Advancing RNA liquid biopsy technology via nanopore sequencing


RNA liquid biopsies enable the systemic profiling of tissues and organs in our bodies in a minimally invasive manner. Cell-free RNAs are dynamically secreted by the cells that comprise our tissues and organs but are thought to be largely degraded in the blood. We performed nanopore sequencing on cell-free RNAs isolated from pancreatic cancer patient plasma and found that thousands of genes are detectable as full-length cell-free RNAs in vivo. Using our repeat-aware COMPLETE-seq RNA liquid biopsy technology, we found that pancreatic cancer patients exhibit high levels of repetitive cell-free RNAs in the blood, with full-length, short interspersed nuclear element (SINE)-derived cell-free RNAs being among the most abundant repetitive RNAs. Moreover, we found that utilizing repetitive cell-free RNA features improved the performance of our machine learning models for cancer classification. Our findings highlight the value of long-read nanopore sequencing of cell-free RNAs for discovering and characterizing novel biomarkers of disease.


Daniel Kim is an Assistant Professor in Biomolecular Engineering at the University of California Santa Cruz, a Visiting Assistant Professor at Stanford University, an Associate Member of the Canary Center at Stanford for Cancer Early Detection, and a Research Scholar of the American Cancer Society. His laboratory develops RNA technologies for precision health, cancer early detection, and RNA medicine. Daniel’s RNA research has been featured in Newsweek, Scientific American, and by the Director of the US National Institutes of Health. His work has been recognized by awards from the Damon Runyon Cancer Research Foundation and the US National Academy of Sciences.

Authors: Daniel Kim