Automated Enrichment of DNA Biomarkers from Large-Volume Samples: Detection of <i>B. burgdorferi</i> Cell-Free DNA in Urine

Liquid biopsies enable rapid and noninvasive analysis for disease biomarkers. However, in the early stages of a disease, biomarkers are often present in extremely dilute concentrations, making them difficult to isolate and quantify. We have developed an Automated Magnetically and Thermally Induced Conical Separator (Auto-MATICS), which enables purification and enrichment of trace biomarkers from large volume biological samples (up to 15 mL) using magnetic beads and thermally responsive alkane partitions (TRAPs). Here, we quantify the enrichment capabilities of the Auto-MATICS and demonstrate a diagnostic application by detecting fragmented genomic DNA from <i>Borrelia burgdorferi</i> (the bacteria that causes Lyme disease) in 15 mL synthetic urine samples. We achieved detection of approximately 0.1 copies/μL of fragmented DNA, nearly 200X better than in a perfectly clean but unenriched sample. We expect that the Auto-MATICS platform can have significant impact on a broad range of diagnostics applications in which trace biomarkers must be detected from large-volume complex biological matrices.