RNA Profiling with the DASL Assay

Microarray analysis of gene expression has proven to be a remarkable tool for biologists, and has the potential to be widely adopted by clinical researchers. One challenge to clinical applications has been the need for high quality, cryopreserved RNA for standard microarray sample labeling. Such samples are of limited availability and must be collected over the course of a disease. In contrast, formalin-fixed, paraffin-embedded (FFPE) tissue samples are readily available and have the added advantage of known patient outcomes. However, the poor integrity of RNA derived from FFPE samples has largely precluded their use in microarray analysis. Illumina has developed a novel gene expression assay for microarrays that is capable of utilizing partially degraded RNA. The cDNA-mediated Annealing, Selection, extension and Ligation (DASL) Assay can monitor RNA expression of up to 1536 sequence targets derived from RNA in FFPE samples stored up to 12 years. Together with the highthroughput capability of Illumina’s microarray platforms, the DASL Assay offers researchers the opportunity to analyze hundreds to thousands of RNA transcripts derived from previously collected, preserved samples. This technical bulletin explains the features of the DASL Assay, describes its performance for measuring RNA derived from both fresh-frozen and FFPE samples and demonstrates its utility in analyzing clinical samples.