Gene Expression Profiling of FFPE Samples: A Titration Test.

Area of Science:

• Molecular Biology
• Genomics
• Biotechnology

Background:

• Formalin-fixed paraffin-embedded (FFPE) tissues are crucial for studying disease progression but often yield degraded RNA.
• Poor RNA quality from FFPE processing hinders accurate gene expression analysis.
• Advancements in genomic technologies offer solutions for analyzing compromised RNA samples.

Purpose of the Study:

• To evaluate RNA extraction methods for FFPE samples.
• To assess the impact of RNA degradation and input quantity on gene expression profiling using the NanoString IO360 panel.
• To determine the reliability of the NanoString nCounter platform for FFPE samples.

Main Methods:

• Tested two RNA extraction methods for FFPE tissues.
• Performed titration experiments with varying RNA input amounts.
• Analyzed FFPE samples with different DV200 values on the NanoString nCounter platform.

Main Results:

• The NanoString nCounter platform demonstrated robustness in gene expression analysis.
• Accurate gene expression profiling was achieved for FFPE samples with DV200 values greater than 30%.
• The platform's performance was consistent across different RNA input levels.

Conclusions:

• The NanoString nCounter platform is a reliable tool for gene expression analysis of FFPE samples.
• The platform's robustness and ease of use are advantageous for clinical settings.
• High-quality gene expression data can be obtained from degraded FFPE RNA with DV200 > 30%.