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Physiol. Genomics (November 25, 2003). doi:10.1152/physiolgenomics.00080.2003
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Submitted on May 9, 2003
Accepted on November 17, 2003

A comparison of oligonucleotide and cDNA-based microarray systems

Nancy Mah1, Anders Thelin2, Tim Lu1, Susanna Nikolaus1, Tanja Kuehbacher1, Yesim Gurbuz3, Holger Eickhoff4, Guenther Kloeppel3, Hans Lehrach4, Bjorn Mellgard2, Christine M Costello1, and Stefan Schreiber1*

1 First Department of Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
2 R&D Molndal, AstraZeneca, Molndal, Sweden
3 Department of Pathology, Christian-Albrechts-University Kiel, Kiel, Germany
4 Department Lehrach, Max-Planck Institute for Molecular Genetics, Berlin, Germany

* To whom correspondence should be addressed. E-mail: s.schreiber{at}mucosa.de.

Large-scale public data mining will become more common as public release of microarray datasets becomes a co-equisite for publication. Therefore, there is an urgent need to clarify whether data from different microarray platforms are comparable. To assess the compatibility of microarray data, results were compared from the two main types of high-throughput microarray expression technologies, namely an oligonucleotide-based and a cDNA-based platform, using RNA obtained from complex tissue (human colonic mucosa) of five individuals. From 715 sequence-verified genes represented on both platforms, 64% of the genes matched in 'present' or 'absent' calls made by both platforms. Calls were influenced by spurious signals caused by Alu repeats in cDNA clones, clone annotation errors or matched probes that were designed to different regions of the gene; however, these factors could not completely account for the level of call discordance observed. Expression levels in sequence-verified, platform-overlapping genes were not related, as demonstrated by weakly positive rank-order correlation. This study demonstrates that there is only moderate overlap in the results from the two array systems. This fact should be carefully considered when performing large-scale analyses on data originating from different microarray platforms.




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