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


BACKGROUND
The model and algorithms will be available upon request to the corresponding author.
Nesvold
Håvard
H
Department of Informatics, University of Oslo, Blindern, Norway.
Kristoffersen
Anja Bråthen
AB
Holst-Jensen
Arne
A
Berdal
Knut G
KG
D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D003198:Computer Simulation; D004252:DNA Mutational Analysis / Q000379:methods*; D015342:DNA Probes / Q000138:chemical synthesis / Q000235:genetics; D004784:Environmental Monitoring / Q000379:methods; D004867:Equipment Design; D019544:Equipment Failure Analysis; D020869:Gene Expression Profiling / Q000379:methods*; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000379:methods*; D030781:Organisms, Genetically Modified / Q000235:genetics*; D018570:Risk Assessment / Q000379:methods*; D012307:Risk Factors
D029681:Arabidopsis Proteins; D015342:DNA Probes