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Oduro KA, Spivey T, Moore EM, Meyerson H, Yoest J, Tomlinson B, Beck R, Alouani D, Sadri N. CLONAL DYNAMICS AND RELAPSE RISK REVEALED BY HIGH SENSITIVITY FLT3-ITD DETECTION IN ACUTE MYELOID LEUKEMIA. Mod Pathol 2024:100534. [PMID: 38852814 DOI: 10.1016/j.modpat.2024.100534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/21/2024] [Accepted: 05/27/2024] [Indexed: 06/11/2024]
Abstract
The ability to detect low level disease is key to our understanding of clonal heterogeneity in acute myeloid leukemia (AML) and residual disease that elude conventional assays and seed relapse. We have developed a high sensitivity next generation sequencing (HS-NGS) clinical assay, able to reliably detect low levels (1x10-5) of FLT3-ITD, a frequent, therapeutically targetable and prognostically relevant mutation in AML. By applying this assay to 289 longitudinal samples from 62 patients at initial diagnosis and/or clinical follow up (mean follow-up of 22 months) we reveal the frequent occurrence of FLT3-ITD subclones at diagnosis and demonstrate a significantly decreased relapse risk when FLT3-ITD is cleared after induction or thereafter. We perform pairwise sequencing of diagnosis and relapse samples from 23 patients to uncover more detailed patterns of FLT3-ITD clonal evolution at relapse than is detectable by less sensitive assays. Lastly, we show that rising ITD level during consecutive biopsies is a harbinger of impending relapse. Our findings corroborate the emerging clinical utility of high sensitivity FLT3-ITD testing and expands our understanding of clonal dynamics in FLT3-ITD positive AML.
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Affiliation(s)
- Kwadwo Asare Oduro
- Department of Pathology & Laboratory Medicine, University of Wisconsin School of Medicine & Public Health; Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine.
| | - Theresa Spivey
- Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine
| | - Erika M Moore
- Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine
| | - Howard Meyerson
- Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine
| | - Jennifer Yoest
- Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine
| | - Benjamin Tomlinson
- Department of Hematology/Oncology, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine
| | - Rose Beck
- Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine
| | - David Alouani
- Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine
| | - Navid Sadri
- Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine.
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2
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Kim SY, Huh HJ. Measurable Residual Disease Testing Using Next-Generation Sequencing in Acute Myeloid Leukemia. Ann Lab Med 2023; 43:323-324. [PMID: 36843399 PMCID: PMC9989539 DOI: 10.3343/alm.2023.43.4.323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023] Open
Affiliation(s)
- Seon Young Kim
- Department of Laboratory Medicine, Chungnam National University College of Medicine, Daejeon, Korea
| | - Hee Jin Huh
- Department of Laboratory Medicine, Dongguk University Ilsan Hospital, Goyang, Korea
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3
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Slade MJ, Ghasemi R, O'Laughlin M, Burton T, Fulton RS, Abel HJ, Duncavage EJ, Ley TJ, Jacoby MA, Spencer DH. Persistent Molecular Disease in Adult Patients With AML Evaluated With Whole-Exome and Targeted Error-Corrected DNA Sequencing. JCO Precis Oncol 2023; 7:e2200559. [PMID: 37079859 PMCID: PMC10530963 DOI: 10.1200/po.22.00559] [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: 10/07/2022] [Revised: 02/03/2023] [Accepted: 03/01/2023] [Indexed: 04/22/2023] Open
Abstract
PURPOSE Persistent molecular disease (PMD) after induction chemotherapy predicts relapse in AML. In this study, we used whole-exome sequencing (WES) and targeted error-corrected sequencing to assess the frequency and mutational patterns of PMD in 30 patients with AML. MATERIALS AND METHODS The study cohort included 30 patients with adult AML younger than 65 years who were uniformly treated with standard induction chemotherapy. Tumor/normal WES was performed for all patients at presentation. PMD analysis was evaluated in bone marrow samples obtained during clinicopathologic remission using repeat WES and analysis of patient-specific mutations and error-corrected sequencing of 40 recurrently mutated AML genes (MyeloSeq). RESULTS WES for patient-specific mutations detected PMD in 63% of patients (19/30) using a minimum variant allele fraction (VAF) of 2.5%. In comparison, MyeloSeq identified persistent mutations above 0.1% VAF in 77% of patients (23/30). PMD was usually present at relatively high levels (>2.5% VAFs), such that WES and MyeloSeq agreed for 73% of patients despite differences in detection limits. Mutations in DNMT3A, ASXL1, and TET2 (ie, DTA mutations) were persistent in 16 of 17 patients, but WES also detected non-DTA mutations in 14 of these patients, which for some patients distinguished residual AML cells from clonal hematopoiesis. Surprisingly, MyeloSeq detected additional variants not identified at presentation in 73% of patients that were consistent with new clonal cell populations after chemotherapy. CONCLUSION PMD and clonal hematopoiesis are both common in patients with AML in first remission. These findings demonstrate the importance of baseline testing for accurate interpretation of mutation-based tumor monitoring assays for patients with AML and highlight the need for clinical trials to determine whether these complex mutation patterns correlate with clinical outcomes in AML.
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Affiliation(s)
- Michael J. Slade
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Reza Ghasemi
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Michelle O'Laughlin
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Tasha Burton
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Robert S. Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Haley J. Abel
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Eric J. Duncavage
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Timothy J. Ley
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Meagan A. Jacoby
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - David H. Spencer
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
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4
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Measurable Residual Disease and Clonal Evolution in Acute Myeloid Leukemia from Diagnosis to Post-Transplant Follow-Up: The Role of Next-Generation Sequencing. Biomedicines 2023; 11:biomedicines11020359. [PMID: 36830896 PMCID: PMC9953407 DOI: 10.3390/biomedicines11020359] [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: 01/09/2023] [Revised: 01/24/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
It has now been ascertained that acute myeloid leukemias-as in most type of cancers-are mixtures of various subclones, evolving by acquiring additional somatic mutations over the course of the disease. The complexity of leukemia clone architecture and the phenotypic and/or genotypic drifts that can occur during treatment explain why more than 50% of patients-in hematological remission-could relapse. Moreover, the complexity and heterogeneity of clone architecture represent a hindrance for monitoring measurable residual disease, as not all minimal residual disease monitoring methods are able to detect genetic mutations arising during treatment. Unlike with chemotherapy, which imparts a relatively short duration of selective pressure on acute myeloid leukemia clonal architecture, the immunological effect related to allogeneic hematopoietic stem cell transplant is prolonged over time and must be overcome for relapse to occur. This means that not all molecular abnormalities detected after transplant always imply inevitable relapse. Therefore, transplant represents a critical setting where a measurable residual disease-based strategy, performed during post-transplant follow-up by highly sensitive methods such as next-generation sequencing, could optimize and improve treatment outcome. The purpose of our review is to provide an overview of the role of next-generation sequencing in monitoring both measurable residual disease and clonal evolution in acute myeloid leukemia patients during the entire course of the disease, with special focus on the transplant phase.
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5
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Duncavage EJ, Bagg A, Hasserjian RP, DiNardo CD, Godley LA, Iacobucci I, Jaiswal S, Malcovati L, Vannucchi AM, Patel KP, Arber DA, Arcila ME, Bejar R, Berliner N, Borowitz MJ, Branford S, Brown AL, Cargo CA, Döhner H, Falini B, Garcia-Manero G, Haferlach T, Hellström-Lindberg E, Kim AS, Klco JM, Komrokji R, Lee-Cheun Loh M, Loghavi S, Mullighan CG, Ogawa S, Orazi A, Papaemmanuil E, Reiter A, Ross DM, Savona M, Shimamura A, Skoda RC, Solé F, Stone RM, Tefferi A, Walter MJ, Wu D, Ebert BL, Cazzola M. Genomic profiling for clinical decision making in myeloid neoplasms and acute leukemia. Blood 2022; 140:2228-2247. [PMID: 36130297 PMCID: PMC10488320 DOI: 10.1182/blood.2022015853] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/27/2022] [Indexed: 11/20/2022] Open
Abstract
Myeloid neoplasms and acute leukemias derive from the clonal expansion of hematopoietic cells driven by somatic gene mutations. Although assessment of morphology plays a crucial role in the diagnostic evaluation of patients with these malignancies, genomic characterization has become increasingly important for accurate diagnosis, risk assessment, and therapeutic decision making. Conventional cytogenetics, a comprehensive and unbiased method for assessing chromosomal abnormalities, has been the mainstay of genomic testing over the past several decades and remains relevant today. However, more recent advances in sequencing technology have increased our ability to detect somatic mutations through the use of targeted gene panels, whole-exome sequencing, whole-genome sequencing, and whole-transcriptome sequencing or RNA sequencing. In patients with myeloid neoplasms, whole-genome sequencing represents a potential replacement for both conventional cytogenetic and sequencing approaches, providing rapid and accurate comprehensive genomic profiling. DNA sequencing methods are used not only for detecting somatically acquired gene mutations but also for identifying germline gene mutations associated with inherited predisposition to hematologic neoplasms. The 2022 International Consensus Classification of myeloid neoplasms and acute leukemias makes extensive use of genomic data. The aim of this report is to help physicians and laboratorians implement genomic testing for diagnosis, risk stratification, and clinical decision making and illustrates the potential of genomic profiling for enabling personalized medicine in patients with hematologic neoplasms.
