1
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You X, Cao Y, Suzuki T, Shao J, Zhu B, Masumura K, Xi J, Liu W, Zhang X, Luan Y. Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing. Nucleic Acids Res 2023; 51:e109. [PMID: 37870450 PMCID: PMC10681716 DOI: 10.1093/nar/gkad909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/25/2023] [Accepted: 10/05/2023] [Indexed: 10/24/2023] Open
Abstract
Error-corrected next-generation sequencing (ecNGS) is an emerging technology for accurately measuring somatic mutations. Here, we report paired-end and complementary consensus sequencing (PECC-Seq), a high-accuracy ecNGS approach for genome-wide somatic mutation detection. We characterize a novel 2-aminoimidazolone lesion besides 7,8-dihydro-8-oxoguanine and the resulting end-repair artifacts originating from NGS library preparation that obscure the sequencing accuracy of NGS. We modify library preparation protocol for the enzymatic removal of end-repair artifacts and improve the accuracy of our previously developed duplex consensus sequencing method. Optimized PECC-Seq shows an error rate of <5 × 10-8 with consensus bases compressed from approximately 25 Gb of raw sequencing data, enabling the accurate detection of low-abundance somatic mutations. We apply PECC-Seq to the quantification of in vivo mutagenesis. Compared with the classic gpt gene mutation assay using gpt delta transgenic mice, PECC-Seq exhibits high sensitivity in quantitatively measuring dose-dependent mutagenesis induced by Aristolochic acid I (AAI). Moreover, PECC-Seq specifically characterizes the distinct genome-wide mutational signatures of AAI, Benzo[a]pyrene, N-Nitroso-N-ethylurea and N-nitrosodiethylamine and reveals the mutational signature of Quinoline in common mouse models. Overall, our findings demonstrate that high-accuracy PECC-Seq is a promising tool for genome-wide somatic mutagenesis quantification and for in vivo mutagenicity testing.
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Affiliation(s)
- Xinyue You
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yiyi Cao
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Takayoshi Suzuki
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Kawasaki 210-9501, Japan
| | - Jie Shao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, The Chinese Academy of Sciences, Beijing 100085, China; The University of Chinese Academy of Sciences, Beijing 100049, China
| | - Benzhan Zhu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, The Chinese Academy of Sciences, Beijing 100085, China; The University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kenichi Masumura
- Division of Risk Assessment, National Institute of Health Sciences, Kawasaki 210-9501, Japan
| | - Jing Xi
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Weiying Liu
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xinyu Zhang
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yang Luan
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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2
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Rosenquist R, Bernard E, Erkers T, Scott DW, Itzykson R, Rousselot P, Soulier J, Hutchings M, Östling P, Cavelier L, Fioretos T, Smedby KE. Novel precision medicine approaches and treatment strategies in hematological malignancies. J Intern Med 2023; 294:413-436. [PMID: 37424223 DOI: 10.1111/joim.13697] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Genetic testing has been applied for decades in clinical routine diagnostics of hematological malignancies to improve disease (sub)classification, prognostication, patient management, and survival. In recent classifications of hematological malignancies, disease subtypes are defined by key recurrent genetic alterations detected by conventional methods (i.e., cytogenetics, fluorescence in situ hybridization, and targeted sequencing). Hematological malignancies were also one of the first disease areas in which targeted therapies were introduced, the prime example being BCR::ABL1 inhibitors, followed by an increasing number of targeted inhibitors hitting the Achilles' heel of each disease, resulting in a clear patient benefit. Owing to the technical advances in high-throughput sequencing, we can now apply broad genomic tests, including comprehensive gene panels or whole-genome and whole-transcriptome sequencing, to identify clinically important diagnostic, prognostic, and predictive markers. In this review, we give examples of how precision diagnostics has been implemented to guide treatment selection and improve survival in myeloid (myelodysplastic syndromes and acute myeloid leukemia) and lymphoid malignancies (acute lymphoblastic leukemia, diffuse large B-cell lymphoma, and chronic lymphocytic leukemia). We discuss the relevance and potential of monitoring measurable residual disease using ultra-sensitive techniques to assess therapy response and detect early relapses. Finally, we bring up the promising avenue of functional precision medicine, combining ex vivo drug screening with various omics technologies, to provide novel treatment options for patients with advanced disease. Although we are only in the beginning of the field of precision hematology, we foresee rapid development with new types of diagnostics and treatment strategies becoming available to the benefit of our patients.
