Background: The ability to identify genetic alterations in cancers is essential for precision medicine however, surgical approaches to obtain brain tumor tissue are invasive. Profiling circulating-tumor DNA (ctDNA) in liquid biopsies has emerged as a promising approach to avoid invasive procedures. Here, we systematically evaluated the feasibility of profiling pediatric brain tumors using ctDNA obtained from plasma, cerebrospinal fluid (CSF) and urine.

Methods: We prospectively collected 564 specimens (257 blood, 240 urine, 67 CSF samples) from 258 patients across all histopathologies. We performed ultra-low pass whole-genome sequencing (ULP-WGS) to assess copy number variations and estimate tumor fraction, and developed a pediatric CNS tumor hybrid-capture panel for deep sequencing of specific mutations and fusions.

Results: ULP-WGS detected copy-number alterations in 9/46 (20%) CSF, 3/230 (1.3%) plasma, 0/153 urine samples. Sequencing detected alterations in 3/10 (30%) CSF, 2/74 (2.7%) plasma, 0/2 urine samples. The only positive results were in high-grade tumors. However, most samples had insufficient somatic mutations (median 1, range 0-39) discoverable by the sequencing panel to provide sufficient power to detect tumor fractions of greater than 0.1%.

Conclusions: Children with brain tumors harbor very low levels of ctDNA in blood, CSF and urine, with CSF having the most DNA detectable. Molecular profiling is feasible in a small subset of high-grade tumors. The level of clonal aberrations per genome is low in most of tumors, posing a challenge for detection using whole genome or even targeted sequencing methods. Substantial challenges therefore remain to genetically characterize pediatric brain tumors from liquid biopsies.

Keywords: Circulating tumor DNA; Hybrid capture sequencing; ULP-WGS; liquid biopsy; pediatric brain tumors.