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The feasibility of using liquid biopsies as a complementary assay for copy number aberration profiling in routinely collected paediatric cancer patient samples

Ruben Van Paemel (UGent) , Charlotte Vandeputte (UGent) , Lennart Raman (UGent) , Jolien Van Thorre, Leen Willems (UGent) , Jo Van Dorpe (UGent) , Malaïka Van der Linden (UGent) , Jilke De Wilde (UGent) , Andries De Koker (UGent) , Björn Menten (UGent) , et al.
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Abstract
Background Paediatric tumours are often characterised by the presence of recurrent DNA copy number alterations (CNAs). These DNA copy number profiles, obtained from a tissue biopsy, can aid in the correct prognostic classification and therapeutic stratification of several paediatric cancer entities (e.g. MYCN amplification in neuroblastoma) and are part of the routine diagnostic practice. Liquid biopsies (LQBs) offer a potentially safer alternative for such invasive tumour tissue biopsies and can provide deeper insight into tumour heterogeneity. Procedure The robustness and reliability of LQB CNA analyses was evaluated. We performed retrospective CNA profiling using shallow whole-genome sequencing (sWGS) on paired plasma circulating cell-free DNA (cfDNA) and tissue DNA samples from routinely collected samples from paediatric patients (n = 128) representing different tumour entities, including osteosarcoma, Ewing sarcoma, rhabdomyosarcoma, Wilms tumour, brain tumours and neuroblastoma. Results Overall, we observed a good concordance between CNAs in tissue DNA and cfDNA. The main cause of CNA discordance was found to be low cfDNA sample quality (i.e. the ratio of cfDNA (<700 bp) and high molecular weight DNA (>700 bp)). Furthermore, CNAs were observed that were present in cfDNA and not in tissue DNA, or vice-versa. In neuroblastoma samples, no false-positives or false-negatives were identified for the detection of the prognostic marker MYCN amplification. Conclusion In future prospective studies, CNA analysis on LQBs that are of sufficient quality can serve as a complementary assay for CNA analysis on tissue biopsies, as either cfDNA or tissue DNA can contain CNAs that cannot be identified in the other biomaterial.
Keywords
Cancer Research, Oncology, cfDNA, pediatric cancer, liquid biopsy

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MLA
Van Paemel, Ruben, et al. “The Feasibility of Using Liquid Biopsies as a Complementary Assay for Copy Number Aberration Profiling in Routinely Collected Paediatric Cancer Patient Samples.” EUROPEAN JOURNAL OF CANCER, vol. 160, 2022, pp. 12–23, doi:10.1016/j.ejca.2021.09.022.
APA
Van Paemel, R., Vandeputte, C., Raman, L., Van Thorre, J., Willems, L., Van Dorpe, J., … Van Roy, N. (2022). The feasibility of using liquid biopsies as a complementary assay for copy number aberration profiling in routinely collected paediatric cancer patient samples. EUROPEAN JOURNAL OF CANCER, 160, 12–23. https://doi.org/10.1016/j.ejca.2021.09.022
Chicago author-date
Van Paemel, Ruben, Charlotte Vandeputte, Lennart Raman, Jolien Van Thorre, Leen Willems, Jo Van Dorpe, Malaïka Van der Linden, et al. 2022. “The Feasibility of Using Liquid Biopsies as a Complementary Assay for Copy Number Aberration Profiling in Routinely Collected Paediatric Cancer Patient Samples.” EUROPEAN JOURNAL OF CANCER 160: 12–23. https://doi.org/10.1016/j.ejca.2021.09.022.
Chicago author-date (all authors)
Van Paemel, Ruben, Charlotte Vandeputte, Lennart Raman, Jolien Van Thorre, Leen Willems, Jo Van Dorpe, Malaïka Van der Linden, Jilke De Wilde, Andries De Koker, Björn Menten, Christine Devalck, Ales Vicha, Marek Grega, Gudrun Schleiermacher, Yasmine Iddir, Mathieu Chicard, Lieke van Zogchel, Janine Stutterheim, Nathalie S.M. Lak, G.A.M. Tytgat, Genevieve Laureys, Franki Speleman, Bram De Wilde, Tim Lammens, Katleen De Preter, and Nadine Van Roy. 2022. “The Feasibility of Using Liquid Biopsies as a Complementary Assay for Copy Number Aberration Profiling in Routinely Collected Paediatric Cancer Patient Samples.” EUROPEAN JOURNAL OF CANCER 160: 12–23. doi:10.1016/j.ejca.2021.09.022.
Vancouver
1.
Van Paemel R, Vandeputte C, Raman L, Van Thorre J, Willems L, Van Dorpe J, et al. The feasibility of using liquid biopsies as a complementary assay for copy number aberration profiling in routinely collected paediatric cancer patient samples. EUROPEAN JOURNAL OF CANCER. 2022;160:12–23.
IEEE
[1]
R. Van Paemel et al., “The feasibility of using liquid biopsies as a complementary assay for copy number aberration profiling in routinely collected paediatric cancer patient samples,” EUROPEAN JOURNAL OF CANCER, vol. 160, pp. 12–23, 2022.
@article{8728822,
  abstract     = {{Background
Paediatric tumours are often characterised by the presence of recurrent DNA copy number alterations (CNAs). These DNA copy number profiles, obtained from a tissue biopsy, can aid in the correct prognostic classification and therapeutic stratification of several paediatric cancer entities (e.g. MYCN amplification in neuroblastoma) and are part of the routine diagnostic practice. Liquid biopsies (LQBs) offer a potentially safer alternative for such invasive tumour tissue biopsies and can provide deeper insight into tumour heterogeneity.