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Affiliation(s)
- Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Elsa Bernard
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, USA
- PRISM Center for Personalized Medicine, Gustave Roussy, Villejuif, France
| | - Tom Erkers
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- SciLifeLab, Stockholm, Sweden
| | - David W Scott
- BC Cancer's Centre for Lymphoid Cancer, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Raphael Itzykson
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, Paris, France
- Département Hématologie et Immunologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Philippe Rousselot
- Department of Hematology, Centre Hospitalier de Versailles, Le Chesnay, France
| | - Jean Soulier
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, Paris, France
- Hématologie Biologique, APHP, Hôpital Saint-Louis, Paris, France
| | - Martin Hutchings
- Department of Haematology and Phase 1 Unit, Rigshospitalet, Copenhagen, Denmark
| | - Päivi Östling
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- SciLifeLab, Stockholm, Sweden
| | - Lucia Cavelier
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Thoas Fioretos
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Karin E Smedby
- Department of Hematology, Karolinska University Hospital, Solna, Stockholm, Sweden
- Division of Clinical Epidemiology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
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3
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Schulz E, Aplan PD, Freeman SD, Pavletic SZ. Moving toward a conceptualization of measurable residual disease in myelodysplastic syndromes. Blood Adv 2023; 7:4381-4394. [PMID: 37267435 PMCID: PMC10432617 DOI: 10.1182/bloodadvances.2023010098] [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: 03/01/2023] [Revised: 05/03/2023] [Accepted: 05/22/2023] [Indexed: 06/04/2023] Open
Abstract
Approximately 90% of patients with myelodysplastic syndromes (MDSs) have somatic mutations that are known or suspected to be oncogenic in the malignant cells. The genetic risk stratification of MDSs has evolved substantially with the introduction of the clinical molecular international prognostic scoring system, which establishes next-generation sequencing at diagnosis as a standard of care. Furthermore, the International Consensus Classification of myeloid neoplasms and acute leukemias has refined the MDS diagnostic criteria with the introduction of a new MDS/acute myeloid leukemia category. Monitoring measurable residual disease (MRD) has historically been used to define remission status, improve relapse prediction, and determine the efficacy of antileukemic drugs in patients with acute and chronic leukemias. However, in contrast to leukemias, assessment of MRD, including tracking of patient-specific mutations, has not yet been formally defined as a biomarker for MDS. This article summarizes current evidence and challenges and provides a conceptual framework for incorporating MRD into the treatment of MDS and future clinical trials.
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Affiliation(s)
- Eduard Schulz
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Myeloid Malignancies Program, National Institutes of Health, Bethesda, MD
| | - Peter D. Aplan
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Myeloid Malignancies Program, National Institutes of Health, Bethesda, MD
| | - Sylvie D. Freeman
- Department of Clinical Immunology, Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Steven Z. Pavletic
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Myeloid Malignancies Program, National Institutes of Health, Bethesda, MD
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4
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Puzo CJ, Tormey CA, Rinder HM, Siddon AJ. Optimizing Donor Chimerism Threshold for Next Generation Sequencing Monitoring of Measurable Residual Disease Post-Allogeneic Stem Cell Transplant for Myeloid Neoplasms. Transplant Cell Ther 2023:S2666-6367(23)01237-X. [PMID: 37062510 DOI: 10.1016/j.jtct.2023.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/30/2023] [Accepted: 04/05/2023] [Indexed: 04/18/2023]
Abstract
BACKGROUND Next-Generation Sequencing (NGS) is used to monitor genetically-measurable residual disease (gMRD) following allogeneic stem cell transplant (aSCT). It is unknown whether an upper limit of chimerism exists such that gMRD NGS testing can be safely forgone. METHODS We reviewed 61 AML and 24 MDS patients between 2016-2020 with at least 1 NGS panel before and after aSCT. Donor chimerism was quantified. Logistic regression characterized which factors predicted gMRD. Receiver operator curves (ROC) determined the optimal chimerism threshold for which gMRD would not be detected. Data from an additional 22 patients with follow-up NGS testing in 2022, was also analyzed to validate our proposed threshold. RESULTS Donor chimerism (OR= 0.38, 95% CI[0.10,0.62], p=0.02), as expected, was a significant predictor of gMRD. Age, gender, conditioning regimen, presence of a related donor, and diagnosis were not associated with gMRD. A chimerism threshold of 92.5% optimized sensitivity (97.7) and specificity (95.4) such that values >92.5% strongly predicted absence of gMRD (AUC= .986). The validation cohort demonstrated similar strongly predictive capability (AUC= .974) with appropriate sensitivity (100%) and specificity (90.9%). CONCLUSION NGS monitoring of gMRD is redundant at chimerism values greater than a more conservative threshold of 92.5% after stem cell transplant.
