390 GPL887

159 Samples

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(Submitter supplied) Microarrays have shown that gene expression patterns can be used to molecularly classify breast cancers into distinct and clinically significant groups. In order to translate these profiles into routine diagnostics, we have recapitulated a microarray breast cancer classification using real-time quantitative (q)RT-PCR. We performed statistical analyses on multiple independent microarray datasets to select an “intrinsic” gene set that can classify breast tumors into four different subtypes designated as Luminal, Normal-like, HER2+/ER-, and Basal-like. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL885 GPL1390 GPL887

126 Samples

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(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:

GPL885 GPL887 GPL1390

170 Samples

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(Submitter supplied) The prognosis of a patient with Estrogen Receptor (ER) and/or Progesterone Receptor (PR)-positive breast cancer is highly variable. Therefore, we developed a gene-expression based outcome predictor for ER+ and/or PR+ (i.e. Luminal) breast cancer patients using biological properties of the tumors. First, we identified estrogen-regulated genes using the ER+ MCF-7 breast cancer cell line treated with estrogen. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

4 related Platforms

174 Samples

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(Submitter supplied) Microarray analysis has been shown to improve risk stratification of breast cancer. Breast tumors analyzed by hierarchical clustering of expression patterns of "intrinsic" genes have been reported to subdivide into at least four molecular subtypes that are associated with distinct patient outcomes. Using a supervised method, a 70-gene expression profile has been identified that predicts the later appearance or absence of clinical metastasis in young breast cancer patients. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL1390 GPL887 GPL885

169 Samples

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(Submitter supplied) Represents about 22K 60-mer oligonucleotide probes which span conserved exons across the transcripts of the targeted full length genes (Incyte Foundation) in the home genome. About 17,000 probes are from Human 1A Oligo Microarray Kit. The other 4000 probes are specifically designed for Dr. Charles Perou Lab at University of North Carolina at Chapel Hill.

Organism:

Homo sapiens

25 Series

597 Samples

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