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- Title
Comparison of the latest commercial short and long oligonucleotide microarray technologies.
- Authors
Reynies, Aurelien de; Geromin, Daniela; Cayuela, Jean-Michel; Petel, Fabien; Dessen, Philippe; Sigaux, Francois; Rickman, David S
- Abstract
Background: We compared the relative precision and accuracy of expression measurements obtained from three different state-of-the-art commercial short and long-oligonucleotide microarray platforms (Affymetrix GeneChip™ , GE Healthcare CodeLink™ and Agilent Technologies). The design of the comparison was chosen to judge each platform in the context of a multi-project program. Results: All wet-lab experiments and raw data acquisitions were performed independently by each commercial platform. Intra-platform reproducibility was assessed using measurements from all available targets. Inter-platform comparisons of relative signal intensities were based on a common and non-redundant set of roughly 3,400 targets chosen for their unique correspondence toward a single transcript. Despite many examples of strong similarities we found several areas of discrepancy between the different platforms. Conclusion: We found a higher level of reproducibility from one-color based microarrays (Affymetrix and CodeLink) compared to the two-color arrays from Agilent. Overall, Affymetrix data had a slightly higher level of concordance with sample-matched real-time quantitative reversetranscriptase polymerase chain reaction (QRT-PCR) data particularly for detecting small changes in gene expression levels.
- Subjects
OLIGONUCLEOTIDES; DNA microarrays; MEDICAL genetics; POLYMERASE chain reaction; GENE expression
- Publication
BMC Genomics, 2006, Vol 7, p51
- ISSN
1471-2164
- Publication type
Article
- DOI
10.1186/1471-2164-7-51