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Affiliation(s)
| | | | - Henry M Rinder
- Yale School of Medicine, Department of Laboratory Medicine, New Haven CT, USA
| | - Alexa J Siddon
- Yale School of Medicine, Department of Laboratory Medicine, New Haven CT, USA; Yale School of Medicine, Department of Pathology, New Haven CT, USA.
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5
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Heuser M, Freeman SD, Ossenkoppele GJ, Buccisano F, Hourigan CS, Ngai LL, Tettero JM, Bachas C, Baer C, Béné MC, Bücklein V, Czyz A, Denys B, Dillon R, Feuring-Buske M, Guzman ML, Haferlach T, Han L, Herzig JK, Jorgensen JL, Kern W, Konopleva MY, Lacombe F, Libura M, Majchrzak A, Maurillo L, Ofran Y, Philippe J, Plesa A, Preudhomme C, Ravandi F, Roumier C, Subklewe M, Thol F, van de Loosdrecht AA, van der Reijden BA, Venditti A, Wierzbowska A, Valk PJM, Wood BL, Walter RB, Thiede C, Döhner K, Roboz GJ, Cloos J. 2021 Update on MRD in acute myeloid leukemia: a consensus document from the European LeukemiaNet MRD Working Party. Blood 2021; 138:2753-2767. [PMID: 34724563 PMCID: PMC8718623 DOI: 10.1182/blood.2021013626] [Citation(s) in RCA: 319] [Impact Index Per Article: 106.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/15/2021] [Indexed: 11/20/2022] Open
Abstract
Measurable residual disease (MRD) is an important biomarker in acute myeloid leukemia (AML) that is used for prognostic, predictive, monitoring, and efficacy-response assessments. The European LeukemiaNet (ELN) MRD Working Party evaluated standardization and harmonization of MRD in an ongoing manner and has updated the 2018 ELN MRD recommendations based on significant developments in the field. New and revised recommendations were established during in-person and online meetings, and a 2-stage Delphi poll was conducted to optimize consensus. All recommendations are graded by levels of evidence and agreement. Major changes include technical specifications for next-generation sequencing-based MRD testing and integrative assessments of MRD irrespective of technology. Other topics include use of MRD as a prognostic and surrogate end point for drug testing; selection of the technique, material, and appropriate time points for MRD assessment; and clinical implications of MRD assessment. In addition to technical recommendations for flow- and molecular-MRD analysis, we provide MRD thresholds and define MRD response, and detail how MRD results should be reported and combined if several techniques are used. MRD assessment in AML is complex and clinically relevant, and standardized approaches to application, interpretation, technical conduct, and reporting are of critical importance.
