Gene Expression Analysis in Breast Cancer Using FFPE Samples
Author Information
Author(s): Kibriya Muhammad G, Jasmine Farzana, Roy Shantanu, Paul-Brutus Rachelle M, Argos Maria, Ahsan Habibul
Primary Institution: The University of Chicago
Hypothesis
Can whole genome DASL assay be effectively used on formalin-fixed paraffin-embedded (FFPE) tissue to draw similar conclusions as fresh frozen (FF) tissues?
Conclusion
The study found that while gene expression experiments using the DASL assay can handle fragmentation issues in FFPE tissues, formalin fixation alters gene expression significantly, necessitating caution in interpretation.
Supporting Evidence
- Gene detection was very good with comparable success between the FFPE and FF samples.
- Reproducibility was high with an r2 value of 0.98.
- Only one-third of differentially expressed genes in tumor tissues from FF samples could be detected in FFPE samples.
Takeaway
Researchers wanted to see if they could study cancer genes in old tissue samples. They found that while they could get some good information, the way the samples were preserved changed some of the results.
Methodology
The study used a whole genome DASL assay on paired breast tumor and surrounding healthy tissues from both FF and FFPE samples.
Potential Biases
The study acknowledges that formalin fixation can introduce significant changes in gene expression, which may differ between tumor and normal tissues.
Limitations
The study did not include gene expression data from breast tissue preserved in RNA stabilization buffer, which would have served as a gold standard.
Participant Demographics
The study involved 21 patients from whom paired tumor and normal breast tissue samples were collected.
Statistical Information
P-Value
2.17 × 10-28
Statistical Significance
p<0.05
Digital Object Identifier (DOI)
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