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The study of gene expression in conventionally processed tissues is hampered by degradation of mRNA. Expensive, low-multiplex, quantitative PCR methods can be unreliable due to the limited template sizes. One way to overcome this problem is to use array-based methods. DASL® technology relies on random priming for production of cDNA, in concert with universal bead arrays to allow the detection and relative quantitation of expression of specific gene subsets.
Using the Illumina DASL® Cancer Panel (500 cancer-associated genes on one array), we evaluated the expression of key genes in archival formalin-fixed, paraffin-embedded tissue samples from 80 breast cancer patients with well-characterised pathological and clinical features. We first assessed transcript integrity in the samples on the basis of levels of mRNA encoding RPL13A, prior to running the Cancer Panel. A subset of genes of interest was then assessed by quantitative PCR to confirm the relative levels observed using the DASL® assay. Finally the expression of the same subset of genes was evaluated at the protein level by immunohistochemistry.
We were able to predict, with good accuracy based upon RPL13A assays, those samples unsuitable for DASL® analysis. Furthermore, the results of DASL® analysis showed good correlation with protein levels, as measured by immunohistochemistry, for a number of key genes including ERBB2 (HER2) and ESR1 (ER). We conclude that DASL® represents a powerful tool for assessing expression of multiple genes in archival tissue.