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Affiliation(s)
- Michael Heuser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Sylvie D Freeman
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Gert J Ossenkoppele
- Department of Hematology, Amsterdam University Medical Center (UMC), Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Francesco Buccisano
- Department of Biomedicine and Prevention, Hematology, University Tor Vergata, Rome, Italy
| | - Christopher S Hourigan
- Laboratory of Myeloid Malignancy, Hematology Branch, National Heart, Lung, and Blood Institute, Bethesda, MD
| | - Lok Lam Ngai
- Department of Hematology, Amsterdam University Medical Center (UMC), Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Jesse M Tettero
- Department of Hematology, Amsterdam University Medical Center (UMC), Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Costa Bachas
- Department of Hematology, Amsterdam University Medical Center (UMC), Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | | | - Marie-Christine Béné
- Department of Hematology and Biology, Centre Hospitalier Universitaire (CHU) Nantes, Nantes, France
| | - Veit Bücklein
- Department of Medicine III, University Hospital, Ludwig Maximilian University Munich, Munich, Germany
| | - Anna Czyz
- Department of Hematology, Blood Neoplasms, and Bone Marrow Transplantation, Wrocław Medical University, Wrocław, Poland
| | - Barbara Denys
- Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University
| | - Richard Dillon
- Department of Medical and Molecular Genetics, King's College, London, United Kingdom
| | | | - Monica L Guzman
- Department of Medicine, Division of Hematology and Oncology, Weill Cornell Medicine, New York, NY
| | | | | | - Julia K Herzig
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | | | | | | | - Francis Lacombe
- Hematology Biology, Flow Cytometry, Bordeaux University Hospital, Pessac, France
| | | | - Agata Majchrzak
- Department of Experimental Hematology, Copernicus Memorial Hospital, Lodz, Poland
| | - Luca Maurillo
- Department of Biomedicine and Prevention, Hematology, University Tor Vergata, Rome, Italy
| | - Yishai Ofran
- Department of Hematology, Shaare Zedek Medical Center Faculty of Medicine Hebrew University, Jerusalem Israel
| | - Jan Philippe
- Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University
| | - Adriana Plesa
- Department of Hematology Laboratory, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
| | | | | | | | - Marion Subklewe
- Department of Medicine III, University Hospital, Ludwig Maximilian University Munich, Munich, Germany
| | - Felicitas Thol
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Arjan A van de Loosdrecht
- Department of Hematology, Amsterdam University Medical Center (UMC), Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Bert A van der Reijden
- Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Adriano Venditti
- Department of Biomedicine and Prevention, Hematology, University Tor Vergata, Rome, Italy
| | | | - Peter J M Valk
- Department of Hematology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Brent L Wood
- Department of Hematopathology, Children's Hospital Los Angeles, CA
| | - Roland B Walter
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Christian Thiede
- Department of Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany; and
- AgenDix GmbH, Dresden, Germany
| | - Konstanze Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Gail J Roboz
- Department of Medicine, Division of Hematology and Oncology, Weill Cornell Medicine, New York, NY
| | - Jacqueline Cloos
- Department of Hematology, Amsterdam University Medical Center (UMC), Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
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6
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Liang EC, Chen C, Lu R, Mannis GN, Muffly L. Measurable residual disease status and FLT3 inhibitor therapy in patients with FLT3-ITD mutated AML following allogeneic hematopoietic cell transplantation. Bone Marrow Transplant 2021; 56:3091-3093. [PMID: 34584238 DOI: 10.1038/s41409-021-01475-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/07/2021] [Accepted: 09/16/2021] [Indexed: 11/09/2022]
Abstract
Measurable residual disease (MRD) is associated with poor prognosis in acute myeloid leukemia (AML), even after allogeneic hematopoietic cell transplantation (HCT). New next-generation sequencing (NGS) methods have emerged as a highly sensitive and specific method to detect MRD. In addition to defining the role of post-HCT MRD monitoring in FLT3-ITD mutated AML, there is great interest in the optimal use of oral FLT3 tyrosine kinase inhibitors (FLT3 inhibitors) to maintain remission following HCT. In this study, we evaluated the clinical impact of sensitive FLT3 MRD testing early after HCT and maintenance FLT3 inhibitor use at our transplant center. We found that there was a trend towards inferior progression-free survival (PFS) for patients with early post-HCT MRD, but that overall survival (OS) was not significantly impacted by MRD. The use of maintenance FLT3 inhibitors led to a significantly superior PFS and OS in our cohort, and improved PFS and OS in both MRD-negative and MRD-positive patients. Altogether, our results demonstrate the prognostic significance of NGS-based MRD monitoring for FLT3-ITD and the ability of post-HCT maintenance therapy to prevent relapse and death in FLT3-ITD mutated AML.
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Affiliation(s)
- Emily C Liang
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Connie Chen
- Department of Medicine, Division of Blood and Marrow Transplantation, Stanford University School of Medicine, Stanford, CA, USA
| | - Rong Lu
- Department of Medicine, Quantitative Sciences Unit, Stanford University School of Medicine, Stanford, CA, USA
| | - Gabriel N Mannis
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lori Muffly
- Department of Medicine, Division of Blood and Marrow Transplantation, Stanford University School of Medicine, Stanford, CA, USA.
