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Journal of Clinical Microbiology, August 2006, p. 2857-2862, Vol. 44, No. 8
0095-1137/06/$08.00+0     doi:10.1128/JCM.00135-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Robust Sequence Selection Method Used To Develop the FluChip Diagnostic Microarray for Influenza Virus

Martin Mehlmann,1,{dagger} Erica D. Dawson,1,{dagger} Michael B. Townsend,1 James A. Smagala,1 Chad L. Moore,1 Catherine B. Smith,2 Nancy J. Cox,2 Robert D. Kuchta,1* and Kathy L. Rowlen1,3

Department of Chemistry and Biochemistry, The University of Colorado at Boulder, UCB #215, Boulder, Colorado 80309,1 Influenza Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd., Atlanta, Georgia 30333,2 InDevR, LLC, 2100 Central Ave., Suite 106, Boulder, Colorado 803013

Received 20 January 2006/ Returned for modification 10 April 2006/ Accepted 14 May 2006

DNA microarrays have proven to be powerful tools for gene expression analyses and are becoming increasingly attractive for diagnostic applications, e.g., for virus identification and subtyping. The selection of appropriate sequences for use on a microarray poses a challenge, particularly for highly mutable organisms such as influenza viruses, human immunodeficiency viruses, and hepatitis C viruses. The goal of this work was to develop an efficient method for mining large databases in order to identify regions of conservation in the influenza virus genome. From these regions of conservation, capture and label sequences capable of discriminating between different viral types and subtypes were selected. The salient features of the method were the use of phylogenetic trees for data reduction and the selection of a relatively small number of capture and label sequences capable of identifying a broad spectrum of influenza viruses. A detailed experimental evaluation of the selected sequences is described in a companion paper. The software is freely available under the General Public License at http://www.colorado.edu/chemistry/RGHP/software/.

* Corresponding author. Mailing address: Department of Chemistry and Biochemistry, University of Colorado, UCB215, Boulder, CO 80303. Phone: (303) 492-7027. Fax: (303) 492-5894. E-mail: kuchta{at}colorado.edu.

{dagger} M. Mehlmann and E. D. Dawson contributed equally to this work.

Journal of Clinical Microbiology, August 2006, p. 2857-2862, Vol. 44, No. 8
0095-1137/06/$08.00+0     doi:10.1128/JCM.00135-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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