Molecular Diagnostics Optimized for Breast Cancer Tissue Samples

A prognostic 70-gene profile assay for early-stage breast cancer has been available for fresh tissue, and improvements in ribonucleic acid (RNA) processing have enabled microarray diagnostics for formalin-fixed, paraffin-embedded (FFPE) tissue.

The test is based on accurate measurement of gene expression by microarray analysis and has been developed and validated for fresh and fresh-frozen tumor tissue to guarantee high-quality RNA for the analysis. Gene expression analysis using FFPE tissue has long been challenging, because of nonstandardized fixation protocols and because of unreliable retrieval of high-quality RNA from FFPE material due to fragmentation of RNA and cross-linking as a result of formalin fixation.


Scientists at the University of Turin (Italy) and colleagues from other organizations, optimized the assay on 157 FFPE samples, and the assay was established using 125 matched FFPE and fresh tissue samples. Validation of the MammaPrint-FFPE assay (Agendia; Irvine, CA, USA), was compared with the company’s MammaPrint-fresh assay and was performed on an independent series of matched tissue for 211 samples from five hospitals.

The MammaPrint assay using FFPE analyte demonstrated an overall equivalence of 91.5% between the 211 independent matched FFPE and fresh tumor samples. Precision was 97.3%, and repeatability was 97.8%, with highly reproducible results between replicate samples of the same tumor and between two laboratories. Precision and repeatability of the FFPE assay were assessed on a set of four diagnostic samples that were processed and analyzed in duplicate for 20 consecutive days. MammaPrint showed very stable results on FFPE, with a very high relative stability for precision.

The authors concluded that the MammaPrint test can be used on core and surgical sections from FFPE tissue as an alternative to fresh tissue. The MammaPrint-FFPE assay has excellent reproducibility, precision, and repeatability, with performance closely similar to that of MammaPrint-fresh. The study was published on December 28, 2013, in the Journal of Molecular Diagnostics.

Related Links:
University of Turin
Agendia