Skip Navigation

Nucleic Acids Research 2005 33(22):e187; doi:10.1093/nar/gni186
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (1301K) Freely available
Right arrow Screen PDF (324K) Freely available
Right arrow Supplementary Material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Thompson, K. L.
Right arrow Articles by Sistare, F. D.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Thompson, K. L.
Right arrow Articles by Sistare, F. D.
Related Collections
Right arrow Microarray
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 23 December 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Methods Online

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

Karol L. Thompson*, Barry A. Rosenzweig, P. Scott Pine, Jacques Retief1, Yaron Turpaz1, Cynthia A. Afshari2, Hisham K. Hamadeh2, Michael A. Damore2, Michael Boedigheimer2, Eric Blomme3, Rita Ciurlionis3, Jeffrey F. Waring3, James C. Fuscoe4, Richard Paules5, Charles J. Tucker5, Thomas Fare6, Ernest M. Coffey6, Yudong He6, Patrick J. Collins7, Kurt Jarnagin8, Susan Fujimoto8, Brigitte Ganter8, Gretchen Kiser9, Tamma Kaysser-Kranich9, Joseph Sina10 and Frank D. Sistare10

Center for Drug Evaluation and Research, US FDA Silver Spring, MD 20993, USA 1Affymetrix Inc. Santa Clara, CA 95051, USA 2Amgen Inc. Thousand Oaks, CA 91320, USA 3Abbott Laboratories Abbott Park, IL 60064, USA 4National Center for Toxicological Research, US FDA Jefferson, AR 72079, USA 5National Center for Toxicogenomics, National Institute of Environmental Health Sciences Research Triangle Park, NC 27709, USA 6Rosetta Inpharmatics LLC Seattle, WA 98109, USA 7Agilent Technologies Palo Alto, CA 94304, USA 8Iconix Pharmaceuticals Inc. Mountain View, CA 94043, USA 9GE Healthcare Chandler, AZ 85248, USA 10Merck & Co. Inc. West Point, PA 19486, USA

*To whom correspondence should be addressed at US Food and Drug Administration, White Oak Life Sciences Building 64, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA. Tel: +1 301 796 0126; Fax: +1 301 796 9818; Email: karol.thompson{at}fda.hhs.gov

Received August 15, 2005. Revised October 20, 2005. Accepted November 21, 2005.

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.

Present address: Jacques Retief, Iconix Pharmaceuticals Inc., Mountain View, CA 94043, USA


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
X. Zheng, H.-C. Huang, W. Li, P. Liu, Q.-Z. Li, and Y. Liu
Modeling nonlinearity in dilution design microarray data
Bioinformatics, June 1, 2007; 23(11): 1339 - 1347.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.