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Chen H, Gu M, Liang J, Song H, Zhang J, Xu W, Zhao F, Shen D, Shen H, Liao C, Tang Y, Xu X. Minimal residual disease detection by next-generation sequencing of different immunoglobulin gene rearrangements in pediatric B-ALL. Nat Commun 2023; 14:7468. [PMID: 37978187 PMCID: PMC10656538 DOI: 10.1038/s41467-023-43171-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
While the prognostic role of immunoglobulin heavy chain locus (IGH) rearrangement in minimal residual disease (MRD) in pediatric B-acute lymphoblastic leukemia (B-ALL) has been reported, the contribution of light chain loci (IGK/IGL) remains elusive. This study is to evaluate the prognosis of IGH and IGK/IGL rearrangement-based MRD detected by next-generation sequencing in B-ALL at the end of induction (EOI) and end of consolidation (EOC). IGK/IGL rearrangements identify 5.5% of patients without trackable IGH clones. Concordance rates for IGH and IGK/IGL are 79.9% (cutoff 0.01%) at EOI and 81.0% (cutoff 0.0001%) at EOC, respectively. Patients with NGS-MRD < 0.01% at EOI or <0.0001% at EOC present excellent outcome, with 3-year event-free survival rates higher than 95%. IGH-MRD is prognostic at EOI/EOC, while IGK-MRD at EOI/EOC and IGL-MRD at EOI are not. At EOI, NGS identifies 26.2% of higher risk patients whose MRD < 0.01% by flow cytometry. However, analyzing IGK/IGL along with IGH fails to identify additional higher risk patients both at EOI and at EOC. In conclusion, IGH is crucial for MRD monitoring while IGK and IGL have relatively limited value.
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Affiliation(s)
- Haipin Chen
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China
| | - Miner Gu
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China
| | - Juan Liang
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China
| | - Hua Song
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China
| | - Jingying Zhang
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China
| | - Weiqun Xu
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China
| | - Fenying Zhao
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China
| | - Diying Shen
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China
| | - Heping Shen
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China
| | - Chan Liao
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China
| | - Yongmin Tang
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China.
| | - Xiaojun Xu
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China.
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2
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Fardoos R, Christensen C, Øbro NF, Overgaard UM, Als-Nielsen B, Madsen HO, Marquart HV. Flow Sorting, Whole Genome Amplification and Next-Generation Sequencing as Combined Tools to Study Heterogeneous Acute Lymphoblastic Leukemia. Diagnostics (Basel) 2023; 13:3306. [PMID: 37958202 PMCID: PMC10650172 DOI: 10.3390/diagnostics13213306] [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: 09/26/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023] Open
Abstract
Next-generation sequencing (NGS) methods have been introduced for immunoglobulin (IG)/T-cell receptor (TR) gene rearrangement analysis in acute lymphoblastic leukemia (ALL) and lymphoma (LBL). These methods likely constitute faster and more sensitive approaches to analyze heterogenous cases of ALL/LBL, yet it is not known whether gene rearrangements constituting low percentages of the total sequence reads represent minor subpopulations of malignant cells or background IG/TR gene rearrangements in normal B-and T-cells. In a comparison of eight cases of B-cell precursor ALL (BCP-ALL) using both the EuroClonality NGS method and the IdentiClone multiplex-PCR/gene-scanning method, the NGS method identified between 29% and 139% more markers than the gene-scanning method, depending on whether the NGS data analysis used a threshold of 5% or 1%, respectively. As an alternative to using low thresholds, we show that IG/TR gene rearrangements in subpopulations of cancer cells can be discriminated from background IG/TR gene rearrangements in normal B-and T-cells through a combination of flow cytometry cell sorting and multiple displacement amplification (MDA)-based whole genome amplification (WGA) prior to the NGS. Using this approach to investigate the clonal evolution in a BCP-ALL patient with double relapse, clonal TR rearrangements were found in sorted leukemic cells at the time of second relapse that could be identified at the time of diagnosis, below 1% of the total sequence reads. These data emphasize that caution should be exerted when interpreting rare sequences in NGS experiments and show the advantage of employing the flow sorting of malignant cell populations in NGS clonality assessments.