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Affiliation(s)
- Eric J. Duncavage
- Department of Pathology and Immunology, Washington University, St. Louis, MO
| | - Adam Bagg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | | | - Courtney D. DiNardo
- Division of Cancer Medicine, Department of Leukemia, MD Anderson Cancer Center, Houston, TX
| | - Lucy A. Godley
- Section of Hematology and Oncology, Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | | | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia & Fondazione IRCCS Policlinico S. Matteo, Pavia, Italy
| | - Alessandro M. Vannucchi
- Department of Hematology, Center Research and Innovation of Myeloproliferative Neoplasms, University of Florence and Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Keyur P. Patel
- Division of Pathology/Lab Medicine, Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Maria E. Arcila
- Department of Pathology, Memorial Sloan Lettering Cancer Center, New York, NY
| | - Rafael Bejar
- Division of Hematology and Oncology, University of California San Diego, La Jolla, CA
| | - Nancy Berliner
- Division of Hematology, Brigham and Women’s Hospital, Harvard University, Boston, MA
| | - Michael J. Borowitz
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Susan Branford
- Department of Genetics and Molecular Pathology, Center for Cancer Biology, SA Pathology, Adelaide, Australia
| | - Anna L. Brown
- Department of Pathology, South Australia Heath Alliance, Adelaide, Australia
| | - Catherine A. Cargo
- Haematological Malignancy Diagnostic Service, St James’s University Hospital, Leeds, United Kingdom
| | - Hartmut Döhner
- Department of Internal Medicine III, Ulm University Hospital, Ulm, Germany
| | - Brunangelo Falini
- Department of Hematology, CREO, University of Perugia, Perugia, Italy
| | | | | | - Eva Hellström-Lindberg
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Annette S. Kim
- Department of Pathology, Brigham and Women’s Hospital, Harvard University, Boston, MA
| | - Jeffery M. Klco
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Rami Komrokji
- Department of Malignant Hematology, Moffitt Cancer Center, Tampa, FL
| | - Mignon Lee-Cheun Loh
- Department of Pediatrics, Ben Towne Center for Childhood Cancer Research, Seattle Children’s Hospital, University of Washington, Seattle, WA
| | - Sanam Loghavi
- Division of Pathology/Lab Medicine, Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Seishi Ogawa
- University of Kyoto School of Medicine, Kyoto, Japan
| | - Attilio Orazi
- Department of Pathology, Texas Tech University Health Sciences Center, El Paso, TX
| | | | - Andreas Reiter
- University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - David M. Ross
- Haematology Directorate, SA Pathology, Adelaide, Australia
| | - Michael Savona
- Department of Medicine, Vanderbilt University, Nashville, TN
| | - Akiko Shimamura
- Dana Farber/Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | - Radek C. Skoda
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Francesc Solé
- MDS Group, Institut de Recerca contra la Leucèmia Josep Carreras, Barcelona, Spain
| | - Richard M. Stone
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | | | - David Wu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Mario Cazzola
- Division of Hematology, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
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6
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Voso MT, Ferrara F, Galimberti S, Rambaldi A, Venditti A. Diagnostic Workup of Acute Myeloid Leukemia: What Is Really Necessary? An Italian Survey. Front Oncol 2022; 12:828072. [PMID: 35251997 PMCID: PMC8893956 DOI: 10.3389/fonc.2022.828072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/26/2022] [Indexed: 11/23/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease with a wide variety of clinical presentations, morphological features, and immunophenotypes. The diagnostic approaches to AML that are adopted in Italy have been explored using an online Delphi-based process to expand the global discussion on mandatory tests for the correct diagnosis and, consequently, for optimal management of AML in clinical practice. The final results of the panel of Italian hematologists involved in this work highlight the importance of genetic evaluation for classification and risk stratification and firmly establish that karyotyping, fluorescence in situ hybridization in cases with non-evaluable karyotype, and molecular tests must be performed in every case of AML, regardless of age. Obtaining clinically relevant genetic data at diagnosis is the basis for the success of patient-tailored therapy. The Italian specialists also confirm the role of multidisciplinary diagnostics for AML, now mandatory and expected to become more important in the future context of “precision” medicine.
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Affiliation(s)
- Maria Teresa Voso
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
- *Correspondence: Maria Teresa Voso,
| | | | - Sara Galimberti
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, Pisa, Italy
| | - Alessandro Rambaldi
- Department of Oncology-Hematology, University of Milan, Milan, Italy
- Azienda Socio Sanitaria Territoriale Papa Giovanni XXIII, Bergamo, Italy
| | - Adriano Venditti
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
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7
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Chen H, Guo X, Li X, Tang Y, Sun H. An increase in DNA G-quadruplex formation in acute myelocytic leukemia is detected by a supramolecular probe. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 260:119968. [PMID: 34049005 DOI: 10.1016/j.saa.2021.119968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/14/2021] [Accepted: 05/16/2021] [Indexed: 06/12/2023]
Abstract
Acute myeloid leukemia (AML) is a common acute leukemia in both adults and children, with poor early detection and diagnosis. Therefore, identifying new indicators for AML detection is significant for effective treatment. Here, we developed a supramolecular probe that exhibits high specificity and sensitivity to G-quadruplex structures in physiological buffer solution, chromosomes, and cells. Using this probe, we tested the DNA extracted from different types of cells and found that the DNA extracted from human acute myeloid leukemia cells HL-60 and KG-1 enhanced the probe fluorescence more significantly than the DNA extracted from other cells. This phenomenon may be related to a large number of G-quadruplexes in acute myeloid leukemia cells, implicating that G-quadruplex levels may be a potential indicator for the detection of acute myeloid leukemia.
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Affiliation(s)
- Hongbo Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; Shenzhou Space Biology Science and Technology Corporation, Ltd, China Academy of Space Technology, Beijing 100190, PR China
| | - Xiaomeng Guo
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xinquan Li
- Department of Hematology, Tsinghua University Affiliated Beijing Tsinghua Changgung Hospital, Beijing 102218, PR China
| | - Yalin Tang
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Hongxia Sun
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China.
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8
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Abstract
Minimal or measurable residual disease (MRD) after therapy is the most important independent prognostic factor in acute myeloid leukemia. MRD measured by multiparametric flow cytometry and real-time quantitative polymerase chain reaction has been integrated into risk stratification and used to guide future treatment strategies. Recent technological advances have allowed the application of the novel molecular method, high-throughput sequencing, in MRD detection in clinical practice to improve sensitivity and specificity. Randomized studies are needed to address outstanding issues, including the optimal methods and timing of MRD testing and interlaboratory standardization to facilitate comparisons, to further improve MRD-directed interventions.
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Affiliation(s)
- Xueyan Chen
- Hematopathology, SCCA G7800, 825 Eastlake Ave E., Seattle, WA 98109, USA
| | - Sindhu Cherian
- Hematopathology, SCCA G7800, 825 Eastlake Ave E., Seattle, WA 98109, USA.
