Detection of cell‐free DNA fragmentation and copy number alterations in cerebrospinal fluid from glioma patients
Abstract Glioma is difficult to detect or characterize using current liquid biopsy approaches. Detection of cell‐free tumor DNA (cftDNA) in cerebrospinal fluid (CSF) has been proposed as an alternative to detection in plasma. We used shallow whole‐genome sequencing (sWGS, at a coverage of < 0.4×)...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Springer Nature
2018-11-01
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| Series: | EMBO Molecular Medicine |
| Subjects: | |
| Online Access: | https://doi.org/10.15252/emmm.201809323 |
| _version_ | 1827015095610245120 |
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| author | Florent Mouliere Richard Mair Dineika Chandrananda Francesco Marass Christopher G Smith Jing Su James Morris Colin Watts Kevin M Brindle Nitzan Rosenfeld |
| author_facet | Florent Mouliere Richard Mair Dineika Chandrananda Francesco Marass Christopher G Smith Jing Su James Morris Colin Watts Kevin M Brindle Nitzan Rosenfeld |
| author_sort | Florent Mouliere |
| collection | DOAJ |
| description | Abstract Glioma is difficult to detect or characterize using current liquid biopsy approaches. Detection of cell‐free tumor DNA (cftDNA) in cerebrospinal fluid (CSF) has been proposed as an alternative to detection in plasma. We used shallow whole‐genome sequencing (sWGS, at a coverage of < 0.4×) of cell‐free DNA from the CSF of 13 patients with primary glioma to determine somatic copy number alterations and DNA fragmentation patterns. This allowed us to determine the presence of cftDNA in CSF without any prior knowledge of point mutations present in the tumor. We also showed that the fragmentation pattern of cell‐free DNA in CSF is different from that in plasma. This low‐cost screening method provides information on the tumor genome and can be used to target those patients with high levels of cftDNA for further larger‐scale sequencing, such as by whole‐exome and whole‐genome sequencing. |
| first_indexed | 2024-03-07T17:10:26Z |
| format | Article |
| id | doaj.art-1ce875fdfe6e48c6ad6369793925f477 |
| institution | Directory Open Access Journal |
| issn | 1757-4676 1757-4684 |
| language | English |
| last_indexed | 2025-02-18T14:17:38Z |
| publishDate | 2018-11-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | EMBO Molecular Medicine |
| spelling | doaj.art-1ce875fdfe6e48c6ad6369793925f4772024-10-28T08:56:58ZengSpringer NatureEMBO Molecular Medicine1757-46761757-46842018-11-0110121610.15252/emmm.201809323Detection of cell‐free DNA fragmentation and copy number alterations in cerebrospinal fluid from glioma patientsFlorent Mouliere0Richard Mair1Dineika Chandrananda2Francesco Marass3Christopher G Smith4Jing Su5James Morris6Colin Watts7Kevin M Brindle8Nitzan Rosenfeld9Cancer Research UK Cambridge Institute, University of CambridgeCancer Research UK Cambridge Institute, University of CambridgeCancer Research UK Cambridge Institute, University of CambridgeCancer Research UK Cambridge Institute, University of CambridgeCancer Research UK Cambridge Institute, University of CambridgeCancer Research UK Cambridge Institute, University of CambridgeCancer Research UK Cambridge Institute, University of CambridgeInstitute of Cancer and Genomic Sciences, University of BirminghamCancer Research UK Cambridge Institute, University of CambridgeCancer Research UK Cambridge Institute, University of CambridgeAbstract Glioma is difficult to detect or characterize using current liquid biopsy approaches. Detection of cell‐free tumor DNA (cftDNA) in cerebrospinal fluid (CSF) has been proposed as an alternative to detection in plasma. We used shallow whole‐genome sequencing (sWGS, at a coverage of < 0.4×) of cell‐free DNA from the CSF of 13 patients with primary glioma to determine somatic copy number alterations and DNA fragmentation patterns. This allowed us to determine the presence of cftDNA in CSF without any prior knowledge of point mutations present in the tumor. We also showed that the fragmentation pattern of cell‐free DNA in CSF is different from that in plasma. This low‐cost screening method provides information on the tumor genome and can be used to target those patients with high levels of cftDNA for further larger‐scale sequencing, such as by whole‐exome and whole‐genome sequencing.https://doi.org/10.15252/emmm.201809323cell‐free DNAcerebrospinal fluidfragmentationgliomashallow WGS |
| spellingShingle | Florent Mouliere Richard Mair Dineika Chandrananda Francesco Marass Christopher G Smith Jing Su James Morris Colin Watts Kevin M Brindle Nitzan Rosenfeld Detection of cell‐free DNA fragmentation and copy number alterations in cerebrospinal fluid from glioma patients EMBO Molecular Medicine cell‐free DNA cerebrospinal fluid fragmentation glioma shallow WGS |
| title | Detection of cell‐free DNA fragmentation and copy number alterations in cerebrospinal fluid from glioma patients |
| title_full | Detection of cell‐free DNA fragmentation and copy number alterations in cerebrospinal fluid from glioma patients |
| title_fullStr | Detection of cell‐free DNA fragmentation and copy number alterations in cerebrospinal fluid from glioma patients |
| title_full_unstemmed | Detection of cell‐free DNA fragmentation and copy number alterations in cerebrospinal fluid from glioma patients |
| title_short | Detection of cell‐free DNA fragmentation and copy number alterations in cerebrospinal fluid from glioma patients |
| title_sort | detection of cell free dna fragmentation and copy number alterations in cerebrospinal fluid from glioma patients |
| topic | cell‐free DNA cerebrospinal fluid fragmentation glioma shallow WGS |
| url | https://doi.org/10.15252/emmm.201809323 |
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