title: Label-free prehybridization DNA microarray imaging using photonic crystals for quantitative spot quality analysis.
abstract: Technical variability during DNA capture probe printing remains an important obstacle to obtaining high quality data from microarray experiments. While methods that use fluorescent labels for visualizing printed arrays prior to hybridization have been presented, the ability to measure spot density using label-free techniques would provide valuable information on spot quality without altering standard microarray protocols. In this study, we present the use of a photonic crystal biosensor surface and a high resolution label-free imaging detection instrument to generate prehybridization images of spotted oligonucleotide microarrays. Spot intensity, size, level of saturation, and local background intensity were measured from these images. This information was used for the automated identification of missed spots (due to mechanical failure or sample depletion) as well as the assignment of a score that reflected the quality of each printed feature. Missed spots were identified with >95% sensitivity. Furthermore, filtering based on spot quality scores increased pairwise correlation of posthybridization spot intensity between replicate arrays, demonstrating that label-free spot quality scores captured the variability in the microarray data. This imaging modality can be applied for the quality control of printed cDNA, oligonucleotide, and protein microarrays.
authors.affiliation: Department of Bioengineering, University of Illinois at Urbana-Champaign, 1304 West Springfield Avenue, Urbana, Illinois 61801, USA.
authors.forename: S
authors.initials: S
authors.lastname: George
authors.forename: I D
authors.initials: ID
authors.lastname: Block
authors.forename: S I
authors.initials: SI
authors.lastname: Jones
authors.forename: P C
authors.initials: PC
authors.lastname: Mathias
authors.forename: V
authors.initials: V
authors.lastname: Chaudhery
authors.forename: P
authors.initials: P
authors.lastname: Vuttipittayamongkol
authors.forename: H-Y
authors.initials: HY
authors.lastname: Wu
authors.forename: L O
authors.initials: LO
authors.lastname: Vodkin
authors.forename: B T
authors.initials: BT
authors.lastname: Cunningham
mesh_terms: D003460:Crystallization; D015342:DNA Probes / Q000032:analysis*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*
chemical_list: D015342:DNA Probes