Simple and Accessible Microfluidic Platform for Single Molecule Sequence Profiling of Tumor-derived DNA within Liquid Biopsies

Project Summary/ Abstract Over 600,000 people in the US will die from cancer this year. It is estimated that 25% of these deaths could have been prevented by detection in earlier stages. Implementation of minimally-invasive routine screening, such as pap smears for cervical cancer, has proven to be an effective approach for reducing cancer mortality. However, several challenges prevent successful implementation of screening in most cancers, especially ones which are not readily accessible for imaging or tissue biopsy. One promising avenue for cancer diagnostics is through use of circulating DNA from so-called “liquid biopsies” or other accessible sample media circulating throughout the body collecting genetic material from tissues, including tumors. Tumor-specific molecular biomarkers, such as DNA mutations and methylation, can be found in minimally-invasive sample media, such as blood, stool, and urine, but are typically only present in very low copy numbers (lt10 copies/mL) and low fractions (lt0.1%) among a high background of healthy DNA. Technical limitations as well as practical inaccessibility of currently available tools have precluded research efforts to discover early-stage cancer- specific DNA biomarker panels and subsequent clinical implementation that could improve patient outcomes. To address this, we previously developed a prototype digital microfluidic platform to facilitate highly sensitive, low-cost detection of cancer-specific DNA methylation patterns by highly parallelized single-molecule thermodynamic sequencing. In this Phase 1 SBIR proposal, we will greatly expand upon the capabilities of this platform to increase accessibility and improve analytical performance towards detection of early-stage disease by significantly increasing its digitization power. We will develop a high-degree multiplexing paradigm for detection and methylation profiling of biomarker panels using a multicolor barcoding technique. We will then incorporate this assay into a microfluidic platform that can interrogate hundreds to thousands of single DNA copies by digitizing template molecules into droplets for high-throughput single molecules analysis. The platform will increase accessibility for biomarker research from liquid biopsies by reducing costs to lt$25 per sample and turnaround time to 4 hours. The platform will enable single-copy detection even among high background populations (lt0.001% sensitivity), which may be necessary for early-stage disease. The proposed work in this Phase 1 project will develop the assay fundamentals for a multiplex, multidimensional analysis of a clinically relevant biomarker panel (Aim 1), incorporate this assay into a highly-parallelized droplet microfluidic platform (Aim 2), and assess its clinical feasibility with plasma samples from a cohort of lung cancer patients and controls (Aim 3). This will lay the groundwork for a subsequent Phase 2 project to design the cartridge and instrumentation for scalable manufacturing and user-friendliness and implement automated, machine- learning image and data analysis pipelines.