Van Paemel Ruben, Vandeputte Charlotte, Raman Lennart, Van Thorre Jolien, Willems Leen, Van Dorpe Jo, Van Der Linden Malaïka, De Wilde Jilke, De Koker Andries, Menten Björn, Devalck Christine, Vicha Ales, Grega Marek, Schleiermacher Gudrun, Iddir Yasmine, Chicard Mathieu, van Zogchel Lieke, Stutterheim Janine, Lak Nathalie S M, Tytgat G A M, Laureys Geneviève, Speleman Frank, De Wilde Bram, Lammens Tim, De Preter Katleen, Van Roy Nadine
Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Research Foundation Flanders, Belgium.
Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
Eur J Cancer. 2022 Jan;160:12-23. doi: 10.1016/j.ejca.2021.09.022. Epub 2021 Nov 16.
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.
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.
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.
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.
儿科肿瘤通常具有反复出现的DNA拷贝数改变（CNA）的特征。从组织活检中获得的这些DNA拷贝数谱有助于对几种儿科癌症实体进行正确的预后分类和治疗分层（例如神经母细胞瘤中的MYCN扩增），并且是常规诊断实践的一部分。液体活检（LQB）为这种侵入性肿瘤组织活检提供了一种潜在更安全的替代方法，并且可以更深入地了解肿瘤异质性。
评估了LQB CNA分析的稳健性和可靠性。我们使用浅层全基因组测序（sWGS）对来自儿科患者（n = 128）常规收集的样本中的配对血浆循环游离DNA（cfDNA）和组织DNA样本进行回顾性CNA分析，这些样本代表不同的肿瘤实体，包括骨肉瘤、尤因肉瘤、横纹肌肉瘤、肾母细胞瘤、脑肿瘤和神经母细胞瘤。
总体而言，我们观察到组织DNA和cfDNA中的CNA之间具有良好的一致性。发现CNA不一致的主要原因是cfDNA样本质量低（即cfDNA（<700 bp）与高分子量DNA（>700 bp）的比率）。此外，还观察到cfDNA中存在而组织DNA中不存在的CNA，反之亦然。在神经母细胞瘤样本中，未发现用于检测预后标志物MYCN扩增的假阳性或假阴性。
在未来的前瞻性研究中，对质量足够的LQB进行CNA分析可作为组织活检CNA分析的补充检测，因为cfDNA或组织DNA都可能包含在其他生物材料中无法识别的CNA。
