title: Sensitivity and fidelity of DNA microarray improved with integration of Amplified Differential Gene Expression (ADGE).
abstract: BACKGROUND
  The ADGE technique is a method designed to magnify the ratios of gene expression before detection. It improves the detection sensitivity to small change of gene expression and requires small amount of starting material. However, the throughput of ADGE is low. We integrated ADGE with DNA microarray (ADGE microarray) and compared it with regular microarray.
  
  
  RESULTS
  When ADGE was integrated with DNA microarray, a quantitative relationship of a power function between detected and input ratios was found. Because of ratio magnification, ADGE microarray was better able to detect small changes in gene expression in a drug resistant model cell line system. The PCR amplification of templates and efficient labeling reduced the requirement of starting material to as little as 125 ng of total RNA for one slide hybridization and enhanced the signal intensity. Integration of ratio magnification, template amplification and efficient labeling in ADGE microarray reduced artifacts in microarray data and improved detection fidelity. The results of ADGE microarray were less variable and more reproducible than those of regular microarray. A gene expression profile generated with ADGE microarray characterized the drug resistant phenotype, particularly with reference to glutathione, proliferation and kinase pathways.
  
  
  CONCLUSIONS
  ADGE microarray magnified the ratios of differential gene expression in a power function, improved the detection sensitivity and fidelity and reduced the requirement for starting material while maintaining high throughput. ADGE microarray generated a more informative expression pattern than regular microarray.
authors.affiliation: Department of Pharmacology, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, PA 19111, USA. z_chen@fccc.edu
authors.forename: Zhijian J
authors.initials: ZJ
authors.lastname: Chen
authors.forename: Laurent
authors.initials: L
authors.lastname: Gaté
authors.forename: Warren
authors.initials: W
authors.lastname: Davis
authors.forename: Kristina E
authors.initials: KE
authors.lastname: Ile
authors.forename: Kenneth D
authors.initials: KD
authors.lastname: Tew
mesh_terms: D002455:Cell Division / Q000235:genetics; D003603:Cytotoxins / Q000494:pharmacology; D019008:Drug Resistance, Neoplasm / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D015971:Gene Expression Regulation, Enzymologic / Q000187:drug effects; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D005978:Glutathione / Q000031:analogs & derivatives* / Q000494:pharmacology; D051549:Glutathione S-Transferase pi; D005982:Glutathione Transferase / Q000235:genetics; D018922:HL-60 Cells; D006801:Humans; D007527:Isoenzymes / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012680:Sensitivity and Specificity
chemical_list: D003603:Cytotoxins; D007527:Isoenzymes; C107479:TER 286; C496556:GSTP1 protein, human; D051549:Glutathione S-Transferase pi; D005982:Glutathione Transferase; D005978:Glutathione