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Journal of Heredity Advance Access published online on November 3, 2005
Journal of Heredity, doi:10.1093/jhered/esi130
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© The American Genetic Association. 2005. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org.

Article

The Development of a High-Density Canine Microarray

J. A. Holzwarth 1*, R. P. Middleton 2, M. Roberts 2, R. Mansourian 1, F. Raymond 1, and S. S. Hannah 2

1 From Nestlé Research Center Lausanne, Nestec Ltd., Vers-chez-les-Blanc, 1000 Lausanne 26, Switzerland
2 From Nestlé Purina Research, Checkerboard Square, St. Louis, MO 63164

* To whom correspondence should be addressed.
J. A. Holzwarth, E-mail: james.holzwarth{at}rdls.nestle.com


  Abstract

DNA microarrays can give global transcriptional views of cellular responses to disease, development, nutrition, and other biological states. They can be used to elucidate biological networks, develop diagnostics, and identify genetic targets and molecular mechanisms. The technology is widely used and can be a valuable complement to more "disease-centric" focused arrays. For these reasons, Nestlé designed a custom canine Affymetrix microarray representing transcripts from multiple tissues for use in areas where a more focused microarray had not already been developed. Sufficient numbers of sequences representing messenger RNAs (mRNAs) or expressed sequence tags (ESTs) is integral for the design of a global microarray chip. This chip was designed using public domain sequences (GenBank) and sequences from a proprietary canine EST database. In order to enrich the chip with annotated transcripts, both of these sequence sets were BLASTed against the nonredundant protein database. The sequences on the microarray were isolated from more than 48 different tissues. The final compliment of sequences had sequences unique to GenBank (3160), unique to the proprietary EST database (17,620), and present in both sources (1996). In comparison with human sequences (RefSeq), 74% of the canine sequences matched a human sequence.


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