Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Quantitative Expression Profiling of RNA from Formalin-Fixed, Paraffin-Embedded (FFPE)and Fresh Frozen (FF) Breast Cancer samples

ABSTRACT: Unluckily, FFPE archival methods lead to partial RNA degradation, limiting the amount of derivable information. This study aims to evaluate if the DASL gene expression assay, designed to generate reproducible data from degraded RNAs, is a reliable method to apply on RNA from FFPE tissues. In order to do that, we analyzed 20 FFPE breast cancer samples and 20 FF (Fresh Frozen) matched samples with the Illumina Whole Genome DASL platform for a genome-wide expression profiling.

ORGANISM(S): Homo sapiens

SUBMITTER: Mittempergher Lorenza

PROVIDER: E-TABM-1081 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Gene expression profiles from formalin fixed paraffin embedded breast cancer tissue are largely comparable to fresh frozen matched tissue.

Mittempergher Lorenza L de Ronde Jorma J JJ Nieuwland Marja M Kerkhoven Ron M RM Simon Iris I Rutgers Emiel J Th EJ Wessels Lodewyk F A LF Van't Veer Laura J LJ

PloS one 20110211 2

<h4>Background and methods</h4>Formalin Fixed Paraffin Embedded (FFPE) samples represent a valuable resource for cancer research. However, the discovery and development of new cancer biomarkers often requires fresh frozen (FF) samples. Recently, the Whole Genome (WG) DASL (cDNA-mediated Annealing, Selection, extension and Ligation) assay was specifically developed to profile FFPE tissue. However, a thorough comparison of data generated from FFPE RNA and Fresh Frozen (FF) RNA using this platform ...[more]

PMID: 21347257

Similar Datasets

Expression profiling of formalin-fixed, paraffin-embedded (FFPE) breast cancer metastases of the lymph node and autopsy tissues

Project description:This SuperSeries is composed of the following subset Series: GSE32488: Expression profiling of formalin-fixed, paraffin-embedded (FFPE) breast cancer metastases of the lymph node and autopsy tissues [DASL HT-12 samples] GSE32489: Expression profiling of formalin-fixed, paraffin-embedded (FFPE) breast cancer metastases of the lymph node and autopsy tissues [DASL HumanRef-v3 samples] Refer to individual Series

2012-10-02 | E-GEOD-32490 | biostudies-arrayexpress

Gene Expression Profiling of Formalin Fixed Paraffin Embedded Familial Breast Tumours Using the Whole Genome-DASL Assay

Project description:Tissue sample acquisition is a limiting step in many studies. There are many thousands of formalin fixed paraffin embedded archival blocks collected around the world, but in contrast relatively few fresh frozen samples in tumor banks. Once samples are fixed in formalin the RNA is degraded and traditional methods for gene expression profiling are not suitable. In this study we have evaluated the whole genome DASL assay from Illumina to perform transcriptomic analysis from archived breast tumor tissue fixed in formalin paraffin embedded blocks. We profiled 76 familial breast tumors from cases carrying a BRCA1, BRCA2 or ATM mutation, or from non-BRCA1/2 families. We found that replicate samples correlated well with each other (r2=0.9-0.98). In 12/15 cases, the matched formalin-fixed and frozen samples predicted the same tumor molecular subtypes with confidence. These results demonstrate that the whole genome DASL assay is a valuable tool to profile degraded RNA from archival FFPE material. This assay will enable transcriptomic analysis of a large number of archival samples that are stored in pathology archives around the globe and consequently will have the potential to improve our understanding and characterisation of many diseases. RNA was extracted from FFPE Familial breast tumours and analysed using the WG-DASL assay for Illumina.

