The Affymetrix branched DNA technol., known com. as QuantiGene, has been used for several years now in the plant biotechnol. industry. Affymetrix has developed assays for direct RNA or gDNA copy number variation anal. using either purified RNA or DNA or sample lysates of plants, bacteria, yeast, whole blood, tissues, cells, and formalin-fixed, paraffin-embedded tissues. Papers using the single-plex technol. have frequently been published since 1999. This linear assay, which allows for the detection of percent changes in gene expression, involves capturing the RNA directly onto an immobilized surface (plate) and then building a signal using a series of oligonucleotide hybridizations (400-fold signal amplification). This is all completed using numerous gene specific probe sets. First, capture extender (CE) probes hybridize to the Universal Capture probes chem. bound to the plate. Then, label extender (LE) probes hybridize to the RNA and become a platform for the bDNA amplifier. A third type of probe sets called blocking probes (BP) are used to help stabilize the RNA. In 2005, the first paper had been published using the QuantiGene Plex 2.0 technol. This version of the assay is a Luminex bead based assay which now allows for the true multiplex measurement of 3-80 different genes at one time in a single sample well. Affymetrix does a full QC to ensure there is no cross hybridization between targets. For an example of this technol. published, please see Qi et al., J Biol Chem. 2012; 287:31482-93.