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Expression Profiling of Formalin-Fixed Parafin-Embedded Primary Breast Tumors

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE25234 | GEO | 2010/12/20

SECONDARY ACCESSION(S): PRJNA134897

REPOSITORIES: GEO

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Expression Profiling of Formalin-Fixed Parafin-Embedded Primary Breast Tumors

Project description:This SuperSeries is composed of the following subset Series: GSE25231: Expression Profiling of Formalin-Fixed Parafin-Embedded Primary Breast Tumors DASL Cancer Panel GSE25233: Expression Profiling of Formalin-Fixed Parafin-Embedded Primary Breast Tumors Whole Genome DASL Refer to individual Series

| S-ECPF-GEOD-25234 | biostudies-other

Expression Profiling of Formalin-Fixed Parafin-Embedded Primary Breast Tumors DASL Cancer Panel

Project description:HER2-positive and HER2-negative samples are compared within this DASL Cancer Panel Platform Two-class comparison

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Expression Profiling of Formalin-Fixed Parafin-Embedded Primary Breast Tumors Whole Genome DASL

Project description:HER2-positive and HER2-negative samples are compared within this Whole Genome Platform Two-class comparison

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Expression Profiling of Formalin-Fixed Parafin-Embedded Primary Breast Tumors

2010-12-20 | E-GEOD-25234 | biostudies-arrayexpress

miRNA expression profiling of formalin-fixed paraffin-embedded (FFPE) hereditary breast tumors.

Project description:Hereditary breast cancer constitutes only 5-10% of all breast cancer cases and is characterized by strong family history of breast and/or other associated cancer types. Only ~ 25% of hereditary breast cancer cases carry a mutation in BRCA1 or BRCA2 gene, while mutations in other rare high and moderate-risk genes and common low penetrance variants may account for additional 20% of the cases. Thus the majority of cases are still unaccounted for and designated as BRCAX tumors. MicroRNAs are small non-coding RNAs that play important roles as regulators of gene expression and are deregulated in cancer. To characterize hereditary breast tumors based on their miRNA expression profiles we performed global microarray miRNA expression profiling on a retrospective cohort of 80 FFPE breast tissues, including 66 hereditary breast tumors (13 BRCA1, 10 BRCA2 and 43 BRCAX), 10 sporadic breast carcinomas and 4 normal breast tissues, using Exiqon miRCURY LNA™ microRNA Array v.11.0. Here we describe in detail the miRNA microarray expression data and tumor samples used for the study of BRCAX tumor heterogeneity (Tanic et al., 2013) and biomarkers associated with positive BRCA1/2 mutation status (Tanic et al., 2014). Additionally, we provide the R code for data preprocessing and quality control.

| S-EPMC4535901 | biostudies-literature

Whole-Genome Gene Expression Profiling of Formalin-Fixed, Paraffin-Embedded Tissue Samples

Project description:This SuperSeries is composed of the SubSeries listed below.

2010-01-13 | GSE17599 | GEO

Expression Profiling of Formalin-Fixed Parafin-Embedded Primary Breast Tumors Whole Genome DASL

Project description:HER2-positive and HER2-negative samples are compared within this Whole Genome Platform

2010-12-20 | GSE25233 | GEO

Expression Profiling of Formalin-Fixed Parafin-Embedded Primary Breast Tumors DASL Cancer Panel

Project description:HER2-positive and HER2-negative samples are compared within this DASL Cancer Panel Platform

2010-12-20 | GSE25231 | GEO

Expression Profiling of Formalin-Fixed Parafin-Embedded Primary Breast Tumors

Project description:Expression Profiling of Formalin-Fixed Parafin-Embedded Primary Breast Tumors

| PRJNA134897 | ENA

Whole Transcriptome Profiling of Adrenocortical Tumors Using Formalin-Fixed Paraffin-Embedded Samples.

Project description:Whole transcriptome profiling is a promising technique in adrenal studies; however, whole transcriptome profiling of adrenal disease using formalin-fixed paraffin-embedded (FFPE) samples has to be further explored. The aim of this study was to evaluate the utility of transcriptome data from FFPE samples of adrenocortical tumors. We performed whole transcriptome profiling of FFPE and fresh frozen samples of adrenocortical carcinoma (ACC, n = 3), aldosterone-producing adenoma (APA, n = 3), and cortisol-producing adenoma (CPA, n = 3), and examined the similarity between the transcriptome data. We further examined whether the transcriptome data of FFPE samples could be used to distinguish tumor types and detect marker genes. The number of read counts was smaller in FFPE samples than in fresh frozen samples (P < 0.01), while the number of genes detected was similar (P = 0.39). The gene expression profiles of FFPE and fresh frozen samples were highly correlated (r = 0.93, P < 0.01). Tumor types could be distinguished by consensus clustering and principal component analysis using transcriptome data from FFPE samples. In the differential expression analysis between ACC and APA-CPA, known marker genes of ACC (e.g., CCNB2, TOP2A, and MAD2L1) were detected in FFPE samples of ACC. In the differential expression analysis between APA and CPA, known marker genes of APA (e.g., CYP11B2, VSNL1, and KCNJ5) were detected in the APA of FFPE samples. The results suggest that FFPE samples may be a reliable alternative to fresh frozen samples for whole transcriptome profiling of adrenocortical tumors.

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