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Bioinformatics Advance Access published online on January 12, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti248
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Bioinformatics © Oxford University Press 2004; all rights reserved.
Received June 29, 2004
Revised November 15, 2004
Accepted December 20, 2004

Article

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

Håvard Nesvold 1, Anja Bråthen Kristoffersen 2, Arne Holst-Jensen 3, and Knut G. Berdal 3*

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

* To whom correspondence should be addressed.
Knut G. Berdal, E-mail: knut.berdal{at}vetinst.no


  Abstract

Motivation: Unknown genetically modified organisms (GMOs) have not undergone a risk evaluation, and hence might be 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 on a set of DNA chip probes containing all possible sequences of uniform length n, creating probes which should be 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 and should be tested further in the laboratory.

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


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