Nanopore barcoding for detecting metastases in liquid biopsies

Diagnosis of primary and metastatic cancer by liquid biopsy has the potential of replacing invasive needle tissue biopsy but remains limited by sensitivity and specificity, and therefore represents an unmet technological and clinical need. Clinical requirements include i) diagnosis: monitor for increasing circulating cell-free (ccf)DNA associated with onset of metastasis and detect earlier before any other tool currently available, ii) prognostic: a shift in molecular targets to inform of changes to molecular subtype, iii) monitor drug resistance: detect appearance tumour cell clones during therapy. Indeed, current ccfDNA detection technologies rely on DNA amplification and, in turn, the detection of low-copy numbers is challenged by DNA-copying errors that occur during amplification, and the skew away from low copy variants. Solid-state nanopores (SSNP) represent a promising, emerging tool for high-throughput and sensitive detection of biomolecules, owing to their intrinsic single-molecule detection capability, high durability and low cost. In this project, we will focus on the integration of SSNP and DNA self-assembly to generate an amplification-free barcoding approach that associates each copy of target mutation in solution with a unique DNA nanostructure that can be detected by nanopore transit with single-copy resolution. This novel integration of solid state and molecular nanotechnologies will be applied to detect initiation of tumour growth (primary and relapse), detect cancer subtype, and possibly determine mutation profile in liquid biopsy by targeting ccfDNA. The PhD candidate will apply current methods in DNA nanotechnology for the design, self-assembly, purification and characterisation of DNA origami nanostructures; molecular biology methods for DNA sample preparation; single-molecule analytical tools for nanostructure characterisation, including solid state nanopore and atomic force microscopy. The sensitivity and specificity of the technology will be assessed by independent sample analysis by means of next-generation sequencing. With this program, the Ph.D. candidate will be part of an international group of scientists and engineer and you will be exposed to cutting-edge interdisciplinary research at the frontier between biomedical and physical sciences.