Assay Validation of Cell-free DNA Amplified DNA Junctions for High Grade Glioma Monitoring

Mayo Clinic Rochester, Rochester MN

Investigators

Abstract

PROJECT SUMMARY/ABSTRACT Grade 4 astrocytomas are primary brain tumors with a median survival of 15-31 months, depending on the isocitrate dehydrogenase (IDH) mutation status. Despite maximal safe surgical resection and aggressive chemoradiation, these tumors inevitably recur fatally. Disease monitoring relies on magnetic resonance imaging (MRI), as assessed by the Response Assessment for Neuro-Oncology criteria (RANO 2.0), which is imperfectly sensitive to disease progression. Specifically, evaluation of disease progression can be hampered by pseudoprogression, or increased contrast-enhancement post-treatment without an actual change in tumor burden. Additionally, significant disease progression must occur before meeting the >25% increase in radiographic size to diagnose progression per current response assessment criteria, preventing early action when disease burden is more minimal. Limited tissue access post-resection underscores the critical need for non-invasive, highly sensitive, and specific monitoring tools. Our project addresses this need by developing a novel liquid biopsy-based assay using plasma circulating tumor DNA (ctDNA) to detect amplified genomic chromosomal junctions unique to each patient. These junctions, resulting from chromosomal rearrangements under selective pressure, are highly specific to the patient's tumor. Leveraging our team's prior experience with this assay in other cancer types, our data to date in patients with high-grade gliomas (HGGs) demonstrate excellent sensitivity and specificity for disease detection, including at baseline and through disease recurrence. In this project, we will perform the technical and clinical validation studies necessary to deploy the amplified junctions ctDNA plasma test as a clinical assay in patients with HGGs. In the UH2 phase, we will validate the technical aspects of our amplified junctions ctDNA assay, starting with low-coverage whole genome sequencing of tumor tissue to identify informative chromosomal junctions. These will be used to generate primers that can then be deployed to detect the abundance of junctions in plasma via PCR. Each step's accuracy, precision, sensitivity, specificity, and quality control measures will be thoroughly assessed, with specific go/no-go criteria required for transition to the clinical validation phase (UH3). The UH3 phase aims to establish the clinical utility of this approach, as defined by the clinical endpoint of detecting changes in disease burden, including response to cytoreduction or disease progression. We will assess changes in junction abundance relative to cytoreductive therapy, stable disease, and progression, distinguishing true increases in disease burden from pseudoprogression. This phase will also evaluate the utility of our assay to detect progression earlier than MRI. In summary, this project not only proposes a robust method for glioma monitoring but also integrates advanced genomic tools and personalized medicine approaches to significantly enhance response assessment accuracy in patients with HGGs, toward our goal of improving outcomes by enabling more timely therapeutic interventions.