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Affiliation(s)
- Rabiah Fardoos
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Claus Christensen
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Nina Friesgaard Øbro
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Ulrik Malthe Overgaard
- Department of Hematology, The University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Bodil Als-Nielsen
- Department of Pediatric and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
- Faculty of Health and Medical Sciences, Institute of Clinical Medicine, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Hans Ole Madsen
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Hanne Vibeke Marquart
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
- Faculty of Health and Medical Sciences, Institute of Clinical Medicine, University of Copenhagen, DK-2100 Copenhagen, Denmark
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3
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Optimizing Molecular Minimal Residual Disease Analysis in Adult Acute Lymphoblastic Leukemia. Cancers (Basel) 2023; 15:cancers15020374. [PMID: 36672325 PMCID: PMC9856386 DOI: 10.3390/cancers15020374] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
Minimal/measurable residual disease (MRD) evaluation has resulted in a fundamental instrument to guide patient management in acute lymphoblastic leukemia (ALL). From a methodological standpoint, MRD is defined as any approach aimed at detecting and possibly quantifying residual neoplastic cells beyond the sensitivity level of cytomorphology. The molecular methods to study MRD in ALL are polymerase chain reaction (PCR) amplification-based approaches and are the most standardized techniques. However, there are some limitations, and emerging technologies, such as digital droplet PCR (ddPCR) and next-generation sequencing (NGS), seem to have advantages that could improve MRD analysis in ALL patients. Furthermore, other blood components, namely cell-free DNA (cfDNA), appear promising and are also being investigated for their potential role in monitoring tumor burden and response to treatment in hematologic malignancies. Based on the review of the literature and on our own data, we hereby discuss how emerging molecular technologies are helping to refine the molecular monitoring of MRD in ALL and may help to overcome some of the limitations of standard approaches, providing a benefit for the care of patients.
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4
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Levy G, Kicinski M, Van der Straeten J, Uyttebroeck A, Ferster A, De Moerloose B, Dresse MF, Chantrain C, Brichard B, Bakkus M. Immunoglobulin Heavy Chain High-Throughput Sequencing in Pediatric B-Precursor Acute Lymphoblastic Leukemia: Is the Clonality of the Disease at Diagnosis Related to Its Prognosis? Front Pediatr 2022; 10:874771. [PMID: 35712632 PMCID: PMC9197340 DOI: 10.3389/fped.2022.874771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
High-throughput sequencing (HTS) of the immunoglobulin heavy chain (IgH) locus is a recent very efficient technique to monitor minimal residual disease of B-cell precursor acute lymphoblastic leukemia (BCP-ALL). It also reveals the sequences of clonal rearrangements, therefore, the multiclonal structure, of BCP-ALL. In this study, we performed IgH HTS on the diagnostic bone marrow of 105 children treated between 2004 and 2008 in Belgium for BCP-ALL in the European Organization for Research and Treatment of Cancer (EORTC)-58951 clinical trial. Patients were included irrespectively of their outcome. We described the patterns of clonal complexity at diagnosis and investigated its association with patients' characteristics. Two indicators of clonal complexity were used, namely, the number of foster clones, described as clones with similar D-N2-J rearrangements but other V-rearrangement and N1-joining, and the maximum across all foster clones of the number of evolved clones from one foster clone. The maximum number of evolved clones was significantly higher in patients with t(12;21)/ETV6:RUNX1. A lower number of foster clones was associated with a higher risk group after prephase and t(12;21)/ETV6:RUNX1 genetic type. This study observes that clonal complexity as accessed by IgH HTS is linked to prognostic factors in childhood BCP-ALL, suggesting that it may be a useful diagnostic tool for BCP-ALL status and prognosis.