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9
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Patkar N, Kakirde C, Shaikh AF, Salve R, Bhanshe P, Chatterjee G, Rajpal S, Joshi S, Chaudhary S, Kodgule R, Ghoghale S, Deshpande N, Shetty D, Khizer SH, Jain H, Bagal B, Menon H, Khattry N, Sengar M, Tembhare P, Subramanian P, Gujral S. Clinical impact of panel-based error-corrected next generation sequencing versus flow cytometry to detect measurable residual disease (MRD) in acute myeloid leukemia (AML). Leukemia 2021; 35:1392-1404. [PMID: 33558666 PMCID: PMC8102181 DOI: 10.1038/s41375-021-01131-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/30/2020] [Accepted: 01/07/2021] [Indexed: 01/30/2023]
Abstract
We accrued 201 patients of adult AML treated with conventional therapy, in morphological remission, and evaluated MRD using sensitive error-corrected next generation sequencing (NGS-MRD) and multiparameter flow cytometry (FCM-MRD) at the end of induction (PI) and consolidation (PC). Nearly 71% of patients were PI NGS-MRD+ and 40.9% PC NGS-MRD+ (median VAF 0.76%). NGS-MRD+ patients had a significantly higher cumulative incidence of relapse (p = 0.003), inferior overall survival (p = 0.001) and relapse free survival (p < 0.001) as compared to NGS-MRD- patients. NGS-MRD was predictive of inferior outcome in intermediate cytogenetic risk and demonstrated potential in favorable cytogenetic risk AML. PI NGS-MRD- patients had a significantly improved survival as compared to patients who became NGS-MRD- subsequently indicating that kinetics of NGS-MRD clearance was of paramount importance. NGS-MRD identified over 80% of cases identified by flow cytometry at PI time point whereas FCM identified 49.3% identified by NGS. Only a fraction of cases were NGS-MRD- but FCM-MRD+. NGS-MRD provided additional information of the risk of relapse when compared to FCM-MRD. We demonstrate a widely applicable, scalable NGS-MRD approach that is clinically informative and synergistic to FCM-MRD in AML treated with conventional therapies. Maximum clinical utility may be leveraged by combining FCM and NGS-MRD modalities.
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Affiliation(s)
- Nikhil Patkar
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Chinmayee Kakirde
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Anam Fatima Shaikh
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Rakhi Salve
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Prasanna Bhanshe
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Gaurav Chatterjee
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Sweta Rajpal
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Swapnali Joshi
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Shruti Chaudhary
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Rohan Kodgule
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Sitaram Ghoghale
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Nilesh Deshpande
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Dhanalaxmi Shetty
- grid.410869.20000 0004 1766 7522Dept of Cytogenetics, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Syed Hasan Khizer
- grid.410869.20000 0004 1766 7522Dept of Cytogenetics, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.410871.b0000 0004 1769 5793Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Hasmukh Jain
- grid.410869.20000 0004 1766 7522Dept of Cytogenetics, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.410871.b0000 0004 1769 5793Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Bhausaheb Bagal
- grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India ,grid.410871.b0000 0004 1769 5793Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Hari Menon
- Haemato-Oncology, CyteCare Cancer Hospital, Bangalore, India
| | - Navin Khattry
- grid.410869.20000 0004 1766 7522Dept of Cytogenetics, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,Haemato-Oncology, CyteCare Cancer Hospital, Bangalore, India
| | - Manju Sengar
- grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India ,grid.410871.b0000 0004 1769 5793Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Prashant Tembhare
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Papagudi Subramanian
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Sumeet Gujral
- grid.410869.20000 0004 1766 7522Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India ,grid.450257.10000 0004 1775 9822Homi Bhabha National Institute (HBNI), Mumbai, India
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Abstract
PURPOSE OF REVIEW Nucleophosmin (NPM1) mutations are encountered in myeloid neoplasia and are present in ~ 30% of de novo acute myeloid leukemia cases. This review summarizes features of mutant NPM1-related disease, with a particular emphasis on recent discoveries relevant to disease monitoring, prognostication, and therapeutic intervention. RECENT FINDINGS Recent studies have shown that HOX/MEIS gene overexpression is central to the survival of NPM1-mutated cells. Two distinct classes of small molecule drugs, BH3 mimetics and menin-MLL interaction inhibitors, have demonstrated exquisite leukemic cell toxicity in preclinical AML models associated with HOX/MEIS overexpression, and the former of these has shown efficacy in older treatment-naïve NPM1-mutated AML patients. The results of ongoing clinical trials further investigating these compounds will be of particular importance and may alter the clinical management of patients with NPM1-mutated myeloid neoplasms. Significant scientific advancements over the last decade, including improved sequencing and disease monitoring techniques, have fostered a much deeper understanding of mutant NPM1 disease biology, prognostication, and opportunities for therapeutic intervention. These discoveries have led to the development of clinical assays that permit the detection and monitoring of mutant NPM1 and have paved the way for future investigation of targeted therapeutics using emerging cutting-edge techniques.
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Affiliation(s)
- Sanjay S Patel
- Division of Hematopathology, Weill Cornell Medical College, New York, NY, USA
| | - Michael J Kluk
- Division of Hematopathology, Weill Cornell Medical College, New York, NY, USA
| | - Olga K Weinberg
- Department of Pathology, Boston Children's Hospital, 300 Longwood Avenue, Bader 126.2, Boston, MA, 02115, USA.
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11
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Wang RQ, Chen CJ, Jing Y, Qin JY, Li Y, Chen GF, Zhou W, Li YH, Wang J, Li DW, Zhao HM, Wang BH, Wang LL, Wang H, Wang MZ, Gao XN, Yu L. Characteristics and prognostic significance of genetic mutations in acute myeloid leukemia based on a targeted next-generation sequencing technique. Cancer Med 2020; 9:8457-8467. [PMID: 32970934 PMCID: PMC7666719 DOI: 10.1002/cam4.3467] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 08/22/2020] [Accepted: 08/27/2020] [Indexed: 12/14/2022] Open
Abstract
To explore the characteristics and prognostic significance of genetic mutations in acute myeloid leukemia (AML), we screened the gene mutation profile of 171 previously untreated AML patients using a next‐generation sequencing technique targeting 127 genes with potential prognostic significance. A total of 390 genetic alterations were identified in 149 patients with a frequency of 87.1%. Younger age and high sensitivity to induction chemotherapy were associated with a lower number of mutations. NPM1 mutation was closely related to DNMT3A and FLT3‐internal tandem duplication (FLT3‐ITD) mutations, but mutually exclusive with ASXL1 mutation and CEBPAdouble mutation. In univariate analysis, ASXL1 or TET2 mutation predicted shorter overall survival (OS) or relapse‐free survival (RFS), DNMT3A, FLT3‐ITD, or RUNX1 mutation predicted a higher likelihood of remission‐induction failure, whereas NRAS mutation or CEBPAdouble mutation predicted longer OS. Concurrent DNMT3A, FLT3‐ITD, and NPM1 mutations predicted shorter OS. Hypomethylation agents could improve the OS in patients with DNA methylation‐related mutations. According to multivariate analysis, TET2 mutation was recognized as an independent prognostic factors for RFS. In summary, our study provided a detailed pattern of gene mutations and their prognostic relevance in Chinese AML patients based on targeted next‐generation sequencing screening.
