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Sparse Sensing DNA Microarray-Based Biosensor: Is It Feasible?
March 2010
Mojdeh Mohtashemi, The MITRE Corporation, MIT CSAIL
Haley Smith, The MITRE Corporation
Felicia Sutton, The MITRE Corporation
David Walburger, The MITRE Corporation
James Diggans, The MITRE Corporation
ABSTRACT
Conventional microarray-based biosensors can only
detect a limited number of organisms, and adding sensor
capabilities requires re-engineering of reagents and devices to
detect the presence of a novel microbial organism. To overcome
these limitations, the size of the microarray may need to be
prohibitively large, an impractical proposition, cost-wise, using
current technology. We hypothesized that a relatively small
number of oligomers is sufficient to design a microarray capable
of differentiating between the genomic signatures of multiple
organisms. To test this hypothesis, we designed a sparse, pseudorandom
prototype microarray-based biosensor by generating
12,600 25bp oligomer probes derived from a mathematical model
based on random selection of DNA sequences from seven
pathogenic prokaryotic genomes. To enable identification of
novel organisms, a reference library of pure genomic DNA was
generated from three simulant organisms that are known to be
phylogenetically distant from the seven base species used to
generate the probes. These simulants were combined to produce
complex DNA samples meant to mimic the uncertainty and
complexity of an unknown environmental genomic background.
A mathematical model was then developed to capture the
signature of each simulant organism. The model detected the
presence of all three simulant organisms in the mixed DNA
samples with high accuracy.
Additional Search Keywords
Biosensor, sparse sensing, DNA microarray, VLMC, PLSR, genomic signature
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