2010-06-16 | E-GEOD-21921 | biostudies-arrayexpress

Molecular characterization of Quebec Cohort of Primary Breast Cancer FFPE Tissues on the Human Cancer Panel

Project description:Analysis of 97 formalin-fixed, paraffin-embedded (FFPE) primary breast tumors using Illumina DASL microarray technology on a Custom Breast Cancer Panel and the Illumina Human Cancer Panel. Molecular markers between the pathology defined subtypes of breast cancer were assessed to hypothesize potential therapeutic targets specific to the subtypes Molecular Characterization of 97 primary breast tumor formalin-fixed, paraffin-embedded (FFPE) specimens including 24 triple negative (TN: ER-, PR-, HER2-), 9 HER2-positive (HER2+: ER-, PR-, HER2+), and 64 hormone receptor-positive (HR+: ER+ and/or PR+). 91 of the 97 specimens were characterized on the Illumina Human Cancer DASL Panel and 86 of 97 specimens were characterized on a custom Breast Cancer DASL Panel, 80 of these specimens were common to both the Human Cancer DASL Panel and the custom Breast Cancer DASL Panel.

2009-10-23 | E-GEOD-17650 | biostudies-arrayexpress

Proteomic profiles of FFPE breast normal and tumor tissue

Project description:Accessing the proteome of formalin fixed, paraffin-embedded (FFPE) tissue could lead to discovery of new biomarkers and development of clinically useful assays. A critical step to realizing this potential is developing a simple and reproducible method to obtain proteomic profiles from FFPE tissue. An objective of this work is to develop and optimize a method to obtain proteomic profiles from FFPE breast tissue using a protocol commonly applied in pathology laboratories. The outcome is a method that incorporates steps used for immunohistochemical analyses of FFPE tissue that results in highly reproducible proteomic profiles. Implementing this assay with normal breast tissue and breast tumor tissue produced proteome profiles that reproducibly demonstrate substantial differences between normal vs. tumor tissue.

2020-07-17 | PXD007088 | Pride

Gene profiling using archival formalin-fixed paraffin-embedded breast cancer specimens can generate informative microarray data: A comparison with matched fresh fine needle aspiration biopsy samples (FFPE samples)

Project description:The Formalin-Fixed Paraffin-Embedded (FFPE) samples on selected breast cancer subtypes (ER+/Her2-, ER+/Her2+, ER-/Her2+, and ER-/Her2-) and their paired fresh fine needle aspirated biopsies (FNA) were investigated. The cases represented different subtypes of breast cancers based on their clinical receptors ER (E) and Her2 (H) status to demonstrate the ability of gene profiles to differentiate these tumors. Compared to FNA specimens, FFPE samples yielded relatively more degraded RNA, and 80% of the samples deemed suitable for cDNA-mediated annealing, selection, extension and ligation (DASL) assay. It is able to demonstrate that gene profiles from FFPE microarrays were reproducible and correlated well with the corresponding gene profiles from FNA microarrays. The gene profiles from both FNA and FFPE could differentiate the four breast cancer subtypes, and the expression levels of corresponding gene set were consistent with qRT-PCR and correlated to the clinical outcomes on published microarray data. It supports the use of FFPE specimens to develop a prognostic tool for breast cancers which can obviate the need for fresh specimens. 25 FFPE specimens were processed for whole genome DASL assays using Illumina Human-Ref8 version 3 BeadChips. Invasive ductal carcinoma (IDC)-type subtypes ER+/Her2-, ER+/Her2+, ER-/Her2+, and ER-/Her2- (ER: estrogen receptor, HER2: human epidermal growth factor receptor 2) were analyzed.

2011-06-22 | E-GEOD-23384 | biostudies-arrayexpress

Gene expression profiling of FFPE breast cancer samples [Affymetrix platform]

Project description:The use of Affymetrix U133 2.0 Plus chips on FFPE samples when coupled with a qPCR-based sample pre-assessment step, yielded satisfactory results from the point of view of biological reliability. When compared with the Illumina DASL WG platform, specifically designed for degraded RNA, the data generated with the Affymetrix platform showed a wider interquartile range (IQR 1.32 vs 0.57, p<2.2x10-16) suggesting a superior discriminatory power within samples as indicated by the good agreement with the immunohistiochemically derived ER status. FFPE primary breast cancer samples profiled using Affymetrix HG-U133 Plus 2.0 microarray platform after RNA amplification with the Nugen WT-Ovation FFPE System The following criteria were considered for a direct comparison of 12 GEPs obtained from Affymetrix and DASL platforms: gene variability as defined by IQR, ESR1 expression in ER status subgroups defined by IHC, distribution of fold changes for predefined ER related genes when comparing ER positive and negative samples.

