Formalin-fixed paraffin-embedded (FFPE) samples are widely used in cancer research and clinical diagnostics for preserving tissue morphology and enabling long-term storage. However, FFPE-induced DNA degradation, crosslinking, and inconsistent quality control significantly hinder their utility in molecular analyses. In this study, we established a robust nanoscale quality control (QC) framework incorporating gel electrophoresis and quantitative polymerase chain reaction (qPCR) to evaluate DNA integrity in clinical tissue FFPE samples. Our findings demonstrate a quantifiable inverse correlation between the degree of DNA fragmentation and amplification efficiency in FFPE samples. Further analysis of 26 single nucleotide polymorphism loci using targeted next-generation sequencing demonstrated substantial improvements in DNA integrity after enzymatic repair. A comparative whole-exome sequencing analysis of endometrial carcinoma samples with different archival durations demonstrated significantly increased damage levels across multiple genomic features in long-term stored specimens, highlighting the cumulative impact of archival duration. These findings emphasize the detrimental effects of prolonged storage on FFPE DNA quality. Our QC framework enables effective sample stratification, facilitating the selection of high-integrity specimens for sequencing and guiding heavily degraded samples toward targeted short-amplicon assays. This comprehensive strategy enhances the reliability of FFPE-derived DNA in clinical genomics, improving the accuracy and reproducibility of archival biospecimen-based research.
