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FFPE Simplified
nCounter and FFPE Analysis

FFPE Simplified

Eliminate the Challenges of Analyzing FFPE Samples

A major reason the nCounter® Analysis System has been well accepted in the oncology community is because of its compatibility with Formalin-Fixed Paraffin-Embedded (FFPE) specimens. These precious specimens offer enormous potential to further scientific enquiry and accelerate the testing of important hypotheses. However, owing to the fact that FFPE preservation was developed to maintain morphology and without any consideration of nucleic acids, genomic analysis of these specimens has proved challenging. nCounter eliminates this challenge. 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 nCounter and many consider it the gold standard method of analysis.

Q&A with Dr. Philippa Webster on FFPE

NanoString Technologies: Q&A with Dr. Philippa Webster on FFPE

FFPE Biobanks are Priceless Archives of Characterized Samples

  • Longitudinal collections
  • Known outcomes
  • Hypothesis testing: months, not years

FFPE Samples are Notoriously Difficult for Molecular Analysis

  • Highly variable
  • Low yield
  • Degradation
  • Sample extraction challenges

nCounter is the Ideal Solution for FFPE Analysis

Get superior reproducibility and generate better data from your samples. nCounter utilizes 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.

Video: Analyzing FFPE Samples with the nCounter System

In this video, Dr. Geiss describes how the technology digitally measures RNA or DNA target molecules directly, with no target amplification or qPCR. Thus, there is less impact of chemically modified bases on the Formalin-Fixed Paraffin-Embedded material. The nCounter technology also detects up to 800 genes in a single reaction/tube, maximizing the amount of data generated from precious samples.

Analyzing FFPE Samples with the nCounter System

Tech Note: FFPE Samples for Gene Expression Analysis with nCounter

FFPE and nCounter

For the past several decades, pathologists have kept samples obtained from tissue resections and biopsies. Typically, these are archived as Formalin-Fixed Paraffin-Embedded blocks, and in some cases are sectioned and preserved on slides. These archived clinical samples are stable for years, and are valuable resources for subsequent investigations. Diagnosis, treatment, disease progression, and other clinical information are associated with many of these samples, making them extremely valuable for clinical research. Moreover, pathologists currently use FFPE blocks and slices as the preferred method to preserve samples from new patients. The ability of new molecular diagnostic tests to use FFPE samples as input material would greatly increase the usability of these tests. However, the fixation and embedding process modifies and degrades RNA, presenting challenges for gene expression studies using these samples. Other currently available gene expression profiling methods such as PCR-based techniques and microarrays have shown a significant decrease in the quality of results when using FFPE samples as input material. Download the Complete Tech Note (PDF)

Data: Unparalleled Performance on Samples

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 Formalin-Fixed Paraffin-Embedded samples.

FFPE Samples: nCounter vs. qPCR