cfRRBS on cfDNA from pediatric cancer

Study ID Alternative Stable ID Type
EGAS00001004194 Other

Study Description

In the clinical management of pediatric solid tumors, histological examination of tumor tissue obtained by a biopsy remains the gold standard to establish a conclusive pathological diagnosis. The DNA methylation pattern of a tumor is known to correlate with the histopathological diagnosis across cancer types and is showing promise in the diagnostic workup of tumor samples. This methylation pattern can be detected in the cell-free DNA. Here, we provide proof-of-concept of histopathologic classification of pediatric tumors using cell-free reduced representation bisulfite sequencing (cf-RRBS) from retrospectively collected plasma and cerebrospinal fluid samples. We determined the correct tumor type in 49 out of 60 (81.6%) samples starting from minute amounts (less than 10 ng) of cell-free DNA. We demonstrate that the majority of misclassifications were associated with sample quality and not with the extent of disease. Our approach has the potential to help tackle some of the remaining diagnostic challenges in pediatric oncology in a cost-effective and minimally invasive manner.

Study Datasets 1 dataset.

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Dataset ID Description Technology Samples
This dataset contains cell-free reduced representation bisulfite sequencing data from 60 pediatric cancer samples. Files are provided in fastq format. Samples were sequenced on a NextSeq 500.
NextSeq 500 60

Who archives the data?

There are no publications available