Proving the Feasibility of Gene Expression Analysis of Preserved Tumor Sections

Whether they are developing diagnostic tools or exploring possible drug targets, cancer researchers depend on preserved tissue samples that are available in limited quantities. To complicate matters, widely used methods such as formalin-fixed paraffin-embedded (FFPE) preservation are very harsh on a sample's RNA. This side effect is especially problematic because RNA is crucial to successful gene expression analysis, which helps reveal the genetic mechanisms of cancer.

The poor quality RNA in FFPE samples has caused researchers to doubt the feasibility of performing comprehensive gene expression studies on preserved tissues. Recently, though, those doubts were dispelled by scientists at Genentech who determined that Agilent's microarray platform can extract accurate, repeatable data from FFPE tissue sections.

Testing FFPE samples

The FFPE procedure is often used to store biopsied tissues for long-term research, and many archived—and current—samples are available only in FFPE format. The method is very effective in its ability to preserve tissue and its morphology, but the crosslinking that occurs during the fixation process causes the degradation of sample RNA.

Given the prevalence of FFPE-treated samples, Genentech wanted to assess the possibility of performing gene expression analysis on fixed tissues. To test that hypothesis, a group of researchers performed a series of experiments on samples of breast and ovarian FFPE tumor sections. All were prepared using Agilent's complete microarray platform: 60-mer oligo microarrays, microarray processing tools and reagents, Feature Extraction Software and the Rosetta Resolver^® data analysis platform. The lab also implemented Agilent's Low RNA Input Fluorescent Linear Amplification Kit protocol.

Proving feasibility

The results were impressive. Studies on well-understood breast tumor sections produced highly correlated data. Further studies on additional genes such as the estrogen receptor confirmed the optimal performance of the microarrays.

To check data reproducibility, the team cut tiny serial sections from ovarian tumor FFPE samples, applied them to microarrays and checked the gene expression patterns. Despite the small tissue samples, there was 98% correlation for all genes. Also, the ability to generate sufficient probe for hybridization from small samples eliminated the need for additional amplification procedures, which can introduce potential bias in the data.

As shown by Genentech, gene expression analysis of FFPE samples is not only feasible but also highly successful. By enabling accurate, repeatable analysis of preserved tissue sections, the Agilent microarray platform can help researchers accelerate the development of new diagnostic tools and possible treatments for cancer.

For more information

You can learn more about Agilent's microarray solutions on the DNA Microarrays page. For information about other Agilent life sciences products and resources, please visit the Life Sciences/Chemical Analysis main page.

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