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

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 Phase I, we demonstrated proof-of-concept for extracting NAs from FFPE using our microfluidic modules in combination with well-established sample prep chemistries. In Phase II, we will fully automate the fluid processing from module to module using our sample prep automation platform, NAxtract.