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Affiliation(s)
- Gabriel Levy
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium.,Ludwig Institute for Cancer Research, Brussels, Belgium.,Department of Pediatric Oncology and Hematology, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Michal Kicinski
- European Organization for Research and Treatment of Cancer (EORTC) Headquarters, Brussels, Belgium
| | - Jona Van der Straeten
- Molecular Hematology Laboratory, Vrije Universiteit Brussel, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - Anne Uyttebroeck
- Department of Pediatric Hemato-Oncology, UZ Leuven, Leuven, Belgium
| | - Alina Ferster
- Department of Pediatric Hematology-Oncology, Children's University Hospital Queen Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Barbara De Moerloose
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Marie-Francoise Dresse
- Department of Pediatrics, Centre Hospitalier Régional (CHR) de la Citadelle, Liège, Belgium
| | - Christophe Chantrain
- Division of Pediatric Hematology-Oncology, Centre Hospitalier Chrétien (CHC) MontLégia, Liège, Belgium
| | - Bénédicte Brichard
- Department of Pediatric Oncology and Hematology, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Marleen Bakkus
- Molecular Hematology Laboratory, Vrije Universiteit Brussel, Universitair Ziekenhuis Brussel, Brussels, Belgium
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5
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Identification of clonal immunoglobulin λ light-chain gene rearrangements in AL amyloidosis using next-generation sequencing. Exp Hematol 2021; 101-102:34-41.e4. [PMID: 34411686 DOI: 10.1016/j.exphem.2021.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/25/2021] [Accepted: 08/08/2021] [Indexed: 11/21/2022]
Abstract
Amyloid light-chain (AL) amyloidosis is caused by deposition of abnormally folded clonal immunoglobulin (Ig) light chains made by malignant plasma cells in the bone marrow (BM), leading to multiorgan dysfunction. However, little is known of the factors that regulate the organ tropism of amyloid deposition in this disease. We aimed to identify the clonal composition of Igλ light-chain variable region (IGLV) genes in BM cells in patients with AL amyloidosis using next-generation sequencing. Based on our definition of the clonal IGLV rearrangement (dominant clone >2.5%, dominant cluster >5%), we identified clonal IGLV in 33 of 38 patients with AL amyloidosis (86.8%), 6 of 9 with monoclonal gammopathy of undetermined significance (67%), and 7 of 7 with multiple myeloma (100%). The clones in AL amyloidosis were significantly smaller than those in multiple myeloma (p < 0.01) but comparable to those in monoclonal gammopathy of undetermined significance. Importantly, in patients with AL amyloidosis, the difference in involved and uninvolved free light chains was not correlated with the clonal size of BM plasma cells in our repertoire analysis using NGS. In summary, the clonal composition of IGLV genes in the BM was successfully identified in most patients with AL amyloidosis using NGS. The clonal size of plasma cells in the BM is small, and small malignant clones of plasma cells may secrete free light chi and cause light chain depositions in AL amyloidosis.
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6
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Kim IS. Minimal residual disease in acute lymphoblastic leukemia: technical aspects and implications for clinical interpretation. Blood Res 2020; 55:S19-S26. [PMID: 32719172 PMCID: PMC7386891 DOI: 10.5045/br.2020.s004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 01/23/2020] [Accepted: 01/23/2020] [Indexed: 12/16/2022] Open
Abstract
Minimal residual disease (MRD) monitoring has proven to be one of the fundamental independent prognostic factors for patients with acute lymphoblastic leukemia (ALL). Sequential monitoring of MRD using sensitive and specific methods, such as real-time quantitative polymerase chain reaction (qPCR) or flow cytometry (FCM), has improved the assessment of treatment response and is currently used for therapeutic stratification and early detection. Although both FCM and qPCR yield highly consistent results with sensitivities of 10‒4, each method has several limitations. For example, qPCR is time-consuming and laborious: designing primers that correspond to the immunoglobulin (IG) and T-cell receptor (TCR) gene rearrangements at diagnosis can take 3‒4 weeks. In addition, the evolution of additional clones beyond the first or index clone during therapy cannot be detected, which might lead to false-negative results. FCM requires experienced technicians and sometimes does not achieve a sensitivity of 10‒4. Accordingly, a next generation sequencing (NGS)-based method has been developed in an attempt to overcome these limitations. With the advent of high-throughput NGS technologies, a more in-depth analysis of IG and/or TCR gene rearrangements is now within reach, which impacts all applications of IG/TR analysis. However, standardization, quality control, and validation of this new technology are warranted prior to its incorporation into routine practice.
