1. ¹Division of Molecular Genetics, Deutsches Krebsforschungszentrum, Heidelberg, Germany
2. ²Chemotherapeutisches Forschungsinstitut Georg-Speyer-Haus, Frankfurt am Main, Germany
3. ³Central Unit Biostatistics, Deutsches Krebsforschungszentrum, Heidelberg, Germany
4. ⁴Department of Otorhinolaryngology, Universitätsklinik, Johann-Wolfgang-Goethe-Universität Frankfurt, Frankfurt, Germany

Correspondence: Dr M Hahn, PhD, Division of Molecular Genetics, Deutsches Krebsforschungszentrum, INF 280, D-69120 Heidelberg, Germany and Dr R Stauber, PhD, Chemotherapeutisches Forschungsinstitut Georg-Speyer-Haus, Paul-Ehrlich-Str. 42-44, D-60596 Frankfurt am Main, Germany. E-mails: m.hahn@dkfz.de, stauber@em.uni-frankfurt.de

^*These two authors contributed equally to this study.

Received 21 February 2005; Revised 8 April 2005; Accepted 9 April 2005; Published online 23 May 2005.

Abstract

The comparison of gene expression measurements obtained with different technical approaches is of substantial interest in order to clarify whether interplatform differences may conceal biologically significant information. To address this concern, we analyzed gene expression in a set of head and neck squamous cell carcinoma patients, using both spotted oligonucleotide microarrays made from a large collection of 70-mer probes and commercial arrays produced by in situ synthesis of sets of multiple 25-mer oligonucleotides per gene. Expression measurements were compared for 4425 genes represented on both platforms, which revealed strong correlations between the corresponding data sets. Of note, a global tendency towards smaller absolute ratios was observed when using the 70-mer probes. Real-time quantitative reverse transcription PCR measurements were conducted to verify expression ratios for a subset of genes and achieved good agreement regarding both array platforms. In conclusion, similar profiles of relative gene expression were obtained using arrays of either single 70-mer or multiple short 25-mer oligonucleotide probes per gene. Although qualitative assessments of the expression of individual genes have to be made with caution, our results indicate that the comparison of gene expression profiles generated on these platforms will help to discover disease-related gene signatures in general.