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

摘要 基因组测序数据适合为临床决策提供信息并提高精度 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可用。的 固定过程使一个现成的，具有成本效益的资源库， 形态学和细胞数据。然而，固定后的提取经常产生少量的 降解的核酸（NAs）。核酸的数量和质量可以在培养过程中得到改善。 提取，然而，当前的工作流程仍然高度依赖于手动方法， 劳动密集、耗时且质量因操作者技能而异。 从FFPE样品中提取核酸需要稳健的方案，其能够维持 始终如一的表现。从人工方法到可靠的自动化方法的转换将至关重要 来推进这个领域。在这个SBIR项目中，我们从FFPE中自动提取核酸 使用创新的微流体解决方案。我们的方法将进行脱蜡，裂解， 以及FFPE组织卷曲的解交联而不需要移液管驱动的混合， 微离心或过滤;然后用微流体磁珠纯化NA 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程 用于自动化的、基于电泳的样品制备。

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.