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Title: Interlaboratory study to determine the reproducibility of toxicogenomics datasets      
dateReleased:
12-31-2011
description:
The application of toxicogenomics as a predictive tool for chemical risk assessment has been under evaluation by the toxicology community for more than a decade. However, toxicogenomics predominately remains a tool for investigative research rather than for regulatory risk assessment. In this study, we aimed to determine whether the current generation of microarray technology in combination with an in vitro experimental design was capable of generating robust, reproducible data of sufficient quality to show promise as a tool for regulatory risk assessment. To this end, we designed a prospective collaborative study to determine the level of inter- and intra-laboratory reproducibility between three independent laboratories. All test sites adopted the same protocols for all aspects of the toxicogenomic experiment including cell culture, chemical exposure, RNA extraction, microarray data generation and analysis. As a case study, the genotoxic carcinogen B[a]P and the human hepatocyte cell line HepG2 were used to generate three comparable toxicogenomic data sets. High levels of technical reproducibility were demonstrated using a widely employed gene expression microarray platform. While differences at the global transcriptome level were still observed between the test sites, a common subset of B[a]P responsive genes was identified across all test sites which included both genes previously reported in the literature as B[a]P responsive in addition to the same most highly up and down regulated genes. Pending further analysis, these preliminary data show promise that the current generation of microarray technology in combination with a standard in vitro experimental design can produce robust data that can be reproducibly generated in independent laboratories. Future work will need to determine whether in vitro model(s) can be not only reproducible but also predictive for a range of toxic chemicals with different mechanisms of action. Such an approach may potentially be part of future in vitro testing regimes for regulatory risk assessment. The aim of this study was to evaluate the inter- and intra-laboratory reproducibility of toxicogenomics data for toxicity testing in a regulatory setting. 3 Test Centres performed the same experimental protocol treating HepG2 cells with 3 mM Benzo[a]pyrene (B[a]P) (in 0.5% DMSO) for 24 hours prior to RNA extraction and microarray analysis. Three biological replicates of B[a]P and DMSO treatments were analysed by microarray analysis in each Test Centre. Two Test Centres analysed one sample in triplicate to determine technical reproducibility of the chosen array platform. One Centre analysed two samples in duplicate. 24 samples in total were used in this study
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-25936
refinement:
raw
alternateIdentifiers:
25936
keywords:
functional genomics
dateModified:
01-10-2012
availability:
available
types:
gene expression
name:
Homo sapiens
ID:
A-AGIL-28
name:
Agilent Whole Human Genome Microarray 4x44K 014850 G4112F (85 cols x 532 rows)
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-25936/E-GEOD-25936.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-25936/E-GEOD-25936.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25936
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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