Ultra-low-input cell-free DNA sequencing for tumor detection and characterization in a real-world pediatric brain tumor cohort.

in Acta neuropathologica communications by Tom T Fischer, Kendra K Maaß, Pitithat Puranachot, Markus Mieskolainen, Martin Sill, Paulina S Schad, Stefanie Volz, Fabian Rosing, Tatjana Wedig, Nathalie Schwarz, Agnes M E Finster, Florian Iser, Jochen Meyer, Felix Sahm, Olli Lohi, Ahmed El Damaty, Benedikt Brors, Hannu Haapasalo, Stefan M Pfister, Joonas Haapasalo, Kristian W Pajtler, Kristiina Nordfors

TLDR

  • A study developed a low-coverage whole genome sequencing assay for detecting cell-free DNA from pediatric CNS tumor patients, demonstrating its potential for guiding diagnostic and therapeutic strategies.

Abstract

Molecular profiling of pediatric central nervous system (CNS) tumors has important clinical utility for guiding diagnostic and therapeutic strategies. Cell-free DNA (cfDNA) from liquid biopsies has been used for minimally invasive tumor profiling and longitudinal disease assessment in adult oncology and pediatric hematology. However, in pediatric neuro-oncology, low cfDNA yields pose a major barrier to translating these assays from bench to bedside. Here, we implemented a low-coverage whole genome sequencing (lcWGS) assay for picogram-level cfDNA inputs and applied it to liquid biopsies from a sizeable, population-based, cross-entity pediatric CNS tumor cohort (n = 56 patients). Applying this protocol, cfDNA whole genome profiles were successfully acquired from all liquid biopsy samples (n = 61/61 serum, n = 56/56 CSF, 100%). Based on copy number variations (CNVs), circulating-tumor DNA (ctDNA) was detected in 2/61 serum (3%) and in 25/56 CSF (45%) samples across various brain tumor entities. The integration of cfDNA results with clinical data demonstrated the utility of CSF lcWGS as a biomarker assay at diagnosis to distinguish cancerous from non-cancerous pineal region lesions (n = 6 patients). Additionally, serial CSF assessment in n = 9 patients (n = 29 CSF samples) enabled minimally invasive disease monitoring, with the added value of molecular profile availability in n = 4/6 (67%) patients at relapse. Proof-of-concept data show the feasibility of serial CSF lcWGS to reveal tumor evolution, tumor heterogeneity and potential therapeutic vulnerabilities in a case of medulloblastoma and germ cell tumor. Our study underscores the clinical utility of a robust lcWGS-based liquid biopsy assay optimized for low-input samples. We identify use-cases for implementing liquid biopsies in the clinical management of pediatric CNS tumor patients and provide a strong rationale for integration into future trials.

Overview

  • The study aimed to develop a low-coverage whole genome sequencing (lcWGS) assay for detecting cell-free DNA (cfDNA) from pediatric central nervous system (CNS) tumor patients at extremely low input levels.
  • The study utilized a sizeable, population-based, cross-entity pediatric CNS tumor cohort (n = 56 patients) and implemented the lcWGS assay for liquid biopsies from serum and cerebrospinal fluid (CSF).
  • The primary objective was to demonstrate the feasibility and clinical utility of the lcWGS-based liquid biopsy assay for guiding diagnostic and therapeutic strategies in pediatric neuro-oncology.

Comparative Analysis & Findings

  • The study reported successful acquisition of cfDNA whole genome profiles from all serum and CSF samples (n = 61/61, n = 56/56, respectively).
  • The integration of cfDNA results with clinical data revealed that CSF lcWGS can distinguish cancerous from non-cancerous pineal region lesions at diagnosis.
  • Serial CSF assessment enabled minimally invasive disease monitoring, with molecular profile availability at relapse in 4/6 patients.

Implications and Future Directions

  • The study provides proof-of-concept data for the feasibility of serial CSF lcWGS to reveal tumor evolution, heterogeneity, and potential therapeutic vulnerabilities.
  • The robust lcWGS-based liquid biopsy assay optimized for low-input samples has significant potential for integrating into clinical management of pediatric CNS tumor patients.
  • Future trials should incorporate this assay to evaluate its utility in guiding personalized therapies and improving outcomes for pediatric CNS tumor patients.
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