GEO DataSets

(Submitter supplied) Experiment: Expression profiling in breast cancer brain metastases (BC) compared to breast cancers (BC) and primary brain tumors (prBT). The objectives are to identify expression profiles that are specific to BCBM in order to identify new molecular biomarkers. The characterization of the BCBM samples included adjacent genetic techniques.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

35 Samples

Download data: CEL

(Submitter supplied) The enumeration of EpCAM-positive circulating tumor cells (CTCs) has allowed clinicians to estimate the overall metastatic burden in breast cancer patients. However, a thorough understanding of CTCs associated with breast cancer brain metastasis (BCBM) is necessary for early identification and evaluation of treatment response to BCBM. In this study, we report that BCBM CTCs are enriched in a distinct sub-population of cells identifiable by their biomarker expression and mutational content. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

10 Samples

Download data: CEL, CHP

(Submitter supplied) Purpose: There is an unmet clinical need for biomarkers to identify breast cancer patients who are at increased risk of developing brain metastases. The objective is to identify gene signatures and biological pathways associated with HER2+ brain metastasis. Experimental Design: Gene expression of 19 HER2+ breast cancer brain metastases was compared with HER2+ nonmetastatic primary tumors. Gene Set Enrichment Analysis was used to identify a signature, which was evaluated for correlation with BRCA1 mutation status and clinical outcome using published microarray datasets and for correlation with pharmacological inhibition by a PARP inhibitor and temozolomide using published microarray datasets of breast cancer cell lines. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS5306

Platform:

GPL1352

38 Samples

Download data: CEL

Analysis of HER2+ breast cancer brain metastasis specimens and HER2+ nonmetastatic primary breast tumors. Samples were matched for patient age upon primary tumor detection and ER status of primary tumor. Results provide insight into the molecular basis of HER2+ breast cancer outgrowth in the brain.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 disease state, 38 other, 38 specimen, 2 tissue sets

Platform:

GPL1352

Series:

GSE43837

38 Samples

Download data: CEL

(Submitter supplied) We hypothesized that circulating miRNAs could work as biomarkers for early detection of breast cancer brain metastasis (BCBM), and their targets could constitute new targets for modulation. We used a mouse model of BCBM and Next-Generation Sequencing to establish the circulating miRNAs alterations along brain metastasis development and performed bioinformatics analysis to identify their targets with relevance in the metastatic process. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16417

6 Samples

Download data: XLSX

(Submitter supplied) Initial screening for potential metastases suppressors down regulated by methylation was performed using breast cancer cell line models specific for site-specific metastasation. Gene expression profiling and qRT-PCR validations were conducted on tumor tissues from primary breast cancer (BC) and BCBM. CADM1 and RECK were further characterized for their methylation patterns and finally the protein expression of CADM1 was validated in a large number of BC and BCBM samples and correlated with clinico-pathologic parameters.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

4 Samples

Download data: TXT

(Submitter supplied) To determine whether breast cancer molecular subtypes and tumor characteristics with demonstrated significance in a primary tumor setting can also confer clinically relevant information in breast cancer metastases. We assessed previously published gene expression modules of seven biological processes and the intrinsic subtypes (PAM50). The translational aspect of the Swedish randomized TEX trial included 112 patients with at least one biopsy from morphologically confirmed loco-regional or distant breast cancer metastasis diagnosed from December 2002 until June 2007. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10379

120 Samples

Download data: CEL

(Submitter supplied) The purpose of this study was to improve prediction of patients at high-risk for metastatic disease utilizing a nested case-control design that uniquely enables enrichment for relevant phenotypes. We identified all women diagnosed with primary breast cancer from January 1, 1997, to December 31, 2005, in the Stockholm health care region. Patients developing distant metastatic disease (cases) were selected and controls (free from distant disease) were randomly matched by adjuvant therapy, age and calendar period at diagnosis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10379

