Formalin-fixed paraffin-embedded (FFPE) samples are extensively utilized in most cancers analysis and medical diagnostics for preserving tissue morphology and enabling long-term storage. Nonetheless, FFPE-induced DNA degradation, crosslinking, and inconsistent high quality management considerably hinder their utility in molecular analyses. On this examine, we established a strong nanoscale high quality management (QC) framework incorporating gel electrophoresis and quantitative polymerase chain response (qPCR) to guage DNA integrity in medical tissue FFPE samples. Our findings reveal a quantifiable inverse correlation between the diploma of DNA fragmentation and amplification effectivity in FFPE samples. Additional evaluation of 26 single nucleotide polymorphism loci utilizing focused next-generation sequencing demonstrated substantial enhancements in DNA integrity after enzymatic restore. A comparative whole-exome sequencing evaluation of endometrial carcinoma samples with completely different archival durations demonstrated considerably elevated harm ranges throughout a number of genomic options in long-term saved specimens, highlighting the cumulative affect of archival length. These findings emphasize the detrimental results of extended storage on FFPE DNA high quality. Our QC framework allows efficient pattern stratification, facilitating the number of high-integrity specimens for sequencing and guiding closely degraded samples towards focused short-amplicon assays. This complete technique enhances the reliability of FFPE-derived DNA in medical genomics, enhancing the accuracy and reproducibility of archival biospecimen-based analysis.
