Where sensitivity meets complexity: Electrophoretic assessment of genomic DNA integrity at low concentrations and for FFPE samples using DIN-based analysis

DNA quality is a critical metric of success in downstream applications such as next-generation sequencing (NGS). However, formalin-fixed paraffin-embedded (FFPE) tissues and low-input sources like dried blood spots and buccal swabs often yield fragmented or chemically modified DNA, complicating quality control and subsequent analysis. To evaluate the impact of various sample sources on sample quality and integrity, genomic DNA (gDNA) was extracted from whole blood, dried blood spots, buccal swabs, saliva, and two FFPE tissue types using various commercial kits. Samples were analyzed on an automated electrophoresis platform and a high-sensitivity assay providing a DNA Integrity Number (DIN) to quantify DNA quality. For all samples DIN values across a broad concentration range were successfully generated showing the varying levels of degradation patterns. DIN values were reproducible across replicates and concentrations, confirming assay robustness, however FFPE samples showed significant DIN variability depending on the extraction method. DIN-based electrophoretic analysis offers a reproducible and objective measure of gDNA integrity, making it suitable for low-concentration and degraded samples in genomics workflows requiring stringent quality control, such as NGS.