Maximizing DNA Yield and Quality from FFPE Samples
02/06/2026
Formalin-fixed paraffin-embedded (FFPE) tissue samples allow scientists to test samples years after fixation. The preservation process, however, damages nucleic acids, requiring unique methods to help mitigate damage and extract usable DNA. Biocompare contributing author Darío Sánchez Martín, Ph.D., spoke with different experts, including NEB NGS Development Scientist Maggie Heider, on how to maximize DNA yield and quality.
Enzymatic repair for artifact and damage reduction post-extraction
Adding a step downstream of extract can reduce artifacts and DNA damage before using FFPE DNA. Partially repairing formalin-induced damage can help both short-read platforms (through mutation and oxidative damage repair) and long-read platforms (through nicks and gaps repair).
The NEBNext FFPE DNA Repair v2 Module is an enzymatic repair option that can be integrated after extraction in any workflow, benefiting all downstream applications.
Finding the right extraction platform
FFPE extraction success depends on sample preparation, QC methods used, human error, and starting with the right approach. Heider highlights protocol standardization, particularly for fixation and extraction. Protocols can be developed to accommodate a range of DNA qualities, which can help researchers pick the best way to obtain useful DNA from their FFPE samples.