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7
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Vonk CM, Al Hinai ASA, Hanekamp D, Valk PJM. Molecular Minimal Residual Disease Detection in Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:5431. [PMID: 34771594 PMCID: PMC8582498 DOI: 10.3390/cancers13215431] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 02/06/2023] Open
Abstract
Initial induction chemotherapy to eradicate the bulk of acute myeloid leukemia (AML) cells results in complete remission (CR) in the majority of patients. However, leukemic cells persisting in the bone marrow below the morphologic threshold remain unaffected and have the potential to proliferate and re-emerge as AML relapse. Detection of minimal/measurable residual disease (MRD) is a promising prognostic marker for AML relapse as it can assess an individual patients' risk profile and evaluate their response to treatment. With the emergence of molecular techniques, such as next generation sequencing (NGS), a more sensitive assessment of molecular MRD markers is available. In recent years, the detection of MRD by molecular assays and its association with AML relapse and survival has been explored and verified in multiple studies. Although most studies show that the presence of MRD leads to a worse clinical outcome, molecular-based methods face several challenges including limited sensitivity/specificity, and a difficult distinction between mutations that are representative of AML rather than clonal hematopoiesis. This review describes the studies that have been performed using molecular-based assays for MRD detection in the context of other MRD detection approaches in AML, and discusses limitations, challenges and opportunities.
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Affiliation(s)
- Christian M Vonk
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands
| | - Adil S A Al Hinai
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands
- National Genetic Center, Ministry of Health, Muscat 111, Oman
| | - Diana Hanekamp
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands
- Department of Hematology, Cancer Center VU University Medical Center, Amsterdam University Medical Centers, 1081 HV Amsterdam, The Netherlands
| | - Peter J M Valk
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands
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8
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Yu T, Chi J, Wang L. Clinical values of gene alterations as marker of minimal residual disease in non-M3 acute myeloid leukemia. Hematology 2021; 26:848-859. [PMID: 34674615 DOI: 10.1080/16078454.2021.1990503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Acute myeloid leukemia (AML) is a malignant disease of the hematopoietic system. Residual leukemic cells after treatment are associated with relapse. Thus, detecting minimal residual disease (MRD) is significant. Major techniques for MRD assessment include multiparameter flow cytometry (MFC), polymerase chain reaction (PCR), and next-generation sequencing (NGS). At a molecular level, AML is the consequence of collaboration of several gene alterations. Some of these gene alterations can also be used as MRD markers to evaluate the level of residual leukemic cells by PCR and NGS. However, when as MRD markers, different gene alterations have different clinical values. This paper aims to summarize the characteristics of various MRD markers, so as to better predict the clinical outcome of AML patients and guide the treatment.
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Affiliation(s)
- Tingyu Yu
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Jianxiang Chi
- Center for the Study of Hematological Malignancies, Nicosia, Cyprus
| | - Li Wang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
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9
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Qin D. Molecular testing for acute myeloid leukemia. Cancer Biol Med 2021; 19:j.issn.2095-3941.2020.0734. [PMID: 34347394 PMCID: PMC8763005 DOI: 10.20892/j.issn.2095-3941.2020.0734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/02/2021] [Indexed: 11/11/2022] Open
Abstract
In the era of personalized medicine, information on molecular change at the gene level is important for patient care. Such information has been used for disease classification, diagnosis, prognosis, risk stratification, and treatment, which is especially important in cancer patient care. Many molecular tests exist and can be used to detect the molecular changes at gene level. These tests include, but are not limited to, karyotyping, endpoint polymerase chain reaction (PCR), real-time PCR, Sanger sequencing, pyrosequencing, next-generation sequencing, and so forth. How to use the right tests for the right patients at the right time is essential for optimal patient outcome. This review puts together some information on molecular testing for acute myeloid leukemia.
