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The potential of li...
The potential of liquid biopsy for detection of the KIAA1549-BRAF fusion in circulating tumor DNA from children with pilocytic astrocytoma
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- Krynina, Olha (author)
- Karolinska Institutet
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- Díaz de Ståhl, Teresita (author)
- Karolinska Inst, Dept Oncol Pathol, Stockholm, Sweden.
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- Jylhä, Cecilia (author)
- Karolinska Inst, Dept Mol Med & Surg, Stockholm, Sweden.;Karolinska Univ Hosp, Clin Genet & Genom, Stockholm, Sweden.
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- Arthur, Cecilia (author)
- Karolinska Institutet
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- Giraud, Geraldine (author)
- Uppsala universitet,Science for Life Laboratory, SciLifeLab,Neuroonkologi och neurodegeneration,Akademiska University Hospital, Uppsala, Sweden,Rudbeck Lab, Sweden; Akadem Univ Hosp, Sweden
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- Nyman, Per (author)
- Linköpings universitet,Avdelningen för diagnostik och specialistmedicin,Medicinska fakulteten,Centrum för medicinsk bildvetenskap och visualisering, CMIV,Region Östergötland, H.K.H. Kronprinsessan Victorias barn- och ungdomssjukhus
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- Fritzberg, Anders (author)
- Clin Pediat Falun Hosp, Daycare Unit Oncol & Hematol, Dalarna, Dalarna Region, Sweden.
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- Sandgren, Johanna (author)
- Karolinska Inst, Dept Oncol Pathol, Stockholm, Sweden.;Karolinska Univ Hosp, Clin Pathol & Canc Diagnost, Stockholm, Sweden.
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- Tham, Emma (author)
- Karolinska Institutet
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- Sandvik, Ulrika (author)
- Karolinska Inst, Dept Clin Neurosci, Div Neurosurg, Stockholm, Sweden.
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Karolinska Institutet Karolinska Inst, Dept Oncol Pathol, Stockholm, Sweden (creator_code:org_t)
- Oxford University Press, 2024
- 2024
- English.
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In: Neuro-Oncology Advances. - : Oxford University Press. - 2632-2498. ; 6:1
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Abstract
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- BackgroundLow-grade gliomas (LGGs) represent children’s most prevalent central nervous system tumor, necessitating molecular profiling to diagnose and determine the most suitable treatment. Developing highly sensitive screening techniques for liquid biopsy samples is particularly beneficial, as it enables the early detection and molecular characterization of tumors with minimally invasive samples.MethodsWe examined CSF and plasma samples from patients with pilocytic astrocytoma (PA) using custom multiplexed droplet digital polymerase chain reaction (ddPCR) assays based on whole genome sequencing data. These assays included a screening test to analyze BRAF duplication and a targeted assay for the detection of patient-specific KIAA1549::BRAF fusion junction sequences or single nucleotide variants.ResultsOur findings revealed that 5 out of 13 individual cerebrospinal fluid (CSF) samples tested positive for circulating tumor DNA (ctDNA). Among these cases, 3 exhibited the KIAA1549::BRAF fusion, which was detected through copy number variation (CNV) analysis (n = 1) or a fusion-specific probe (n = 2), while 1 case each displayed the BRAF V600E mutation and the FGFR1 N577K mutation. Additionally, a quantitative analysis of cell-free DNA (cfDNA) concentrations in PA CSF samples showed that most cases had low cfDNA levels, below the limit of detection of our assay (<1.9 ng).ConclusionsWhile CNV analysis of CSF samples from LGGs still has some limitations, it has the potential to serve as a valuable complementary tool. Furthermore, it can also be multiplexed with other aberrations, for example, to the BRAF V600 test, to provide important insights into the molecular characteristics of LGGs.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Cancer och onkologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Cancer and Oncology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
Keyword
- cerebrospinal fluid
- cfDNA
- ddPCR
- KIAA1549::BRAF
- pilocytic astrocytoma
Publication and Content Type
- ref (subject category)
- art (subject category)
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- By the author/editor
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Krynina, Olha
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Díaz de Ståhl, T ...
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Jylhä, Cecilia
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Arthur, Cecilia
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Giraud, Geraldin ...
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Nyman, Per
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Fritzberg, Ander ...
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Sandgren, Johann ...
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Tham, Emma
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Sandvik, Ulrika
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- About the subject
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Clinical Medicin ...
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and Cancer and Oncol ...
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Basic Medicine
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and Medical Genetics
- Articles in the publication
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Neuro-Oncology A ...
- By the university
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Uppsala University
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Linköping University
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Karolinska Institutet