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REVIEW article

Front. Oncol.
Sec. Pediatric Oncology
Volume 14 - 2024 | doi: 10.3389/fonc.2024.1513073
This article is part of the Research Topic Recent Biological Insights into Pediatric Brain Tumors View all articles

Targeted detection of sequence variants in cell-free DNA from cerebrospinal fluid in pediatric central nervous system tumors

Provisionally accepted
Katrina O'Halloran Katrina O'Halloran 1,2*Erin Crotty Erin Crotty 3Eirini Christodoulou Eirini Christodoulou 4Sarah Leary Sarah Leary 3Alexandra Miller Alexandra Miller 5,6Vera Paulson Vera Paulson 7Christina M Lockwood Christina M Lockwood 7Ashley Sloane Margol Ashley Sloane Margol 1,2Jaclyn A Biegel Jaclyn A Biegel 8
  • 1 Cancer and Blood Disease Institute, Children’s Hospital Los Angeles, Los Angeles, United States
  • 2 Keck School of Medicine, University of Southern California, Los Angeles, United States
  • 3 Ben Towne Center for Childhood Cancer and Blood Disorders Research and the Department of Pediatrics, Seattle Children’s Hospital, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, United States
  • 4 Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, United States
  • 5 Brain and Spine Tumor Center, Perlmutter Cancer Center, New York University Langone, New York, United States
  • 6 Department of Neurology, New York University-Langone Health, New York, United States
  • 7 Genetics and Solid Tumor Laboratory, Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, United States
  • 8 Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, United States

The final, formatted version of the article will be published soon.

    The emergence of liquid biopsy technologies holds great promise in the cancer setting, including in pediatric central nervous system (CNS) tumors. In contrast to broad lower-depth sequencing, commonly referred to as low pass whole genome sequencing (WGS), targeted platforms with a higher depth of coverage have also been established. Here, we review targeted liquid biopsy techniques with applicability to pediatric CNS tumors. These include polymerase chain reaction (PCR), both droplet digital PCR and reverse transcription-based PCR, Sanger sequencing, and next-generation sequencing approaches that incorporate amplicon-and hybrid capture-based methods. The goal of this paper is to facilitate an understanding of these targeted techniques and provide a context for clinical relevance within disease categories, as well as a discussion on optimizing real-world implementation for pediatric CNS tumors.

    Keywords: Pediatric Neuro-Oncology, Cerebrospinal Fluid, liquid biopsy, targeted sequencing, Sequence variant

    Received: 17 Oct 2024; Accepted: 29 Nov 2024.

    Copyright: © 2024 O'Halloran, Crotty, Christodoulou, Leary, Miller, Paulson, Lockwood, Margol and Biegel. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Katrina O'Halloran, Cancer and Blood Disease Institute, Children’s Hospital Los Angeles, Los Angeles, United States

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.