Genomewide copy number alteration screening of circulating plasma DNA: potential for the detection of incipient tumors

L. Lenaerts, P. Vandenberghe, N. Brison, H. Che, M. Neofytou, M. Verheecke, L. Leemans, C. Maggen, B. Dewaele, L. Dehaspe, S. Vanderschueren, D. Dierickx, V. Vandecaveye, F. Amant and J. R. Vermeesch 2019. Genomewide copy number alteration screening of circulating plasma DNA: potential for the detection of incipient tumors. Annals of Oncology. 30 (1), pp. p85-95. https://doi.org/10.1093/annonc/mdy476

TitleGenomewide copy number alteration screening of circulating plasma DNA: potential for the detection of incipient tumors
TypeJournal article
AuthorsL. Lenaerts, P. Vandenberghe, N. Brison, H. Che, M. Neofytou, M. Verheecke, L. Leemans, C. Maggen, B. Dewaele, L. Dehaspe, S. Vanderschueren, D. Dierickx, V. Vandecaveye, F. Amant and J. R. Vermeesch
Abstract

Background
Early cancer diagnosis might improve survival rates. As circulating tumor DNA (ctDNA) carries cancer-specific modifications, it has great potential as a noninvasive biomarker for detection of incipient tumors.
Patients and methods
We collected cell-free DNA (cfDNA) samples of 1002 elderly without a prior malignancy, carried out whole-genome massive parallel sequencing and scrutinized the mapped sequences for the presence of (sub)chromosomal copy number alterations (CNAs) predictive for a malignancy. When imbalances were detected, 6-monthly clinical follow-up was carried out.
Results
In 3% of participants chromosomal imbalances were detected. Follow-up analyses, including whole-body MRI screening, confirmed the presence of five hematologic malignancies: one Hodgkin lymphoma (HL), stage II; three non-HL (type chronic lymphocytic leukemia, Rai I–Binet A; type SLL, stage III; type mucosa-associated lymphoid tissue, stage I) and one myelodysplastic syndrome with excess blasts, stage II. The CNAs detected in cfDNA were tumor-specific. Furthermore, one case was identified with monoclonal B-cell lymphocytosis, a potential precursor of B-cell malignancy. In 24 additional individuals, CNAs were identified but no cancer diagnosis was made. For 9 of them, the aberrant cfDNA profile originated from peripheral blood cells. For 15 others the origin of aberrations in cfDNA remains undetermined.
Conclusion(s)
Genomewide profiling of cfDNA in apparently healthy individuals enables the detection of incipient hematologic malignancies as well as clonal mosaicism with unknown clinical significance. CNA screening of cellular DNA of peripheral blood in elderly has established that clonal mosaicism for these chromosomal anomalies predicts a 5- to 10-fold enhanced risk of a subsequent cancer. We demonstrate that cfDNA screening detects CNAs, which are not only derived from peripheral blood, but even more from other tissues. Since the clinical relevance of clonal mosaics in other tissues remains unknown, long-term follow-up is warranted. Taken together, this study demonstrates that genomewide cfDNA analysis has potential as an unbiased screening approach for hematological malignancies and premalignant conditions.

JournalAnnals of Oncology
Journal citation30 (1), pp. p85-95
ISSN0923-7534
Year2019
PublisherElsevier
Publisher's version
License
CC BY-NC-ND 4.0
File Access Level
Open (open metadata and files)
Digital Object Identifier (DOI)https://doi.org/10.1093/annonc/mdy476
PubMed ID30371735
Web address (URL)https://www.annalsofoncology.org/article/S0923-7534(19)30990-1/fulltext
Publication dates
Published08 Jan 2019
Supplemental file
File Access Level
Open (open metadata and files)

Related outputs

Noninvasive prenatal diagnosis by genome-wide haplotyping of cell-free plasma DNA
Neofytou, M. 2020. Noninvasive prenatal diagnosis by genome-wide haplotyping of cell-free plasma DNA. Genetics in Medicine. 22 (5), pp. 962-973. https://doi.org/10.1038/s41436-019-0748-y

