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van den Brand M, Rijntjes J, Möbs M, Steinhilber J, van der Klift MY, Heezen KC, Kroeze LI, Reigl T, Porc J, Darzentas N, Luijks JACW, Scheijen B, Davi F, ElDaly H, Liu H, Anagnostopoulos I, Hummel M, Fend F, Langerak AW, Groenen PJTA. Next-Generation Sequencing-Based Clonality Assessment of Ig Gene Rearrangements: A Multicenter Validation Study by EuroClonality-NGS. J Mol Diagn 2021; 23:1105-1115. [PMID: 34186174 DOI: 10.1016/j.jmoldx.2021.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 05/17/2021] [Accepted: 06/01/2021] [Indexed: 11/18/2022] Open
Abstract
Ig gene (IG) clonality analysis has an important role in the distinction of benign and malignant B-cell lymphoid proliferations and is mostly performed with the conventional EuroClonality/BIOMED-2 multiplex PCR protocol and GeneScan fragment size analysis. Recently, the EuroClonality-NGS Working Group developed a method for next-generation sequencing (NGS)-based IG clonality analysis. Herein, we report the results of an international multicenter biological validation of this novel method compared with the gold standard EuroClonality/BIOMED-2 protocol, based on 209 specimens of reactive and neoplastic lymphoproliferations. NGS-based IG clonality analysis showed a high interlaboratory concordance (99%) and high concordance with conventional clonality analysis (98%) for the molecular conclusion. Detailed analysis of the individual IG heavy chain and kappa light chain targets showed that NGS-based clonality analysis was more often able to detect a clonal rearrangement or yield an interpretable result. NGS-based and conventional clonality analysis detected a clone in 96% and 95% of B-cell neoplasms, respectively, and all but one of the reactive cases were scored polyclonal. We conclude that NGS-based IG clonality analysis performs comparable to conventional clonality analysis. We provide critical parameters for interpretation and discuss a first step toward a quantitative scoring approach for NGS clonality results. Considering the advantages of NGS-based clonality analysis, including its high sensitivity and possibilities for accurate clonal comparison, this supports implementation in diagnostic practice.
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Affiliation(s)
- Michiel van den Brand
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Jos Rijntjes
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Markus Möbs
- Institute of Pathology, Charité-Universitätsmedizin, Berlin, Germany
| | - Julia Steinhilber
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Michèle Y van der Klift
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Kim C Heezen
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Leonie I Kroeze
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tomas Reigl
- Molecular Medicine Program, Central European Institute of Technology, Brno, Czech Republic
| | - Jakub Porc
- Molecular Medicine Program, Central European Institute of Technology, Brno, Czech Republic
| | - Nikos Darzentas
- Molecular Medicine Program, Central European Institute of Technology, Brno, Czech Republic; Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Jeroen A C W Luijks
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Blanca Scheijen
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Frédéric Davi
- Hematology Department, Hospital Pitié-Salpêtrière and Sorbonne University, Paris, France
| | - Hesham ElDaly
- Histopathology Department, Coventry University Hospitals National Health Service Trust, Coventry, United Kingdom; Clinical Pathology Department, Cairo University, Cairo, Egypt
| | - Hongxiang Liu
- Haematopathology and Oncology Diagnostics Service, Addenbrooke's Hospital, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, United Kingdom
| | | | - Michael Hummel
- Institute of Pathology, Charité-Universitätsmedizin, Berlin, Germany
| | - Falko Fend
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Anton W Langerak
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
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Scheijen B, Meijers RWJ, Rijntjes J, van der Klift MY, Möbs M, Steinhilber J, Reigl T, van den Brand M, Kotrová M, Ritter JM, Catherwood MA, Stamatopoulos K, Brüggemann M, Davi F, Darzentas N, Pott C, Fend F, Hummel M, Langerak AW, Groenen PJTA. Next-generation sequencing of immunoglobulin gene rearrangements for clonality assessment: a technical feasibility study by EuroClonality-NGS. Leukemia 2019; 33:2227-2240. [PMID: 31197258 PMCID: PMC6756030 DOI: 10.1038/s41375-019-0508-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/25/2019] [Accepted: 04/26/2019] [Indexed: 11/09/2022]
Abstract
One of the hallmarks of B lymphoid malignancies is a B cell clone characterized by a unique footprint of clonal immunoglobulin (IG) gene rearrangements that serves as a diagnostic marker for clonality assessment. The EuroClonality/BIOMED-2 assay is currently the gold standard for analyzing IG heavy chain (IGH) and κ light chain (IGK) gene rearrangements of suspected B cell lymphomas. Here, the EuroClonality-NGS Working Group presents a multicentre technical feasibility study of a novel approach involving next-generation sequencing (NGS) of IGH and IGK loci rearrangements that is highly suitable for detecting IG gene rearrangements in frozen and formalin-fixed paraffin-embedded tissue specimens. By employing gene-specific primers for IGH and IGK amplifying smaller amplicon sizes in combination with deep sequencing technology, this NGS-based IG clonality analysis showed robust performance, even in DNA samples of suboptimal DNA integrity, and a high clinical sensitivity for the detection of clonal rearrangements. Bioinformatics analyses of the high-throughput sequencing data with ARResT/Interrogate, a platform developed within the EuroClonality-NGS Working Group, allowed accurate identification of clonotypes in both polyclonal cell populations and monoclonal lymphoproliferative disorders. This multicentre feasibility study is an important step towards implementation of NGS-based clonality assessment in clinical practice, which will eventually improve lymphoma diagnostics.
