title: Quantitative data analysis methods for bead-based DNA hybridization assays using generic flow cytometry platforms.
abstract: Bead-based assays are in demand for rapid genomic and proteomic assays for both research and clinical purposes. Standard quantitative procedures addressing raw data quality and analysis are required to ensure the data are consistent and reproducible across laboratories independent of flow platform. Quantitative procedures have been introduced spanning raw histogram analysis through to absolute target quantitation. These included models developed to estimate the absolute number of sample molecules bound per bead (Langmuir isotherm), relative quantitative comparisons (two-sided t-tests), and statistical analyses investigating the quality of raw fluorescence data. The absolute target quantitation method revealed a concentration range (below probe saturation) of Cy5-labeled synthetic cytokeratin 19 (K19) RNA of c.a. 1 x 10(4) to 500 x 10(4) molecules/bead, with a binding constant of c.a. 1.6 nM. Raw hybridization frequency histograms were observed to be highly reproducible across 10 triplex assay replicates and only three assay replicates were required to distinguish overlapping peaks representing small sequence mismatches. This study provides a quantitative scheme for determining the absolute target concentration in nucleic acid hybridization reactions and the equilibrium binding constants for individual probe/target pairs. It is envisaged that such studies will form the basis of standard analytical procedures for bead-based cytometry assays to ensure reproducibility in inter- and intra-platform comparisons of data between laboratories.
authors.affiliation: Nanotechnology and Biomaterials Centre, Level 5, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia.
authors.forename: S R
authors.initials: SR
authors.lastname: Corrie
authors.forename: G A
authors.initials: GA
authors.lastname: Lawrie
authors.forename: B J
authors.initials: BJ
authors.lastname: Battersby
authors.forename: K
authors.initials: K
authors.lastname: Ford
authors.forename: A
authors.initials: A
authors.lastname: Rühmann
authors.forename: K
authors.initials: K
authors.lastname: Koehler
authors.forename: D E
authors.initials: DE
authors.lastname: Sabath
authors.forename: M
authors.initials: M
authors.lastname: Trau
mesh_terms: D004247:DNA / Q000235:genetics*; D003627:Data Interpretation, Statistical; D005434:Flow Cytometry / Q000379:methods* / Q000706:statistics & numerical data; D005456:Fluorescent Dyes; D006801:Humans; D053539:Keratin-19 / Q000235:genetics; D015336:Molecular Probe Techniques; D009693:Nucleic Acid Hybridization / Q000379:methods*; D015345:Oligonucleotide Probes / Q000235:genetics; D012313:RNA / Q000032:analysis / Q000235:genetics; D012984:Software
chemical_list: D005456:Fluorescent Dyes; D053539:Keratin-19; D015345:Oligonucleotide Probes; D012313:RNA; D004247:DNA