Combinatorial Probes for High-Throughput Electrochemical Analysis of Circulating Nucleic Acids in Clinical Samples

The analysis of circulating tumour nucleic acids (ctNAs) provides a minimally invasive way to assess the mutational spectrum of a tumour. However, effective and practical methods for analyzing this emerging class of markers are lacking. Analysis of ctNAs using a sensor-based approach has notable challenges, as it is vital to differentiate nucleic acids from normal cells from mutation-bearing sequences emerging from tumours. Moreover, many genes related to cancer have dozens of different mutations. Herein, we report an electrochemical approach that directly detects genes with mutations in patient serum by using combinatorial probes (CPs). The CPs enable detection of all of the mutant alleles derived from the same part of the gene. As a proof of concept, we analyze mutations of the EGFR gene, which has more than 40 clinically relevant alterations that include deletions, insertions, and point mutations. Our CP-based approach accurately detects mutant sequences directly in patient serum.Research reported in this publication was supported by the Province of Ontario though the Ministry of Research, Innovation and Science (Grant #RE05-009), the Canadian Institutes of Health Research (Emerging Team Grant #RMF-111625), the Canadian Cancer Society Research Institute (Grant #70241), and the Natural Sciences and Engineering Research Council of Canada (Grant #2016-06090). The opinions, results and conclusions are solely the responsibility of the authors and no endorsement by the funding agencies is intended or inferred