Abstract
Conventional response monitoring relies on imperfect tools like MRI and cerebrospinal fluid (CSF) cytology to detect measurable residual disease (MRD) in children with brain tumors. “Liquid biopsy” techniques provide a minimally-invasive method for MRD detection by identifying fragments of cell-free DNA (cfDNA) shed from tumor cells following cell death. Early detection of MRD has been proposed as a clinically actionable biomarker that may allow clinicians to reliably detect tumor versus treatment effect, intensify therapy prior to relapse, and minimize toxicity. Our center is currently evaluating low-pass whole genome sequencing (LP-WGS) in children with brain tumors receiving standard of care therapy for real-time MRD assessment. Following informed consent, patients are enrolled on the Seattle Children’s Hospital Tissue Banking and Biology Protocol, and CSF samples are collected prospectively by lumbar puncture during routine clinical care. LP-WGS is performed in a CAP/CLIA certified environment with return of results to the referring clinician. In addition to feasibility as a prognostic and predictive biomarker, correlative studies will investigate if neuroinflammatory and immunologic profiles change with the presence of MRD using CNS cytokine signatures, including CXCL-12, CCL-2, MMPs, CD163, and GFAP. Preliminary cfDNA studies of children with embryonal tumors suggest LP-WGS is both a sensitive and clinically valuable test to detect tumor-associated copy number variants (CNVs). Thirty of thirty-one (97%) of CSF samples from 17 patients demonstrated adequate cfDNA for LP-WGS testing. Key CNVs detected included monosomy 6, isodicentric chromosome 17, and amplifications of MYCN and TTYH1. Among 8 samples obtained at initial tumor staging, LP-WGS detected tumor in 7/8 (1 negative ATRT without CNVs), whereas only 2/8 were positive by cytology. Two samples acquired additional chromosomal alterations at progression beyond those observed in the original tumor. Future prospective clinical trials are warranted to determine how MRD will transform clinical care and patient outcomes.