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Reading the B-cell receptor immunome in chronic lymphocytic leukemia: revelations and applications. Exp Hematol 2020; 93:14-24. [PMID: 32976948 DOI: 10.1016/j.exphem.2020.09.194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/25/2020] [Accepted: 09/19/2020] [Indexed: 12/19/2022]
Abstract
B-Cell receptor (BCR) sequencing has been the force driving many recent advances in chronic lymphocytic leukemia (CLL) research. Here, we discuss the general principles, revelations, and applications of reading the BCR immunome in the context of CLL. First, IGHV mutational status, obtained by measuring the mutational imprint on the IGHV gene of the CLL clonotype, is the cornerstone of CLL risk stratification. Furthermore, the discovery of "BCR-stereotyped" groups of unrelated patients that share not only a highly similar BCR on their leukemic clone, but also certain clinical characteristics has provided insights key to understanding disease ontogeny. Additionally, whereas the BCR repertoire of most CLL patients is characterized by a single dominant rearrangement, next-generation sequencing (NGS) has revealed a rich subclonal landscape in a larger than previously expected proportion of CLL patients. We review the mechanisms underlying these "multiple dominant" cases, including V(D)J-recombination errors, failure of allelic exclusion, intraclonal diversification, and "true" bi- or oligoclonality, and their implications, in detail. Finally, BCR repertoire sequencing can be used for sensitive quantification of minimal residual disease to potentially unprecedented depth. To surmount pitfalls inherent to this approach and develop internationally harmonized protocols, the EuroClonality-NGS Working Group has been established.
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52
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Caution encouraged in next-generation sequencing immunogenetic analyses in acute lymphoblastic leukemia. Blood 2020; 136:1105-1107. [PMID: 32438392 DOI: 10.1182/blood.2020005613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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53
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Hess JF, Kotrová M, Calabrese S, Darzentas N, Hutzenlaub T, Zengerle R, Brüggemann M, Paust N. Automation of Amplicon-Based Library Preparation for Next-Generation Sequencing by Centrifugal Microfluidics. Anal Chem 2020; 92:12833-12841. [DOI: 10.1021/acs.analchem.0c01202] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Jacob Friedrich Hess
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Michaela Kotrová
- Unit for Hematological Diagnostics, II. Medical Department, University Medical Center Schleswig Holstein, Langer Segen 8-10, 24105 Kiel, Germany
| | - Silvia Calabrese
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Nikos Darzentas
- Unit for Hematological Diagnostics, II. Medical Department, University Medical Center Schleswig Holstein, Langer Segen 8-10, 24105 Kiel, Germany
| | - Tobias Hutzenlaub
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Roland Zengerle
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Monika Brüggemann
- Unit for Hematological Diagnostics, II. Medical Department, University Medical Center Schleswig Holstein, Langer Segen 8-10, 24105 Kiel, Germany
| | - Nils Paust
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
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Drexler HG, Quentmeier H. The LL-100 Cell Lines Panel: Tool for Molecular Leukemia-Lymphoma Research. Int J Mol Sci 2020; 21:ijms21165800. [PMID: 32823535 PMCID: PMC7461097 DOI: 10.3390/ijms21165800] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/04/2020] [Accepted: 08/11/2020] [Indexed: 12/17/2022] Open
Abstract
Certified cell line models provide ideal experimental platforms to answer countless scientific questions. The LL-100 panel is a cohort of cell lines that are broadly representative of all leukemia–lymphoma entities (including multiple myeloma and related diseases), rigorously authenticated and validated, and comprehensively annotated. The process of the assembly of the LL-100 panel was based on evidence and experience. To expand the genetic characterization across all LL-100 cell lines, we performed whole-exome sequencing and RNA sequencing. Here, we describe the conception of the panel and showcase some exemplary applications with a focus on cancer genomics. Due diligence was paid to exclude cross-contaminated and non-representative cell lines. As the LL-100 cell lines are so well characterized and readily available, the panel will be a valuable resource for identifying cell lines with mutations in cancer genes, providing superior model systems. The data also add to the current knowledge of the molecular pathogenesis of leukemia–lymphoma. Additional efforts to expand the breadth of available high-quality cell lines are clearly warranted.
