Targeted detection of sequence variants in cell-free DNA from cerebrospinal fluid in pediatric central nervous system tumors
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 co...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2025-01-01
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| Series: | Frontiers in Oncology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fonc.2024.1513073/full |
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| author | Katrina O’Halloran Katrina O’Halloran Erin E. Crotty Eirini Christodoulou Sarah E. Leary Alexandra Miller Alexandra Miller Vera A. Paulson Christina M. Lockwood Ashley S. Margol Ashley S. Margol Jaclyn A. Biegel Jaclyn A. Biegel |
| author_facet | Katrina O’Halloran Katrina O’Halloran Erin E. Crotty Eirini Christodoulou Sarah E. Leary Alexandra Miller Alexandra Miller Vera A. Paulson Christina M. Lockwood Ashley S. Margol Ashley S. Margol Jaclyn A. Biegel Jaclyn A. Biegel |
| author_sort | Katrina O’Halloran |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-87307bcea6044f3489fcf629ae06d4f8 |
| institution | DOAJ |
| issn | 2234-943X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Oncology |
| spelling | doaj-art-87307bcea6044f3489fcf629ae06d4f82025-08-20T02:43:36ZengFrontiers Media S.A.Frontiers in Oncology2234-943X2025-01-011410.3389/fonc.2024.15130731513073Targeted detection of sequence variants in cell-free DNA from cerebrospinal fluid in pediatric central nervous system tumorsKatrina O’Halloran0Katrina O’Halloran1Erin E. Crotty2Eirini Christodoulou3Sarah E. Leary4Alexandra Miller5Alexandra Miller6Vera A. Paulson7Christina M. Lockwood8Ashley S. Margol9Ashley S. Margol10Jaclyn A. Biegel11Jaclyn A. Biegel12Cancer and Blood Disease Institute, Children’s Hospital Los Angeles, Los Angeles, CA, United StatesKeck School of Medicine, University of Southern California, Los Angeles, CA, United StatesBen 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, WA, United StatesDepartment of Pathology, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, United StatesBen 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, WA, United StatesBrain and Spine Tumor Center, Perlmutter Cancer Center, New York University Langone, New York, NY, United StatesDepartment of Neurology, New York University-Langone Health, New York, NY, United StatesGenetics and Solid Tumor Laboratory, Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United StatesGenetics and Solid Tumor Laboratory, Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United StatesCancer and Blood Disease Institute, Children’s Hospital Los Angeles, Los Angeles, CA, United StatesKeck School of Medicine, University of Southern California, Los Angeles, CA, United StatesKeck School of Medicine, University of Southern California, Los Angeles, CA, United StatesDepartment of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United StatesThe 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.https://www.frontiersin.org/articles/10.3389/fonc.2024.1513073/fullpediatric neuro-oncologycerebrospinal fluidliquid biopsytargeted sequencingsequence variant |
| spellingShingle | Katrina O’Halloran Katrina O’Halloran Erin E. Crotty Eirini Christodoulou Sarah E. Leary Alexandra Miller Alexandra Miller Vera A. Paulson Christina M. Lockwood Ashley S. Margol Ashley S. Margol Jaclyn A. Biegel Jaclyn A. Biegel Targeted detection of sequence variants in cell-free DNA from cerebrospinal fluid in pediatric central nervous system tumors Frontiers in Oncology pediatric neuro-oncology cerebrospinal fluid liquid biopsy targeted sequencing sequence variant |
| title | Targeted detection of sequence variants in cell-free DNA from cerebrospinal fluid in pediatric central nervous system tumors |
| title_full | Targeted detection of sequence variants in cell-free DNA from cerebrospinal fluid in pediatric central nervous system tumors |
| title_fullStr | Targeted detection of sequence variants in cell-free DNA from cerebrospinal fluid in pediatric central nervous system tumors |
| title_full_unstemmed | Targeted detection of sequence variants in cell-free DNA from cerebrospinal fluid in pediatric central nervous system tumors |
| title_short | Targeted detection of sequence variants in cell-free DNA from cerebrospinal fluid in pediatric central nervous system tumors |
| title_sort | targeted detection of sequence variants in cell free dna from cerebrospinal fluid in pediatric central nervous system tumors |
| topic | pediatric neuro-oncology cerebrospinal fluid liquid biopsy targeted sequencing sequence variant |
| url | https://www.frontiersin.org/articles/10.3389/fonc.2024.1513073/full |
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