A novel ctDNA analysis solution for the next-generation of liquid biopsy assays

/ABSTRACT Detection and analysis of the mutations and methylation changes that occur in cancer cells is a foundational element of cancer research and care. Rapidly emerging technologies such as ‘Liquid Biopsy’ (LBx) based on circulating tumor DNA (ctDNA) are hindered by the limitations of current DNA analysis methods, primarily next- generation sequencing (NGS). These limitations include low accuracy and the requirement for indirect, even more inaccurate methods to readout methylation. To address this challenge, XGenomes is developing an entirely novel DNA analysis platform that directly reads both mutations and methylation changes, achieving accuracy for each over 100x greater than current DNA sequencing platforms. This technology is based around measuring the kinetic binding of a repertoire of short, fluorescently labelled oligonucleotide probes, using super-resolution microscopy. The changes in binding kinetics allow for direct measurement of methylation, without the need for prior bisulfite conversion or similar treatment. As each nucleotide of the target DNA is measured by multiple overlapping probes, this technique provides unprecedented accuracy. This technology will facilitate a transformative advancement in both cancer research and clinical care. XGenomes has demonstrated all key elements of the platform in principle. In this project, the platform will be further developed to the point where proof-of-concept (POC) assays in cancer therapy selection and methylation analysis can be conducted. Specific Aim 1 involves integrating hybridization capture into XGenomes' workflow. Specific Aim 2 will focus on designing and optimizing a targeted methylation assay for the BRCA1 gene promoter—a critical factor in breast and ovarian cancer. The tests developed in this project will act as proof of concept for broader applications, laying the foundation for development of more complex assays. This validation of XGenomes’ platform achieved in this project will help secure further investment, both federal and venture, thereby accelerating the platform's application across cancer research and care, and ultimately transforming the field. Project Number: 1R43CA295403-01A1 | Fiscal Year: 2025 | NIH Institute/Center: National Cancer Institute (NCI) | Principal Investigator: Kalim Mir | Institution: XGENOMES CORP., CAMBRIDGE, MA | Award Amount: $399,816 | Activity Code: R43 | Study Section: Special Emphasis Panel[ZCA1 RPRB-L (M3)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11254540