Detection of cell-free DNA fragmentation and copy number alterations in cerebrospinal fluid from glioma patients

Glioma is difficult to detect or characterise 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 < 0.4x) 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.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

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Dataset ID	Description	Technology	Samples
EGAD00001004425	FASTQ files from sequencing to < 0.4x depth of coverage of thirteen glioma patients. Indexed sequencing libraries were prepared using a commercially available kit (ThruPLEX-Plasma Seq, Rubicon Genomics). Libraries were pooled in equimolar amounts and sequenced on a HiSeq 4000 (Illumina) generating 150-bp paired-end reads.	Illumina HiSeq 4000	13

Publications	Citations
Detection of cell-free DNA fragmentation and copy number alterations in cerebrospinal fluid from glioma patients. Mouliere F, Mair R, Chandrananda D, Marass F, Smith CG, Su J, Morris J, Watts C, Brindle KM, Rosenfeld N. EMBO Mol Med 10: 2018 e9323	74