Research article

Robust interlaboratory reproducibility of a gene expression signature measurement consistent with the needs of a new generation of diagnostic tools

Robert A Ach¹ , Arno Floore² , Bo Curry¹ , Vladimir Lazar³ , Annuska M Glas² , Rob Pover² , Anya Tsalenko¹ , Hugues Ripoche³ , Fatima Cardoso⁴ , Mahasti Saghatchian d'Assignies³ , Laurakay Bruhn¹ and Laura J Van't Veer²

¹  Molecular Technology Lab, Agilent Laboratories, Agilent Technologies, 5301 Stevens Creek Blvd., Santa Clara, CA 95051, USA

²  Agendia BV, Slotervaart Medical Center 9D, Louwesweg 6, 1066 EC Amsterdam, The Netherlands

³  Institut Gustave-Roussy, 39 rue Camille Desmoulins, 94805 Villejuif Cedex, France

⁴  Institut Jules Bordet, 121 Blvd de Waterloo, B-1000 Brussels, Belgium

author email corresponding author email

BMC Genomics 2007, 8:148doi:10.1186/1471-2164-8-148

Published:	7 June 2007

Abstract

Background

The increasing use of DNA microarrays in biomedical research, toxicogenomics, pharmaceutical development, and diagnostics has focused attention on the reproducibility and reliability of microarray measurements. While the reproducibility of microarray gene expression measurements has been the subject of several recent reports, there is still a need for systematic investigation into what factors most contribute to variability of measured expression levels observed among different laboratories and different experimenters.

Results

We report the results of an interlaboratory comparison of gene expression array measurements on the same microarray platform, in which the RNA amplification and labeling, hybridization and wash, and slide scanning were each individually varied. Identical input RNA was used for all experiments. While some sources of variation have measurable influence on individual microarray signals, they showed very low influence on sample-to-reference ratios based on averaged triplicate measurements in the two-color experiments. RNA labeling was the largest contributor to interlaboratory variation.

Conclusion

Despite this variation, measurement of one particular breast cancer gene expression signature in three different laboratories was found to be highly robust, showing a high intralaboratory and interlaboratory reproducibility when using strictly controlled standard operating procedures.