title: Quantitative assessment of a novel flow-through porous microarray for the rapid analysis of gene expression profiles.
abstract: A novel microarray system that utilizes a porous aluminum-oxide substrate and flow-through incubation has been developed for rapid molecular biological testing. To assess its utility in gene expression analysis, we determined hybridization kinetics, variability, sensitivity and dynamic range of the system using amplified RNA. To show the feasibility with complex biological RNA, we subjected Jurkat cells to heat-shock treatment and analyzed the transcriptional regulation of 23 genes. We found that trends (regulation or no change) acquired on this platform are in good agreement with data obtained from real-time quantitative PCR and Affymetrix GeneChips. Additionally, the system demonstrates a linear dynamic range of 3 orders of magnitude and at least 10-fold decreased hybridization time compared to conventional microarrays. The minimum amount of transcript that could be detected in 20 microl volume is 2-5 amol, which enables the detection of 1 in 300,000 copies of a transcript in 1 microg of amplified RNA. Hybridization and subsequent analysis are completed within 2 h. Replicate hybridizations on 24 identical arrays with two complex biological samples revealed a mean coefficient of variation of 11.6%. This study shows the potential of flow-through porous microarrays for the rapid analysis of gene expression profiles in clinical applications.
authors.affiliation: PamGene International BV, Nieuwstraat 30, PO Box 1345, 5200 BJ 's-Hertogenbosch, The Netherlands. ywu@pamgene.com
authors.forename: Ying
authors.initials: Y
authors.lastname: Wu
authors.forename: Peggy
authors.initials: P
authors.lastname: de Kievit
authors.forename: Lars
authors.initials: L
authors.lastname: Vahlkamp
authors.forename: Dirk
authors.initials: D
authors.lastname: Pijnenburg
authors.forename: Maarten
authors.initials: M
authors.lastname: Smit
authors.forename: Martijn
authors.initials: M
authors.lastname: Dankers
authors.forename: Diana
authors.initials: D
authors.lastname: Melchers
authors.forename: Martijn
authors.initials: M
authors.lastname: Stax
authors.forename: Piet J
authors.initials: PJ
authors.lastname: Boender
authors.forename: Colin
authors.initials: C
authors.lastname: Ingham
authors.forename: Niek
authors.initials: N
authors.lastname: Bastiaensen
authors.forename: Rik
authors.initials: R
authors.lastname: de Wijn
authors.forename: Dirk
authors.initials: D
authors.lastname: van Alewijk
authors.forename: Henk
authors.initials: H
authors.lastname: van Damme
authors.forename: Anton K
authors.initials: AK
authors.lastname: Raap
authors.forename: Alan B
authors.initials: AB
authors.lastname: Chan
authors.forename: Rinie
authors.initials: R
authors.lastname: van Beuningen
mesh_terms: D000537:Aluminum Oxide / Q000737:chemistry; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D019169:Jurkat Cells; D007700:Kinetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results; D013997:Time Factors
chemical_list: D000537:Aluminum Oxide