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; J. R. Vermeesch


Ann Oncol. 2019;30(1):85-95. 

In This Article

Abstract and Introduction


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.


With the increasing ageing population and concurrent expanding cancer incidence rates, a heavier focus on early cancer detection is required to complement new and improved treatments. As circulating tumor DNA (ctDNA) carries cancer-specific modifications, including DNA mutations and copy number alterations (CNAs), interest in its use as a noninvasive biomarker for detection of incipient tumors has been growing vastly. ctDNA represents a subset of the plasma cell-free DNA (cfDNA), the latter being normally present at low levels in the blood of healthy individuals and suggested to be primarily derived from normal cells of the hematopoietic lineage.[1] Most reports on ctDNA as a cancer marker focused on the detection of specific point mutations. Owing to its targeted nature, this approach only provides a partial glimpse of the tumor genome in plasma and must be customized for each patient based on a known tumor mutation profile. This is not feasible for screening purposes. CNAs, such as point mutations, are common for a large proportion of cancer types. About 90% of solid tumors and 50% of blood-related cancers are aneuploid and have somatic CNAs.[2] Furthermore, genomewide sequencing of plasma-derived DNA from cancer patients enabled the detection of tumor-associated copy number profiles in selected tumors prone to CNAs.[3,4]

We recently established a genomewide cfDNA analysis pipeline, coined Genomic Imbalance Profiling from cfDNA SEQuencing (GIPseq) for noninvasive prenatal testing, allowing genomewide detection of fetal and maternal chromosomal imbalances. Using this pipeline in ~50 000 asymptomatic pregnant women we incidentally identified 8 malignancies upon the detection of cancer-like CNAs in cfDNA[4,5] (unpublished data). Furthermore, we demonstrated that this approach allows detecting CNAs in cfDNA of patients with solid and hematological tumors.[4,6] Building on these observations, we aimed to test this noninvasive unbiased genomewide GIPseq as a tool for cancer screening in people with an elevated risk of developing cancer. Plasma cfDNA of a large cohort of cancer-free, elderly individuals was screened for the presence of chromosomal aberrations that might reveal the presence of a malignancy. Participants were subjected to a 6-month clinical follow-up when aberrancies were detected. Furthermore, CNAs, present in cfDNA in otherwise healthy elderly, were cataloged, creating a unique map of anomalies in cfDNA in this ageing population.