Formalin-Fixed, Paraffin-Embedded (FFPE) samples represent an invaluable resource in biomedical research and clinical diagnostics. With vast archives of preserved tumor tissues and rare clinical cases, FFPE samples offer a window into historical pathology and molecular signatures. However, the very fixation and storage methods that make them durable also introduce significant challenges—DNA extracted from FFPE samples is often degraded, cross-linked, and heavily fragmented, making it difficult to generate high-quality libraries for next-generation sequencing (NGS).
In recent years, the demand for extracting genomic insights from FFPE materials has surged, especially in cancer genomics, biomarker discovery, and retrospective clinical studies. Yet the bottleneck remains: how to recover usable DNA from compromised FFPE input.
That’s where efficient DNA repair technologies come into play. By addressing the damage induced during fixation—such as nicks, abasic sites, and crosslinks—these repair solutions can restore DNA integrity, improve fragment quality, and dramatically increase the success rate of library preparation. With the right tools, even heavily degraded FFPE DNA can yield reliable, high-coverage NGS data—turning a once "unusable" sample into a genomic goldmine.
Unlocking the Value of FFPE Repair Reagents
To overcome these DNA damages, DNA repair prior to library preparation has become essential. Recognizing this need, Yeasen has developed the Hieff NGSTM FFPE DNA Repair Reagent (Cat#12606ES) — an optimized enzyme mixture specifically formulated to repair common types of FFPE-induced DNA damage. This reagent has been validated to significantly improve library yields from low-quality FFPE samples, without introducing sequence bias, thereby enhancing the overall success rate of NGS library preparation.
|
Type of Damage |
Repair Capability |
|
Cytosine deamination to uracil |
✔ Repaired |
|
Nicks and gaps |
✔ Repaired |
|
Oxidized bases |
✔ Repaired |
|
3′-end blockage |
✔ Repaired |
|
Fragmentation |
✘ Not repaired |
|
DNA–protein crosslinking |
✘ Not repaired |
Improved Library Yields in Low-Quality FFPE Samples
In a comparative experiment, FFPE DNA from the same sample was processed with and without the repair reagent added during the end-repair and A-tailing step of library construction. The results were clear: the FFPE repair reagent significantly improved library yield for low-quality FFPE samples. In contrast, minimal difference was observed in high-quality samples, indicating that the reagent specifically benefits compromised DNA without affecting intact inputs.
With its powerful damage-specific repair performance and compatibility with standard NGS workflows, Hieff NGSTM FFPE DNA Repair Reagent helps unlock the full potential of FFPE samples—bringing degraded clinical archives back to life for genomic discovery.
Figure 1. Performance and Stability of FFPE DNA Repair Reagent
Related Products
|
Category |
Name |
Cat No. |
|
FFPE Repair |
12606ES |
|
|
DNA Lib Prep for NGS |
12927ES |
|
|
12972ES |
||
|
12316ES |
||
|
DNA Lib Prep for TGS |
13301ES |