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Detection of tumor-derived cell-free DNA in cerebrospinal fluid using a clinically validated targeted sequencing panel for pediatric brain tumors

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Abstract

Purpose

Clinical sequencing of tumor DNA is necessary to render an integrated diagnosis and select therapy for children with primary central nervous system (CNS) tumors, but neurosurgical biopsy is not without risk. In this study, we describe cell-free DNA (cfDNA) in blood and cerebrospinal fluid (CSF) as sources for “liquid biopsy” in pediatric brain tumors.

Methods

CSF samples were collected by lumbar puncture, ventriculostomy, or surgery from pediatric patients with CNS tumors. Following extraction, CSF-derived cfDNA was sequenced using UW-OncoPlex™, a clinically validated next-generation sequencing platform. CSF-derived cfDNA results and paired plasma and tumor samples concordance was also evaluated.

Results

Seventeen CSF samples were obtained from 15 pediatric patients with primary CNS tumors. Tumor types included medulloblastoma (n = 7), atypical teratoid/rhabdoid tumor (n = 2), diffuse midline glioma with H3 K27 alteration (n = 4), pilocytic astrocytoma (n = 1), and pleomorphic xanthoastrocytoma (n = 1). CSF-derived cfDNA was detected in 9/17 (53%) of samples, and sufficient for sequencing in 8/10 (80%) of extracted samples. All somatic mutations and copy-number variants were also detected in matched tumor tissue, and tumor-derived cfDNA was absent in plasma samples and controls. Tumor-derived cfDNA alterations were detected in the absence of cytological evidence of malignant cells in as little as 200 µl of CSF. Several clinically relevant alterations, including a KIAA1549::BRAF fusion were detected.

Conclusions

Clinically relevant genomic alterations are detectable using CSF-derived cfDNA across a range of pediatric brain tumors. Next-generation sequencing platforms are capable of producing a high yield of DNA alterations with 100% concordance rate with tissue analysis.

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Data availability

CSF data analysis available by request.

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Funding

Seattle Children’s Pediatric Brain Tumor Research Fund (PBTRF), Brotman Baty Institute (BBI) for Precision Medicine, Ruth L. Kirschstein National Research Service Award Institutional Research Training Grant [T32CA009351].

Author information

Authors and Affiliations

  1. Division of Hematology/Oncology, Department of Pediatrics, Seattle Children’s Hospital, University of Washington, Seattle, WA, US

    Rebecca Ronsley, Kristine A. Karvonen, Jeff Stevens, Erin E. Crotty & Sarah E. S. Leary

  2. Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA, US

    Rebecca Ronsley, Kristine A. Karvonen, Jeff Stevens, Erin E. Crotty & Sarah E. S. Leary

  3. Fred Hutchinson Cancer Research Center, Seattle, WA, US

    Rebecca Ronsley, Kristine A. Karvonen, Erin E. Crotty & Sarah E. S. Leary

  4. Department of Laboratories, Seattle Children’s Hospital, University of Washington, Seattle, WA, US

    Bonnie Cole & Shannon M. Stasi

  5. Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, US

    Bonnie Cole, Vera Paulson & Christina M. Lockwood

  6. Division of Neurosurgery, Department of Neurological Surgery, Seattle Children’s Hospital, University of Washington, Seattle, WA, US

    Jason Hauptman & Amy Lee

  7. Genetics and Solid Tumor Laboratory, Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA

    Vera Paulson & Christina M. Lockwood

  8. Seattle Children’s Hospital, Mail Stop MB.8.501, 4800 Sand Point Way NE, Seattle, WA, 98105, USA

    Rebecca Ronsley

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  1. Rebecca Ronsley
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Contributions

Experimental design: SESL, CL, BC. Experimental implementation: JH, AL, BC, CL, JS, VP. Analysis and interpretation: SESL, RR, EEC, CL, BC, KAK, VP. Manuscript preparation and critical review: All authors.

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Correspondence to Rebecca Ronsley.

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Ronsley, R., Karvonen, K.A., Cole, B. et al. Detection of tumor-derived cell-free DNA in cerebrospinal fluid using a clinically validated targeted sequencing panel for pediatric brain tumors. J Neurooncol 168, 215–224 (2024). https://doi.org/10.1007/s11060-024-04645-y

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  • DOI: https://doi.org/10.1007/s11060-024-04645-y

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