Point-of-need screening device for lung cancer in low-resource settings

Darwin Biosciences, Inc., Broomfield CO

Investigators

Abstract

PROJECT SUMMARY- Lung cancer is the leading cause of cancer death worldwide (estimated to be about 18% of all cancer deaths), but an early diagnosis can substantially reduce mortality. In the US, an annual low-dose computed tomography (LDCT) scan is the recommended screening method for those who are deemed as high- risk due to age and smoking history. Merely 5.8% of eligible Americans were screened for lung cancer in 2021 and there exists a significant socioeconomic disparity in screening. Among underprivileged populations in developing countries, lung cancer screening is practically non-existent due to resource constraints. The low rate of lung cancer screening via LDCT is often attributed to the high frequency of false-positives and the lack of LDCT infrastructure and trained operators in low-resource settings. Further, non-smokers are typically not included in screening programs, although lung cancer rates have increased significantly in this group, particularly in developing countries. There is a significant unmet need for a lung cancer screening tool that can be deployed at the point-of-need to improve screening in vulnerable populations. To meet this need, Darwin Biosciences is developing a low-cost, easy to use, handheld, and non-invasive lung cancer screening device that can be used in low-resource settings in the US and worldwide, such as in community health centers, rural clinics, and in healthcare facilities of developing countries. In ongoing work, under a $12 million contract with the DOD, Darwin Biosciences has developed the first prototype of a handheld device that incorporates sample collection and processing, isothermal recombinase polymerase amplification (RPA) of nucleic acid biomarkers, and a visual readout of amplicons on lateral flow strips. This work was done for detecting pathogen-agnostic infection biomarkers. In this Phase I project, this platform will be adapted for the detection of circulating tumor DNA biomarkers which are validated in non-small cell lung cancer. The goal of this Phase I project is to develop and optimize robust and sensitive assays for the detection of 3 biomarkers which are variants of EGFR (EGFR exon 19 deletion, EGFR Leu858Arg, EGFR Thr790Met) using saliva and capillary blood as biospecimens to enable non-invasive testing. Aim 1: Primer selection for the 3 assays for EGFR-variant biomarkers: Primers for RPA will be designed in silico and locked nucleic acids will be incorporated in the primers to enhance the discrimination of single nucleotide variants. The designed primers will be bench tested to select one primer set for each assay that shows minimal noise in the no-template control and strong signal in the template reaction. Aim 2: Analytical characterization of the assays: The analytical performance of the 3 assays will be determined in buffer and in biospecimens - saliva and capillary blood - by using samples with known amounts of spiked templates. The target LOD will be a clinically relevant range of 10-100 copies/reaction and target specificity will be <10% false positive with wild-type EGFR. Successful completion of this Phase I project is proof- of-concept demonstration of detection of 3 lung cancer biomarkers in a portable, low-cost device.