PO.MCB08.03 · 分子与细胞生物学
当灵敏度遇上复杂性：使用基于DIN的分析对低浓度基因组DNA及FFPE样本的完整性进行电泳评估
Where sensitivity meets complexity: Electrophoretic assessment of genomic DNA integrity at low concentrations and for FFPE samples using DIN-based analysis
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
DNA质量是二代测序（NGS）等下游应用成功与否的关键指标。然而，福尔马林固定石蜡包埋（FFPE）组织以及干血斑和口腔拭子等低输入量来源常产生片段化或化学修饰的DNA，使质量控制和后续分析复杂化。为评估各种样本来源对样本质量和完整性的影响，我们使用各种商用试剂盒从全血、干血斑、口腔拭子、唾液以及两种FFPE组织类型中提取了基因组DNA（gDNA）。样本在自动化电泳平台上采用高灵敏度检测进行分析，提供DNA完整性数值（DIN）以量化DNA质量。对于所有样本，均成功生成了广泛浓度范围内的DIN值，显示出不同程度的降解模式。DIN值在重复样本和不同浓度之间可重现，证实了检测的稳健性；然而FFPE样本的DIN变异性显著，取决于提取方法。基于DIN的电泳分析提供了一种可重现且客观的gDNA完整性度量，使其适用于基因组学工作流程中需要严格质量控制的低浓度和降解样本，例如NGS。
查看英文原文 English abstract
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.
利益披露 Disclosure
S. Borg, None..
I. Priester, None.