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Affiliation(s)
- Hans G. Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany;
- Faculty of Life Sciences, Technical University of Braunschweig, 38124 Braunschweig, Germany
- Correspondence:
| | - Hilmar Quentmeier
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany;
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55
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Hess J, Kohl T, Kotrová M, Rönsch K, Paprotka T, Mohr V, Hutzenlaub T, Brüggemann M, Zengerle R, Niemann S, Paust N. Library preparation for next generation sequencing: A review of automation strategies. Biotechnol Adv 2020; 41:107537. [DOI: 10.1016/j.biotechadv.2020.107537] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/27/2020] [Accepted: 03/16/2020] [Indexed: 01/08/2023]
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56
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Bartram J, Patel B, Fielding AK. Monitoring MRD in ALL: Methodologies, technical aspects and optimal time points for measurement. Semin Hematol 2020; 57:142-148. [PMID: 33256904 DOI: 10.1053/j.seminhematol.2020.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 06/02/2020] [Indexed: 01/21/2023]
Abstract
The accurate determination of minimal or measurable residual disease (MRD) during the early months of therapy in acute lymphoblastic leukemia is well established as the most important independent prognostic biomarker, predicting response to combination chemotherapy. Stratification based on MRD maximizes treatment effectiveness while minimizing adverse effects. Allele-specific real-time quantitative PCR of clone-defining immunoglobin/T-cell receptor gene rearrangements in the patients' leukemic clones and/or multiparametric flow cytometric tracking of leukemia-associated immunophenotypes are considered standard of care. Following recent advances in high throughput sequencing (HTS; next generation sequencing), much attention has been devoted to the development of HTS-based MRD assays, which can increase sensitivity; theoretically only limited by the number of cells input into the assay. Knowledge of the methods and limitations of each technology, along with awareness of the sensitivity and specificity of MRD at particular treatment time points is important in interpretation of the MRD value. MRD negativity at pre-established protocol-appropriate time points guides continuance with consolidation/maintenance chemotherapy, whereas positivity leads to a change to a biological therapy such as blinatumomab and intensification of therapy to allogeneic stem cell transplant. Positivity after maintenance may herald impending relapse enabling treatment intervention. MRD has been integral to the introduction of novel agents and cellular therapies into clinical trials and standard of care, but the long-term predictive value of MRD on outcome of novel therapies is not yet established. Integration of somatic genetics with MRD may further improve accurate identification of patients with the lowest and highest risk of relapse.
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Affiliation(s)
- Jack Bartram
- Department of Haematology, Great Ormond Street Hospital for Children, London, UK; Cancer Section, DBC Programme, University College London, London, UK.
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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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58
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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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59
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Giusti GNN, Jotta PY, Lopes CDO, Ganazza MA, de Azevedo AC, Brandalise SR, Meidanis J, Yunes JA. Test trial of spike-in immunoglobulin heavy-chain (IGH) controls for next generation sequencing quantification of minimal residual disease in acute lymphoblastic leukaemia. Br J Haematol 2020; 189:e150-e154. [PMID: 32187384 DOI: 10.1111/bjh.16571] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 02/18/2020] [Indexed: 10/24/2022]
Affiliation(s)
- Guilherme Navarro Nilo Giusti
- Laboratório de Biologia Molecular, Centro Infantil Boldrini, Campinas, São Paulo, Brazil.,Graduate Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo, Brazil
| | | | | | | | | | | | - João Meidanis
- Laboratório de Biologia Molecular, Centro Infantil Boldrini, Campinas, São Paulo, Brazil.,Institute of Computing, University of Campinas, Campinas, São Paulo, Brazil
| | - José Andrés Yunes
- Laboratório de Biologia Molecular, Centro Infantil Boldrini, Campinas, São Paulo, Brazil.,Genetics Department, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
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60
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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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61
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Komkov A, Miroshnichenkova A, Nugmanov G, Popov A, Pogorelyy M, Zapletalova E, Jelinkova H, Pospisilova S, Lebedev Y, Chudakov D, Olshanskaya Y, Plevova K, Maschan M, Mamedov I. High‐throughput sequencing of T‐cell receptor alpha chain clonal rearrangements at the DNA level in lymphoid malignancies. Br J Haematol 2019; 188:723-731. [DOI: 10.1111/bjh.16230] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/04/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Alexander Komkov