Procedure
The robustness and reliability of LQB CNA analyses was evaluated. We performed retrospective CNA profiling using shallow whole-genome sequencing (sWGS) on paired plasma circulating cell-free DNA (cfDNA) and tissue DNA samples from routinely collected samples from paediatric patients (n = 128) representing different tumour entities, including osteosarcoma, Ewing sarcoma, rhabdomyosarcoma, Wilms tumour, brain tumours and neuroblastoma.

Results
Overall, we observed a good concordance between CNAs in tissue DNA and cfDNA. The main cause of CNA discordance was found to be low cfDNA sample quality (i.e. the ratio of cfDNA (<700 bp) and high molecular weight DNA (>700 bp)). Furthermore, CNAs were observed that were present in cfDNA and not in tissue DNA, or vice-versa. In neuroblastoma samples, no false-positives or false-negatives were identified for the detection of the prognostic marker MYCN amplification.

Conclusion
In future prospective studies, CNA analysis on LQBs that are of sufficient quality can serve as a complementary assay for CNA analysis on tissue biopsies, as either cfDNA or tissue DNA can contain CNAs that cannot be identified in the other biomaterial.}},
  author       = {{Van Paemel, Ruben and Vandeputte, Charlotte and Raman, Lennart and Van Thorre, Jolien and Willems, Leen and Van Dorpe, Jo and Van der Linden, Malaïka and De Wilde, Jilke and De Koker, Andries and Menten, Björn and Devalck, Christine and Vicha, Ales and Grega, Marek and Schleiermacher, Gudrun and Iddir, Yasmine and Chicard, Mathieu and van Zogchel, Lieke and Stutterheim, Janine and Lak, Nathalie S.M. and Tytgat, G.A.M. and Laureys, Genevieve and Speleman, Franki and De Wilde, Bram and Lammens, Tim and De Preter, Katleen and Van Roy, Nadine}},
  issn         = {{0959-8049}},
  journal      = {{EUROPEAN JOURNAL OF CANCER}},
  keywords     = {{Cancer Research,Oncology,cfDNA,pediatric cancer,liquid biopsy}},
  language     = {{eng}},
  pages        = {{12--23}},
  title        = {{The feasibility of using liquid biopsies as a complementary assay for copy number aberration profiling in routinely collected paediatric cancer patient samples}},
  url          = {{http://dx.doi.org/10.1016/j.ejca.2021.09.022}},
  volume       = {{160}},
  year         = {{2022}},
}

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