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Affiliation(s)
- Rui-Qi Wang
- Department of Hematology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China.,Medicine School, Nankai University, Tianjin, China
| | - Chong-Jian Chen
- Annoroad Gene Technology Co, Beijing Economic-Technological Development Area, Beijing, China
| | - Yu Jing
- Department of Hematology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Jia-Yue Qin
- Annoroad Gene Technology Co, Beijing Economic-Technological Development Area, Beijing, China
| | - Yan Li
- Department of Hematology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Guo-Feng Chen
- Department of Hematology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Wei Zhou
- Department of Hematology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Yong-Hui Li
- Department of Hematology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Juan Wang
- Annoroad Gene Technology Co, Beijing Economic-Technological Development Area, Beijing, China
| | - Da-Wei Li
- Annoroad Gene Technology Co, Beijing Economic-Technological Development Area, Beijing, China
| | - Hong-Mei Zhao
- Annoroad Gene Technology Co, Beijing Economic-Technological Development Area, Beijing, China
| | - Bian-Hong Wang
- Beijing Tsinghua Changgung Hospital, Changping District, Beijing, China
| | - Li-Li Wang
- Department of Hematology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Hong Wang
- Department of Hematology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Meng-Zhen Wang
- Department of Hematology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Xiao-Ning Gao
- Department of Hematology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Li Yu
- Department of Hematology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China.,Department of Hematology-Oncology, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University Health Science Center, Shenzhen, China
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12
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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: 15] [Impact Index Per Article: 3.8] [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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13
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Moffitt AB, Spector MS, Andrews P, Kendall J, Alexander J, Stepansky A, Ma B, Kolitz J, Chiorazzi N, Allen SL, Krasnitz A, Wigler M, Levy D, Wang Z. Multiplex accurate sensitive quantitation (MASQ) with application to minimal residual disease in acute myeloid leukemia. Nucleic Acids Res 2020; 48:e40. [PMID: 32083660 PMCID: PMC7144909 DOI: 10.1093/nar/gkaa090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 01/22/2020] [Accepted: 02/04/2020] [Indexed: 11/30/2022] Open
Abstract
Measuring minimal residual disease in cancer has applications for prognosis, monitoring treatment and detection of recurrence. Simple sequence-based methods to detect nucleotide substitution variants have error rates (about 10−3) that limit sensitive detection. We developed and characterized the performance of MASQ (multiplex accurate sensitive quantitation), a method with an error rate below 10−6. MASQ counts variant templates accurately in the presence of millions of host genomes by using tags to identify each template and demanding consensus over multiple reads. Since the MASQ protocol multiplexes 50 target loci, we can both integrate signal from multiple variants and capture subclonal response to treatment. Compared to existing methods for variant detection, MASQ achieves an excellent combination of sensitivity, specificity and yield. We tested MASQ in a pilot study in acute myeloid leukemia (AML) patients who entered complete remission. We detect leukemic variants in the blood and bone marrow samples of all five patients, after induction therapy, at levels ranging from 10−2 to nearly 10−6. We observe evidence of sub-clonal structure and find higher target variant frequencies in patients who go on to relapse, demonstrating the potential for MASQ to quantify residual disease in AML.
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Affiliation(s)
- Andrea B Moffitt
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Mona S Spector
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Peter Andrews
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jude Kendall
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Joan Alexander
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Asya Stepansky
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - BeiCong Ma
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jonathan Kolitz
- The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY 11030, USA.,Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Nicholas Chiorazzi
- The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY 11030, USA.,Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Steven L Allen
- The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY 11030, USA.,Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Alex Krasnitz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Michael Wigler
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Dan Levy
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Zihua Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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14
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Ghannam J, Dillon LW, Hourigan CS. Next-generation sequencing for measurable residual disease detection in acute myeloid leukaemia. Br J Haematol 2019; 188:77-85. [PMID: 31804716 DOI: 10.1111/bjh.16362] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Acute myeloid leukaemia (AML) is a blood cancer characterized by acquired genetic mutations. There is great interest in accurately establishing measurable residual disease (MRD) burden in AML patients in remission after treatment but at risk of relapse. However, inter- and intrapatient genetic diversity means that, unlike in the chronic myeloid and acute promyelocytic leukaemias, no single genetic abnormality is pathognomonic for all cases of AML MRD. Next-generation sequencing offers the opportunity to test broadly and deeply for potential genetic evidence of residual AML, and while not currently accepted for such use clinically, is likely to be increasingly used for AML MRD testing in the future.
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Affiliation(s)
- Jack Ghannam
- Laboratory of Myeloid Malignancies, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Laura W Dillon
- Laboratory of Myeloid Malignancies, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Christopher S Hourigan
- Laboratory of Myeloid Malignancies, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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15
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Ritterhouse LL, Parilla M, Zhen CJ, Wurst MN, Puranik R, Henderson CM, Joudeh NZ, Hartley MJ, Haridas R, Wanjari P, Furtado LV, Kadri S, Segal JP. Clinical Validation and Implementation of a Measurable Residual Disease Assay for NPM1 in Acute Myeloid Leukemia by Error-Corrected Next-Generation Sequencing. Mol Diagn Ther 2019; 23:791-802. [DOI: 10.1007/s40291-019-00436-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Next-generation sequencing-based minimal residual disease monitoring in patients receiving allogeneic hematopoietic stem cell transplantation for acute myeloid leukemia or myelodysplastic syndrome. Curr Opin Hematol 2019; 25:425-432. [PMID: 30281033 DOI: 10.1097/moh.0000000000000464] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
PURPOSE OF REVIEW The monitoring of minimal residual disease (MRD) has important clinical implications in both the pre and postallogeneic stem cell transplant (SCT) setting in acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). Next-generation sequencing (NGS) is a rapidly improving technology whose application to the monitoring of MRD is an active area of research. We aim to describe existing methods of MRD in AML and MDS, with a focus on the utility of NGS in patients undergoing SCT. RECENT FINDINGS Flow cytometry and quantitative PCR have been recommended by the European Leukemia Net as the preferred methods of MRD in AML and MDS, but these methods have limitations in cases without a disease-defining phenotype and genotype. Clinical trials are currently ongoing to assess the use of NGS in the setting of SCT for MDS and AML. Few studies have so far assessed the optimal method of MRD monitoring in the posttransplant setting. SUMMARY The optimal method for the monitoring of MRD in AML and MDS both pre and post transplant may require more than one technology. NGS holds great promise for the monitoring of MRD, with prospective trials currently ongoing to evaluate its efficacy in this regard.
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17
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Jung J, Cho BS, Kim HJ, Han E, Jang W, Han K, Lee JW, Chung NG, Cho B, Kim M, Kim Y. Reclassification of Acute Myeloid Leukemia According to the 2016 WHO Classification. Ann Lab Med 2019; 39:311-316. [PMID: 30623623 PMCID: PMC6340847 DOI: 10.3343/alm.2019.39.3.311] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 10/08/2018] [Accepted: 12/19/2018] [Indexed: 01/22/2023] Open
Abstract
We reviewed our leukemia database to reclassify 610 patients previously diagnosed as having acute myeloid leukemia (AML) according to the updated 2016 WHO classification. Nine patients were categorized as having myelodysplastic syndrome and myeloid neoplasms with germline predisposition. AML with recurrent genetic abnormalities accounted for 57.4% (345/601) of the patients under the 2016 WHO classification. AML with mutated NPM1 was the most common form (16.5%), with the majority associated with monocytic differentiation (63.6%). AML with double CEBPA mutations accounted for 8.3% of these cases, and the majority were previously diagnosed as AML with/without maturation (78.0%). These newly classified mutations were mutually exclusive without overlapping with other forms of AML with recurrent genetic abnormalities. AML with mutated NPM1 and AML with myelodysplasia-related changes comprised the oldest patients, whereas AML with RUNX1-RUNX1T1 included the youngest patients. The leukocyte count was highest in AML with mutated NPM1, and the percentage of peripheral blood blasts was the highest in AML with double CEBPA mutations. Our results indicate that implementation of the 2016 WHO classification of AML would not pose major difficulties in clinical practice. Hematopathologists should review and prepare genetic tests for the new classification, according to their clinical laboratory conditions.
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Affiliation(s)
- Jin Jung
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Byung Sik Cho
- Department of Hematology, Seoul St. Mary's Hematology Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Leukemia Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hee Je Kim
- Department of Hematology, Seoul St. Mary's Hematology Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Leukemia Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Eunhee Han
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Woori Jang
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kyungja Han
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jae Wook Lee
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Nack Gyun Chung
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Bin Cho
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.
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18
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Toth LN, Green D, Peterson J, Deharvengt SJ, de Abreu FB, Loo EY. Variant allele frequencies do not correlate well with myeloblast counts in a clinically validated gene sequencing panel for routine acute myeloid leukemia workup. Leuk Lymphoma 2019; 60:2415-2422. [DOI: 10.1080/10428194.2019.1587757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Laura N. Toth
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center One Medical Center Drive, Lebanon, NH, USA
| | - Donald Green
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center One Medical Center Drive, Lebanon, NH, USA
| | - Jason Peterson
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center One Medical Center Drive, Lebanon, NH, USA
| | - Sophie J. Deharvengt
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center One Medical Center Drive, Lebanon, NH, USA
| | - Francine B. de Abreu
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center One Medical Center Drive, Lebanon, NH, USA
| | - Eric Y. Loo
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center One Medical Center Drive, Lebanon, NH, USA
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19
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Sabath DE. The Next Generation in Detection of Leukemia-Associated Translocations. J Mol Diagn 2019; 21:16-18. [PMID: 30268945 DOI: 10.1016/j.jmoldx.2018.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 08/10/2018] [Indexed: 11/17/2022] Open
Abstract
This commentary highlights the article by Kim et al that suggests use of two different next-generation sequencing-based assays for detection of fusion RNAs in patients with acute leukemia.
