Enhanced recovery of high-quality DNA from limited FFPE tissue for advancing cancer genomics

Archived formalin-fixed paraffin-embedded (FFPE) tissue samples are crucial assets in cancer research. However, despite the availability of commercial DNA purification kits, researchers face persistent challenges. The limited tissue availability, formalin-induced crosslinking, and DNA fragmentation in FFPE blocks often results in low DNA yield and compromised quality, hindering downstream applications. In this study, we optimized and standardized DNA purification methods to achieve high-yield, high-integrity DNA, making it ideal for DNA library preparation and high-throughput sequencing. Therefore, we optimized DNA extraction protocols using two Qiagen kits, the QIAamp DNA FFPE Tissue Kit and the QIAamp DNA FFPE Advanced Kit. The optimized methods significantly improved the yield and integrity of DNA isolated from limited FFPE tissue samples, with the advanced kit demonstrating superior performance and efficiency. This resulted in a two- to threefold increase in DNA concentration, as determined by spectrophotometric (NanoDrop) and fluorometric (Qubit) analyses. Gel electrophoresis and DNA integrity number (DIN) assessments confirm enhanced fragment preservation, suitable for downstream applications. Libraries prepared using DNA from the advanced protocol demonstrated higher sequencing quality and microbial diversity resolution. This study demonstrated that optimizing DNA purification methods for FFPE tissue samples can substantially improve the yield and integrity of DNA, paving the way for more accurate and comprehensive genomic analyses.