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 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.