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Affiliation(s)
- In-Suk Kim
- Department of Laboratory Medicine, Pusan National University Yangsan Hospital, Yangsan, Korea.,Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Korea
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7
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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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8
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Coccaro N, Anelli L, Zagaria A, Specchia G, Albano F. Next-Generation Sequencing in Acute Lymphoblastic Leukemia. Int J Mol Sci 2019; 20:ijms20122929. [PMID: 31208040 PMCID: PMC6627957 DOI: 10.3390/ijms20122929] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/04/2019] [Accepted: 06/14/2019] [Indexed: 12/25/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer and accounts for about a quarter of adult acute leukemias, and features different outcomes depending on the age of onset. Improvements in ALL genomic analysis achieved thanks to the implementation of next-generation sequencing (NGS) have led to the recent discovery of several novel molecular entities and to a deeper understanding of the existing ones. The purpose of our review is to report the most recent discoveries obtained by NGS studies for ALL diagnosis, risk stratification, and treatment planning. We also report the first efforts at NGS use for minimal residual disease (MRD) assessment, and early studies on the application of third generation sequencing in cancer research. Lastly, we consider the need for the integration of NGS analyses in clinical practice for genomic patients profiling from the personalized medicine perspective.
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Affiliation(s)
- Nicoletta Coccaro
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
| | - Luisa Anelli
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
| | - Antonella Zagaria
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
| | - Giorgina Specchia
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
| | - Francesco Albano
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
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9
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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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10
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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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Considerations for monitoring minimal residual disease using immunoglobulin clonality in patients with precursor B-cell lymphoblastic leukemia. Clin Chim Acta 2018; 488:81-89. [PMID: 30389459 DOI: 10.1016/j.cca.2018.10.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 10/08/2018] [Accepted: 10/29/2018] [Indexed: 11/23/2022]
Abstract
BACKGROUND Minimal residual disease (MRD) monitoring is a powerful tool to predict the risk of relapse. Herein, we present an MRD monitoring strategy for B-cell lymphoblastic leukemia (B-ALL) using high-throughput sequencing (HTS) of immunoglobulin (Ig) clonality before implementation into routine practice. METHODS We selected 74 bone marrow (BM) specimens from 47 patients who were diagnosed with B-ALL. Ig clonality was analyzed using both fragment analysis and HTS. The performance of Ig clonality was evaluated through comparison of the results from real-time quantitative polymerase chain reaction (qPCR) of leukemia-specific fusion transcripts and flow cytometry. RESULTS IGH clonality was observed in all patients, and the sum of clonal burden varied (9.47%-96.77%). IGK clonality was identified in 70% of patients and availed in cases with low IGH clonal burden. The total IGH clonal burden was significantly correlated with the proportion of leukemic blasts, leukemia-specific fusion transcripts, and flow cytometry. We recognized the different responses of each clone and emerging clones originating from the trace of Ig rearrangement presented in the initial specimen. IGH clonal burden after chemotherapy represented patient outcomes well. IGH assay also provided information of repertoire diversity of IGH rearrangement. CONCLUSION The Ig clonality assay via HTS will be a promising tool for MRD monitoring of B-ALL through an adequate strategy to identify and monitor individual clones and determine repertoire diversity.
