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Nguyen PC, Nguyen T, Wilson C, Tiong IS, Baldwin K, Nguyen V, Came N, Blombery P, Westerman DA. Evaluation of T-cell clonality by anti-TRBC1 antibody-based flow cytometry and correlation with T-cell receptor sequencing. Br J Haematol 2024; 204:910-920. [PMID: 38098188 DOI: 10.1111/bjh.19252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/08/2023] [Accepted: 11/28/2023] [Indexed: 03/14/2024]
Abstract
Flow cytometry (FC) incorporating the T-cell receptor β constant chain-1 (TRBC1) has been recently proposed as a new standard in T-cell clonality assessment. While early studies demonstrated high sensitivity in samples with conspicuous tumour burden, performance in real-world samples, including those with low tumour burden and correlation with molecular methods has been limited. We evaluated TRBC1-FC performance and correlated the results with high-throughput TRB sequencing and a targeted next-generation sequencing gene panel. Our cohort consisted of 90 evaluable samples from 57 patients. TRBC1-FC confirmed T-cell clonality in 37 out of 38 samples (97%) that were involved in a mature T-cell neoplasm (MTCN). T-cell clonality was also identified in nine samples from patients lacking a current or prior diagnosis of MTCN, consistent with the emerging entity T-cell clonality of uncertain significance. TRBC-FC was polyclonal in all samples and negative for disease involvement by standard pathology assessment. However, correlation with TRB sequencing in 17 of these samples identified two cases that harboured the known clonal sequence from index testing, indicating the presence of measurable residual disease not otherwise detected. Our study provides real-world correlative validation of TRBC1-FC, highlighting the strengths and limitations pertinent to its increasing implementation by general diagnostic laboratories.
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Affiliation(s)
- Phillip C Nguyen
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Tamia Nguyen
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Clarissa Wilson
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Ing Soo Tiong
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Kylie Baldwin
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Vuong Nguyen
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Neil Came
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Piers Blombery
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
- Department of Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - David A Westerman
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
- Department of Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia
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2
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Grants JM, May C, Bridgers J, Huang S, Gillis S, Meissner B, Boyle M, Ben-Neriah S, Hung S, Duns G, Hilton L, Gerrie AS, Marra M, Kridel R, Sabatini PJB, Steidl C, Scott DW, Karsan A. Chronic Lymphocytic Leukemia IGHV Somatic Hypermutation Detection by Targeted Capture Next-Generation Sequencing. Clin Chem 2024; 70:273-284. [PMID: 38175592 DOI: 10.1093/clinchem/hvad147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/13/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Somatic hypermutation (SHM) status of the immunoglobulin heavy variable (IGHV) gene plays a crucial role in determining the prognosis and treatment of patients with chronic lymphocytic leukemia (CLL). A common approach for determining SHM status is multiplex polymerase chain reaction and Sanger sequencing of the immunoglobin heavy locus; however, this technique is low throughput, is vulnerable to failure, and does not allow multiplexing with other diagnostic assays. METHODS Here we designed and validated a DNA targeted capture approach to detect immunoglobulin heavy variable somatic hypermutation (IGHV SHM) status as a submodule of a larger next-generation sequencing (NGS) panel that also includes probes for ATM, BIRC3, CHD2, KLHL6, MYD88, NOTCH1, NOTCH2, POT1, SF3B1, TP53, and XPO1. The assay takes as input FASTQ files and outputs a report containing IGHV SHM status and V allele usage following European Research Initiative on CLL guidelines. RESULTS We validated the approach on 35 CLL patient samples, 34 of which were characterized using Sanger sequencing. The NGS panel identified the IGHV SHM status of 34 of 35 CLL patients. We showed 100% sensitivity and specificity among the 33 CLL samples with both NGS and Sanger sequencing calls. Furthermore, we demonstrated that this panel can be combined with additional targeted capture panels to detect prognostically important CLL single nucleotide variants, insertions/deletions, and copy number variants (TP53 copy number loss). CONCLUSIONS A targeted capture approach to IGHV SHM detection can be integrated into broader sequencing panels, allowing broad CLL prognostication in a single molecular assay.
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Affiliation(s)
- Jennifer M Grants
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Christina May
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Josh Bridgers
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Shujun Huang
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Sierra Gillis
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Barbara Meissner
- Centre for Lymphoid Cancer, BC Cancer Centre, Vancouver, BC, Canada
| | - Merrill Boyle
- Centre for Lymphoid Cancer, BC Cancer Centre, Vancouver, BC, Canada
| | | | - Stacy Hung
- Centre for Lymphoid Cancer, BC Cancer Centre, Vancouver, BC, Canada
| | - Gerben Duns
- Centre for Lymphoid Cancer, BC Cancer Centre, Vancouver, BC, Canada
| | - Laura Hilton
- Centre for Lymphoid Cancer, BC Cancer Centre, Vancouver, BC, Canada
| | - Alina S Gerrie
- Centre for Lymphoid Cancer, BC Cancer Centre, Vancouver, BC, Canada
| | - Marco Marra
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Robert Kridel
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Peter J B Sabatini
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer Centre, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, BC Cancer Centre, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Aly Karsan
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
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3
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Gazzola A, Navari M, Mannu C, Donelli R, Etebari M, Piccaluga PP. Single-Step IGHV Next-Generation Sequencing Detects Clonality and Somatic Hypermutation in Lymphoid Malignancies: A Phase III Diagnostic Accuracy Study. Cancers (Basel) 2023; 15:4624. [PMID: 37760593 PMCID: PMC10526376 DOI: 10.3390/cancers15184624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Multiplex PCR based on consensus primers followed by capillary electrophoresis and Sanger sequencing are considered as the gold standard method for the evaluation of clonality and somatic hypermutation in lymphoid malignancies. As an alternative, the next-generation sequencing (NGS) of immune receptor genes has recently been proposed as a solution, due to being highly effective and sensitive. Here, we designed a phase III diagnostic accuracy study intended to compare the current gold standard methods versus the first commercially available NGS approaches for testing immunoglobulin heavy chain gene rearrangements. METHODS We assessed IGH rearrangements in 68 samples by means of both the NGS approach (LymphoTrack® IGH assay, and LymphoTrack® IGH somatic hypermutation assay, run on Illumina MiSeq) and capillary electrophoresis/Sanger sequencing to assess clonality and somatic hypermutations (SHM). RESULTS In comparison to the routine capillary-based analysis, the NGS clonality assay had an overall diagnostic accuracy of 96% (63/66 cases). Other studied criteria included sensitivity (95%), specificity (100%), positive predictive value (100%) and negative predictive value (75%). In discrepant cases, the NGS results were confirmed by a different set of primers that provided coverage of the IGH leader sequence. Furthermore, there was excellent agreement of the SHM determination with both the LymphoTrack® FR1 and leader assays when compared to the Sanger sequencing analysis (84%), with NGS able to assess the SHM rate even in cases where the conventional approach failed. CONCLUSION Overall, conventional Sanger sequencing and next-generation-sequencing-based clonality and somatic hypermutation analyses gave comparable results. For future use in a routine diagnostic workflow, NGS-based approaches should be evaluated prospectively and an analysis of cost-effectiveness should be performed.