Maternal liver transplant: Another cause of discordant fetal sex determination using cell-free DNA.
Maria Neofytou, Nathalie Brison, Kris Van den Bogaert, Luc Dehaspe, Koen Devriendt, Anja Geerts and Joris R. Vermeesch 2018. Maternal liver transplant: Another cause of discordant fetal sex determination using cell-free DNA. Prenatal Diagnosis. 38 (2), pp. 148-150. https://doi.org/10.1002/pd.5194

MeDIP combined with in-solution targeted enrichment followed by NGS: Inter-individual methylation variability of fetal-specific biomarkers and their implementation in a proof of concept study for NIPT
Anna Keravnou, Marios Ioannides, Charalambos Loizides, Kyriakos Tsangaras, Achilleas Achilleos, Petros Mina, Elena Kypri, Michael D. Hadjidaniel, Maria Neofytou, Skevi Kyriacou, Carolina Sismani, George Koumbaris and Philippos C. Patsalis 2018. MeDIP combined with in-solution targeted enrichment followed by NGS: Inter-individual methylation variability of fetal-specific biomarkers and their implementation in a proof of concept study for NIPT. PLoS ONE. 13 (6) e0199010. https://doi.org/10.1371/journal.pone.0199010

Predicting fetoplacental chromosomal mosaicism during non-invasive prenatal testing
Nathalie Brison, Maria Neofytou, Luc Dehaspe, Baran Bayindir, Kris Van Den Bogaert, Griet Van Buggenhout, Leila Dardour, Hilde Peeters, Hilde Van Esch, Annick Vogels, Thomy de Ravel, Eric Legius, Koen Devriendt and Joris R. Vermeesch 2018. Predicting fetoplacental chromosomal mosaicism during non-invasive prenatal testing. Prenatal Diagnosis. 38 (4), pp. 258-266. https://doi.org/10.1002/pd.5223

Whole-genome fetal and maternal DNA methylation analysis using MeDIP-NGS for the identification of differentially methylated regions
Anna Keravnou, Marios Ioannides, Kyriakos Tsangaras, Charalambos Loizides, Michael D. Hadjidaniel, Elisavet a. Papageorgiou, Skevi Kyriakou, Pavlos Antoniou, Petros Mina, Achilleas Achilleos, Maria Neofytou, Elena Kypri, Carolina Sismani, George koumbaris and Philippos C. Patsalis 2016. Whole-genome fetal and maternal DNA methylation analysis using MeDIP-NGS for the identification of differentially methylated regions. Genetics Research. 98 e15. https://doi.org/10.1017/S0016672316000136

Cell-free DNA analysis of targeted genomic regions in maternal plasma for non-invasive prenatal testing of trisomy 21, trisomy 18, trisomy 13, and fetal sex
George Koumbaris, Elena Kypri, Kyriakos Tsangaras, Achilleas Achilleos, Petros Mina, Maria Neofytou, Voula Velissariou, Georgia Christopoulou, Ioannis Kallikas, Alicia González-Liñán, Egle Benusiene, Anna Latos-Bielenska, Pietryga Marek, Alfredo Santana, Nikoletta Nagy, Márta Széll, Piotr Laudanski, Elisavet A. Papageorgiou, Marios Ioannides and Philippos C. Patsalis 2016. Cell-free DNA analysis of targeted genomic regions in maternal plasma for non-invasive prenatal testing of trisomy 21, trisomy 18, trisomy 13, and fetal sex. Clinical Chemistry. 62 (6), pp. 848-855. https://doi.org/10.1373/clinchem.2015.252502

Permalink - https://westminsterresearch.westminster.ac.uk/item/wyy8w/genomewide-copy-number-alteration-screening-of-circulating-plasma-dna-potential-for-the-detection-of-incipient-tumors


Share this

Usage statistics

6 total views
1 total downloads
These values cover views and downloads from WestminsterResearch and are for the period from September 2nd 2018, when this repository was created.