title: Optimal amounts of fluorescent dye improve expression microarray results in tumor specimens.
abstract: Expression microarrays have great potential for clinical use but variability of the results represents a challenge for reliable practical application. The amount of fluorescent dye used in microarray experiments is a significant source of variability that has not been systematically studied. Here we demonstrate that the quantity of Cy3 dye affects microarray results performed on tumor specimens. Signal-to-noise ratios and coefficients of variation are significantly improved by increasing Cy3 to 150-180 pmol, but any further increase does not improve the data. In conclusion, optimal amounts of dye reduce variability and improve reliability of expression microarray experiments.
authors.affiliation: Cancer Genomics Program, Department of Oncology, University of Cambridge, Hutchison/MRC Research Center, Hills Road, Cambridge CB2 2XZ, UK. an258@cam.ac.uk
authors.forename: Ali
authors.initials: A
authors.lastname: Naderi
authors.forename: Ahmed A
authors.initials: AA
authors.lastname: Ahmed
authors.forename: Yanzhong
authors.initials: Y
authors.lastname: Wang
authors.forename: James D
authors.initials: JD
authors.lastname: Brenton
authors.forename: Carlos
authors.initials: C
authors.lastname: Caldas
mesh_terms: D002232:Carbocyanines / Q000592:standards*; D005456:Fluorescent Dyes / Q000592:standards*; D020869:Gene Expression Profiling / Q000379:methods* / Q000592:standards; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000592:standards*
chemical_list: D002232:Carbocyanines; D005456:Fluorescent Dyes; C089187:cyanine dye 3