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Affiliation(s)
- Anna Gazzola
- Hematopathology Unit, IRCCS Azienda Opedaliera-Universitaria di Bologna S. Orsola-Malpighi, 40138 Bologna, Italy; (A.G.); (C.M.)
| | - Mohsen Navari
- Department of Medical Biotechnology, School of Paramedical Sciences, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh 95196-33787, Iran;
- Research Center of Advanced Technologies in Medicine, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh 95196-33787, Iran
- Bioinformatics Research Center, Mashhad University of Medical Sciences, Mashhad 91779-48564, Iran
| | - Claudia Mannu
- Hematopathology Unit, IRCCS Azienda Opedaliera-Universitaria di Bologna S. Orsola-Malpighi, 40138 Bologna, Italy; (A.G.); (C.M.)
| | - Riccardo Donelli
- Biobank of Research, IRCCS Azienda Opedaliera-Universitaria di Bologna, 40138 Bologna, Italy;
- Department of Medical and Surgical Sciences, Institute of Hematology and Medical Oncology “L&A Seràgnoli”, Bologna University School of Medicine, 40126 Bologna, Italy
| | - Maryam Etebari
- Health Sciences Research Center, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh 33787-95196, Iran;
| | - Pier Paolo Piccaluga
- Biobank of Research, IRCCS Azienda Opedaliera-Universitaria di Bologna, 40138 Bologna, Italy;
- Department of Medical and Surgical Sciences, Institute of Hematology and Medical Oncology “L&A Seràgnoli”, Bologna University School of Medicine, 40126 Bologna, Italy
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4
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Genuardi E, Alessandria B, Civita AM, Ferrero S. Targeted Locus Amplification as Marker Screening Approach to Detect Immunoglobulin (IG) Translocations in B-Cell Non-Hodgkin Lymphomas. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2453:119-132. [PMID: 35622324 DOI: 10.1007/978-1-0716-2115-8_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although MRD monitoring by the classic polymerase chain reaction (PCR) approach is a powerful outcome predictor, about 20% of mantle cell lymphoma (MCL) and 50% of follicular lymphoma (FL) patients still lack a molecular marker and are thus resulting not eligible for MRD monitoring. Targeted locus amplification (TLA), a new NGS technology, has been revealed as a feasible marker screening approach able to identify uncommon B-cell leukemia/lymphoma 1 (BCL1) and B-cell leukemia/lymphoma 2 (BCL2) rearrangements in MCL and FL cases defined as having "no marker" by the classic PCR approach.
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Affiliation(s)
- Elisa Genuardi
- Hematology Division, Department of Molecular Biotechnologies and Health Sciences, University of Torino, Torino, Italy
| | - Beatrice Alessandria
- Hematology Division, Department of Molecular Biotechnologies and Health Sciences, University of Torino, Torino, Italy
| | - Aurora Maria Civita
- Hematology Division, Department of Molecular Biotechnologies and Health Sciences, University of Torino, Torino, Italy
| | - Simone Ferrero
- Hematology Division, Department of Molecular Biotechnologies and Health Sciences, University of Torino, Torino, Italy. .,Hematology Division, AOU "Città della Salute e della Scienza di Torino", Torino, Italy.
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5
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Giudice ID, Starza ID, Foà R. Does MRD have a role in the management of iNHL? HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2021; 2021:320-330. [PMID: 34889425 PMCID: PMC8791119 DOI: 10.1182/hematology.2021000312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Among indolent non-Hodgkin lymphomas (iNHLs), the analysis of measurable/minimal residual disease (MRD) has been extensively applied to follicular lymphoma (FL). Treatment combinations have deeply changed over the years, as well as the techniques to measure MRD, which is currently evaluated only in the setting of clinical trials. Here, we discuss the evidence on the role of molecular monitoring in the management of FL. Mature data support the quantification of molecular tumor burden at diagnosis as a tool to stratify patients in risk categories and of MRD evaluation at the end of treatment to predict progression-free survival and overall survival. Moreover, MRD deserves further studies as a tool to refine the clinical/metabolic response and to modulate treatment intensity/duration. Patients with a higher relapse probability can be identified, but the relevance of continuous molecular follow-up should be clarified by kinetic models of MRD analysis. Being the BCL2/heavy chain immunoglobulin gene hybrid rearrangement detectable in about 50% to 60% of advanced FL and in 30% of positron emission tomography/computed tomography-staged localized FL, technical advancements such as next-generation sequencing/target locus amplification may allow broadening the FL population carrying a molecular marker. Droplet digital polymerase chain reaction can better quantify MRD at low levels, and novel sources of DNA, such as cell-free DNA, may represent a noninvasive tool to monitor MRD. Finally, MRD in other iNHLs, such as lymphoplasmacytic lymphoma/Waldenström macroglobulinemia and marginal zone lymphoma, is beginning to be explored.
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Affiliation(s)
- Ilaria Del Giudice
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Irene Della Starza
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Robin Foà
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
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6
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Agathangelidis A, Vlachonikola E, Davi F, Langerak AW, Chatzidimitriou A. High-Throughput immunogenetics for precision medicine in cancer. Semin Cancer Biol 2021; 84:80-88. [PMID: 34757183 DOI: 10.1016/j.semcancer.2021.10.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 01/20/2023]
Abstract
Cancer is characterized by an extremely complex biological background, which hinders personalized therapeutic interventions. Precision medicine promises to overcome this obstacle through integrating information from different 'subsystems', including the host, the external environment, the tumor itself and the tumor micro-environment. Immunogenetics is an essential tool that allows dissecting both lymphoid cancer ontogeny at both a cell-intrinsic and a cell-extrinsic level, i.e. through characterizing micro-environmental interactions, with a view to precision medicine. This is particularly thanks to the introduction of powerful, high-throughput approaches i.e. next generation sequencing, which allow the comprehensive characterization of immune repertoires. Indeed, NGS immunogenetic analysis (Immune-seq) has emerged as key to both understanding cancer pathogenesis and improving the accuracy of clinical decision making in oncology. Immune-seq has applications in lymphoid malignancies, assisting in the diagnosis e.g. through differentiating from reactive conditions, as well as in disease monitoring through accurate assessment of minimal residual disease. Moreover, Immune-seq facilitates the study of T cell receptor clonal dynamics in critical clinical contexts, including transplantation as well as innovative immunotherapy for solid cancers. The clinical utility of Immune-seq represents the focus of the present contribution, where we highlight what can be achieved but also what must be addressed in order to maximally realize the promise of Immune-seq in precision medicine in cancer.
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Affiliation(s)
- Andreas Agathangelidis
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece; Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
| | - Elisavet Vlachonikola
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece; Department of Genetics and Molecular Biology, Faculty of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Frederic Davi
- Department of Hematology, APHP, Hôpital Pitié-Salpêtrière and Sorbonne University, Paris, France
| | - Anton W Langerak
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, Rotterdam, the Netherlands
| | - Anastasia Chatzidimitriou
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece; Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75236, Sweden.
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7
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Mansouri L, Thorvaldsdottir B, Laidou S, Stamatopoulos K, Rosenquist R. Precision diagnostics in lymphomas - Recent developments and future directions. Semin Cancer Biol 2021; 84:170-183. [PMID: 34699973 DOI: 10.1016/j.semcancer.2021.10.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 01/03/2023]
Abstract
Genetics is an integral part of the clinical diagnostics of lymphomas that improves disease subclassification and patient risk-stratification. With the introduction of high-throughput sequencing technologies, a rapid, in-depth portrayal of the genomic landscape in major lymphoma entities was achieved. Whilst a few lymphoma entities were characterized by a predominant gene mutation (e.g. Waldenström's macroglobulinemia and hairy cell leukemia), the vast majority demonstrated a very diverse genetic landscape with a high number of recurrent gene mutations (e.g. chronic lymphocytic leukemia and diffuse large B cell lymphoma), indeed reflecting the great clinical heterogeneity among lymphomas. These studies have allowed better understanding of the ontogeny and evolution of different lymphomas, while also identifying new genetic markers that can complement lymphoma diagnostics and improve prognostication. However, despite these efforts, there is still a limited number of gene mutations with predictive impact that can guide treatment selection. In this review, we will highlight clinically relevant diagnostic, prognostic and predictive markers in lymphomas that are used today in routine diagnostics. We will also discuss how comprehensive genomic characterization using broad sequencing panels, allowing for the simultaneous detection of different types of genetic aberrations, may aid future development of precision diagnostics in lymphomas. This may in turn pave the way for the implementation of tailored precision therapy strategies at the individual patient level.
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Affiliation(s)
- Larry Mansouri
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Birna Thorvaldsdottir
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Stamatia Laidou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Kostas Stamatopoulos
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Solna, Sweden.