2015-02-25 | E-GEOD-51450 | biostudies-arrayexpress

Quantitative proteomic analysis identifies TUBB2A as a novel protein biomarker for prediction of distant metastatic breast cancer

Project description:Metastasis of breast cancer to other distant organs is fatal to patients. However, few studies have revealed biomarkers associated with distant metastatic breast cancer. Furthermore, the inability of current biomarkers such as HER2, ER and PR, in accurately differentiating between distant metastatic breast cancers from non-distant metastatic ones necessitates the development of novel biomarkers. An integrated proteomics approach that combines filter-aided sample preparation, tandem mass tag labeling (TMT), high pH fractionation, and high resolution MS was applied to acquire in-depth proteome data of distant metastatic breast cancer FFPE tissue. Bioinformatics analyses for gene ontology and signaling pathways using differentially expressed proteins (DEPs) were performed to investigate molecular characteristics of distant metastatic breast cancer. In addition, real-time polymerase chain reaction (RT-PCR) and invasion/migration assays were performed to validate the differential regulation and functional capability of biomarker candidates. A total of 9,459 and 8,760 proteins were identified from the pooled sample set and the individual sample set, respectively. Through our stringent criteria, TUBB2A was selected as a novel biomarker. The metastatic functions of the candidate were subsequently validated. Bioinformatics analysis using DEPs were able to characterize the overall molecular features of distant metastasis as well as investigate the differences across breast cancer subtypes. Our study is the first to explore the distant metastatic breast cancer proteome using FFPE tissue. The depth of our dataset enabled the discovery of novel biomarker and the investigation of proteomic characteristics of distant metastatic breast cancer. The distinct molecular features of breast cancer subtypes were also observed. Our proteomic data has important utility as a valuable resource for the research on distant metastatic breast cancer.

2020-06-05 | PXD016061 | Pride

Cross-laboratory validation of the OncoScan FFPE Assay, a multiplex tool for whole genome tumour profiling

Project description:162 FFPE samples, representing six different tumour types, were profiled in triplicate across three independent laboratories. OncoScan¬ FFPE assay data was then analysed for reproducibility of genome-wide copy number, loss of heterozygosity and somatic mutations.

2015-02-18 | E-MTAB-2914 | biostudies-arrayexpress

Tumors with neoadjuvant chemotherapy

Project description:Using whole genome mRNA expression profiling of primary human tumors and unsupervised hierarchical cluster analyses, 3 novel molecular subsets (basal, luminal and p53-like subsets) of muscle-invasive bladder cancer (MIBC) were identified. 23 MVAC treated samples were used for the validation of three MIBC subsets MVAC cohort consisted of 23 FFPE pretreatment tumors (TURs) from a Phase III clinical trial were used to validate 3 molecular subsets including basal, luminal and p53-like subsets We used Illumina cDNA-mediated Annealing, Selection, Extension, and Ligation (DASL) assay that is specifically designed for the gene expression of RNA that is extracted from FFPE.

2014-02-10 | E-GEOD-52219 | biostudies-arrayexpress

Genes associated with prostate cancer are differentially expressed in African American and European American men (tumor specimens)

Project description:A total of 1,507 probes measured the expression of 517 genes on the custom Illumina DASL assay testing if select genes showed cancer-specific differential expression according to race. Genes were chosen for inclusion in the assay based on existing evidence from the literature and our own data for their importance to prostate cancer, prostate cancer aggressiveness, or cancer in general. 639 FFPE tumor samples (270 African American, 369 European American)

2013-01-31 | E-GEOD-41967 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data