- Department of Genomics of Adaptive Immunity Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry Moscow Russia
- Laboratory of Cytogenetics and Molecular Genetics Dmitry Rogachev National Medical and Research Centre of Paediatric Haematology, Oncology and Immunology Moscow Russia
| | - Anna Miroshnichenkova
- Laboratory of Cytogenetics and Molecular Genetics Dmitry Rogachev National Medical and Research Centre of Paediatric Haematology, Oncology and Immunology Moscow Russia
| | - Gaiaz Nugmanov
- Department of Genomics of Adaptive Immunity Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry Moscow Russia
| | - Alexander Popov
- Laboratory of Cytogenetics and Molecular Genetics Dmitry Rogachev National Medical and Research Centre of Paediatric Haematology, Oncology and Immunology Moscow Russia
| | - Mikhail Pogorelyy
- Department of Genomics of Adaptive Immunity Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry Moscow Russia
- Department of Molecular Technologies Pirogov Russian National Research Medical University Moscow Russia
| | - Eva Zapletalova
- Department of Internal Medicine, Haematology and Oncology University Hospital Brno and Faculty of Medicine Masaryk University Brno Czech Republic
| | - Hana Jelinkova
- Department of Internal Medicine, Haematology and Oncology University Hospital Brno and Faculty of Medicine Masaryk University Brno Czech Republic
| | - Sarka Pospisilova
- Department of Internal Medicine, Haematology and Oncology University Hospital Brno and Faculty of Medicine Masaryk University Brno Czech Republic
- Central European Institute of Technology Masaryk University Brno Czech Republic
| | - Yuri Lebedev
- Department of Genomics of Adaptive Immunity Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry Moscow Russia
- Department of Molecular Technologies Pirogov Russian National Research Medical University Moscow Russia
| | - Dmitriy Chudakov
- Department of Genomics of Adaptive Immunity Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry Moscow Russia
- Department of Molecular Technologies Pirogov Russian National Research Medical University Moscow Russia
- Central European Institute of Technology Masaryk University Brno Czech Republic
| | - Yulia Olshanskaya
- Laboratory of Cytogenetics and Molecular Genetics Dmitry Rogachev National Medical and Research Centre of Paediatric Haematology, Oncology and Immunology Moscow Russia
| | - Karla Plevova
- Department of Internal Medicine, Haematology and Oncology University Hospital Brno and Faculty of Medicine Masaryk University Brno Czech Republic
- Central European Institute of Technology Masaryk University Brno Czech Republic
| | - Michael Maschan
- Laboratory of Cytogenetics and Molecular Genetics Dmitry Rogachev National Medical and Research Centre of Paediatric Haematology, Oncology and Immunology Moscow Russia
| | - Ilgar Mamedov
- Department of Genomics of Adaptive Immunity Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry Moscow Russia
- Laboratory of Cytogenetics and Molecular Genetics Dmitry Rogachev National Medical and Research Centre of Paediatric Haematology, Oncology and Immunology Moscow Russia
- Department of Molecular Technologies Pirogov Russian National Research Medical University Moscow Russia
- Central European Institute of Technology Masaryk University Brno Czech Republic
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62
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Liu X, He H, Li Y, Huang Y, Li G, Yu Q, Li W, Li D. The application of antigen receptor gene rearrangement of BIOMED-2 in the pathologic diagnosis of 348 cases with non-Hodgkin lymphoma in a single institution in Southwest of China. Pathol Res Pract 2019; 215:152615. [PMID: 31562020 DOI: 10.1016/j.prp.2019.152615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 08/12/2019] [Accepted: 08/23/2019] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To explore the clinical value of immunoglobulin (Ig) and T cell receptor (TCR) gene rearrangement in the diagnosis of non-Hodgkin lymphoma. METHODS Using the standardized BIOMED-2 multiplex PCR strategy to detect IgH, IgK and TCR in 272 cases of mature B-cell lymphoma, 55 cases of mature T-cell lymphoma, 21 cases of extranodal NK/ T-cell lymphoma, nasal type, and 20 cases of lymphoid tissue reactive hyperplasia. RESULTS Among all mature B-cell lymphomas, the sensitivity of Ig gene rearrangement was 91.18% (248/272), IgH and IgK gene rearrangement was 76.47% (208/272) and 75.00% (204/272), respectively, meanwhile the sensitivity of TCRγ rearrangement was 3.68% (10/272). In the 55 cases of mature T-cell lymphoma, the sensitivity of the detection of TCRγ was 76.36% (44/55), at the same time the sensitivity of Ig gene rearrangement was 14.55% (8/55), IgH and IgK gene rearrangement was 7.27% (4/55) and 12.73% (7/55), respectively. In 21 cases of extranodal NK/T cell lymphoma, nasal type, and 20 cases of reactive lymphoid hyperplasia, no gene rearrangement was found in the samples of IgH, IgK and TCR. The sensitivity of gene rearrangement in Ig/TCR in B and T-cell lymphoma was significantly different from that in the control group (P < 0.05). CONCLUSION The Ig/TCR gene rearrangement of BIOMED-2 multiplex PCR strategy has important auxiliary value in the diagnosis of B/T-cell non-Hodgkin lymphoma respectively, however, a few B-cell lymphomas may company TCR gene rearrangement as well as a few T-cell lymphomas may accompany Ig gene rearrangement, it must be comprehensively judged with the combination of morphology, immunohistochemistry and clinical features.