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8
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Validation of the EuroClonality-NGS DNA capture panel as an integrated genomic tool for lymphoproliferative disorders. Blood Adv 2021; 5:3188-3198. [PMID: 34424321 DOI: 10.1182/bloodadvances.2020004056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/16/2021] [Indexed: 11/20/2022] Open
Abstract
Current diagnostic standards for lymphoproliferative disorders include multiple tests for detection of clonal immunoglobulin (IG) and/or T-cell receptor (TCR) rearrangements, translocations, copy-number alterations (CNAs), and somatic mutations. The EuroClonality-NGS DNA Capture (EuroClonality-NDC) assay was designed as an integrated tool to characterize these alterations by capturing IGH switch regions along with variable, diversity, and joining genes of all IG and TCR loci in addition to clinically relevant genes for CNA and mutation analysis. Diagnostic performance against standard-of-care clinical testing was assessed in a cohort of 280 B- and T-cell malignancies from 10 European laboratories, including 88 formalin-fixed paraffin-embedded samples and 21 reactive lesions. DNA samples were subjected to the EuroClonality-NDC protocol in 7 EuroClonality-NGS laboratories and analyzed using a bespoke bioinformatic pipeline. The EuroClonality-NDC assay detected B-cell clonality in 191 (97%) of 197 B-cell malignancies and T-cell clonality in 71 (97%) of 73 T-cell malignancies. Limit of detection (LOD) for IG/TCR rearrangements was established at 5% using cell line blends. Chromosomal translocations were detected in 145 (95%) of 152 cases known to be positive. CNAs were validated for immunogenetic and oncogenetic regions, highlighting their novel role in confirming clonality in somatically hypermutated cases. Single-nucleotide variant LOD was determined as 4% allele frequency, and an orthogonal validation using 32 samples resulted in 98% concordance. The EuroClonality-NDC assay is a robust tool providing a single end-to-end workflow for simultaneous detection of B- and T-cell clonality, translocations, CNAs, and sequence variants.
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9
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Rosenquist R. Molecular diagnostics and reporting in lymphoid malignancies: Current status and beyond. Hematol Oncol 2021; 39 Suppl 1:73-77. [PMID: 34105808 DOI: 10.1002/hon.2849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Indexed: 11/05/2022]
Affiliation(s)
- Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
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10
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Navrkalova V, Plevova K, Hynst J, Pal K, Mareckova A, Reigl T, Jelinkova H, Vrzalova Z, Stranska K, Pavlova S, Panovska A, Janikova A, Doubek M, Kotaskova J, Pospisilova S. LYmphoid NeXt-Generation Sequencing (LYNX) Panel: A Comprehensive Capture-Based Sequencing Tool for the Analysis of Prognostic and Predictive Markers in Lymphoid Malignancies. J Mol Diagn 2021; 23:959-974. [PMID: 34082072 DOI: 10.1016/j.jmoldx.2021.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 04/21/2021] [Accepted: 05/03/2021] [Indexed: 02/07/2023] Open
Abstract
B-cell neoplasms represent a clinically heterogeneous group of hematologic malignancies with considerably diverse genomic architecture recently endorsed by next-generation sequencing (NGS) studies. Because multiple genetic defects have a potential or confirmed clinical impact, a tendency toward more comprehensive testing of diagnostic, prognostic, and predictive markers is desired. This study introduces the design, validation, and implementation of an integrative, custom-designed, capture-based NGS panel titled LYmphoid NeXt-generation sequencing (LYNX) for the analysis of standard and novel molecular markers in the most common lymphoid neoplasms (chronic lymphocytic leukemia, acute lymphoblastic leukemia, diffuse large B-cell lymphoma, follicular lymphoma, and mantle cell lymphoma). A single LYNX test provides the following: i) accurate detection of mutations in all coding exons and splice sites of 70 lymphoma-related genes with a sensitivity of 5% variant allele frequency, ii) reliable identification of large genome-wide (≥6 Mb) and recurrent chromosomal aberrations (≥300 kb) in at least 20% of the clonal cell fraction, iii) the assessment of immunoglobulin and T-cell receptor gene rearrangements, and iv) lymphoma-specific translocation detection. Dedicated bioinformatic pipelines were designed to detect all markers mentioned above. The LYNX panel represents a comprehensive, up-to-date tool suitable for routine testing of lymphoid neoplasms with research and clinical applicability. It allows a wide adoption of capture-based targeted NGS in clinical practice and personalized management of patients with lymphoproliferative diseases.
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Affiliation(s)
- Veronika Navrkalova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karla Plevova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Jakub Hynst
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karol Pal
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Department of Internal Medicine II - Hematology and Oncology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Andrea Mareckova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Tomas Reigl
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Hana Jelinkova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Zuzana Vrzalova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Kamila Stranska
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Sarka Pavlova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Anna Panovska
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Andrea Janikova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Michael Doubek
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Jana Kotaskova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic.
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11
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Tosi M, Spinelli O, Leoncin M, Cavagna R, Pavoni C, Lussana F, Intermesoli T, Frison L, Perali G, Carobolante F, Viero P, Skert C, Rambaldi A, Bassan R. MRD-Based Therapeutic Decisions in Genetically Defined Subsets of Adolescents and Young Adult Philadelphia-Negative ALL. Cancers (Basel) 2021; 13:cancers13092108. [PMID: 33925541 PMCID: PMC8123823 DOI: 10.3390/cancers13092108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/05/2022] Open
Abstract
Simple Summary In acute lymphoblastic leukemia (ALL), once a complete remission is achieved following induction chemotherapy, the study of submicroscopic minimal residual disease (MRD) represents a highly sensitive tool to assess the efficacy of early chemotherapy courses and predict outcome. Because of the significant therapeutic progress occurred in adolescent and young adult (AYA) ALL, the importance of MRD in this peculiar age setting has grown considerably, to refine individual prognostic scores within different genetic subsets and support specific risk and MRD-oriented programs. The evidence coming from the most recent MRD-based studies and the new therapeutic directions for AYA ALL are critically reviewed according to ALL subset and risk category. Abstract In many clinical studies published over the past 20 years, adolescents and young adults (AYA) with Philadelphia chromosome negative acute lymphoblastic leukemia (Ph− ALL) were considered as a rather homogeneous clinico-prognostic group of patients suitable to receive intensive pediatric-like regimens with an improved outcome compared with the use of traditional adult ALL protocols. The AYA group was defined in most studies by an age range of 18–40 years, with some exceptions (up to 45 years). The experience collected in pediatric ALL with the study of post-induction minimal residual disease (MRD) was rapidly duplicated in AYA ALL, making MRD a widely accepted key factor for risk stratification and risk-oriented therapy with or without allogeneic stem cell transplantation and experimental new drugs for patients with MRD detectable after highly intensive chemotherapy. This combined strategy has resulted in long-term survival rates of AYA patients of 60–80%. The present review examines the evidence for MRD-guided therapies in AYA’s Ph− ALL, provides a critical appraisal of current treatment pitfalls and illustrates the ways of achieving further therapeutic improvement according to the massive knowledge recently generated in the field of ALL biology and MRD/risk/subset-specific therapy
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Affiliation(s)
- Manuela Tosi
- Hematology Unit, Azienda Socio Sanitaria Territoriale (ASST), Ospedale Papa Giovanni XXIII, 24127 Bergamo, Italy; (M.T.); (O.S.); (R.C.); (C.P.); (F.L.); (T.I.); (A.R.)
| | - Orietta Spinelli
- Hematology Unit, Azienda Socio Sanitaria Territoriale (ASST), Ospedale Papa Giovanni XXIII, 24127 Bergamo, Italy; (M.T.); (O.S.); (R.C.); (C.P.); (F.L.); (T.I.); (A.R.)
| | - Matteo Leoncin
- Hematology Unit, Azienda Ulss3 Serenissima, Ospedale dell’Angelo, 30174 Venezia-Mestre, Italy; (M.L.); (L.F.); (G.P.); (F.C.); (P.V.); (C.S.)
