Ultra-low-input cell-free DNA sequencing for tumor detection and characterization in a real-world pediatric brain tumor cohort
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...
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2025-06-01
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| Series: | Acta Neuropathologica Communications |
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| Online Access: | https://doi.org/10.1186/s40478-025-02024-w |
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| author | 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 |
| author_facet | 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 |
| author_sort | Tom T. Fischer |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-9587743f1f8643da8b65d568b4ac4ddc |
| institution | OA Journals |
| issn | 2051-5960 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | BMC |
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| series | Acta Neuropathologica Communications |
| spelling | doaj-art-9587743f1f8643da8b65d568b4ac4ddc2025-08-20T02:35:40ZengBMCActa Neuropathologica Communications2051-59602025-06-0113111910.1186/s40478-025-02024-wUltra-low-input cell-free DNA sequencing for tumor detection and characterization in a real-world pediatric brain tumor cohortTom T. Fischer0Kendra K. Maaß1Pitithat Puranachot2Markus Mieskolainen3Martin Sill4Paulina S. Schad5Stefanie Volz6Fabian Rosing7Tatjana Wedig8Nathalie Schwarz9Agnes M. E. Finster10Florian Iser11Jochen Meyer12Felix Sahm13Olli Lohi14Ahmed El Damaty15Benedikt Brors16Hannu Haapasalo17Stefan M. Pfister18Joonas Haapasalo19Kristian W. Pajtler20Kristiina Nordfors21Hopp Children’s Cancer Center (KiTZ)Hopp Children’s Cancer Center (KiTZ)Princess Srisavangavadhana Faculty of Medicine, Chulabhorn Royal AcademyDepartment of Neurosurgery, Tampere University Hospital and Tampere UniversityHopp Children’s Cancer Center (KiTZ)Hopp Children’s Cancer Center (KiTZ)Hopp Children’s Cancer Center (KiTZ)Hopp Children’s Cancer Center (KiTZ)Hopp Children’s Cancer Center (KiTZ)Hopp Children’s Cancer Center (KiTZ)Hopp Children’s Cancer Center (KiTZ)Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ)Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ)Hopp Children’s Cancer Center (KiTZ)Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere UniversityHeidelberg Faculty of Medicine, Department of Neurosurgery, Heidelberg University, Heidelberg University HospitalNational Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University HospitalDepartment of Pathology, Fimlab Laboratories LtdHopp Children’s Cancer Center (KiTZ)Department of Neurosurgery, Tampere University Hospital and Tampere UniversityHopp Children’s Cancer Center (KiTZ)Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere UniversityAbstract 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.https://doi.org/10.1186/s40478-025-02024-wCerebrospinal fluid liquid biopsiesCell-free DNALow-input samplesCirculating-tumor DNACopy number variation profilingLow-coverage whole genome sequencing |
| spellingShingle | 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 Ultra-low-input cell-free DNA sequencing for tumor detection and characterization in a real-world pediatric brain tumor cohort Acta Neuropathologica Communications Cerebrospinal fluid liquid biopsies Cell-free DNA Low-input samples Circulating-tumor DNA Copy number variation profiling Low-coverage whole genome sequencing |
| title | Ultra-low-input cell-free DNA sequencing for tumor detection and characterization in a real-world pediatric brain tumor cohort |
| title_full | Ultra-low-input cell-free DNA sequencing for tumor detection and characterization in a real-world pediatric brain tumor cohort |
| title_fullStr | Ultra-low-input cell-free DNA sequencing for tumor detection and characterization in a real-world pediatric brain tumor cohort |
| title_full_unstemmed | Ultra-low-input cell-free DNA sequencing for tumor detection and characterization in a real-world pediatric brain tumor cohort |
| title_short | Ultra-low-input cell-free DNA sequencing for tumor detection and characterization in a real-world pediatric brain tumor cohort |
| title_sort | ultra low input cell free dna sequencing for tumor detection and characterization in a real world pediatric brain tumor cohort |
| topic | Cerebrospinal fluid liquid biopsies Cell-free DNA Low-input samples Circulating-tumor DNA Copy number variation profiling Low-coverage whole genome sequencing |
| url | https://doi.org/10.1186/s40478-025-02024-w |
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