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Minimally invasive classification of pediatric solid tumors using reduced representation bisulfite sequencing of cell-free DNA : a proof-of-principle study

(2021) EPIGENETICS. 16(2). p.196-208
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Abstract
In the clinical management of paediatric solid tumours, histological examination of tumour tissue obtained by a biopsy remains the gold standard to establish a conclusive pathological diagnosis. The DNA methylation pattern of a tumour is known to correlate with the histopathological diagnosis across cancer types and is showing promise in the diagnostic workup of tumour samples. This methylation pattern can be detected in the cell-free DNA. Here, we provide proof-of-concept of histopathologic classification of paediatric tumours using cell-free reduced representation bisulphite sequencing (cf-RRBS) from retrospectively collected plasma and cerebrospinal fluid samples. We determined the correct tumour 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 paediatric oncology in a cost-effective and minimally invasive manner.
Keywords
DNA methylation, cell-free DNA, liquid biopsy, pediatric oncology, biomarker, diagnosis, infinium, reduced representation bisulfite sequencing, METHYLATION, PATHOLOGY

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MLA
Van Paemel, Ruben, et al. “Minimally Invasive Classification of Pediatric Solid Tumors Using Reduced Representation Bisulfite Sequencing of Cell-Free DNA : A Proof-of-Principle Study.” EPIGENETICS, vol. 16, no. 2, 2021, pp. 196–208, doi:10.1080/15592294.2020.1790950.
APA
Van Paemel, R., De Koker, A., Vandeputte, C., van Zogchel, L., Lammens, T., Laureys, G., … De Wilde, B. (2021). Minimally invasive classification of pediatric solid tumors using reduced representation bisulfite sequencing of cell-free DNA : a proof-of-principle study. EPIGENETICS, 16(2), 196–208. https://doi.org/10.1080/15592294.2020.1790950
Chicago author-date
Van Paemel, Ruben, Andries De Koker, Charlotte Vandeputte, Lieke van Zogchel, Tim Lammens, Genevieve Laureys, Jo Vandesompele, et al. 2021. “Minimally Invasive Classification of Pediatric Solid Tumors Using Reduced Representation Bisulfite Sequencing of Cell-Free DNA : A Proof-of-Principle Study.” EPIGENETICS 16 (2): 196–208. https://doi.org/10.1080/15592294.2020.1790950.
Chicago author-date (all authors)
Van Paemel, Ruben, Andries De Koker, Charlotte Vandeputte, Lieke van Zogchel, Tim Lammens, Genevieve Laureys, Jo Vandesompele, Gudrun Schleiermacher, Mathieu Chicard, Nadine Van Roy, Ales Vicha, Godelieve A. M. Tytgat, Nico Callewaert, Katleen De Preter, and Bram De Wilde. 2021. “Minimally Invasive Classification of Pediatric Solid Tumors Using Reduced Representation Bisulfite Sequencing of Cell-Free DNA : A Proof-of-Principle Study.” EPIGENETICS 16 (2): 196–208. doi:10.1080/15592294.2020.1790950.
Vancouver
1.
Van Paemel R, De Koker A, Vandeputte C, van Zogchel L, Lammens T, Laureys G, et al. Minimally invasive classification of pediatric solid tumors using reduced representation bisulfite sequencing of cell-free DNA : a proof-of-principle study. EPIGENETICS. 2021;16(2):196–208.
IEEE
[1]
R. Van Paemel et al., “Minimally invasive classification of pediatric solid tumors using reduced representation bisulfite sequencing of cell-free DNA : a proof-of-principle study,” EPIGENETICS, vol. 16, no. 2, pp. 196–208, 2021.
@article{8668827,
  abstract     = {{In the clinical management of paediatric solid tumours, histological examination of tumour tissue obtained by a biopsy remains the gold standard to establish a conclusive pathological diagnosis. The DNA methylation pattern of a tumour is known to correlate with the histopathological diagnosis across cancer types and is showing promise in the diagnostic workup of tumour samples. This methylation pattern can be detected in the cell-free DNA. Here, we provide proof-of-concept of histopathologic classification of paediatric tumours using cell-free reduced representation bisulphite sequencing (cf-RRBS) from retrospectively collected plasma and cerebrospinal fluid samples. We determined the correct tumour 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 paediatric oncology in a cost-effective and minimally invasive manner.}},
  author       = {{Van Paemel, Ruben and De Koker, Andries and Vandeputte, Charlotte and van Zogchel, Lieke and Lammens, Tim and Laureys, Genevieve and Vandesompele, Jo and Schleiermacher, Gudrun and Chicard, Mathieu and Van Roy, Nadine and Vicha, Ales and Tytgat, Godelieve A. M. and Callewaert, Nico and De Preter, Katleen and De Wilde, Bram}},
  issn         = {{1559-2294}},
  journal      = {{EPIGENETICS}},
  keywords     = {{DNA methylation,cell-free DNA,liquid biopsy,pediatric oncology,biomarker,diagnosis,infinium,reduced representation bisulfite sequencing,METHYLATION,PATHOLOGY}},
  language     = {{eng}},
  number       = {{2}},
  pages        = {{196--208}},
  title        = {{Minimally invasive classification of pediatric solid tumors using reduced representation bisulfite sequencing of cell-free DNA : a proof-of-principle study}},
  url          = {{http://dx.doi.org/10.1080/15592294.2020.1790950}},
  volume       = {{16}},
  year         = {{2021}},
}

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