Comparison of the latest commercial short and long oligonucleotide microarray technologies.
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.


CONCLUSIONS
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 reverse-transcriptase polymerase chain reaction (QRT-PCR) data particularly for detecting small changes in gene expression levels.
de Reyniès
Aurélien
A
Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France. ReyniesA@ligue-cancer.net
Geromin
Daniela
D
Cayuela
Jean-Michel
JM
Petel
Fabien
F
Dessen
Philippe
P
Sigaux
François
F
Rickman
David S
DS
D045744:Cell Line, Tumor; D016000:Cluster Analysis; D020869:Gene Expression Profiling / Q000295:instrumentation / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods; D015203:Reproducibility of Results