Arraying Archives

Microarray manufacturer Affymetrix of Santa Clara, Calif., http://www.affymetrix.com and laser-capture microdissection company Arcturus of Mountain View, Calif. http://www.arctur.com, have teamed up, offering the GeneChip X3P array and the Paradise™ reagent system, respectively, to enable gene expression analysis of archived formalin-fixed, paraffin-embedded (FFPE) samples. "These samples represent a treasure trove for genomic discovery efforts, because they generally are associated with known clinical outcomes," says Peter Dansky, formerly vice president of marketing at Arcturus.

Extracting high-quality mRNA suitable for microarray analyses from FFPE samples was not feasible in the past, says Renata Coudry, a research pathologist in the chemoprevention program at Fox Chase Cancer Center in Philadelphia. Previously, Coudry and colleagues could characterize only a small subset of molecular markers in colitis-associated colorectal dysplasias; they now can analyze the expression of a vast number of genes.

Since these samples tend to yield shorter RNAs, the X3P's probes contain an extreme 3' bias, ...