Probe Design for Compressive Sensing DNA Microarrays

Abstract—Compressive Sensing Microarrays (CSM) are DNAbased sensors that operate using group testing and compressive sensing (CS) principles. In contrast to conventional DNA microarrays, in which each genetic sensor is designed to respond to a single target, in a CSM each sensor responds to a group of targets. We study the problem of designing CS probes that simultaneously account for both the constraints from group testing theory and the biochemistry of probe-target DNA hybridization. Our results show that, in order to achieve accurate hybridization profiling, consensus probe sequences are required to have sequence homology of at least 80% with all targets to be detected. Furthermore, experiments show that outof-equilibrium datasets are usually as accurate as those obtained from equilibrium conditions. Consequently, one can use CSMs in applications for which only short hybridization times are allowed.

• Type: Conference
• Year: 2008
• Where: BIBM
• Authors: Wei Dai, Olgica Milenkovic, Mona A. Sheikh, Richard G. Baraniuk
• Keywords: Abstract—Compressive Sensing Microarrays, BIBM 2008, Bioinformatics, Conventional Dna Microarrays, Group Testing