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Theunissen PMJ, de Bie M, van Zessen D, de Haas V, Stubbs AP, van der Velden VHJ. Next-generation antigen receptor sequencing of paired diagnosis and relapse samples of B-cell acute lymphoblastic leukemia: Clonal evolution and implications for minimal residual disease target selection. Leuk Res 2018; 76:98-104. [PMID: 30389174 DOI: 10.1016/j.leukres.2018.10.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/01/2018] [Accepted: 10/18/2018] [Indexed: 11/26/2022]
Abstract
Antigen receptor gene rearrangements are frequently applied as molecular targets for detection of minimal residual disease (MRD) in B-cell precursor acute lymphoblastic leukemia patients. Since such targets may be lost at relapse, appropriate selection of antigen receptor genes as MRD-PCR target is critical. Recently, next-generation sequencing (NGS) - much more sensitive and quantitative than classical PCR-heteroduplex approaches - has been introduced for identification of MRD-PCR targets. We evaluated 42 paired diagnosis-relapse samples by NGS (IGH, IGK, TRG, TRD, and TRB) to evaluate clonal evolution patterns and to design an algorithm for selection of antigen receptor gene rearrangements most likely to remain stable at relapse. Overall, only 393 out of 1446 (27%) clonal rearrangements were stable between diagnosis and relapse. If only index clones with a frequency >5% at diagnosis were taken into account, this number increased to 65%; including only index clones with an absolute read count >10,000, indicating truly major clones, further increased the stability to 84%. Over 90% of index clones at relapse were also present as index clone at diagnosis. Our data provide detailed information about the stability of antigen receptor gene rearrangements, based on which we propose an algorithm for selecting stable MRD-PCR targets, successful in >97% of patients.
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Affiliation(s)
- Prisca M J Theunissen
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Maaike de Bie
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - David van Zessen
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, The Netherlands; Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | | | - Andrew P Stubbs
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, The Netherlands
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Cheng S, Inghirami G, Cheng S, Tam W. Simple deep sequencing-based post-remission MRD surveillance predicts clinical relapse in B-ALL. J Hematol Oncol 2018; 11:105. [PMID: 30134947 PMCID: PMC6103872 DOI: 10.1186/s13045-018-0652-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/13/2018] [Indexed: 01/01/2023] Open
Abstract
Background Next-generation sequencing (NGS) of the rearranged immunoglobulin heavy-chain gene has emerged as a highly sensitive method to detect minimal residual disease (MRD) in B acute lymphoblastic leukemia/lymphoma (B-ALL). However, a sensitive and easily implemented NGS methodology for routine clinical laboratories is lacking and clinical utility of NGS-MRD surveillance in a post-remission setting to predict clinical relapse has not been determined. Methods Here we described a simple and quantitative NGS platform and assessed its performance characteristics, quantified NGS-MRD levels in 122 B-ALL samples from 30 B-ALL patients, and explored the clinical merit of NGS-based MRD surveillance. Results The current NGS platform has an analytic sensitivity of 0.0001% with excellent specificity and reproducibility. Overall, it performs better than routine multi-color flow cytometry (MCF) in detecting MRD. Utilizing this assay in MRD surveillance in a post-remission setting showed that it detected conversion to positive MRD (CPMRD) in patients with NGS-based molecular remission much earlier than MCF, and that positive MRD conversion could be detected as early as 25.6 weeks prior to clinical relapse in closely surveilled patients. Post-remission CPMRD, but not NGS-based MRD positivity at end of induction, can accurately predict clinical relapse in our limited cohort of B-ALL patients. Conclusions This pilot proof-of-concept study illustrates the clinical utility of a simple, sensitive, and clinically feasible MRD detection platform in post-remission NGS-based MRD surveillance and early relapse detection in B-ALL patients. Electronic supplementary material The online version of this article (10.1186/s13045-018-0652-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shuhua Cheng
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Shuo Cheng
- Department of Computer Science, School of Engineering, Cornell University, Ithaca, New York, NY, 14853, USA
| | - Wayne Tam
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10021, USA.