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Affiliation(s)
- Daniel E Sabath
- Departments of Laboratory Medicine and Medicine, University of Washington School of Medicine, Seattle, Washington.
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20
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Delsing Malmberg E, Rehammar A, Pereira MB, Abrahamsson J, Samuelsson T, Ståhlman S, Asp J, Tierens A, Palmqvist L, Kristiansson E, Fogelstrand L. Accurate and Sensitive Analysis of Minimal Residual Disease in Acute Myeloid Leukemia Using Deep Sequencing of Single Nucleotide Variations. J Mol Diagn 2019; 21:149-162. [DOI: 10.1016/j.jmoldx.2018.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 07/18/2018] [Accepted: 08/30/2018] [Indexed: 12/26/2022] Open
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21
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Patkar N, Kodgule R, Kakirde C, Raval G, Bhanshe P, Joshi S, Chaudhary S, Badrinath Y, Ghoghale S, Kadechkar S, Khizer SH, Kannan S, Shetty D, Gokarn A, Punatkar S, Jain H, Bagal B, Menon H, Sengar M, Khattry N, Tembhare P, Subramanian P, Gujral S. Clinical impact of measurable residual disease monitoring by ultradeep next generation sequencing in NPM1 mutated acute myeloid leukemia. Oncotarget 2018; 9:36613-36624. [PMID: 30564301 PMCID: PMC6290958 DOI: 10.18632/oncotarget.26400] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 11/16/2018] [Indexed: 01/18/2023] Open
Abstract
Detection of measurable residual disease (MRD) by mutation specific techniques has prognostic relevance in NPM1 mutated AML (NPM1mut AML). However, the clinical utility of next generation sequencing (NGS) to detect MRD in AML remains unproven. We analysed the clinical significance of monitoring MRD using ultradeep NGS (NGS-MRD) and flow cytometry (FCM-MRD) in 137 samples obtained from 83 patients of NPM1mut AML at the end of induction (PI) and consolidation (PC). We could monitor 12 different types of NPM1 mutations at a sensitivity of 0.001% using NGS-MRD. We demonstrated a significant correlation between NGS-MRD and real time quantitative PCR (RQ-PCR). Based upon a one log reduction between PI and PC time points we could classify patients as NGS-MRD positive (<1log reduction) or negative (>1log reduction). NGS-MRD, FCM-MRD as well as DNMT3A mutations were predictive of inferior overall survival (OS) and relapse free survival (RFS). On a multivariate analysis NGS-MRD emerged as an independent, most important prognostic factor predictive of inferior OS (hazard ratio, 3.64; 95% confidence interval [CI] 1.58 to 8.37) and RFS (hazard ratio, 4.8; 95% CI:2.24 to 10.28). We establish that DNA based NPM1 NGS MRD is a highly useful test for prediction of relapse and survival in NPM1mut AML.
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Affiliation(s)
- Nikhil Patkar
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Rohan Kodgule
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India.,Homi Bhabha National Institute, Training School Complex, Mumbai, India
| | - Chinmayee Kakirde
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Goutham Raval
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Prasanna Bhanshe
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Swapnali Joshi
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Shruti Chaudhary
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Y Badrinath
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Sitaram Ghoghale
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Shraddha Kadechkar
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Syed Hasan Khizer
- Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Sadhana Kannan
- Biostatistics, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Dhanalaxmi Shetty
- Dept of Cytogenetics, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Anant Gokarn
- Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Sachin Punatkar
- Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Hasmukh Jain
- Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Bhausaheb Bagal
- Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Hari Menon
- Haemato-Oncology, CyteCare Cancer Hospital, Bangalore, India
| | - Manju Sengar
- Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Navin Khattry
- Adult Haematolymphoid Disease Management Group, Tata Memorial Centre, Mumbai, India
| | - Prashant Tembhare
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | | | - Sumeet Gujral
- Haematopathology Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
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22
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Minimal/Measurable Residual Disease Monitoring in NPM1-Mutated Acute Myeloid Leukemia: A Clinical Viewpoint and Perspectives. Int J Mol Sci 2018; 19:ijms19113492. [PMID: 30404199 PMCID: PMC6274702 DOI: 10.3390/ijms19113492] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/02/2018] [Accepted: 11/03/2018] [Indexed: 02/06/2023] Open
Abstract
Acute myeloid leukemia (AML) with NPM1 gene mutations is currently recognized as a distinct entity, due to its unique biological and clinical features. We summarize here the results of published studies investigating the clinical application of minimal/measurable residual disease (MRD) in patients with NPM1-mutated AML, receiving either intensive chemotherapy or hematopoietic stem cell transplantation. Several clinical trials have so far demonstrated a significant independent prognostic impact of molecular MRD monitoring in NPM1-mutated AML and, accordingly, the Consensus Document from the European Leukemia Net MRD Working Party has recently recommended that NPM1-mutated AML patients have MRD assessment at informative clinical timepoints during treatment and follow-up. However, several controversies remain, mainly with regard to the most clinically significant timepoints and the MRD thresholds to be considered, but also with respect to the optimal source to be analyzed, namely bone marrow or peripheral blood samples, and the correlation of MRD with other known prognostic indicators. Moreover, we discuss potential advantages, as well as drawbacks, of newer molecular technologies such as digital droplet PCR and next-generation sequencing in comparison to conventional RQ-PCR to quantify NPM1-mutated MRD. In conclusion, further prospective clinical trials are warranted to standardize MRD monitoring strategies and to optimize MRD-guided therapeutic interventions in NPM1-mutated AML patients.
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23
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Onecha E, Linares M, Rapado I, Ruiz-Heredia Y, Martinez-Sanchez P, Cedena T, Pratcorona M, Oteyza JP, Herrera P, Barragan E, Montesinos P, Vela JAG, Magro E, Anguita E, Figuera A, Riaza R, Martinez-Barranco P, Sanchez-Vega B, Nomdedeu J, Gallardo M, Martinez-Lopez J, Ayala R. A novel deep targeted sequencing method for minimal residual disease monitoring in acute myeloid leukemia. Haematologica 2018; 104:288-296. [PMID: 30093399 PMCID: PMC6355493 DOI: 10.3324/haematol.2018.194712] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 08/08/2018] [Indexed: 12/11/2022] Open
Abstract
A high proportion of patients with acute myeloid leukemia who achieve minimal residual disease negative status ultimately relapse because a fraction of pathological clones remains undetected by standard methods. We designed and validated a high-throughput sequencing method for minimal residual disease assessment of cell clonotypes with mutations of NPM1, IDH1/2 and/or FLT3-single nucleotide variants. For clinical validation, 106 follow-up samples from 63 patients in complete remission were studied by sequencing, evaluating the level of mutations detected at diagnosis. The predictive value of minimal residual disease status by sequencing, multiparameter flow cytometry, or quantitative polymerase chain reaction analysis was determined by survival analysis. The sequencing method achieved a sensitivity of 10−4 for single nucleotide variants and 10−5 for insertions/deletions and could be used in acute myeloid leukemia patients who carry any mutation (86% in our diagnostic data set). Sequencing–determined minimal residual disease positive status was associated with lower disease-free survival (hazard ratio 3.4, P=0.005) and lower overall survival (hazard ratio 4.2, P<0.001). Multivariate analysis showed that minimal residual disease positive status determined by sequencing was an independent factor associated with risk of death (hazard ratio 4.54, P=0.005) and the only independent factor conferring risk of relapse (hazard ratio 3.76, P=0.012). This sequencing-based method simplifies and standardizes minimal residual disease evaluation, with high applicability in acute myeloid leukemia. It is also an improvement upon flow cytometry- and quantitative polymerase chain reaction-based prediction of outcomes of patients with acute myeloid leukemia and could be incorporated in clinical settings and clinical trials.
