The feasibility of using liquid biopsies as a complementary assay for copy number aberration profiling in routinely collected paediatric cancer patient samples
Jazyk angličtina Země Anglie, Velká Británie Médium print-electronic
Typ dokumentu časopisecké články, práce podpořená grantem
PubMed
34794856
DOI
10.1016/j.ejca.2021.09.022
PII: S0959-8049(21)00613-4
Knihovny.cz E-zdroje
- Klíčová slova
- Biomarker, Copy number aberrations, Liquid biopsy, Shallow whole-genome sequencing, cfDNA,
- MeSH
- dítě MeSH
- lidé MeSH
- mladiství MeSH
- nádorové biomarkery genetika MeSH
- předškolní dítě MeSH
- prospektivní studie MeSH
- retrospektivní studie MeSH
- studie proveditelnosti MeSH
- tekutá biopsie metody MeSH
- variabilita počtu kopií segmentů DNA genetika MeSH
- volné cirkulující nukleové kyseliny genetika MeSH
- Check Tag
- dítě MeSH
- lidé MeSH
- mladiství MeSH
- mužské pohlaví MeSH
- předškolní dítě MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- nádorové biomarkery MeSH
- volné cirkulující nukleové kyseliny MeSH
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.
Center for Medical Genetics Ghent University Hospital Ghent Belgium
Hôpital Universitaire des Enfants Reine Fabiola Brussels Belgium
Princess Máxima Center for Pediatric Oncology Utrecht the Netherlands
Translational Pediatric Oncology Centre de recherche de l'Institut Curie Paris France
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