cfRRBS on cfDNA from pediatric cancer

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.

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

1 Dataset 1 Publication

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001005928	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

Publications	Citations
Minimally invasive classification of paediatric solid tumours using reduced representation bisulphite sequencing of cell-free DNA: a proof-of-principle study. Van Paemel R, De Koker A, Vandeputte C, van Zogchel L, Lammens T, Laureys G, Vandesompele J, Schleiermacher G, Chicard M, Van Roy N, Vicha A, Tytgat GAM, Callewaert N, De Preter K, De Wilde B. Epigenetics 16: 2021 196-208	27