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Affiliation(s)
- Dahui Qin
- Moffitt Cancer Center, Tampa, FL 33612-9416, USA
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10
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Yamato G, Deguchi T, Terui K, Toki T, Watanabe T, Imaizumi T, Hama A, Iwamoto S, Hasegawa D, Ueda T, Yokosuka T, Tanaka S, Yanagisawa R, Koh K, Saito AM, Horibe K, Hayashi Y, Adachi S, Mizutani S, Taga T, Ito E, Watanabe K, Muramatsu H. Predictive factors for the development of leukemia in patients with transient abnormal myelopoiesis and Down syndrome. Leukemia 2021; 35:1480-1484. [PMID: 33654203 PMCID: PMC8102190 DOI: 10.1038/s41375-021-01171-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 01/08/2021] [Accepted: 01/28/2021] [Indexed: 12/20/2022]
Affiliation(s)
- Genki Yamato
- Department of Hematology/Oncology, Gunma Children's Medical Center, Gunma, Japan.,Department of Pediatrics, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Takao Deguchi
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Kiminori Terui
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Aomori, Japan
| | - Tsutomu Toki
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Aomori, Japan
| | - Tomoyuki Watanabe
- Department of Nutritional Science, Faculty of Psychological and Physical Science, Aichi Gakuin University, Aichi, Japan
| | - Takahiro Imaizumi
- Department of Advanced Medicine, Nagoya University Hospital, Nagoya, Japan
| | - Asahito Hama
- Department of Hematology and Oncology, Children's Medical Center, Japanese Red Cross Nagoya First Hospital, Nagoya, Japan
| | - Shotaro Iwamoto
- Department of Pediatrics, Mie University Graduate School of Medicine, Mie, Japan
| | - Daisuke Hasegawa
- Department of Pediatrics, St Luke's International Hospital, Tokyo, Japan
| | - Takahiro Ueda
- Department of Pediatrics, Nippon Medical School, Tokyo, Japan
| | - Tomoko Yokosuka
- Department of Hematology/Oncology, Kanagawa Children's Medical Center, Kanagawa, Japan
| | - Shiro Tanaka
- Clinical Biostatistics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ryu Yanagisawa
- Department of Hematology and Oncology, Nagano Children's Hospital, Nagano, Japan
| | - Katsuyoshi Koh
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Akiko M Saito
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Keizo Horibe
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Yasuhide Hayashi
- Department of Hematology/Oncology, Gunma Children's Medical Center, Gunma, Japan.,Institute of Physiology and Medicine, Jobu University, Gunma, Japan
| | - Souichi Adachi
- Department of Human Health Sciences, Kyoto University, Kyoto, Japan
| | - Shuki Mizutani
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takashi Taga
- Department of Pediatrics, Shiga University of Medical Science, Otsu, Japan
| | - Etsuro Ito
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Aomori, Japan
| | - Kenichiro Watanabe
- Department of Hematology and Oncology, Shizuoka Children's Hospital, Shizuoka, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan.
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11
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Aguirre-Ruiz P, Ariceta B, Viguria MC, Zudaire MT, Blasco-Iturri Z, Arnedo P, Aguilera-Diaz A, Jauregui A, Mañú A, Prosper F, Mateos MC, Fernández-Mercado M, Larráyoz MJ, Redondo M, Calasanz MJ, Vázquez I, Bandrés E. Assessment of Minimal Residual Disease by Next Generation Sequencing in Peripheral Blood as a Complementary Tool for Personalized Transplant Monitoring in Myeloid Neoplasms. J Clin Med 2020; 9:jcm9123818. [PMID: 33255857 PMCID: PMC7760908 DOI: 10.3390/jcm9123818] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/30/2022] Open
Abstract
Patients with myeloid neoplasms who relapsed after allogenic hematopoietic stem cell transplant (HSCT) have poor prognosis. Monitoring of chimerism and specific molecular markers as a surrogate measure of relapse is not always helpful; therefore, improved systems to detect early relapse are needed. We hypothesized that the use of next generation sequencing (NGS) could be a suitable approach for personalized follow-up post-HSCT. To validate our hypothesis, we analyzed by NGS, a retrospective set of peripheral blood (PB) DNA samples previously evaluated by high-sensitive quantitative PCR analysis using insertion/deletion polymorphisms (indel-qPCR) chimerism engraftment. Post-HCST allelic burdens assessed by NGS and chimerism status showed a similar time-course pattern. At time of clinical relapse in 8/12 patients, we detected positive NGS-based minimal residual disease (NGS-MRD). Importantly, in 6/8 patients, we were able to detect NGS-MRD at time points collected prior to clinical relapse. We also confirmed the disappearance of post-HCST allelic burden in non-relapsed patients, indicating true clinical specificity. This study highlights the clinical utility of NGS-based post-HCST monitoring in myeloid neoplasia as a complementary specific analysis to high-sensitive engraftment testing. Overall, NGS-MRD testing in PB is widely applicable for the evaluation of patients following HSCT and highly valuable to personalized early treatment intervention when mixed chimerism is detected.
