Ultra-rapid tumor burden measurements for molecularly-guided surgery

/ABSTRACT The discovery of the mutations that commonly drive cancer has revolutionized cancer research and spurred the development of novel treatments. However, current genetic testing methods physically take hours to perform and clinically often take days to weeks to return results. Consequently, information about cancer- driving mutations is rarely available during cancer surgeries whose time must be minimized for safety. Thus, the past two decades of genetic discoveries have had little impact on cancer resection surgeries that are a primary treatment for many types of cancer. This project aims to bring the era of molecular-genetic information into the operating room, not just at one timepoint, but in a manner that is rapid and cost- effective to repeat across many tissue samples throughout a cancer resection surgery. Specifically, we will develop a method for ultra-rapid droplet digital PCR (ddPCR) that can repeatedly and accurately quantify cancer-driving mutations in tissue samples to both provide surgeons with a molecular profile guiding overall resection strategy (for example, distinguishing low- versus high-grade tumors), and to aid surgeons in maximally resecting tumor tissue while minimizing resection of healthy tissue. ddPCR is an established technology for targeted quantification of mutation burdens with high sensitivity, but standard ddPCR takes 3 hours to perform. We previously developed an ultra-rapid ddPCR method that combines ultra-rapid DNA extraction in 4 minutes with ultra-rapid ddPCR thermal cycling in only 3 minutes while achieving the same performance as standard ddPCR to detect tumor cell percentages as low as 0.1% and < 10 tumor cells/mm3. However, our current method is not scalabe as it requires many manual steps. In this project, we will: 1) develop a microfluidic device that performs all steps of ultra-rapid ddPCR in one chip to profile 8 tissue samples in parallel in only < 15 minutes; 2) create multiplex ddPCR assays spanning most common cancer hotspot mutations; 3) implement the device and assays in the operating room for low-grade glioma brain tumors, followed by comparison of results to clinical-grade assays and high-fidelity sequencing. We have assembled an interdisciplinary engineering and clinical academic team that will work closely with our industrial partner Wainamics, a company with extensive experience designing commercial microfluidic devices and biosensors. This academic-industrial partnership will ensure that our device is designed for scalable and cost- effective manufacturing, and that it meets industry-standard testing metrics for future regulatory requirements. As such, the device we develop will be ready for advancement to commercialization immediately after completion of this project. Our development of a “commercialization-ready” microfluidic device for unprecedented speed and scale in quantifying mutation burdens in tissue samples will unlock a new dimension in how cancer resection surgeries are performed. Our technology will likely also find utility in many other areas of medicine that benefit from point-of-care diagnostics. Project Number: 1R01CA307127-01 | Fiscal Year: 2026 | NIH Institute/Center: National Cancer Institute (NCI) | Principal Investigator: Gilad Evrony (+2 co-PIs) | Institution: NEW YORK UNIVERSITY SCHOOL OF MEDICINE, NEW YORK, NY | Award Amount: $703,227 | Activity Code: R01 | Study Section: Special Emphasis Panel[ZRG1 CTH-E (57)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11268390