| | - Roberta Cavagna
- Hematology Unit, Azienda Socio Sanitaria Territoriale (ASST), Ospedale Papa Giovanni XXIII, 24127 Bergamo, Italy; (M.T.); (O.S.); (R.C.); (C.P.); (F.L.); (T.I.); (A.R.)
| | - Chiara Pavoni
- Hematology Unit, Azienda Socio Sanitaria Territoriale (ASST), Ospedale Papa Giovanni XXIII, 24127 Bergamo, Italy; (M.T.); (O.S.); (R.C.); (C.P.); (F.L.); (T.I.); (A.R.)
| | - Federico Lussana
- Hematology Unit, Azienda Socio Sanitaria Territoriale (ASST), Ospedale Papa Giovanni XXIII, 24127 Bergamo, Italy; (M.T.); (O.S.); (R.C.); (C.P.); (F.L.); (T.I.); (A.R.)
| | - Tamara Intermesoli
- Hematology Unit, Azienda Socio Sanitaria Territoriale (ASST), Ospedale Papa Giovanni XXIII, 24127 Bergamo, Italy; (M.T.); (O.S.); (R.C.); (C.P.); (F.L.); (T.I.); (A.R.)
| | - Luca Frison
- Hematology Unit, Azienda Ulss3 Serenissima, Ospedale dell’Angelo, 30174 Venezia-Mestre, Italy; (M.L.); (L.F.); (G.P.); (F.C.); (P.V.); (C.S.)
| | - Giulia Perali
- Hematology Unit, Azienda Ulss3 Serenissima, Ospedale dell’Angelo, 30174 Venezia-Mestre, Italy; (M.L.); (L.F.); (G.P.); (F.C.); (P.V.); (C.S.)
| | - Francesca Carobolante
- Hematology Unit, Azienda Ulss3 Serenissima, Ospedale dell’Angelo, 30174 Venezia-Mestre, Italy; (M.L.); (L.F.); (G.P.); (F.C.); (P.V.); (C.S.)
| | - Piera Viero
- Hematology Unit, Azienda Ulss3 Serenissima, Ospedale dell’Angelo, 30174 Venezia-Mestre, Italy; (M.L.); (L.F.); (G.P.); (F.C.); (P.V.); (C.S.)
| | - Cristina Skert
- Hematology Unit, Azienda Ulss3 Serenissima, Ospedale dell’Angelo, 30174 Venezia-Mestre, Italy; (M.L.); (L.F.); (G.P.); (F.C.); (P.V.); (C.S.)
| | - Alessandro Rambaldi
- Hematology Unit, Azienda Socio Sanitaria Territoriale (ASST), Ospedale Papa Giovanni XXIII, 24127 Bergamo, Italy; (M.T.); (O.S.); (R.C.); (C.P.); (F.L.); (T.I.); (A.R.)
- Department of Oncology-Hematology, University of Milan, 20122 Milan, Italy
| | - Renato Bassan
- Hematology Unit, Azienda Ulss3 Serenissima, Ospedale dell’Angelo, 30174 Venezia-Mestre, Italy; (M.L.); (L.F.); (G.P.); (F.C.); (P.V.); (C.S.)
- Correspondence: ; Tel.: +39-041-965-7362
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12
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Johansson G, Kaltak M, Rîmniceanu C, Singh AK, Lycke J, Malmeström C, Hühn M, Vaarala O, Cardell S, Ståhlberg A. Ultrasensitive DNA Immune Repertoire Sequencing Using Unique Molecular Identifiers. Clin Chem 2021; 66:1228-1237. [PMID: 32814950 DOI: 10.1093/clinchem/hvaa159] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/25/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Immune repertoire sequencing of the T-cell receptor can identify clonotypes that have expanded as a result of antigen recognition or hematological malignancies. However, current sequencing protocols display limitations with nonuniform amplification and polymerase-induced errors during sequencing. Here, we developed a sequencing method that overcame these issues and applied it to γδ T cells, a cell type that plays a unique role in immunity, autoimmunity, homeostasis of intestine, skin, adipose tissue, and cancer biology. METHODS The ultrasensitive immune repertoire sequencing method used PCR-introduced unique molecular identifiers. We constructed a 32-panel assay that captured the full diversity of the recombined T-cell receptor delta loci in γδ T cells. The protocol was validated on synthetic reference molecules and blood samples of healthy individuals. RESULTS The 32-panel assay displayed wide dynamic range, high reproducibility, and analytical sensitivity with single-nucleotide resolution. The method corrected for sequencing-depended quantification bias and polymerase-induced errors and could be applied to both enriched and nonenriched cells. Healthy donors displayed oligoclonal expansion of γδ T cells and similar frequencies of clonotypes were detected in both enrichment and nonenriched samples. CONCLUSIONS Ultrasensitive immune repertoire sequencing strategy enables quantification of individual and specific clonotypes in a background that can be applied to clinical as well as basic application areas. Our approach is simple, flexible, and can easily be implemented in any molecular laboratory.
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Affiliation(s)
- Gustav Johansson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Translational Science & Experimental Medicine, Research and Early Development, Respiratory, Inflammation and Autoimmune (RIA), Gothenburg, Sweden
| | - Melita Kaltak
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Cristiana Rîmniceanu
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 7A, University of Gothenburg, Gothenburg, Sweden
| | - Avadhesh K Singh
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 7A, University of Gothenburg, Gothenburg, Sweden
| | - Jan Lycke
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Clas Malmeström
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Michael Hühn
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory, Inflammation and Autoimmune (RIA), Gothenburg, Sweden
| | - Outi Vaarala
- Respiratory Inflammation and Autoimmunity, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Susanna Cardell
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 7A, University of Gothenburg, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
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13
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Correia RP, Puga RD, Muto NH, Lee MLDM, Torres DC, Hassan R, Bacal NS, Hamerschlak N, Campregher PV. High-throughput sequencing of immunoglobulin heavy chain for minimal residual disease detection in B-lymphoblastic leukemia. Int J Lab Hematol 2021; 43:724-731. [PMID: 33393719 DOI: 10.1111/ijlh.13453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/24/2020] [Accepted: 12/17/2020] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Minimal residual disease (MRD) is a cornerstone for stratification of upfront B-lymphoblastic leukemia (B-ALL) treatment protocols to decrease relapse risk. Although its detection by flow cytometry (FC) and real-time quantitative polymerase has clinical usefulness, evidence suggests that methods with increased sensitivity could lead to improved outcomes. The aim of this study was to develop an amplicon-based assay followed by high-throughput sequencing of the immunoglobulin heavy chain variable region for MRD detection in B-ALL. METHODS We analyzed 84 samples, 27 from diagnosis, 5 from relapse, 40 from post-treatment samples, and 12 from healthy controls. RESULTS Our assay was able to identify more neoplastic clones at diagnosis than Sanger sequencing including incomplete DJ rearrangements. From the 40 MRD samples evaluated 21 were positive by our new approach on high-throughput sequencing assay, but only 15 of these were positive by FC. The remaining 19 were negative by the two techniques. CONCLUSION We have developed a novel approach on high-sensitive assay for MRD detection in B-ALL, which could add clinical value in the management of patients, especially in cases negative for MRD by FC.
