FFPE Analysis Simplified

Molecular analysis of Formalin-Fixed Paraffin-Embedded (FFPE) samples is notoriously difficult, as they are highly variable and produce low yield. Most of these samples are highly degraded, making them a difficult sample type for nucleic acid extractions and amplifications.

The nCounter® Analysis system eliminates these challenges by utilizing molecular “barcodes” and single molecule imaging to detect and count hundreds of unique transcripts in a single reaction without any amplification steps that might introduce bias to the results. With a single curl of FFPE material, nCounter can generate data that is on par with that generated on matched fresh frozen material.

Our customers have analyzed 1000s of these specimens with the nCounter Analysis System.

Performance Data

Independent research by Reis PP, et al., "mRNA Transcript Quantification in Archival Samples Using Multiplexed, Color-coded Probes," evaluates the results of FFPE analysis performed on the nCounter System compared to qPCR. The figure on the left shows nCounter data which has a correlation coefficient between FFPE and fresh-frozen of 0.90, and the figure on the right shows equivalent data for qPCR with a correlation coefficient of 0.50. This illustrates the superiority of nCounter data to that of qPCR for gene expression analysis of FFPE samples.


Analyzing FFPE Samples with the nCounter® System
Q&A with Dr. Philippa Webster on FFPE



For Research Use Only. Not for use in diagnostic procedures.