Gene Expression Profiling of Archival Tumors
Author Information
Author(s): Linton K M, Hey Y, Saunders E, Jeziorska M, Denton J, Wilson C L, Swindell R, Dibben S, Miller C J, Pepper S D, Radford J A, Freemont A J
Primary Institution: Cancer Research UK Department of Medical Oncology, Christie Hospital NHS Foundation Trust
Hypothesis
Can archival FFPET profiles be used to generate valid quantitative prognostic data?
Conclusion
Reliable clinically relevant data can be obtained from archival FFPET, but protocol amendments are needed to improve the sensitivity and broad application of this approach.
Supporting Evidence
- FFPET sensitivity was low (∼50%) but specificity was high (95%).
- RT–PCR validated the regulation pattern for 19 of 24 candidate genes.
- Prognostic significance was confirmed for several genes including RECQL4, FRRS1, CFH, and MET.
Takeaway
Researchers found that they can get useful information from old tumor samples, but they need to improve their methods to get better results.
Methodology
The study used RNA extraction and Affymetrix microarray technology to analyze archival FFPET samples.
Potential Biases
Potential biases due to 'block effects' from tissue processing and storage conditions.
Limitations
The sensitivity of FFPET arrays was low (∼50%) compared to fresh-frozen tissue.
Participant Demographics
Patients with completely resected, localized extremity soft tissue sarcomas.
Statistical Information
P-Value
p<0.05
Statistical Significance
p<0.05
Digital Object Identifier (DOI)
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