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Transcriptional signatures of normal human mammary epithelial cells in response to benzo[a]pyrene exposure: a comparison of three microarray platforms.

Authors
Gwinn-MR; Keshava-C; Olivero-OA; Humsi-JA; Poirier-MC; Weston-A
Source
OMICS 2005 Dec; 9(4):334-350
NIOSHTIC No.
20029409
Abstract
Microarrays are used to study gene expression in a variety of biological systems. A number of different platforms have been developed, but few studies exist that have directly compared the performance of one platform with another. The goal of this study was to determine array variation by analyzing the same RNA samples with three different array platforms. Using gene expression responses to benzo[a]pyrene exposure in normal human mammary epithelial cells (NHMECs), we compared the results of gene expression profiling using three microarray platforms: photolithographic oligonucleotide arrays (Affymetrix), spotted oligonucleotide arrays (Amersham), and spotted cDNA arrays (NCI). While most previous reports comparing microarrays have analyzed pre-existing data from different platforms, this comparison study used the same sample assayed on all three platforms, allowing for analysis of variation from each array platform. In general, poor correlation was found with corresponding measurements from each platform. Each platform yielded different gene expression profiles, suggesting that while microarray analysis is a useful discovery tool, further validation is needed to extrapolate results for broad use of the data. Also, microarray variability needs to be taken into consideration, not only in the data analysis but also in specific probe selection for each array type.
Keywords
Genes; Biological-systems; Sampling; Sampling-methods; Exposure-assessment; Cell-cultures
Contact
Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, 1095 Willowdale Road, Morgantown, WV 26505-2888, USA
Publication Date
20051201
Document Type
Journal Article
Fiscal Year
2006
NTIS Accession No.
NTIS Price
Issue of Publication
4
ISSN
1536-2310
NIOSH Division
HELD
Source Name
OMICS: A Journal of Integrative Biology
State
WV; DC; MD
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