The DNA Integrity Number (DIN) Provided by the Agilent 2200 TapeStation System is an Ideal Tool to Optimize FFPE Extraction

One of the most widely used methods for clinical sample preservation and archiving is the preparation of formalin-fi xed paraffi n-embedded (FFPE) tissue. Thin sections of FFPE blocks are commonly subjected to histopathology with the remaining sample being archived. These FFPE tissue archives represent a valuable source for retrospective studies of gene expression and mutation analysis. However, DNA extraction from FFPE samples has proved to be challenging1. The most common issues are cross-linking and fragmentation of DNA during tissue processing and storage. Formalin, used for tissue fi xation, causes cross-linking of nucleic acids and proteins, increasing the susceptibility of DNA to mechanical stress and decreasing the accessibility for enzymes. In addition, formalin may be oxidized to formic acid, which causes DNA depurination and DNA strand breaks. Therefore, the fi xation conditions can signifi cantly impact the quality of the extracted DNA2. In addition, the DNA extraction method is crucial for DNA integrity and the performance of downstream applications such as PCR3. Standard DNA isolation procedures often result in low amounts of suitable DNA. Therefore, specially tailored procedures were developed to extract DNA from FFPE tissue blocks. These procedures include steps to release the DNA from the FFPE tissue, but also to reverse the formalin cross-linking and, therefore, improve yield as well as DNA performance in downstream assays.