ID #729 LBSeq4Kids clinical liquid biopsy platform demonstrates a high detection rate in CSF at diagnosis and facilitates sequential CSF monitoring for high-risk pediatric brain tumors

Abstract

The LBSeqKids clinically validated liquid biopsy platform combines low passage whole genome sequencing (LP-WGS) to detect copy number alterations (CNAs) and a 136 gene targeted sequencing panel (TSP) to detect mutations in cerebrospinal fluid (CSF), aqueous humor of the eye and plasma in patients with solid tumors. We analyzed 80 CSF specimens from 42 patients who had CSF samples banked at the time of diagnosis and/or recurrence, with additional samples obtained at clinical disease assessment (on therapy, post-treatment, surveillance or relapse). The cohort included patients with embryonal tumors (n = 23: medulloblastoma=14; ATRT= 6; ETMR= 2; pineoblastoma=1) as well as high-grade gliomas (n = 7), ependymoma (n = 6), choroid plexus carcinoma (CPC, n = 3) and others (n = 3). LP-WGS was successful for 73 of 80 (91%) samples with as little as 0.2 ng input cfDNA isolated from 1-2 ml of CSF. TSP was performed on 49 of those 73 samples. Tumor-matched CNAs or sequence alterations were detected in 22/42 (52%) of patients, including medulloblastoma (7/14, 50%), ATRT (6/6, 100%), CPC (2/3, 67%), ETMR (2/2, 100%), DMG, H3-K27M-altered (2/3, 67%), astroblastoma, pineoblastoma and infant-hemispheric HGG (1/1 each), expanding the clinical utility of this assay to rare tumors. Notably, however, we observed low cfDNA yield and no detectable CNAs or mutations in six ependymomas. Sequential disease evaluation (≥3 CSF samples) was performed in nine patients with MB (n = 3), CPC (n = 3), ETMR (n = 2) and ATRT (n = 1). In a case of ETMR with early disease progression, sequential cfDNA monitoring correlated with clinical and radiographic progression and revealed novel genetic alterations compared to the diagnostic tumor sample. Our findings support the utilization of sequential cfDNA monitoring for a variety of high-grade brain tumors, not limited to medulloblastoma or HGG. Including CSF-cfDNA assays in prospective clinical trials will be imperative to accurately assess their prognostic utility for different tumor types.