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Affiliation(s)
- Paula Aguirre-Ruiz
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, 31008 Pamplona, Navarra, Spain; (P.A.-R.); (B.A.); (Z.B.-I.); (A.M.); (M.F.-M.); (M.J.L.); (M.J.C.)
| | - Beñat Ariceta
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, 31008 Pamplona, Navarra, Spain; (P.A.-R.); (B.A.); (Z.B.-I.); (A.M.); (M.F.-M.); (M.J.L.); (M.J.C.)
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Navarra, Spain; (M.C.V.); (M.T.Z.); (A.A.-D.); (F.P.); (M.C.M.); (M.R.)
| | - María Cruz Viguria
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Navarra, Spain; (M.C.V.); (M.T.Z.); (A.A.-D.); (F.P.); (M.C.M.); (M.R.)
- Hematology Department, Complejo Hospitalario de Navarra, 31008 Pamplona, Navarra, Spain; (P.A.); (A.J.)
| | - María Teresa Zudaire
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Navarra, Spain; (M.C.V.); (M.T.Z.); (A.A.-D.); (F.P.); (M.C.M.); (M.R.)
- Hematology Department, Complejo Hospitalario de Navarra, 31008 Pamplona, Navarra, Spain; (P.A.); (A.J.)
| | - Zuriñe Blasco-Iturri
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, 31008 Pamplona, Navarra, Spain; (P.A.-R.); (B.A.); (Z.B.-I.); (A.M.); (M.F.-M.); (M.J.L.); (M.J.C.)
| | - Patricia Arnedo
- Hematology Department, Complejo Hospitalario de Navarra, 31008 Pamplona, Navarra, Spain; (P.A.); (A.J.)
| | - Almudena Aguilera-Diaz
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Navarra, Spain; (M.C.V.); (M.T.Z.); (A.A.-D.); (F.P.); (M.C.M.); (M.R.)
- Advanced Genomics Laboratory, Hemato-Oncology, Center for Applied Medical Research (CIMA), 31008 Pamplona, Navarra, Spain
| | - Axier Jauregui
- Hematology Department, Complejo Hospitalario de Navarra, 31008 Pamplona, Navarra, Spain; (P.A.); (A.J.)
| | - Amagoia Mañú
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, 31008 Pamplona, Navarra, Spain; (P.A.-R.); (B.A.); (Z.B.-I.); (A.M.); (M.F.-M.); (M.J.L.); (M.J.C.)
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Navarra, Spain; (M.C.V.); (M.T.Z.); (A.A.-D.); (F.P.); (M.C.M.); (M.R.)
| | - Felipe Prosper
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Navarra, Spain; (M.C.V.); (M.T.Z.); (A.A.-D.); (F.P.); (M.C.M.); (M.R.)
- Advanced Genomics Laboratory, Hemato-Oncology, Center for Applied Medical Research (CIMA), 31008 Pamplona, Navarra, Spain
- Hematology Department, Clinica Universidad de Navarra (CUN), 31008 Pamplona, Navarra, Spain
| | - María Carmen Mateos
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Navarra, Spain; (M.C.V.); (M.T.Z.); (A.A.-D.); (F.P.); (M.C.M.); (M.R.)
- Hematology Department, Complejo Hospitalario de Navarra, 31008 Pamplona, Navarra, Spain; (P.A.); (A.J.)
| | - Marta Fernández-Mercado
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, 31008 Pamplona, Navarra, Spain; (P.A.-R.); (B.A.); (Z.B.-I.); (A.M.); (M.F.-M.); (M.J.L.); (M.J.C.)
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Navarra, Spain; (M.C.V.); (M.T.Z.); (A.A.-D.); (F.P.); (M.C.M.); (M.R.)