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Affiliation(s)
- Blanca Scheijen
- Department of Pathology, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Ruud W J Meijers
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Jos Rijntjes
- Department of Pathology, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Michèle Y van der Klift
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Markus Möbs
- Charité-Universitätsmedizin Berlin, Institute of Pathology, D-10117, Berlin, Germany
| | - Julia Steinhilber
- Institute of Pathology and Neuropathology, Comprehensive Cancer Center, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Tomas Reigl
- Molecular Medicine Program, Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Michiel van den Brand
- Department of Pathology, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Michaela Kotrová
- Department of Hematology, University Hospital Schleswig-Holstein, 24105, Kiel, Germany
| | - Julia-Marie Ritter
- Charité-Universitätsmedizin Berlin, Institute of Pathology, D-10117, Berlin, Germany
| | - Mark A Catherwood
- Department of Haematology, Belfast City Hospital, Belfast BT9 7AB, UK
| | | | - Monika Brüggemann
- Department of Hematology, University Hospital Schleswig-Holstein, 24105, Kiel, Germany
| | - Frédéric Davi
- Hematology Department, Hospital Pitié-Salpêtrière and Sorbonne University, 75013, Paris, France
| | - Nikos Darzentas
- Molecular Medicine Program, Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic.,Department of Hematology, University Hospital Schleswig-Holstein, 24105, Kiel, Germany
| | - Christiane Pott
- Department of Hematology, University Hospital Schleswig-Holstein, 24105, Kiel, Germany
| | - Falko Fend
- Institute of Pathology and Neuropathology, Comprehensive Cancer Center, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Michael Hummel
- Charité-Universitätsmedizin Berlin, Institute of Pathology, D-10117, Berlin, Germany
| | - Anton W Langerak
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Patricia J T A Groenen
- Department of Pathology, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands.
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Kallemeijn MJ, Kavelaars FG, van der Klift MY, Wolvers-Tettero ILM, Valk PJM, van Dongen JJM, Langerak AW. Next-Generation Sequencing Analysis of the Human TCRγδ+ T-Cell Repertoire Reveals Shifts in Vγ- and Vδ-Usage in Memory Populations upon Aging. Front Immunol 2018; 9:448. [PMID: 29559980 PMCID: PMC5845707 DOI: 10.3389/fimmu.2018.00448] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/19/2018] [Indexed: 12/20/2022] Open
Abstract
Immunological aging remodels the immune system at several levels. This has been documented in particular for the T-cell receptor (TCR)αβ+ T-cell compartment, showing reduced naive T-cell outputs and an accumulation of terminally differentiated clonally expanding effector T-cells, leading to increased proneness to autoimmunity and cancer development at older age. Even though TCRαβ+ and TCRγδ+ T-cells follow similar paths of development involving V(D)J-recombination of TCR genes in the thymus, TCRγδ+ T-cells tend to be more subjected to peripheral rather than central selection. However, the impact of aging in shaping of the peripheral TRG/TRD repertoire remains largely elusive. Next-generation sequencing analysis methods were optimized based on a spike-in method using plasmid vector DNA-samples for accurate TRG/TRD receptor diversity quantification, resulting in optimally defined primer concentrations, annealing temperatures and cycle numbers. Next, TRG/TRD repertoire diversity was evaluated during TCRγδ+ T-cell ontogeny, showing a broad, diverse repertoire in thymic and cord blood samples with Gaussian CDR3-length distributions, in contrast to the more skewed repertoire in mature circulating TCRγδ+ T-cells in adult peripheral blood. During aging the naive repertoire maintained its diversity with Gaussian CDR3-length distributions, while in the central and effector memory populations a clear shift from young (Vγ9/Vδ2 dominance) to elderly (Vγ2/Vδ1 dominance) was observed. Together with less clear Gaussian CDR3-length distributions, this would be highly suggestive of differentially heavily selected repertoires. Despite the apparent age-related shift from Vγ9/Vδ2 to Vγ2/Vδ1, no clear aging effect was observed on the Vδ2 invariant T nucleotide and canonical Vγ9-Jγ1.2 selection determinants. A more detailed look into the healthy TRG/TRD repertoire revealed known cytomegalovirus-specific TRG/TRD clonotypes in a few donors, albeit without a significant aging-effect, while Mycobacterium tuberculosis-specific clonotypes were absent. Notably, in effector subsets of elderly individuals, we could identify reported TRG and TRD receptor chains from TCRγδ+ T-cell large granular lymphocyte leukemia proliferations, which typically present in the elderly population. Collectively, our results point to relatively subtle age-related changes in the human TRG/TRD repertoire, with a clear shift in Vγ/Vδ usage in memory cells upon aging.
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Affiliation(s)
- Martine J Kallemeijn
- Laboratory for Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - François G Kavelaars
- Department of Hematology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Michèle Y van der Klift
- Laboratory for Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Ingrid L M Wolvers-Tettero
- Laboratory for Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Peter J M Valk
- Department of Hematology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Jacques J M van Dongen
- Laboratory for Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Anton W Langerak
- Laboratory for Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
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