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Affiliation(s)
- Esther Onecha
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid
| | - Maria Linares
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid
| | - Inmaculada Rapado
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid
| | - Yanira Ruiz-Heredia
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid
| | | | - Teresa Cedena
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid.,Complutense University, Madrid
| | - Marta Pratcorona
- Hematology Department, Hospital Santa Creu i Sant Pau, Barcelona
| | | | - Pilar Herrera
- Hematology Department, Hospital Universitario Ramon y Cajal, Madrid
| | - Eva Barragan
- Complutense University, Madrid.,Hematology Department, Hospital Universitario La Fe, Valencia
| | - Pau Montesinos
- Complutense University, Madrid.,Hematology Department, Hospital Universitario La Fe, Valencia
| | | | - Elena Magro
- Hematology Department, Hospital Universitario Principe de Asturias, Madrid
| | - Eduardo Anguita
- Hematology Department, Hospital Clínico San Carlos, IdISSC, UCM, Madrid
| | - Angela Figuera
- Hematology Department, Hospital Universitario de la Princesa, Madrid
| | - Rosalia Riaza
- Hematology Department, Hospital Universitario Severo Ochoa, Madrid
| | | | - Beatriz Sanchez-Vega
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid
| | - Josep Nomdedeu
- Hematology Department, Hospital Santa Creu i Sant Pau, Barcelona
| | - Miguel Gallardo
- Hematological Malignancies Clinical Research Unit, CNIO, Madrid
| | - Joaquin Martinez-Lopez
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid.,Complutense University, Madrid
| | - Rosa Ayala
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid .,Hematological Malignancies Clinical Research Unit, CNIO, Madrid.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid.,Complutense University, Madrid
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24
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Delsing Malmberg E, Johansson Alm S, Nicklasson M, Lazarevic V, Ståhlman S, Samuelsson T, Lenhoff S, Asp J, Ehinger M, Palmqvist L, Brune M, Fogelstrand L. Minimal residual disease assessed with deep sequencing of NPM1 mutations predicts relapse after allogeneic stem cell transplant in AML. Leuk Lymphoma 2018; 60:409-417. [DOI: 10.1080/10428194.2018.1485910] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Erik Delsing Malmberg
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Sofie Johansson Alm
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Malin Nicklasson
- Department of Medicine, Section of Hematology and Coagulation, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Vladimir Lazarevic
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Sara Ståhlman
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Tore Samuelsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Stig Lenhoff
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Julia Asp
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Mats Ehinger
- Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Lars Palmqvist
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Mats Brune
- Department of Medicine, Section of Hematology and Coagulation, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Linda Fogelstrand
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
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25
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Abstract
The presence of measurable ("minimal") residual disease (MRD) after induction and/or consolidation chemotherapy is a significant risk factor for relapse in patients with acute myeloid leukemia (AML). In recognition of the clinical significance of AML MRD, the European LeukemiaNet (ELN) recently recommended the establishment of CR-MRDNegative as a separate category of treatment response. This recommendation represents a major milestone in the integration of AML MRD testing in standard clinical practice. This review article summarizes the methodologies employed in AML MRD detection and their application in clinical studies that provide evidence supporting the clinical utility of AML MRD testing. Future MRD evaluations in AML likely will require an integrated approach combining multi-parameter flow cytometry and high-sensitivity molecular techniques applied to time points during and after completion of therapy in order to provide the most accurate and comprehensive assessment of treatment response.
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26
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Selim AG, Moore AS. Molecular Minimal Residual Disease Monitoring in Acute Myeloid Leukemia. J Mol Diagn 2018; 20:389-397. [DOI: 10.1016/j.jmoldx.2018.03.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 02/22/2018] [Accepted: 03/27/2018] [Indexed: 01/22/2023] Open
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27
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Bacher U, Porret N, Joncourt R, Sanz J, Aliu N, Wiedemann G, Jeker B, Banz Y, Pabst T. Pitfalls in the molecular follow up of NPM1 mutant acute myeloid leukemia. Haematologica 2018; 103:e486-e488. [PMID: 29903758 DOI: 10.3324/haematol.2018.192104] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Ulrike Bacher
- Department of Hematology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Center of Laboratory Medicine (ZLM) Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Naomi Porret
- Department of Hematology, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Raphael Joncourt
- Department of Hematology, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Javier Sanz
- Division of Human Genetics, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Nijas Aliu
- Division of Human Genetics, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Gertrud Wiedemann
- Department of Hematology, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Barbara Jeker
- Department of Medical Oncology, Inselspital, Bern University Hospital, Switzerland
| | - Yara Banz
- Institute of Pathology, University of Bern, Switzerland
| | - Thomas Pabst
- Department of Medical Oncology, Inselspital, Bern University Hospital, Switzerland
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28
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Evaluating measurable residual disease in acute myeloid leukemia. Blood Adv 2018; 2:1356-1366. [PMID: 29895626 PMCID: PMC5998930 DOI: 10.1182/bloodadvances.2018016378] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/23/2018] [Indexed: 02/03/2023] Open
Abstract
Mounting evidence indicates that the presence of measurable ("minimal") residual disease (MRD), defined as posttherapy persistence of leukemic cells at levels below morphologic detection, is a strong, independent prognostic marker of increased risk of relapse and shorter survival in patients with acute myeloid leukemia (AML) and can be used to refine risk-stratification and treatment response assessment. Because of the association between MRD and relapse risk, it has been postulated that testing for MRD posttreatment may help guide postremission treatment strategies by identifying high-risk patients who might benefit from preemptive treatment. This strategy, which remains to be formally tested, may be particularly attractive with availability of agents that could be used to specifically eradicate MRD. This review examines current methods of MRD detection, challenges to adopting MRD testing in routine clinical practice, and recent recommendations for MRD testing in AML issued by the European LeukemiaNet MRD Working Party. Inclusion of MRD as an end point in future randomized clinical trials will provide the data needed to move toward standardizing MRD assays and may provide a more accurate assessment of therapeutic efficacy than current morphologic measures.
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29
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Deep NPM1 Sequencing Following Allogeneic Hematopoietic Cell Transplantation Improves Risk Assessment in Adults with NPM1-Mutated AML. Biol Blood Marrow Transplant 2018; 24:1615-1620. [PMID: 29684564 DOI: 10.1016/j.bbmt.2018.04.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/12/2018] [Indexed: 12/12/2022]
Abstract
Relapse is the major cause of death in patients with acute myeloid leukemia (AML) after allogeneic hematopoietic cell transplantation (HCT). Measurable residual disease (MRD) detected by multiparameter flow cytometry (MFC) before and after HCT is a strong, independent risk factor for relapse. As next-generation sequencing (NGS) is increasingly applied in AML MRD detection, it remains to be determined if NGS can improve prediction of post-HCT relapse. Herein, we investigated pre-HCT MRD detected by MFC and NGS in 59 adult patients with NPM1-mutated AML in morphologic remission; 45 of the 59 had post-HCT MRD determined by MFC and NGS around day 28. Before HCT, MRD detected by MFC was the most significant risk factor for relapse (hazard ratio [HR], 4.63; P < .001), whereas MRD detected only by NGS was not. After HCT, MRD detected by either MFC or NGS was significant risk factor for relapse (HR, 4.96, P = .004 and HR, 4.36, P = .002, respectively). Combining pre- and post-HCT MRD provided the best prediction for relapse (HR, 5.25; P < .001), with a sensitivity at 83%. We conclude that NGS testing of mutated NPM1 post-HCT improves the risk assessment for relapse, whereas pre-HCT MFC testing identifies a subset of high-risk patients in whom additional therapy should be tested.
