Abstract Background: Liquid biopsies from the gynecological tract can be useful for analysis of cell free DNA (cfDNA) (1, 2, 3). Sampling procedure and optimal preanalytical handling are poorly investigated. In this study, we aimed to evaluate how the profile and integrity of DNA, sampled from the female genital tract, were affected by preanalytical handling. Methods: Biobanked/archival (stored at -80℃ after 48h at room temperature (RT)) and freshly obtained clinical samples were analyzed together with standardized in vitro samples. Archival and in vitro samples were preserved in methanol-based solution, imitating clinical handling of endocervical samples which are initially stored at RT for 48h before further handling. The fragmentation profile of archival and in vitro samples was analyzed. Time series of in vitro samples at RT and 4℃, with extraction at 6-hour intervals from 0 to 96h, were performed. The fresh clinical samples were collected from the endocervix in methanol-based solution and from the vagina in a solution designed to preserve DNA and placed at 4℃ resp RT. Extraction was performed within 4h and at 48h. Results: Accumulation of short DNA fragments were observed in the archival samples and in the in vitro samples, indicating that fragmentation was initiated prior to 48h. Time series showed that the quantity of short DNA fragments gradually increased with time at both RT and 4℃ but at a slower rate in 4℃. At RT the percentage of fragments between 100-350bp increased 12-fold (0.39% vs 4.75%, p=0.002). The freshly obtained endocervical samples showed a similar significant increase in short fragments in samples stored at RT compared with samples stored at 4℃ (p= 0.02 for 100-230bp; p= 0.007 for 230-350bp; p= 0.03 for 100-2500bp) at 4h-48h. Conclusion: Pre-analytical handling of endocervical samples can be optimized. Lowering temperature from RT to 4℃ immediately haltered DNA fragmentation. Citation Format: Jacob Malchau Lauesgaard, Therese Carlsson, Anna Linder, Sara Schumacher, Karin Sundfeldt. DNA integrity and preanalytical handling of endocervical samples for use in liquid biopsy-based diagnostics and monitoring of gynecological cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6081.
Read full abstract