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Affiliation(s)
- Rodolfo P Correia
- Departments of Clinical Pathology Laboratory, Hematology and Hemotherapy, Research Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Renato D Puga
- Departments of Clinical Pathology Laboratory, Hematology and Hemotherapy, Research Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Nair H Muto
- Departments of Clinical Pathology Laboratory, Hematology and Hemotherapy, Research Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | | | - Davi C Torres
- Bone Marrow Transplantation Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Rocio Hassan
- Bone Marrow Transplantation Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Nydia S Bacal
- Departments of Clinical Pathology Laboratory, Hematology and Hemotherapy, Research Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil.,Centro de Hematologia de São Paulo, São Paulo, Brazil
| | - Nelson Hamerschlak
- Departments of Clinical Pathology Laboratory, Hematology and Hemotherapy, Research Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Paulo V Campregher
- Departments of Clinical Pathology Laboratory, Hematology and Hemotherapy, Research Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
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14
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Capture-based Next-Generation Sequencing Improves the Identification of Immunoglobulin/T-Cell Receptor Clonal Markers and Gene Mutations in Adult Acute Lymphoblastic Leukemia Patients Lacking Molecular Probes. Cancers (Basel) 2020; 12:cancers12061505. [PMID: 32526928 PMCID: PMC7352935 DOI: 10.3390/cancers12061505] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/23/2020] [Accepted: 06/05/2020] [Indexed: 01/08/2023] Open
Abstract
The monitoring of minimal residual disease (MRD) in Philadelphia-negative acute lymphoblastic leukemia (ALL) requires the identification at diagnosis of immunoglobulin/T-cell receptor (Ig/TCR) rearrangements as clonality markers. Aiming to simplify and possibly improve the patients' initial screening, we designed a capture-based next-generation sequencing (NGS) panel combining the Ig/TCR rearrangement detection with the profiling of relevant leukemia-related genes. The validation of the assay on well-characterized samples allowed us to identify all the known Ig/TCR rearrangements as well as additional clonalities, including rare rearrangements characterized by uncommon combinations of variable, diversity, and joining (V-D-J) gene segments, oligoclonal rearrangements, and low represented clones. Upon validation, the capture NGS approach allowed us to identify Ig/TCR clonal markers in 87% of a retrospective cohort (MRD-unknown within the Northern Italy Leukemia Group (NILG)-ALL 09/00 clinical trial) and in 83% of newly-diagnosed ALL cases in which conventional method failed, thus proving its prospective applicability. Finally, we identified gene variants in 94.7% of patients analyzed for mutational status with the same implemented capture assay. The prospective application of this technology could simplify clonality assessment and improve standard assay development for leukemia monitoring, as well as provide information about the mutational status of selected leukemia-related genes, potentially representing new prognostic elements, MRD markers, and targets for specific therapies.
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15
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Gupta SK, Viswanatha DS, Patel KP. Evaluation of Somatic Hypermutation Status in Chronic Lymphocytic Leukemia (CLL) in the Era of Next Generation Sequencing. Front Cell Dev Biol 2020; 8:357. [PMID: 32509784 PMCID: PMC7248390 DOI: 10.3389/fcell.2020.00357] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/21/2020] [Indexed: 01/22/2023] Open
Abstract
Somatic hypermutation (SHM) status provides an important prognostic indicator for chronic lymphocytic leukemia (CLL), a very common type of mature B-cell leukemia. Owing to the adverse prognosis associated with an unmutated immunoglobulin heavy chain variable (IGHV) status, SHM testing is performed as a standard of care in CLL. Conventionally, SHM testing has been performed using labor intensive and primarily analog Sanger sequencing method following PCR amplification of the clonal immunoglobulin heavy chain gene rearrangements in CLL cells. In comparison, recent availability of next generation sequencing (NGS) allows more versatile detection and direct identification of clonal immunoglobulin gene rearrangements in neoplastic B-cell populations. The ability to identify specific clonal IGHV signature(s) in both baseline (diagnostic) and post-treatment settings enables unique clinical applications of NGS such as determination of SHM status, minimal residual disease (MRD) monitoring, clonal heterogeneity and B cell receptor IG stereotypy. We provide a review of current practices and recommendations for SHM determination using NGS including examples of difficult cases.
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Affiliation(s)
- Sanjeev Kumar Gupta
- Laboratory Oncology Unit, Dr. B.R.A IRCH, All India Institute of Medical Sciences, New Delhi, New Delhi, India
| | | | - Keyur P. Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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16
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Droplet Digital PCR Quantification of Mantle Cell Lymphoma Follow-up Samples From Four Prospective Trials of the European MCL Network. Hemasphere 2020; 4:e347. [PMID: 32309784 PMCID: PMC7162081 DOI: 10.1097/hs9.0000000000000347] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/21/2020] [Accepted: 01/27/2020] [Indexed: 12/25/2022] Open
Abstract
Minimal residual disease (MRD) has been increasingly investigated in mantle cell lymphoma (MCL), including for individual therapeutic stratification and pre-emptive treatment in clinical trials. Although patient/allele specific real-time quantitative polymerase chain reaction (qPCR) of IGH or BCL1-IGH clonal markers is the gold-standard method, its reliance on a standard curve for relative quantification limits quantification of low-level positivity within the 1E-4 to 1E-5 range; over half of positive MRD samples after treatment fall below the quantitative range (BQR) of the standard curve. Droplet digital PCR (ddPCR), in contrast, allows absolute quantification, including for samples with no baseline determination of tumor infiltration by multicolor flow cytometry (MFC), avoiding the need for a reference standard curve. Using updated, optimized, ddPCR criteria we compared it with qPCR in 416 MRD samples (and with MFC in 63), with over-representation (61%) of BQR results by qPCR, from a total of 166 patients from four prospective MCL clinical trials. ddPCR, qPCR and MFC gave comparable results in MRD samples with at least 0.01% (1E-4) positivity. ddPCR was preferable to qPCR since it provided more robust quantification at positivity between 1E-4 and 1E-5. Amongst 240 BQR samples with duplicate or triplicate analysis, 39% were positive by ddPCR, 49% negative and only 12% remained positive below quantifiable ddPCR limits. The prognostic relevance of ddPCR is currently under assessment in the context of prospective trials within the European MCL Network.
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17
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Characterization of novel, recurrent genomic rearrangements as sensitive MRD targets in childhood B-cell precursor ALL. Blood Cancer J 2019; 9:96. [PMID: 31784504 PMCID: PMC6884523 DOI: 10.1038/s41408-019-0257-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/01/2019] [Accepted: 11/06/2019] [Indexed: 12/20/2022] Open
Abstract
B-cell precursor (BCP) ALL carry a variety of classical V(D)J rearrangements as well as genomic fusions and translocations. Here, we assessed the value of genomic capture high-throughput sequencing (gc-HTS) in BCP ALL (n = 183) for the identification and implementation of targets for minimal residual disease (MRD) testing. For TRδ, a total of 300 clonal rearrangements were detected in 158 of 183 samples (86%). Beside clonal Vδ2-Dδ3, Dδ2-Dδ3, and Vδ2-Jα we identified a novel group of recurrent Dδ-Jα rearrangements, comprising Dδ2 or Dδ3 segments fused predominantly to Jα29. For IGH-JH, 329 clonal rearrangements were identified in 172 of 183 samples (94%) including novel types of V(D)J joining. Oligoclonality was found in ~1/3 (n = 57/183) of ALL samples. Genomic breakpoints were identified in 71 BCP-ALL. A distinct MRD high-risk subgroup of IGH-V(D)J-germline ALL revealed frequent deletions of IKZF1 (n = 7/11) and the presence of genomic fusions (n = 10/11). Quantitative measurement using genomic fusion breakpoints achieved equivalent results compared to conventional V(D)J-based MRD testing and could be advantageous upon persistence of a leukemic clone. Taken together, selective gc-HTS expands the spectrum of suitable MRD targets and allows for the identification of genomic fusions relevant to risk and treatment stratification in childhood ALL.