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30
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Wu D, Waalkes A, Penewit K, Salipante SJ. Ultrasensitive Detection of Chimerism by Single-Molecule Molecular Inversion Probe Capture and High-Throughput Sequencing of Copy Number Deletion Polymorphisms. Clin Chem 2018; 64:938-949. [PMID: 29549183 DOI: 10.1373/clinchem.2017.284737] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/21/2018] [Indexed: 11/06/2022]
Abstract
BACKGROUND Genomic chimerism, the co-occurrence of cells from different genetic origins, provides important diagnostic information in diverse clinical contexts, including graft injury detection and longitudinal surveillance of hematopoietic stem cell transplantation patients, but existing assays are limiting. Here we applied single-molecule molecular inversion probes (smMIPs), a high-throughput sequencing technology combining multiplexed target capture with read quantification mediated by unique molecular identifiers, to detect chimerism based on the presence or absence of polymorphic genomic loci. METHODS We designed a 159-smMIP panel targeting 40 autosomal regions of frequent homozygous deletion across human populations and 2 sex-linked loci. We developed methods for detecting and quantitating loci absent from 1 cell population but present in another, which could be used to sensitively identify chimeric cell populations. RESULTS Unrelated individuals and first-degree relatives were highly polymorphic across the loci examined. Using synthetic DNA mixtures, limits of detection of at least 1 in 10000 chimeric cells were demonstrated without prior knowledge of genotypes, and mixtures of up to 4 separate donors could be deconvoluted. Quantitative linearity over 4 orders of magnitude and false-positive rates <1 in 85000 events were achieved. Eleven of 11 posttransplant clinical specimens from patients with hematological malignancies testing positive for residual cancer by conventional methods had detectable chimeric populations by smMIP, whereas 11 of 11 specimens testing negative by conventional methods were low-positive for chimerism by smMIP. CONCLUSIONS smMIPs are scalable to high sensitivity and large numbers of informative markers, enabling ultrasensitive chimerism detection for many clinical purposes.
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Affiliation(s)
- David Wu
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | - Adam Waalkes
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | - Kelsi Penewit
- Department of Laboratory Medicine, University of Washington, Seattle, WA
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31
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Blombery P, Jones K, Doig K, Ryland G, McBean M, Thompson E, Yannakou CK, Westerman D. Sensitive NPM1 Mutation Quantitation in Acute Myeloid Leukemia Using Ultradeep Next-Generation Sequencing in the Diagnostic Laboratory. Arch Pathol Lab Med 2018; 142:606-612. [PMID: 29425073 DOI: 10.5858/arpa.2017-0229-oa] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Context Detection of measurable residual disease after therapy is an important predictor of outcome in acute myeloid leukemia. Objective To investigate the feasibility of using next-generation sequencing (NGS) in the diagnostic laboratory to perform quantitative NPM1 mutation assessment using ultradeep (approximately 300 000×-500 000×) sequencing (NGS-q NPM1) as a method of assessing residual disease burden in patients with acute myeloid leukemia. Design A flexible NGS-based assay for the detection and quantitation of NPM1 mutations was developed by polymerase chain reaction amplification of target DNA sequences, sequencing on an Illumina (San Diego, California) MiSeq, and analyzing data with an in-house-designed bioinformatic pipeline. NGS-q NPM1 was compared with current NPM1 quantitation methods (real-time quantitative-polymerase chain reaction and multiparameter flow cytometry). Results The NGS-q NPM1 assay had a sensitivity of between 10-4 and 10-5 and showed high concordance and correlation with reference methodologies. Moreover, the NGS-q NPM1 assay was able to be integrated into the laboratory's existing, targeted amplicon-based sequencing workflow. Conclusions An NGS-based, quantitative NPM1-mutation assessment can be used to monitor patients with acute myeloid leukemia, and it has some practical advantages over existing modalities.
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Affiliation(s)
| | | | | | | | | | | | | | - David Westerman
- From the Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Australia (Drs Blombery, Jones, Ryland, Thompson, Yannakou, and Westerman; Mr Doig; and Ms McBean); and the Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia (Drs Blombery, Thompson, Yannakou, and Westerman). Drs Blombery and Jones contributed equally to this work
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32
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Waalkes A, Penewit K, Wood BL, Wu D, Salipante SJ. Ultrasensitive detection of acute myeloid leukemia minimal residual disease using single molecule molecular inversion probes. Haematologica 2017; 102:1549-1557. [PMID: 28572161 PMCID: PMC5685235 DOI: 10.3324/haematol.2017.169136] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/31/2017] [Indexed: 12/11/2022] Open
Abstract
The identification of minimal residual disease is the primary diagnostic finding which predicts relapse in patients treated for acute myeloid leukemia. Ultrasensitive detection of minimal residual disease would enable better patient risk stratification and could open opportunities for early therapeutic intervention. Herein we apply single molecule molecular inversion probe capture, a technology combining multiplexed targeted sequencing with error correction schemes based on molecular barcoding, in order to detect mutations identifying minimal residual disease with ultrasensitive and quantitative precision. We designed a single molecule molecular inversion probe capture panel spanning >50 kb and targeting 32 factors relevant to acute myeloid leukemia pathogenesis. We demonstrate linearity and quantitative precision over 100-fold relative abundance of mutant cells (1 in 100 to 1 in 1,500), with estimated error rates approaching 1 in 1,200 base pairs sequenced and maximum theoretical limits of detection exceeding 1 in 60,000 mutant alleles. In 3 of 4 longitudinally collected specimens from patients with acute myeloid leukemia, we find that single molecule molecular inversion probe capture detects somatic mutations identifying minimal residual disease at substantially earlier time points and with greater sensitivity than clinical diagnostic approaches used as current standard of care (flow cytometry and conventional molecular diagnosis), and identifies persisting neoplastic cells during clinical remission. In 2 patients, single molecule molecular inversion probe capture detected heterogeneous, subclonal acute myeloid leukemia populations carrying distinct mutational signatures. Single molecule molecular inversion probe technology uniquely couples scalable target enrichment with sequence read error correction, providing an integrated, ultrasensitive approach for detecting minimal residual disease identifying mutations.
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Affiliation(s)
- Adam Waalkes
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Kelsi Penewit
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Brent L Wood
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - David Wu
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
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33
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Mencia-Trinchant N, Hu Y, Alas MA, Ali F, Wouters BJ, Lee S, Ritchie EK, Desai P, Guzman ML, Roboz GJ, Hassane DC. Minimal Residual Disease Monitoring of Acute Myeloid Leukemia by Massively Multiplex Digital PCR in Patients with NPM1 Mutations. J Mol Diagn 2017; 19:537-548. [PMID: 28525762 DOI: 10.1016/j.jmoldx.2017.03.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/17/2017] [Accepted: 03/23/2017] [Indexed: 12/27/2022] Open
Abstract
The presence of minimal residual disease (MRD) is widely recognized as a powerful predictor of therapeutic outcome in acute myeloid leukemia (AML), but methods of measurement and quantification of MRD in AML are not yet standardized in clinical practice. There is an urgent, unmet need for robust and sensitive assays that can be readily adopted as real-time tools for disease monitoring. NPM1 frameshift mutations are an established MRD marker present in half of patients with cytogenetically normal AML. However, detection is complicated by the existence of hundreds of potential frameshift insertions, clonal heterogeneity, and absence of sequence information when the NPM1 mutation is identified using capillary electrophoresis. Thus, some patients are ineligible for NPM1 MRD monitoring. Furthermore, a subset of patients with NPM1-mutated AML will have false-negative MRD results because of clonal evolution. To simplify and improve MRD testing for NPM1, we present a novel digital PCR technique composed of massively multiplex pools of insertion-specific primers that selectively detect mutated but not wild-type NPM1. By measuring reaction end points using digital PCR technology, the resulting single assay enables sensitive and specific quantification of most NPM1 exon 12 mutations in a manner that is robust to clonal heterogeneity, does not require NPM1 sequence information, and obviates the need for maintenance of hundreds of type-specific assays and associated plasmid standards.
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Affiliation(s)
- Nuria Mencia-Trinchant
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Yang Hu
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Maria Antonina Alas
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Fatima Ali
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Bas J Wouters
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Sangmin Lee
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Ellen K Ritchie
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Pinkal Desai
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Monica L Guzman
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Gail J Roboz
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Duane C Hassane
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York.
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34
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Chen X, Wood BL. Monitoring minimal residual disease in acute leukemia: Technical challenges and interpretive complexities. Blood Rev 2017; 31:63-75. [DOI: 10.1016/j.blre.2016.09.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 09/20/2016] [Accepted: 09/30/2016] [Indexed: 01/04/2023]
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35
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Paietta E. Minimal Residual Disease in AML: Why Has It Lagged Behind Pediatric ALL? CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2016; 15 Suppl:S2-6. [PMID: 26297274 DOI: 10.1016/j.clml.2015.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 02/03/2015] [Indexed: 12/16/2022]
Abstract
Although the concept of minimal residual disease (MRD) as an indicator for the quality of treatment response is the same in acute myeloid leukemia (AML) and acute lymphoid leukemia (ALL), the practice of measuring MRD levels for monitoring response and guiding therapy after induction has been implemented much more rapidly in ALL, particularly pediatric ALL, than in AML. In this perspective we examine the facts and discuss why ALL appears to be more amenable to MRD-shaped risk allocation and a revised definition of complete remission.
