Improving extraction success of FFPE samples with automated and reliable microfluidic sample preparation

摘要 基因组测序数据适用于临床决策和提高精确度 医药。虽然新鲜冷冻组织是下一代测序的黄金标准，但只有 固定石蜡包埋(FFPE)组织块在临床工作流程中广泛使用。这个 固定过程支持随时可用、经济高效的资源库，并保存 形态和细胞数据。然而，固定后的提取通常会产生少量的 降解核酸(Nas)。在此期间，核酸的数量和质量都可以得到改善 然而，当前的工作流仍然高度依赖手动方法，这些方法 劳动强度大、耗时长、质量因操作员技能而异。 从FFPE样本中提取核酸需要强大的协议，并能够保持 性能始终如一。从人工方法到可靠的自动化方法的转换将是至关重要的 为推进这一领域而干杯。在这个SBIR项目中，我们自动从FFPE中提取核酸 使用创新的微流控溶液采集样品。我们的方法将执行脱蜡，裂解， 以及FFPE组织卷曲的解交联而不需要吸管驱动的混合， 微离心或过滤；然后用微流控磁珠进行纯化 技术在随后的第二阶段项目中，我们将在我们的平台上完全自动化此工作流 用于自动的、基于墨盒的样品准备。

Abstract Genomic sequencing data is suitable for informing clinical decisions and advancing precision medicine. While fresh-frozen tissues are the gold standard for next-generation sequencing, only fixed paraffin-embedded (FFPE) tissue blocks are widely available in clinical workflows. The fixation process enables a readily available, cost-effective resource repository with preserved morphology and cellular data. However, extraction after fixation frequently yields low quantities of degraded nucleic acids (NAs). The quantity and quality of nucleic acids can be improved during extraction, however current workflows remain highly dependent on manual methods that are labor-intensive, time-consuming, and vary in quality by operator skill. Extracting nucleic acids from FFPE samples requires robust protocols with the ability to maintain consistent performance. The translation from manual to reliable automated methods will be crucial to advancing the field. In this SBIR project, we automate extraction of nucleic acids from FFPE samples using an innovate microfluidic solution. Our method will perform deparaffinization, lysis, and decrosslinking of FFPE tissue curls without the need for pipet-driven mixing, microcentrifugation, or filtration; NAs will then be purified with a microfluidic magnetic bead technology. In a subsequent Phase II project we will fully automate this workflow on our platform for automated, cartridge-based sample prep.