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Rocher T, Giraud M, Salson M. Indexing labeled sequences. PeerJ Comput Sci 2018; 4:e148. [PMID: 33816803 PMCID: PMC7924554 DOI: 10.7717/peerj-cs.148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 02/01/2018] [Indexed: 06/12/2023]
Abstract
BACKGROUND Labels are a way to add some information on a text, such as functional annotations such as genes on a DNA sequences. V(D)J recombinations are DNA recombinations involving two or three short genes in lymphocytes. Sequencing this short region (500 bp or less) produces labeled sequences and brings insight in the lymphocyte repertoire for onco-hematology or immunology studies. METHODS We present two indexes for a text with non-overlapping labels. They store the text in a Burrows-Wheeler transform (BWT) and a compressed label sequence in a Wavelet Tree. The label sequence is taken in the order of the text (TL-index) or in the order of the BWT (TLBW-index). Both indexes need a space related to the entropy of the labeled text. RESULTS These indexes allow efficient text-label queries to count and find labeled patterns. The TLBW-index has an overhead on simple label queries but is very efficient on combined pattern-label queries. We implemented the indexes in C++ and compared them against a baseline solution on pseudo-random as well as on V(D)J labeled texts. DISCUSSION New indexes such as the ones we proposed improve the way we index and query labeled texts as, for instance, lymphocyte repertoire for hematological and immunological studies.
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Duez M, Giraud M, Herbert R, Rocher T, Salson M, Thonier F. Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing. PLoS One 2016; 11:e0166126. [PMID: 27835690 PMCID: PMC5106020 DOI: 10.1371/journal.pone.0166126] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/24/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The B and T lymphocytes are white blood cells playing a key role in the adaptive immunity. A part of their DNA, called the V(D)J recombinations, is specific to each lymphocyte, and enables recognition of specific antigenes. Today, with new sequencing techniques, one can get billions of DNA sequences from these regions. With dedicated Repertoire Sequencing (RepSeq) methods, it is now possible to picture population of lymphocytes, and to monitor more accurately the immune response as well as pathologies such as leukemia. METHODS AND RESULTS Vidjil is an open-source platform for the interactive analysis of high-throughput sequencing data from lymphocyte recombinations. It contains an algorithm gathering reads into clonotypes according to their V(D)J junctions, a web application made of a sample, experiment and patient database and a visualization for the analysis of clonotypes along the time. Vidjil is implemented in C++, Python and Javascript and licensed under the GPLv3 open-source license. Source code, binaries and a public web server are available at http://www.vidjil.org and at http://bioinfo.lille.inria.fr/vidjil. Using the Vidjil web application consists of four steps: 1. uploading a raw sequence file (typically a FASTQ); 2. running RepSeq analysis software; 3. visualizing the results; 4. annotating the results and saving them for future use. For the end-user, the Vidjil web application needs no specific installation and just requires a connection and a modern web browser. Vidjil is used by labs in hematology or immunology for research and clinical applications.
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Affiliation(s)
- Marc Duez
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
- SIRIC ONCOLille, 59000 Lille, France
| | - Mathieu Giraud
- Université de Lille, CNRS, UMR 9189 – CRIStAL – Centre de Recherche en Informatique Signal et Automatique de Lille, 59000 Lille, France
- Inria Lille, 59650 Villeneuve d’Ascq, France
- * E-mail:
| | - Ryan Herbert
- Université de Lille, CNRS, UMR 9189 – CRIStAL – Centre de Recherche en Informatique Signal et Automatique de Lille, 59000 Lille, France
- Inria Lille, 59650 Villeneuve d’Ascq, France
| | - Tatiana Rocher
- Université de Lille, CNRS, UMR 9189 – CRIStAL – Centre de Recherche en Informatique Signal et Automatique de Lille, 59000 Lille, France
- Inria Lille, 59650 Villeneuve d’Ascq, France
| | - Mikaël Salson
- Université de Lille, CNRS, UMR 9189 – CRIStAL – Centre de Recherche en Informatique Signal et Automatique de Lille, 59000 Lille, France
- Inria Lille, 59650 Villeneuve d’Ascq, France
| | - Florian Thonier
- Inserm, Hôpital Necker – Enfants Malades, 75015 Paris, France
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