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Affiliation(s)
- Elisabeth Paietta
- Montefiore Medical Center-North Division, Albert Einstein College of Medicine, Bronx, NY.
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36
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Malmberg EB, Ståhlman S, Rehammar A, Samuelsson T, Alm SJ, Kristiansson E, Abrahamsson J, Garelius H, Pettersson L, Ehinger M, Palmqvist L, Fogelstrand L. Patient-tailored analysis of minimal residual disease in acute myeloid leukemia using next-generation sequencing. Eur J Haematol 2016; 98:26-37. [DOI: 10.1111/ejh.12780] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Erik B.R. Malmberg
- Department of Clinical Chemistry and Transfusion Medicine; Institute of Biomedicine; Sahlgrenska Academy at University of Gothenburg; Gothenburg Sweden
| | - Sara Ståhlman
- Department of Clinical Chemistry and Transfusion Medicine; Institute of Biomedicine; Sahlgrenska Academy at University of Gothenburg; Gothenburg Sweden
| | - Anna Rehammar
- Mathematical Sciences; Chalmers University of Technology and University of Gothenburg; Gothenburg Sweden
| | - Tore Samuelsson
- Department of Medical Biochemistry and Cell Biology; Institute of Biomedicine; Sahlgrenska Academy at University of Gothenburg; Gothenburg Sweden
| | - Sofie J. Alm
- Department of Clinical Chemistry and Transfusion Medicine; Institute of Biomedicine; Sahlgrenska Academy at University of Gothenburg; Gothenburg Sweden
| | - Erik Kristiansson
- Mathematical Sciences; Chalmers University of Technology and University of Gothenburg; Gothenburg Sweden
| | - Jonas Abrahamsson
- Department of Pediatrics; Institute of Clinical Sciences; Sahlgrenska Academy at University of Gothenburg; Gothenburg Sweden
| | - Hege Garelius
- Department of Medicine; Section of Hematology and Coagulation; Sahlgrenska University Hospital; Gothenburg Sweden
| | - Louise Pettersson
- Department of Pathology; Hallands Hospital Halmstad; Halmstad Sweden
| | - Mats Ehinger
- Division of Oncology and Pathology; Lund University; Lund Sweden
| | - Lars Palmqvist
- Department of Clinical Chemistry and Transfusion Medicine; Institute of Biomedicine; Sahlgrenska Academy at University of Gothenburg; Gothenburg Sweden
- Department of Clinical Chemistry; Sahlgrenska University Hospital; Gothenburg Sweden
| | - Linda Fogelstrand
- Department of Clinical Chemistry and Transfusion Medicine; Institute of Biomedicine; Sahlgrenska Academy at University of Gothenburg; Gothenburg Sweden
- Department of Clinical Chemistry; Sahlgrenska University Hospital; Gothenburg Sweden
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37
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Duncavage EJ, Tandon B. The utility of next-generation sequencing in diagnosis and monitoring of acute myeloid leukemia and myelodysplastic syndromes. Int J Lab Hematol 2016; 37 Suppl 1:115-21. [PMID: 25976969 DOI: 10.1111/ijlh.12361] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 03/13/2015] [Indexed: 11/28/2022]
Abstract
Myeloid malignancies including acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) are a heterogeneous group of disorders that share a common biology and are a major source of morbidity and mortality. In the last several years, studies using next-generation sequencing (NGS) have identified a core set of recurrently mutated myeloid malignancy genes in the majority of patients with AML and MDS, including those with normal cytogenetics. DNA-level mutations in several of these genes including NPM1, FLT3, and CEBPA in AML and ASXL1, ETV6, EZH2, RUNX1, and TP53 in MDS are associated with changes in patient outcomes and are now tested for in clinical laboratories. In addition to providing prognostic information, these gene mutations can be used to monitor patient disease burden through the use of ultrasensitive detection techniques. In this review, we will focus on the clinical utility of various NGS-based methods including whole-genome sequencing, exome sequencing, and targeted panel-based sequencing in the initial diagnosis and management of AML and MDS and cover recent methodological advances for the molecular monitoring of AML and MDS.
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Affiliation(s)
- E J Duncavage
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - B Tandon
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
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38
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The role of multiparametric flow cytometry in the detection of minimal residual disease in acute leukaemia. Pathology 2015; 47:609-21. [DOI: 10.1097/pat.0000000000000319] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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39
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Wood BL. Principles of minimal residual disease detection for hematopoietic neoplasms by flow cytometry. CYTOMETRY PART B-CLINICAL CYTOMETRY 2015; 90:47-53. [PMID: 25906832 DOI: 10.1002/cyto.b.21239] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/09/2015] [Accepted: 03/18/2015] [Indexed: 01/22/2023]
Abstract
Flow cytometry has become an indispensible tool for the diagnosis and classification of hematopoietic neoplasms. The ability to rapidly distinguish cellular subpopulations via multiparametric assessment of quantitative differences in antigen expression on single cells and enumerate the relative sizes of the resulting subpopulations is a key feature of the technology. More recently, these capabilities have been expanded to include the identification and enumeration of rare subpopulations within complex cellular mixtures, for example, blood or bone marrow, leading to the application for post-therapeutic monitoring or minimal residual disease detection. This review will briefly present the principles to be considered in the construction and use of flow cytometric assays for minimal residual disease detection including the use of informative antibody combinations, the impact of immunophenotypic instability, enumeration, assay sensitivity, and reproducibility.
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Affiliation(s)
- Brent L Wood
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington
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40
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Yeung CCS, Gerds AT, Fang M, Scott BL, Flowers MED, Gooley T, Deeg HJ. Relapse after Allogeneic Hematopoietic Cell Transplantation for Myelodysplastic Syndromes: Analysis of Late Relapse Using Comparative Karyotype and Chromosome Genome Array Testing. Biol Blood Marrow Transplant 2015; 21:1565-1575. [PMID: 25953732 DOI: 10.1016/j.bbmt.2015.04.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/24/2015] [Indexed: 12/01/2022]
Abstract
Relapse is a major cause of failure after allogeneic hematopoietic cell transplantation (HCT) in patients with myelodysplastic syndromes (MDS). We analyzed the relapse pattern in 1007 patients who underwent transplantation for MDS to identify factors that may determine the timing of relapse. Overall, 254 patients relapsed: 213 before 18 months and 41 later than 18 months after HCT, a time point frequently used in clinical trials. The hazard of relapse declined progressively with time since transplantation. A higher proportion of patients with early relapse had high-risk cytogenetics compared with patients with late relapse (P = .009). Patients with late relapse had suggestively longer postrelapse survival than patients who relapsed early, although the difference was not statistically significant (P = .07). Among 41 late relapsing patients, sequential cytogenetic data were available in 36. In 41% of these, new clonal abnormalities in addition to pre-HCT findings were identified at relapse; in 30% pre-HCT abnormalities were replaced by new clones, in 17.3% the same clone was present before HCT and at relapse, and in 9.7%, no abnormalities were present either before HCT or at relapse. Comparative chromosomal genomic array testing in 3 patients with late relapse showed molecular differences not detectable by cytogenetics between the pre-HCT clones and the clones at relapse. These data show that late relapses are not infrequent in patients who undergo transplantation for MDS. The pattern of new cytogenetic alterations at late relapse is similar to that observed in patients with early relapse and supports the concept that MDS relapse early and late after HCT is frequently due to the emergence of clones not detectable before HCT.
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Affiliation(s)
- Cecilia C S Yeung
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Pathology, University of Washington, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington
| | - Aaron T Gerds
- Department of Hematology and Oncology, Cleveland Clinic, Cleveland, Ohio
| | - Min Fang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Pathology, University of Washington, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington
| | - Bart L Scott
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Medicine, University of Washington, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington
| | - Mary E D Flowers
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Medicine, University of Washington, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington
| | - Ted Gooley
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Biostatistics, University of Washington, Seattle, Washington
| | - H Joachim Deeg
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Medicine, University of Washington, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington
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