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Affiliation(s)
- Xueni Liu
- Department of Pathology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Hong He
- Department of Internal Medicine, The First Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Yuanxin Li
- Department of Pathology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Ying Huang
- Department of Pathology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Gang Li
- Molecular Medical Laboratory, Chongqing Medical University, Chongqing, China
| | - Qiubo Yu
- Molecular Medical Laboratory, Chongqing Medical University, Chongqing, China
| | - Wenwen Li
- Department of Pathology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Dan Li
- Department of Pathology, College of Basic Medicine, Chongqing Medical University, Chongqing, China.
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63
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Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study. Leukemia 2019; 33:2241-2253. [PMID: 31243313 PMCID: PMC6756028 DOI: 10.1038/s41375-019-0496-7] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/20/2019] [Indexed: 01/09/2023]
Abstract
Amplicon-based next-generation sequencing (NGS) of immunoglobulin (IG) and T-cell receptor (TR) gene rearrangements for clonality assessment, marker identification and quantification of minimal residual disease (MRD) in lymphoid neoplasms has been the focus of intense research, development and application. However, standardization and validation in a scientifically controlled multicentre setting is still lacking. Therefore, IG/TR assay development and design, including bioinformatics, was performed within the EuroClonality-NGS working group and validated for MRD marker identification in acute lymphoblastic leukaemia (ALL). Five EuroMRD ALL reference laboratories performed IG/TR NGS in 50 diagnostic ALL samples, and compared results with those generated through routine IG/TR Sanger sequencing. A central polytarget quality control (cPT-QC) was used to monitor primer performance, and a central in-tube quality control (cIT-QC) was spiked into each sample as a library-specific quality control and calibrator. NGS identified 259 (average 5.2/sample, range 0–14) clonal sequences vs. Sanger-sequencing 248 (average 5.0/sample, range 0–14). NGS primers covered possible IG/TR rearrangement types more completely compared with local multiplex PCR sets and enabled sequencing of bi-allelic rearrangements and weak PCR products. The cPT-QC showed high reproducibility across all laboratories. These validated and reproducible quality-controlled EuroClonality-NGS assays can be used for standardized NGS-based identification of IG/TR markers in lymphoid malignancies.
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64
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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: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [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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Sánchez R, Ayala R, Martínez-López J. Minimal Residual Disease Monitoring with Next-Generation Sequencing Methodologies in Hematological Malignancies. Int J Mol Sci 2019; 20:ijms20112832. [PMID: 31185671 PMCID: PMC6600313 DOI: 10.3390/ijms20112832] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/05/2019] [Accepted: 06/07/2019] [Indexed: 12/15/2022] Open
Abstract
Ultra-deep next-generation sequencing has emerged in recent years as an important diagnostic tool for the detection and follow-up of tumor burden in most of the known hematopoietic malignancies. Meticulous and high-throughput methods for the lowest possible quantified disease are needed to address the deficiencies of more classical techniques. Precision-based approaches will allow us to correctly stratify each patient based on the minimal residual disease (MRD) after a treatment cycle. In this review, we consider the most prominent ways to approach next-generation sequencing methodologies to follow-up MRD in hematological neoplasms.
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Affiliation(s)
- Ricardo Sánchez
- Servicio de Hematología y Hemoterapia. Hospital Universitario 12 de Octubre, 28041 Madrid, Spain.
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain.
| | - Rosa Ayala
- Servicio de Hematología y Hemoterapia. Hospital Universitario 12 de Octubre, 28041 Madrid, Spain.
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain.
- Universidad Complutense de Madrid (UCM), 28040 Madrid, Spain.
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain.
| | - Joaquín Martínez-López
- Servicio de Hematología y Hemoterapia. Hospital Universitario 12 de Octubre, 28041 Madrid, Spain.
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain.
- Universidad Complutense de Madrid (UCM), 28040 Madrid, Spain.
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain.
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