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18
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Galimberti S, Genuardi E, Mazziotta F, Iovino L, Morabito F, Grassi S, Ciabatti E, Guerrini F, Petrini M. The Minimal Residual Disease in Non-Hodgkin's Lymphomas: From the Laboratory to the Clinical Practice. Front Oncol 2019; 9:528. [PMID: 31293969 PMCID: PMC6606710 DOI: 10.3389/fonc.2019.00528] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/31/2019] [Indexed: 01/05/2023] Open
Abstract
Minimal residual disease (MRD) in non-Hodgkin's lymphomas (NHLs) still represents matter of interest and debate: indeed, the new available treatments offer higher rates of complete responses and MRD negativity than in the past, with a positive impact on the long-term survival. Furthermore, the introduction of more sensitive and accurate molecular techniques, such as digital PCR (ddPCR) and the next generation sequencing techniques (NGS), increased the possibility of identifying molecular targets to be followed after therapy (such as rearrangement of immunoglobulins, fusion genes, or mutations). This review focused on how molecular biology can help to detect MRD in different types of NHLs and how MRD can change the clinical practice in 2019. In follicular lymphoma (FL), contamination of the grafts and molecular disease persistence after transplantation represent a negative prognostic factors. The combination of Rituximab or Obinutuzumab with Bendamustine seems to be the most effective way to clear MRD in FL patients receiving chemo-immunotherapy (further studies are in progress), and also 90Yttrium-Ibritumomab-Tiuxetan offers a deep clearance of molecular disease. Finally, molecular MRD can further stratify PET-negative cases, with subjects both PET- and MRD-negative presenting the best outcome. In aggressive lymphomas, MRD has a relevant prognostic power and can represent the platform for immunotherapy (such as CAR-T). In diffuse large B-cell lymphoma (DLBCL), the assessment of MRD in the plasma (where cell-free DNA and exosomes circulate) seems to be more predictive than the bone marrow analysis or peripheral blood mononuclear cells. Finally, NGS technologies could be more useful than the classical "patient allele-specific PCR" because they can identify any possible clone emerging during the treatment or follow-up, even if different from that identified at diagnosis, thus predicting relapse. After all, the present available molecular approaches can move MRD from the bench side to the clinical practice.
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Affiliation(s)
- Sara Galimberti
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Elisa Genuardi
- Department of Molecular Biotechnologies and Health Sciences, University of Torino, Turin, Italy
| | - Francesco Mazziotta
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.,GeNOMEC School of Doctorate, University of Siena, Siena, Italy
| | - Lorenzo Iovino
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.,Clinical and Translational Sciences School of Doctorate, University of Pisa, Pisa, Italy
| | - Fortunato Morabito
- Hematology Oncology Department, Augusta Victoria Hospital, East Jerusalem, Israel.,Biotechnology Research Unit, Cosenza, Italy
| | - Susanna Grassi
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.,GeNOMEC School of Doctorate, University of Siena, Siena, Italy
| | - Elena Ciabatti
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Francesca Guerrini
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Mario Petrini
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
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19
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Knecht H, Reigl T, Kotrová M, Appelt F, Stewart P, Bystry V, Krejci A, Grioni A, Pal K, Stranska K, Plevova K, Rijntjes J, Songia S, Svatoň M, Froňková E, Bartram J, Scheijen B, Herrmann D, García-Sanz R, Hancock J, Moppett J, van Dongen JJM, Cazzaniga G, Davi F, Groenen PJTA, Hummel M, Macintyre EA, Stamatopoulos K, Trka J, Langerak AW, Gonzalez D, Pott C, Brüggemann M, Darzentas N. Quality control and quantification in IG/TR next-generation sequencing marker identification: protocols and bioinformatic functionalities by EuroClonality-NGS. Leukemia 2019; 33:2254-2265. [PMID: 31227779 PMCID: PMC6756032 DOI: 10.1038/s41375-019-0499-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/23/2019] [Accepted: 04/23/2019] [Indexed: 12/29/2022]
Abstract
Assessment of clonality, marker identification and measurement of minimal residual disease (MRD) of immunoglobulin (IG) and T cell receptor (TR) gene rearrangements in lymphoid neoplasms using next-generation sequencing (NGS) is currently under intensive development for use in clinical diagnostics. So far, however, there is a lack of suitable quality control (QC) options with regard to standardisation and quality metrics to ensure robust clinical application of such approaches. The EuroClonality-NGS Working Group has therefore established two types of QCs to accompany the NGS-based IG/TR assays. First, a central polytarget QC (cPT-QC) is used to monitor the primer performance of each of the EuroClonality multiplex NGS assays; second, a standardised human cell line-based DNA control is spiked into each patient DNA sample to work as a central in-tube QC and calibrator for MRD quantification (cIT-QC). Having integrated those two reference standards in the ARResT/Interrogate bioinformatic platform, EuroClonality-NGS provides a complete protocol for standardised IG/TR gene rearrangement analysis by NGS with high reproducibility, accuracy and precision for valid marker identification and quantification in diagnostics of lymphoid malignancies.
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Affiliation(s)
- Henrik Knecht
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Tomas Reigl
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Michaela Kotrová
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Franziska Appelt
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Peter Stewart
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Vojtech Bystry
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Adam Krejci
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Andrea Grioni
- Centro Ricerca Tettamanti, University of Milano Bicocca, Monza, Italy
| | - Karol Pal
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Kamila Stranska
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Karla Plevova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jos Rijntjes
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Simona Songia
- Centro Ricerca Tettamanti, University of Milano Bicocca, Monza, Italy
| | - Michael Svatoň
- CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, University Hospital Motol, Prague, Czech Republic
| | - Eva Froňková
- CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, University Hospital Motol, Prague, Czech Republic
| | - Jack Bartram
- Department of Paediatric Haematology, Great Ormond Street Hospital, London, UK
| | - Blanca Scheijen
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Dietrich Herrmann
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Ramón García-Sanz
- IBMCC-CSIC, Hospital Universitario de Salamanca-IBSAL, Salamanca, Spain
| | - Jeremy Hancock
- Bristol Genetics Laboratory, Southmead Hospital, Bristol, UK
| | - John Moppett
- Department of Pediatric Haematology, Bristol Royal Hospital for Children, Bristol, UK
| | - Jacques J M van Dongen
- Department of Immunohematology and Blood Transfusion (IHB), Leiden University Medical Center, Leiden, The Netherlands
| | | | - Frédéric Davi
- Department of Hematology, Hopital Pitié-Salpêtrière, Paris, France
| | | | - Michael Hummel
- Insititute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Elizabeth A Macintyre
- Department of Hematology, APHP Necker-Enfants Malades and Paris Descartes University, Paris, France
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Jan Trka
- CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, University Hospital Motol, Prague, Czech Republic
| | - Anton W Langerak
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
| | - David Gonzalez
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Christiane Pott
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Monika Brüggemann
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Nikos Darzentas
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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20
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Catherwood MA, Gonzalez D, Donaldson D, Clifford R, Mills K, Thornton P. Relevance of TP53 for CLL diagnostics. J Clin Pathol 2019; 72:343-346. [PMID: 30712002 DOI: 10.1136/jclinpath-2018-205622] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 01/14/2019] [Accepted: 01/14/2019] [Indexed: 12/12/2022]
Abstract
TP53 disruption in chronic lymphocytic leukaemia (CLL) is a well-established prognostic marker and informs on the appropriate course of treatment for patients. TP53 status is commonly assessed by fluorescence in situ hybridisation for del(17 p) and Sanger sequencing for TP53 mutations. At present, current screening methods for TP53 mutations fail to detect diagnostically relevant mutations potentially leading to inappropriate treatment decisions. In addition, low levels of mutations that are proving to be clinically relevant may not be discovered with current less sensitive techniques. This review describes the structure, function and regulation of the TP53 protein, the mutations found in cancer and CLL, the relevance of TP53 disruption in CLL and the current screening methods for TP53 mutations including next-generation sequencing.
