1
|
Raman L, Van der Linden M, De Vriendt C, Van den Broeck B, Muylle K, Deeren D, Dedeurwaerdere F, Verbeke S, Dendooven A, De Grove K, Baert S, Claes K, Menten B, Offner F, Van Dorpe J. Shallow-depth sequencing of cell-free DNA for Hodgkin and diffuse large B-cell lymphoma (differential) diagnosis: a standardized approach with underappreciated potential. Haematologica 2020; 107:211-220. [PMID: 33299235 PMCID: PMC8719079 DOI: 10.3324/haematol.2020.268813] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Indexed: 11/17/2022] Open
Abstract
Shallow-depth sequencing of cell-free DNA, an inexpensive and standardized approach to obtain molecular information on tumors non-invasively, has been insufficiently explored for the diagnosis of lymphoma and disease follow-up. This study collected 318 samples, including longitudinal liquid and paired solid biopsies, from a prospectively- recruited cohort of 38 Hodgkin lymphoma (HL) and 85 aggressive B-cell non-HL patients, represented by 81 diffuse large B-cell lymphoma (DLBCL) cases. Following sequencing, copy number alterations and viral read fractions were derived and analyzed. At diagnosis, liquid biopsies showed detectable copy number alterations in 84.2% of HL patients (88.6% for classical HL) and 74.1% of DLBCL patients. Of the DLBCL patients, copy number profiles between liquid-solid pairs were highly concordant (r=0.815±0.043); and, compared to tissue, HL liquid biopsies had abnormalities with higher amplitudes (P=0.010). This implies that tumor DNA is more abundant in plasma. Additionally, 39.5% of HL and 13.6% of DLBCL cases had a significantly elevated number of plasma Epstein-Barr virus DNA fragments, achieving a sensitivity of 100% compared to the current standard. A longitudinal analysis determined that, when detectable, copy number patterns were similar across (re)staging moments in refractory or relapsed patients. Further, the overall profile anomaly correlated highly with the total metabolic tumor volume (P<0.001). To conclude, as a proof of principle, we demonstrate that liquid biopsy-derived copy numbers can aid diagnosis: e.g., by differentiating HL from DLBCL, random forest modeling is represented by an area under the receiver operating characteristic curve of 0.967. This application is potentially useful when tissue is difficult to obtain or when biopsies are small and inconclusive.
Collapse
Affiliation(s)
- Lennart Raman
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium; Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent University Hospital, Ghent
| | - Malaïka Van der Linden
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium; Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent University Hospital, Ghent
| | - Ciel De Vriendt
- Department of Clinical Hematology, Ghent University, Ghent University Hospital, Ghent
| | | | | | | | | | - Sofie Verbeke
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent
| | - Amélie Dendooven
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium; Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk
| | - Katrien De Grove
- Department of Clinical Hematology, Ghent University, Ghent University Hospital, Ghent
| | - Saskia Baert
- Department of Clinical Hematology, Ghent University, Ghent University Hospital, Ghent
| | - Kathleen Claes
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent University Hospital, Ghent
| | - Björn Menten
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent University Hospital, Ghent
| | - Fritz Offner
- Department of Clinical Hematology, Ghent University, Ghent University Hospital, Ghent
| | - Jo Van Dorpe
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent.
| |
Collapse
|