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Published online 25 May 2004

Nucleic Acids Research, 2004, Vol. 32, No. 9 e74
© 2004 Oxford University Press

Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements

Brigham H. Mecham, Gregory T. Klus1, Jeffrey Strovel2, Meena Augustus2, David Byrne3, Peter Bozso3, Daniel Z. Wetmore, Thomas J. Mariani, Isaac S. Kohane3 and Zoltan Szallasi*,1,3

Division of Pulmonary and Critical Care Medicine, Department of Medicine and Pulmonary Bioinformatics, The Lung Biology Center, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA, 1 Department of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA, 2 Avalon Pharmaceuticals, Germantown, MD 20876, USA and 3 Children’s Hospital Informatics Program, Harvard Medical School, Boston, MA 02115, USA

*To whom correspondence should be addressed at Harvard Medical School, Children’s Hospital Informatics Program, 300 Longwood Avenue, Boston, MA 02215, USA. Tel: +1 617 355 2179; Fax: +1 617 730 0253; Email: zszallasi{at}chip.org

Received March 21, 2004; Revised and Accepted April 21, 2004

Cancer derived microarray data sets are routinely produced by various platforms that are either commercially available or manufactured by academic groups. The fundamental difference in their probe selection strategies holds the promise that identical observations produced by more than one platform prove to be more robust when validated by biology. However, cross-platform comparison requires matching corresponding probe sets. We are introducing here sequence-based matching of probes instead of gene identifier-based matching. We analyzed breast cancer cell line derived RNA aliquots using Agilent cDNA and Affymetrix oligonucleotide microarray platforms to assess the advantage of this method. We show, that at different levels of the analysis, including gene expression ratios and difference calls, cross-platform consistency is significantly improved by sequence- based matching. We also present evidence that sequence-based probe matching produces more consistent results when comparing similar biological data sets obtained by different microarray platforms. This strategy allowed a more efficient transfer of classification of breast cancer samples between data sets produced by cDNA microarray and Affymetrix gene-chip platforms.


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