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Affiliation(s)
- Mark A Catherwood
- Haematology Department, Belfast Health and Social Care Trust, Belfast, UK
| | - David Gonzalez
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, UK
| | - David Donaldson
- Haematology Department, Belfast Health and Social Care Trust, Belfast, UK
| | - Ruth Clifford
- Department of Haematology, University Hospital Limerick, Ireland
| | - Ken Mills
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, UK
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21
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Arcila ME, Yu W, Syed M, Kim H, Maciag L, Yao J, Ho C, Petrova K, Moung C, Salazar P, Rijo I, Baldi T, Zehir A, Landgren O, Park J, Roshal M, Dogan A, Nafa K. Establishment of Immunoglobulin Heavy (IGH) Chain Clonality Testing by Next-Generation Sequencing for Routine Characterization of B-Cell and Plasma Cell Neoplasms. J Mol Diagn 2018; 21:330-342. [PMID: 30590126 DOI: 10.1016/j.jmoldx.2018.10.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 10/09/2018] [Accepted: 10/26/2018] [Indexed: 01/03/2023] Open
Abstract
Immunoglobulin heavy chain (IGH) clonality testing by next-generation sequencing (NGS) offers unique advantages over current low-throughput methods in the assessment of B-cell lineage neoplasms. Clinical use remains limited because assays are not standardized and validation/implementation guidelines are not yet developed. Herein, we describe our clinical validation and implementation of NGS IGH clonality testing and summarize our experience based on extensive routine use. NGS-based clonality testing targeting IGH FR1, FR2, FR3, and the conserved leader sequence upstream of FR1 was validated using commercially available kits. Data were analyzed by commercial and in-house-developed bioinformatics pipelines. Performance characteristics were evaluated directly comparing with capillary electrophoresis (CE) assays (BIOMED-2 primers). Assays were monitored after implementation (>1.5 years), concurrently testing by CE methods. A total of 1189 clinical samples were studied (94 validation, 1095 postimplementation). NGS showed superior performance compared with CE assays. For initial assessment, clonality detection rate was >97% for all malignancy types. Concordance with CE was 96%; discordances were related to higher sensitivity/resolution of NGS and improved detection in cases with high somatic hypermutation. Routine NGS clonality assessment is feasible and superior to existing assays, enabling accurate and specific index clone assessment and future tracking of all rearrangements in a patient sample. Successful implementation requires new standardization, validation, and implementation processes, which should be performed as a multicenter and multidisciplinary collaboration.
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Affiliation(s)
- Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Wayne Yu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mustafa Syed
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hannah Kim
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lidia Maciag
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - JinJuan Yao
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Caleb Ho
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kseniya Petrova
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christine Moung
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paulo Salazar
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ivelise Rijo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tessara Baldi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ola Landgren
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jae Park
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mikhail Roshal
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Dogan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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22
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CCND2 and CCND3 hijack immunoglobulin light-chain enhancers in cyclin D1 - mantle cell lymphoma. Blood 2018; 133:940-951. [PMID: 30538135 DOI: 10.1182/blood-2018-07-862151] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 12/01/2018] [Indexed: 12/15/2022] Open
Abstract
Mantle cell lymphoma (MCL) is characterized by the t(11;14)(q13;q32) translocation resulting in overexpression of cyclin D1. However, a small subset of cyclin D1- MCL has been recognized, and approximately one-half of them harbor CCND2 translocations while the primary event in cyclin D1-/D2- MCL remains elusive. To identify other potential mechanisms driving MCL pathogenesis, we investigated 56 cyclin D1-/SOX11+ MCL by fluorescence in situ hybridization (FISH), whole-genome/exome sequencing, and gene-expression and copy-number arrays. FISH with break-apart probes identified CCND2 rearrangements in 39 cases (70%) but not CCND3 rearrangements. We analyzed 3 of these negative cases by whole-genome/exome sequencing and identified IGK (n = 2) and IGL (n = 1) enhancer hijackings near CCND3 that were associated with cyclin D3 overexpression. By specific FISH probes, including the IGK enhancer region, we detected 10 additional cryptic IGK juxtapositions to CCND3 (6 cases) and CCND2 (4 cases) in MCL that overexpressed, respectively, these cyclins. A minor subset of 4 cyclin D1- MCL cases lacked cyclin D rearrangements and showed upregulation of CCNE1 and CCNE2. These cases had blastoid morphology, high genomic complexity, and CDKN2A and RB1 deletions. Both genomic and gene-expression profiles of cyclin D1- MCL cases were indistinguishable from cyclin D1+ MCL. In conclusion, virtually all cyclin D1- MCLs carry CCND2/CCND3 rearrangements with immunoglobulin genes, including a novel IGK/L enhancer hijacking mechanism. A subset of cyclin D1-/D2-/D3- MCL with aggressive features has cyclin E dysregulation. Specific FISH probes may allow the molecular identification and diagnosis of cyclin D1- MCL.
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23
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A clinical perspective on immunoglobulin heavy chain clonal heterogeneity in B cell acute lymphoblastic leukemia. Leuk Res 2018; 75:15-22. [DOI: 10.1016/j.leukres.2018.10.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 12/15/2022]
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24
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Wang HW, Raffeld M. Molecular assessment of clonality in lymphoid neoplasms. Semin Hematol 2018; 56:37-45. [PMID: 30573043 DOI: 10.1053/j.seminhematol.2018.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 05/08/2018] [Indexed: 02/03/2023]
Abstract
Molecular clonality assays in B- and T-cell lymphoproliferative disorders often provide critical information in establishing a diagnosis of a lymphoproliferative disorder. These assays rely on the unique genetic structures that serve as assay targets, created in the process of generating immunoglobulin and T-cell receptors during B- and T-cell development. Molecular clonality assays are generally used when flow cytometry or immunohistochemistry has not sufficiently clarified the benign or malignant nature of a lymphoid proliferation. Additionally, since molecular clonality assays are tumor specific, they allow the clinician to distinguish recurrences from second tumors, and have the sensitivity to monitor minimal residual disease. In this review, we discuss the principles underlying these tests, the current approaches to clonality testing, some of the pitfalls in their interpretation, and the future applications of next generation sequencing technology to clonality testing.
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Affiliation(s)
- Hao-Wei Wang
- Hematopathology Section, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Mark Raffeld
- Molecular Diagnostics Section, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD.
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25
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Ibata S, Kobune M, Kikuchi S, Yoshida M, Miura S, Horiguchi H, Murase K, Iyama S, Takada K, Miyanishi K, Kato J. High expression of nucleoporin 133 mRNA in bone marrow CD138+ cells is a poor prognostic factor in multiple myeloma. Oncotarget 2018; 9:25127-25135. [PMID: 29861858 PMCID: PMC5982762 DOI: 10.18632/oncotarget.25350] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 04/24/2018] [Indexed: 12/13/2022] Open
Abstract
Recent advances in plasma cell biology and molecularly-targeted therapy enable us to employ various types of drugs including immunomodulatory drugs, proteasome inhibitors, and immunotherapy. However, the optimal therapeutic strategies to introduce these drugs for heterogeneous patients with multiple myeloma (MM) have not yet been clarified. In the present study, we attempted to identify a new factor indicating poor prognosis in CD138+ myeloma cells using accumulated Gene Expression Omnibus (GEO) datasets from studies of MM and to assess the relationship between gene expression and survival using MAQC-II Project Myeloma (GSE24080). Five GEO datasets (GSE5900, GSE58133, GSE68871, GSE57317 and GSE16791) which were analyzed by the same microarray platform (GLP570) were combined into one MM database including various types of MM. However, we found that gene expression levels were quite heterogeneous. Hence, we focused on the differentially-expressed genes (DEGs) between newly-diagnosed MM and relapsed/refractory MM and found that the expression levels of more than 20 genes changed two-fold or more. Additionally, pathway analysis indicated that six pathways including Hippo signaling were significantly enriched. Then, we applied all DEGs and genes associated with core enrichment for GSE24080 to evaluate their involvement in disease prognosis. We found that nucleoporin 133 (NUP133) is an independent poor prognostic factor by Cox proportional hazard analysis. These results suggested that high expression of NUP133 could be useful when choosing the appropriate MM therapy and may be a new target of MM therapy.
