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Clin Cancer Res. 2017 Oct 15;23(20):6305-6314. doi: 10.1158/1078-0432.CCR-17-0675. Epub 2017 Jul 14.

Shallow Whole Genome Sequencing on Circulating Cell-Free DNA Allows Reliable Noninvasive Copy-Number Profiling in Neuroblastoma Patients.

Author information

1
Center for Medical Genetics, Ghent University, Ghent, Belgium.
2
Cancer Research Institute Ghent, Ghent University, Ghent, Belgium.
3
Department of Pathology, Ghent University, Ghent, Belgium.
4
Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium.
5
Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Leuven University Hospital, Leuven, Belgium.
6
Center for Medical Genetics, Ghent University, Ghent, Belgium. katleen.depreter@ugent.be.

Abstract

Purpose: Neuroblastoma (NB) is a heterogeneous disease characterized by distinct clinical features and by the presence of typical copy-number alterations (CNAs). Given the strong association of these CNA profiles with prognosis, analysis of the CNA profile at diagnosis is mandatory. Therefore, we tested whether the analysis of circulating cell-free DNA (cfDNA) present in plasma samples of patients with NB could offer a valuable alternative to primary tumor DNA for CNA profiling.Experimental Design: In 37 patients with NB, cfDNA analysis using shallow whole genome sequencing (sWGS) was compared with arrayCGH analysis of primary tumor tissue.Results: Comparison of CNA profiles on cfDNA showed highly concordant patterns, particularly in high-stage patients. Numerical chromosome imbalances as well as large and focal structural aberrations including MYCN and LIN28B amplification and ATRX deletion could be readily detected with sWGS using a low input of cfDNA.Conclusions: In conclusion, sWGS analysis on cfDNA offers a cost-effective, noninvasive, rapid, robust and sensitive alternative for tumor DNA copy-number profiling in most patients with NB. Clin Cancer Res; 23(20); 6305-14. ©2017 AACR.

PMID:
28710315
DOI:
10.1158/1078-0432.CCR-17-0675
[Indexed for MEDLINE]
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