Abstract 4085: Assessing RNA integrity in FFPE samples with the DV200 quality metric for automated electrophoresis systems

Abstract Introduction: Formalin-fixation and paraffin-embedding (FFPE) is a pivotal technique in pathology, enabling the long-term preservation of tissue specimens. This method not only maintains the cellular structure but also allows repeated analyses of the same sample without the need for additional collection. Despite its benefits, FFPE poses significant challenges for nucleic acid extraction and analysis, particularly for RNA, which is essential for gene expression studies. The fixation process can lead to RNA degradation and fragmentation, creating obstacles for researchers who require high-quality RNA for sequencing purposes. Implementing a quality control system to evaluate RNA integrity post-FFPE extraction is crucial for determining the viability of a sample for downstream analyses like next-generation sequencing. Methods: FFPE RNA samples extracted from different sources were analyzed on the Agilent 2100 Bioanalyzer system with the Agilent RNA 6000 Nano kit and the Agilent RNA 6000 Pico kit, and on the 4200 TapeStation system with the Agilent RNA ScreenTape and High Sensitivity RNA ScreenTape with corresponding reagents. Data analysis on the Agilent 2100 Bioanalyzer Expert software was completed using the DV200 assay configuration file. Analysis using the TapeStation was performed with the region mode, setting a region of 200 to 10, 000 nucleotides to obtain the DV200 metric. Results: The obtained electropherograms from both systems exhibited similar overall patterns, with slight differences. Despite these differences in electropherogram appearance, the comparison of DV200 values demonstrated highly comparable results. The Bioanalyzer and TapeStation systems showed consistent DV200 scores across different FFPE RNA samples, demonstrating their interchangeability and reliability. Conclusions: The results demonstrate that each system is capable of similarly assessing the quality of FFPE RNA samples. Additionally, the data points out that a consistent measurement can be obtained regardless of the assay or kit being used within each system. This comparison allows users for confident use of the DV200 quality metric in their workflows. For Research Use Only. Not for use in diagnostic procedures. Citation Format: Isabell Priester, Annika Dorn, Tim Butler. Assessing RNA integrity in FFPE samples with the DV200 quality metric for automated electrophoresis systems [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4085.