Quantitative expression profiling of RNA from formalin-fixed, paraffin-embedded tissues using randomly assembled bead arrays.

Formalin-fixed, paraffin-embedded (FFPE) tissues represent an invaluable resource for gene expression analysis, as they are the most widely available materials for studies of human disease. However, degradation of RNA during tissue fixation and storage makes FFPE-derived RNAs hard to work with using conventional microarray technology. Most gene expression studies done using FFPE tissues rely on quantitative RT-PCR (qPCR), but this approach has had limited success because of the short cDNA templates available in these samples. In this chapter, we describe the DASL (cDNA-mediated annealing, selection, extension, and ligation) Assay, a flexible, sensitive, and reproducible gene expression profiling system for parallel analysis of several hundred mRNA transcripts on the BeadArray platform. This technology is especially useful for determining cancer prognosis or therapy response, because it allows not only prospective studies but also retrospective analyses. Using the DASL Assay, gene expression analyses can be performed on routinely stored tumor specimens from patients with known outcomes.