Archiving of clinical materials as Formalin-Fixed, Paraffin-Embedded (FFPE) samples is a common practice. However, the methods used for fixation and storage significantly damage and compromise the quality of nucleic acids from these samples. As a result, it can be challenging to obtain useful information, including high-quality sequence data, especially when sample amounts are limited. The
NEBNext FFPE DNA Repair Mix is a cocktail of enzymes formulated to repair DNA, and specifically optimized and validated for repair of FFPE DNA samples.
The DNA repair step is easily integrated into sequencing workflows for any platform, upstream of library preparation, and treatment results in both increased library yields and increased library quality.
Table 1: Types of FFPE DNA damage and their ability to be repaired by the NEBNext FFPE DNA Repair Mix
FFPE DAMAGE TYPE
REPAIRED BY THE FFPE DNA ENZYME REPAIR MIX?
Deamination of cytosine to uracil
Nicks and gaps
Blocked 3´ ends
Figure 1: Effect of DNA Repair on Sequence Quality from FFPE Samples
Genomic DNA was extracted using standard DNA purification. Each DNA sample was treated with the NEBNext FFPE DNA Repair Mix, or was untreated, before library construction and Illumina® sequencing.
Panel A: The effect of DNA repair on the percentage of mappable reads. Reads were mapped to the human genome (hg19) using BWA (1).
Panel B: The effect of DNA repair on the percentage of reads that were properly paired from a paired-end sequencing protocol.