- Advanced Genomics Laboratory, Hemato-Oncology, Center for Applied Medical Research (CIMA), 31008 Pamplona, Navarra, Spain
| | - María José Larráyoz
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, 31008 Pamplona, Navarra, Spain; (P.A.-R.); (B.A.); (Z.B.-I.); (A.M.); (M.F.-M.); (M.J.L.); (M.J.C.)
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Navarra, Spain; (M.C.V.); (M.T.Z.); (A.A.-D.); (F.P.); (M.C.M.); (M.R.)
| | - Margarita Redondo
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Navarra, Spain; (M.C.V.); (M.T.Z.); (A.A.-D.); (F.P.); (M.C.M.); (M.R.)
- Hematology Department, Complejo Hospitalario de Navarra, 31008 Pamplona, Navarra, Spain; (P.A.); (A.J.)
| | - María José Calasanz
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, 31008 Pamplona, Navarra, Spain; (P.A.-R.); (B.A.); (Z.B.-I.); (A.M.); (M.F.-M.); (M.J.L.); (M.J.C.)
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Navarra, Spain; (M.C.V.); (M.T.Z.); (A.A.-D.); (F.P.); (M.C.M.); (M.R.)
| | - Iria Vázquez
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, 31008 Pamplona, Navarra, Spain; (P.A.-R.); (B.A.); (Z.B.-I.); (A.M.); (M.F.-M.); (M.J.L.); (M.J.C.)
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Navarra, Spain; (M.C.V.); (M.T.Z.); (A.A.-D.); (F.P.); (M.C.M.); (M.R.)
- Correspondence: (I.V.); (E.B.); Tel.: +34-948194700-1000 (I.V.)
| | - Eva Bandrés
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Navarra, Spain; (M.C.V.); (M.T.Z.); (A.A.-D.); (F.P.); (M.C.M.); (M.R.)
- Hematology Department, Complejo Hospitalario de Navarra, 31008 Pamplona, Navarra, Spain; (P.A.); (A.J.)
- Correspondence: (I.V.); (E.B.); Tel.: +34-948194700-1000 (I.V.)
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12
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Haferlach T. Advancing leukemia diagnostics: Role of Next Generation Sequencing (NGS) in acute myeloid leukemia. Hematol Rep 2020; 12:8957. [PMID: 33042506 PMCID: PMC7520852 DOI: 10.4081/hr.2020.8957] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Indexed: 02/08/2023] Open
Abstract
AML diagnostics, initially based solely on morphological evaluation, now relies on multiple disciplines to reach its full potential. Only by integrating the results of cytomorphology, cytochemistry, immunophenotyping, cytogenetics and molecular genetics it is possible to fulfil WHO classification and ELN prognostication systems. Especially molecular genetics has gained a lot of interest over the last decade, mainly through the introduction of next generation sequencing (NGS). NGS application ranges from the investigation of single genes and panels to even whole exomes, transcriptomes and genomes. In routine AML diagnostics panels are the preferred NGS methodology. Here, we will review the power and limitations of NGS in the context of diagnosis, prognosis and precision medicine. Due to high dimensionality, NGS data interpretation is challenging but it also offers a unique investigatory chance and the opportunity to apply data mining techniques such as artificial intelligence. We will also reflect on how the incorporation of the improved knowledge base into routine diagnostics can pave the way for better treatment and more cure in AML.
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13
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Yoest JM, Shirai CL, Duncavage EJ. Sequencing-Based Measurable Residual Disease Testing in Acute Myeloid Leukemia. Front Cell Dev Biol 2020; 8:249. [PMID: 32457898 PMCID: PMC7225302 DOI: 10.3389/fcell.2020.00249] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/24/2020] [Indexed: 12/31/2022] Open
Abstract
Next generation sequencing (NGS) methods have allowed for unprecedented genomic characterization of acute myeloid leukemia (AML) over the last several years. Further advances in NGS-based methods including error correction using unique molecular identifiers (UMIs) have more recently enabled the use of NGS-based measurable residual disease (MRD) detection. This review focuses on the use of NGS-based MRD detection in AML, including basic methodologies and clinical applications.
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Affiliation(s)
- Jennifer M Yoest
- Department of Pathology, Case Western Reserve University, Cleveland, OH, United States
| | - Cara Lunn Shirai
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, United States
| | - Eric J Duncavage
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, United States
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