School of Medicine Publications
Document Type
Article
Publication Date
5-23-2026
Abstract
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.
Recommended Citation
Singh, S., Vidaurri, S., Perez, A., Dhasmana, A., Dhasmana, S., Betancourt-Garcia, M. M., ... & Khan, S. (2026). Enhanced recovery of high-quality DNA from limited FFPE tissue for advancing cancer genomics. Scientific Reports. https://doi.org/10.1038/s41598-026-51594-9
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Publication Title
Scientific Reports
DOI
10.1038/s41598-026-51594-9
Academic Level
faculty
Mentor/PI Department
Immunology and Microbiology
Comments
This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made.