RT Journal Article
SR Electronic
T1 Minimally invasive classification of pediatric solid tumors using reduced representation bisulfite sequencing of cell-free DNA: a proof-of-principle study
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 795047
DO 10.1101/795047
A1 Ruben Van Paemel
A1 Andries De Koker
A1 Charlotte Vandeputte
A1 Lieke van Zogchel
A1 Tim Lammens
A1 Geneviève Laureys
A1 Jo Vandesompele
A1 Gudrun Schleiermacher
A1 Mathieu Chicard
A1 Nadine Van Roy
A1 Ales Vicha
A1 G.A.M. Tytgat
A1 Nico Callewaert
A1 Katleen De Preter
A1 Bram De Wilde
YR 2019
UL http://biorxiv.org/content/early/2019/10/08/795047.abstract
AB 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.Translational relevance Obtaining a correct diagnosis in pediatric oncology can be challenging in some tumor types, especially in renal tumors or central nervous system tumors. Furthermore, the diagnostic odyssey can result in anxiety and discomfort for these children. By applying a novel technique, reduced representation bisulfite sequencing on cell-free DNA (cf-RRBS), we show the feasibility of obtaining the histopathological diagnosis with a minimally invasive test on either plasma or cerebrospinal fluid. Furthermore, we were able to derive the copy number profile or tumor subtype from the same assay. Given that primary tumor material might be difficult to obtain, in particular in critically ill children or depending on the tumor location, and might be limited in terms of quantity or quality, our assay could become complementary to the classical tissue biopsy in difficult cases.