PAM50 breast cancer intrinsic classifier: Clinical validation of a multianalyte laboratory developed test.

10597 Background: Invasive breast cancers can be classified by gene expression profiling into 4 major biologic subtypes referred to as Luminal A, Luminal B, HER2-enriched, and Basal-like. Subtypes have been identified using several technologies including microarray, immunohistochemistry, and RT-qPCR. In 2009, a 50-gene signature (PAM50) was proposed to standardize breast cancer subtyping. We present the clinical validation of this signature by RT-qPCR. Methods: RNA was extracted from 171 breast samples (155 invasive cancers and 16 “normal” breast tissues) procured in formalin-fixed paraffin-embedded tissue blocks. The RNA was reverse transcribed and cDNA was amplified by PCR using the LC480 instrument (Roche®). A statistical analysis (SigClust) was applied to hierarchical clustering of RT-qPCR data to identify prototypes for each subtype. Robustness of the PAM50 subtype assignment was assessed using a 10-fold cross validation. Subtype centroids were used to develop a single-sample subtype predictor by Spe...