623 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL570 GPL10123

9 Samples

Download data: CEL, TXT

(Submitter supplied) Primary SCEC is a rare malignancy without established treatment strategy. Although previous studies suggested that there were similarities between SCEC and SCLC in clinical manifestation and pathological morphology, genetic studies on this highly malignant tumour remains sparse. This study was designed to investigate the copy number variations (CNVs) of SCEC.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10123

3 Samples

Download data: TXT

(Submitter supplied) Primary SCEC is a rare malignancy without established treatment strategy. Although previous studies suggested that there were similarities between SCEC and SCLC in clinical manifestation and pathological morphology, genetic studies on this highly malignant tumour remained sparse. This study was designed to investigate the gene expression profile of SCEC, and compare it with the known expression data of SCLC and EC.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

6 Samples

Download data: CEL

(Submitter supplied) Experiment a) Establishment of expression profiles in conventional papillary thyroid carcinomas (PTCs) with a BRAF mutation vs. PTCs without a BRAF mutation and using normal thyroid (TN) specimens as reference. Experiment b) Establishment of expression profiles in follicular adenomas (FAs) of the thyroid and follicular variant of papillary thyroid carcinomas (FVPTCs).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

45 Samples

Download data: CEL, CHP

(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

Download data

(Submitter supplied) We used DNA content-based flow cytometry to distinguish and isolate nuclei of clonal tumor populations from resected triple negative breast cancer tissues. We then interrogated each sorted tumor population with whole genome aCGH and next generation sequencing (NGS). The genomic data was correlated with IHC staining for PD-1 and PD-L1.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL19387

48 Samples

Download data: TXT

(Submitter supplied) The survival of women with brain metastases (BM) from breast cancer remains very poor, and more than 80% will die within a year of their diagnosis. Here we define the function of IL13Rα2 in outgrowth of breast cancer brain metastases (BCBM) in vitro and in vivo, and postulate IL13Rα2 as a suitable therapeutic target for BM. Experimental design: We performed IHC staining of IL13Rα2 in BCBM to define its prognostic value. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28337

6 Samples

Download data: TXT

(Submitter supplied) In our combinatorial CRISPR screenings, we screened for tumor/growth promoting GIs between 52 tumor suppressor genes (TSGs). In this part, we systematically profiled single-cell transcriptomes of double knocking-out (DKO) and single knocking-out (SKO) cells of GI pairs identified in our GI screenings, and tried to decipher the role of transcription in the phenotypic effects of GIs.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

20 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) Comparative genomic hybridization analysis for detection of copy number variation for cancer genes in breast cancer mestastatic brain tumors DNA was isolated and analyzed in a two-color experiment using Cancer CGH+SNP 180Kx4 arrays from Agilent and Agilent SureScan system: Cy5-labeled specimen DNA and Cy3-labeled reference Agilent (female) reference DNA

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL16237

18 Samples

Download data: TXT

(Submitter supplied) Analysis of breast cancer gene expression profiles. The hypothesis tested in the present study was that if differential profiles exsist between early and late onset breast cancer. Results provide important information regarding up- or down-regulated genes playing a mechanistic role in cancer.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL6884 GPL6947

38 Samples

Download data: TXT

(Submitter supplied) In this study we want to compare the expression profiles of E-cadherin high and low tumor cells from 4 different mice with breast cancer brain metastasis. We used a breast cancer brain metastasis model derived from the PyMT E-cadherin-mCFP breast cancer model (Beerling et al. Cell Reports 2016) and FACS sorted samples based on endogenous E-cadherin-mCFP expression.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

8 Samples

Download data: TXT

(Submitter supplied) In this study we studied the presence of tumor cells that underwent epithelial-to-mesenchymal transition within polyoma middle T antigen (PyMT) breast tumors. For this we dissociated tumors and isolated Ecad positive tumor cells by FACS sorting. We confirmed that PyMT tumors contain a small set of tumor cells that have undergone EMT in the primary tumor and that E-cadherin can be used as a marker on single cell level for mesenchymal status in this model.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL19057

7 Samples

Download data: CSV, TXT