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Bioinformatics Advance Access originally published online on January 12, 2005
Bioinformatics 2005 21(9):1917-1926; doi:10.1093/bioinformatics/bti248
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Design of a DNA chip for detection of unknown genetically modified organisms (GMOs)

Håvard Nesvold 1,2, Anja Bråthen Kristoffersen 1, Arne Holst-Jensen 2 and Knut G. Berdal 2,*

1Department of Informatics, University of Oslo PO Box 1080 Blindern, 0316 Oslo, Norway
2Section of Food and Feed Microbiology, National Veterinary Institute PO Box 8156 Dep., 0033 Oslo, Norway

*To whom correspondence should be addressed.

Motivation: Unknown genetically modified organisms (GMOs) have not undergone a risk evaluation, and hence might pose a danger to health and environment. There are, today, no methods for detecting unknown GMOs. In this paper we propose a novel method intended as a first step in an approach for detecting unknown genetically modified (GM) material in a single plant.

Results: A model is designed where biological and combinatorial reduction rules are applied to a set of DNA chip probes containing all possible sequences of uniform length n, creating probes capable of detecting unknown GMOs. The model is theoretically tested for Arabidopsis thaliana Columbia, and the probabilities for detecting inserts and receiving false positives are assessed for various parameters for this organism. From a theoretical standpoint, the model looks very promising but should be tested further in the laboratory.

Availability: The model and algorithms will be available upon request to the corresponding author.

Contact: knut.berdal{at}vetinst.no


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