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Flagship Bio Rolls out RNA Analysis Services on Affy's QuantiGene ViewRNA Platform

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Flagship Biosciences will use Affymetrix Quantigene ViewRNA assays as part of a new tissue-based RNA in situ hybridization analysis service.

Central to the company's service are internally developed image analysis algorithms that combine tissue pattern recognition with cell-based analysis to "offer pharmaceutical clients improved approaches to measuring RNA expression while preserving the tissue context," according to a company statement.

Flagship said that the algorithms can be used to "simplify and standardize" the identification of the regions of interest in relevant and surrounding tissue and to also identify cells and the chromogenic expression patterns of the various RNA products.

The service identifies the cells of interest and associates the ISH probe with individual cells. Individual ISH dots are measured by number, size, intensity, or in a summary form more familiar to pathological evaluations, the firm said. This "solves the problem of interpreting the significance of the ISH dots and allows data reporting and evaluation more consistent with customary pathological approaches."

Flagship's service relies on Affy's Panomics QuantiGene ViewRNA for ISH, which enables the detection of RNA transcripts at single-cell resolution in formalin-fixed, paraffin-embedded tissues, core biopsies, and fine needle aspirates in singleplex and multiplex formats. Earlier this year, Affy announced a deal with Leica Microsystems, a Danaher company, to automate the assay on the Leica Bond RX staining platform for research applications (BAN 8/7/2012). Flagship cited the assay's multiplexed two-color approaches and its availability on an automated immunohistochemistry autostainer platform as factors in its adoption of the product.

"While the quantitation of RNA in situ is still in its infancy, our ability to combine Flagship's image analysis techniques with Affymetrix's technology is a valuable step in the right direction," Flagship's CEO Steven Potts said in a statement. "Evaluating RNA expression in the localized tissue context is a valuable addition to many pharmaceutical companion diagnostics and research programs," he added.

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