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DNA Quantity and Quality Comparisons between Cryopreserved and FFPE Tumors from Matched Pan-Cancer Samples
Jeffrey Okojie1,2, Nikole O'Neal2, Mackenzie Burr1
1Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA.
Current Oncology (Toronto, Ont.)
|May 24, 2024
Summary
Cryopreserved tissue provides superior DNA yield and quality compared to formalin-fixed, paraffin-embedded (FFPE) tissue for molecular cancer diagnostics. This finding supports cryopreserved samples as a better option for advanced DNA characterization in personalized cancer care.
Area of Science:
- Oncology
- Molecular Biology
- Biotechnology
Background:
- Personalized cancer care relies on molecular characterization of tumors.
- Formalin-fixed, paraffin-embedded (FFPE) tissue is the standard clinical source, while frozen tissue is preferred for research.
- Emerging DNA technologies require high-molecular-weight DNA, necessitating a comparison between FFPE and cryopreserved samples.
Purpose of the Study:
- To compare DNA yield and quality between FFPE and cryopreserved human tumor samples.
- To evaluate the suitability of different tissue preservation methods for advanced molecular assays.
- To determine if cryopreserved samples offer superior DNA metrics for cancer research and diagnostics.
Main Methods:
- A head-to-head comparison of DNA metrics from 38 human tumors.
- Analysis included both FFPE and cryopreserved tissue samples.
- DNA quantity and purity assessed by UV spectrophotometry; DNA quality assessed by fragment microelectrophoresis.
Main Results:
- Cryopreserved tissue yielded 4.2-fold more DNA per mg than FFPE tissue (p < 0.001).
- DNA from cryopreserved samples showed a 223% increase in DNA quality number.
- Cryopreserved tissue yielded 9-fold more DNA fragments over 40,000 bp compared to FFPE (p < 0.0001).
Conclusions:
- DNA extracted from cryopreserved tumor tissues is demonstrably superior to that from FFPE tissues.
- Cryopreservation offers significantly higher DNA yield and quality, crucial for advanced molecular analyses.
- These findings advocate for the use of cryopreserved samples in clinical settings for enhanced personalized cancer care.
