Journal Article

Use of a mixed tissue RNA design for performance assessments on multiple microarray formats

Karol L. Thompson, Barry A. Rosenzweig, P. Scott Pine, Jacques Retief, Yaron Turpaz, Cynthia A. Afshari, Hisham K. Hamadeh, Michael A. Damore, Michael Boedigheimer, Eric Blomme, Rita Ciurlionis, Jeffrey F. Waring, James C. Fuscoe, Richard Paules, Charles J. Tucker, Thomas Fare, Ernest M. Coffey, Yudong He, Patrick J. Collins, Kurt Jarnagin, Susan Fujimoto, Brigitte Ganter, Gretchen Kiser, Tamma Kaysser-Kranich, Joseph Sina and Frank D. Sistare

in Nucleic Acids Research

Volume 33, issue 22, pages e187-e187
Published in print December 2005 | ISSN: 0305-1048
Published online December 2005 | e-ISSN: 1362-4962 | DOI: https://dx.doi.org/10.1093/nar/gni186

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The comparability and reliability of data generated using microarray technology would be enhanced by use of a common set of standards that allow accuracy, reproducibility and dynamic range assessments on multiple formats. We designed and tested a complex biological reagent for performance measurements on three commercial oligonucleotide array formats that differ in probe design and signal measurement methodology. The reagent is a set of two mixtures with different proportions of RNA for each of four rat tissues (brain, liver, kidney and testes). The design provides four known ratio measurements of >200 reference probes, which were chosen for their tissue-selectivity, dynamic range coverage and alignment to the same exemplar transcript sequence across all three platforms. The data generated from testing three biological replicates of the reagent at eight laboratories on three array formats provides a benchmark set for both laboratory and data processing performance assessments. Close agreement with target ratios adjusted for sample complexity was achieved on all platforms and low variance was observed among platforms, replicates and sites. The mixed tissue design produces a reagent with known gene expression changes within a complex sample and can serve as a paradigm for performance standards for microarrays that target other species.

Journal Article.  9868 words.  Illustrated.

Subjects: Research Methods in Life Sciences

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