Highly multiplexed detection of cancer biomarkers from clinical samples using nanopore sequencing

The unmet need in cancer diagnostics lies in the discovery and detection of novel biomarkers with both prognostic and predictive value. This is essential for enhancing early detection, optimizing treatment strategies and improving patient outcomes through personalized care. Currently, the majority of blood tests are conducted within a clinical environment and only examine a limited number of indicators. The potential for clinical diagnostics to progress beyond the customary single biomarker model lies in developing an inexpensive, rapid, and highly multiplexed platforms. To this end, we propose the creation of a novel technology that leverages nanopore sequencing and barcoded molecular probes building on work from our groups as shown in Koch et al. Nature Nanotechnology, 18, 1483 (2023). This innovative approach will facilitate the simultaneous multiplexed detection of analytes implicated in liver cancer within a single sample. The platform will allow for precise de-multiplexing of single molecule detection, enabling the simultaneous quantitative detection of hundreds of miRNAs and proteins and the generation of large single molecule data sets to build Modified Hidden Markov ML models. This adaptable method can also be expanded to detect a vast array of molecules, depending on the specific application required. To ensure the success of this project, we have assembled a team composed of Imperial physical and life scientists as well as an industrial partner, Oxford Nanopore Technologies (ONT), who we will collaborate with to deliver proof of concept and preclinical studies.