Rapid extraction of DNA from limited FFPE material derived from lung tumour of engineered mice

Biological material obtained from biopsies is highly valuable for clinical diagnostics, as well as pharmacological/clinical research. Millions of these tissues are preserved and archived in formalin-fixed paraffin-embedded (FFPE) blocks. These blocks are cut into slides and these slides are used for down-stream analysis such as immunohistochemistry, qPCR/PCR and sequencing. Several commercially available nucleic acid extraction kits require a minimum of one 10µm slide of starting material to extract enough genomic DNA (gDNA) for down-stream analysis. These blocks are extremely precious as they are obtained from human patients, Therefore, the kit used for
extraction is crucial as it determines the size of the slide needed and therefore the number of analyses that can be carried out on each FFPE block. This limitation reduces the number of possible applications as some archived tissues are too small and cannot satisfy this criterion. In addition, DNA extraction with these kits can be time-consuming.

In this Application Note, prepGEM Universal kits for DNA extraction using a thermocycler (cat #PUN0100) and PDQeX prepGEM Universal kits for DNA extraction using the PDQeX nucleic acid extractor (cat #XPU0100 and XMA) were tested by extracting gDNA from FFPE slides of 2µm and 5µm collected from lung tumour of engineered mice. prepGEM Universal is a simple, rapid DNA extraction
solution that leverages a temperature-driven and single-tube approach. The thermostable proteinase is activated at 75°C and inactivated at 95°C, and does not require toxic detergents such as SDS to work properly. In addition, the single-tube approach allows users to virtually recover 100% of the extracted material and preserve its integrity. The results showed that prepGEM Universal can extract gDNA sufficient for PCR-based applications from both 2µm and 5µm slides in 20 minutes, saving precious
material and time. These findings were confirmed by Munkhbaatar et al. 2020 (Nat. Comm.), who used
prepGEM Universal to extract gDNA from 5µm FFPE slides to evaluate Mcl-1 copy number in KrasG12D/+p53Δ/Δ deletion lesions1.