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Affiliation(s)
- Soushi Ibata
- Department of Hematology, Sapporo Medical University School of Medicine, Sapporo, Japan.,Department of Medical Oncology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Masayoshi Kobune
- Department of Hematology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Shohei Kikuchi
- Department of Hematology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Masahiro Yoshida
- Department of Hematology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Shogo Miura
- Department of Hematology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroto Horiguchi
- Department of Hematology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Kazuyuki Murase
- Department of Hematology, Sapporo Medical University School of Medicine, Sapporo, Japan.,Department of Medical Oncology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Satoshi Iyama
- Department of Hematology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Kohichi Takada
- Department of Hematology, Sapporo Medical University School of Medicine, Sapporo, Japan.,Department of Medical Oncology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Koji Miyanishi
- Department of Medical Oncology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Junji Kato
- Department of Medical Oncology, Sapporo Medical University School of Medicine, Sapporo, Japan
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26
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Pugh TJ. Circulating Tumour DNA for Detecting Minimal Residual Disease in Multiple Myeloma. Semin Hematol 2018; 55:38-40. [PMID: 29759151 DOI: 10.1053/j.seminhematol.2018.03.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 03/05/2018] [Indexed: 12/23/2022]
Abstract
Circulating tumor DNA faithfully recapitulates somatic mutations detected in bone marrow aspirates from patients with newly diagnosed or relapsed or recurrent myeloma. Extending these methods to enable detection of minimal residual disease will require increased sensitivity and breadth of genomic assays to maximize information content from small quantities of cell-free DNA; as well as definition of a clinically meaningful ctDNA concentration in comparison with conventional bone marrow cell-count thresholds. This review describes the use of cell-free DNA sequencing in myeloma to date, identifies challenges associated with pushing limit of detection of these assays into the realm of detecting minimal residual disease, and describes potential strategies to overcome these challenges.
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Affiliation(s)
- Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada.
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27
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Ferrero S, Dreyling M. Minimal residual disease in mantle cell lymphoma: are we ready for a personalized treatment approach? Haematologica 2017; 102:1133-1136. [PMID: 28655809 PMCID: PMC5566011 DOI: 10.3324/haematol.2017.167627] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Simone Ferrero
- Division of Hematology, Department of Molecular Biotechnologies and Health Sciences, University of Torino, Italy
| | - Martin Dreyling
- Department of Medicine III, Hospital of the University LMU München, Germany
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28
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Díez P, Ibarrola N, Dégano RM, Lécrevisse Q, Rodriguez-Caballero A, Criado I, Nieto WG, Góngora R, González M, Almeida J, Orfao A, Fuentes M. A systematic approach for peptide characterization of B-cell receptor in chronic lymphocytic leukemia cells. Oncotarget 2017; 8:42836-42846. [PMID: 28467808 PMCID: PMC5522109 DOI: 10.18632/oncotarget.17076] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/22/2017] [Indexed: 01/09/2023] Open
Abstract
A wide variety of immunoglobulins (Ig) is produced by the immune system thanks to different mechanisms (V(D)J recombination, somatic hypermutation, and antigen selection). The profiling of Ig sequences (at both DNA and peptide levels) are of great relevance to developing targeted vaccines or treatments for specific diseases or infections. Thus, genomics and proteomics techniques (such as Next-Generation Sequencing (NGS) and mass spectrometry (MS)) have notably increased the knowledge in Ig sequencing and serum Ig peptide profiling in a high-throughput manner. However, the peptide characterization of membrane-bound Ig (e.g., B-cell receptors, BCR) is still a challenge mainly due to the poor recovery of mentioned Ig.Herein, we have evaluated three different sample processing methods for peptide sequencing of BCR belonging to chronic lymphocytic leukemia (CLL) B cells identifying up to 426 different peptide sequences (MS/MS data are available via ProteomeXchange with identifier PXD004466). Moreover, as a consequence of the results here obtained, recommended guidelines have been described for BCR-sequencing of B-CLL samples by MS approaches.For this purpose, an in-house algorithm has been designed and developed to compare the MS/MS results with those obtained by molecular biology in order to integrate both proteomics and genomics results and establish the steps to follow when sequencing membrane-bound Ig by MS/MS.
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MESH Headings
- Aged
- Aged, 80 and over
- Amino Acid Sequence
- Female
- Genomics/methods
- High-Throughput Nucleotide Sequencing
- Humans
- Immunoglobulin Heavy Chains/chemistry
- Immunoglobulin Heavy Chains/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Male
- Middle Aged
- Peptide Fragments/chemistry
- Peptide Fragments/genetics
- Proteomics/methods
- Receptors, Antigen, B-Cell/chemistry
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/metabolism
- Tandem Mass Spectrometry
- Workflow
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Affiliation(s)
- Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Nieves Ibarrola
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Rosa M. Dégano
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Quentin Lécrevisse
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Arancha Rodriguez-Caballero
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Ignacio Criado
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Wendy G. Nieto
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Rafael Góngora
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Marcos González
- Hematology Service, Institute of Biomedical Research of Salamanca, University Hospital of Salamanca, Cancer Research and Institute of Molecular Biology and Cellular Oncology, 37007 Salamanca, Spain
| | - Julia Almeida
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Alberto Orfao
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
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29
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Kotrova M, Trka J, Kneba M, Brüggemann M. Is Next-Generation Sequencing the way to go for Residual Disease Monitoring in Acute Lymphoblastic Leukemia? Mol Diagn Ther 2017; 21:481-492. [DOI: 10.1007/s40291-017-0277-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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30
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Langerak AW, Brüggemann M, Davi F, Darzentas N, van Dongen JJM, Gonzalez D, Cazzaniga G, Giudicelli V, Lefranc MP, Giraud M, Macintyre EA, Hummel M, Pott C, Groenen PJTA, Stamatopoulos K. High-Throughput Immunogenetics for Clinical and Research Applications in Immunohematology: Potential and Challenges. THE JOURNAL OF IMMUNOLOGY 2017; 198:3765-3774. [PMID: 28416603 DOI: 10.4049/jimmunol.1602050] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/09/2017] [Indexed: 11/19/2022]
Abstract
Analysis and interpretation of Ig and TCR gene rearrangements in the conventional, low-throughput way have their limitations in terms of resolution, coverage, and biases. With the advent of high-throughput, next-generation sequencing (NGS) technologies, a deeper analysis of Ig and/or TCR (IG/TR) gene rearrangements is now within reach, which impacts on all main applications of IG/TR immunogenetic analysis. To bridge the generation gap from low- to high-throughput analysis, the EuroClonality-NGS Consortium has been formed, with the main objectives to develop, standardize, and validate the entire workflow of IG/TR NGS assays for 1) clonality assessment, 2) minimal residual disease detection, and 3) repertoire analysis. This concerns the preanalytical (sample preparation, target choice), analytical (amplification, NGS), and postanalytical (immunoinformatics) phases. Here we critically discuss pitfalls and challenges of IG/TR NGS methodology and its applications in hemato-oncology and immunology.
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Affiliation(s)
- Anton W Langerak
- Department of Immunology, Laboratory for Medical Immunology, Erasmus MC, University Medical Center, 3015 CN Rotterdam, the Netherlands;
| | - Monika Brüggemann
- Second Medical Department, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Frédéric Davi
- Département d'Hématologie, Assistance Publique - Hôpitaux de Paris Hopital Pitié-Salpêtrière and Université Pierre et Marie Curie - Université Paris IV, 75005 Paris, France
| | - Nikos Darzentas
- Molecular Medicine Program, Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Jacques J M van Dongen
- Department of Immunology, Laboratory for Medical Immunology, Erasmus MC, University Medical Center, 3015 CN Rotterdam, the Netherlands;
| | - David Gonzalez
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast BT9 7AE, United Kingdom
| | - Gianni Cazzaniga
- Centro Ricerca Tettamanti, Clinica Pediatrica Università Milano-Bicocca, 20900 Monza, Italy
| | | | | | - Mathieu Giraud
- Centre de Recherche en Informatique Signal et Automatique de Lille, CNRS, Université de Lille, 59000 Lille, France
| | - Elizabeth A Macintyre
- Département d'Hématologie, Assistance Publique - Hôpitaux de Paris Necker-Enfants Malades and Paris Descartes, 75015 Paris, France
| | - Michael Hummel
- Institut für Pathologie, Charité - Universitätsmedizin Berlin, D-10117 Berlin, Germany
| | - Christiane Pott
- Second Medical Department, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Patricia J T A Groenen
- Department of Pathology, Radboud University Nijmegen Medical Center, 6525 GA Nijmegen, the Netherlands; and
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Center for Research and Technology Hellas, GR-57001 Thessaloniki, Greece
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