Challenges of FFPE Sample Materials – Where Does Variation in Quantity of Purified DNA Come From?

In this webinar we will discuss variability in quantity and purity of DNA purified from FFPE samples manually or with automated procedures, assessed by different quantification and quality control methods. Formalin-fixation and paraffin-embedding is a standard method for long-term preservation of tissue biopsies, and many unprocessed FFPE samples are archived in tissue banks and biorepositories. These stored samples are a valuable tool for studying diseases such as cancer, especially when they are histologically and pathologically well characterized, and follow-up clinical data is available.

The quality of nucleic acids extracted from FFPE samples depends on a number of factors, including how the samples were handled before, during and after fixation and embedding. There are several difficulties when purifying nucleic acids from FFPE samples. Formaldehyde, the effective component of formalin, generates crosslinks between nucleic acids and proteins, and use of low pH formalin causes acid-mediated hydrolytic nucleic acid fragmentation. Moreover, often only a limited amount of sample material is available for analyte purification and downstream analysis, requiring highly efficient purification procedures to recover as much usable analyte as possible.