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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-Internal Tandem Duplication Detection in Acute Myeloid Leukemia. Mod Pathol 2024; 37:100534. [PMID: 38852814 DOI: 10.1016/j.modpat.2024.100534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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 developed a high-sensitivity next-generation sequencing (HS-NGS) clinical assay, able to reliably detect low levels (1 × 10-5) 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. Finally, 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 and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine, Cleveland, Ohio.
| | - Theresa Spivey
- Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Erika M Moore
- Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Howard Meyerson
- Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Jennifer Yoest
- Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Benjamin Tomlinson
- Department of Hematology/Oncology, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Rose Beck
- Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - David Alouani
- Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Navid Sadri
- Department of Pathology and Laboratory Medicine, University Hospitals Cleveland Medical Center & Case Western Reserve University School of Medicine, Cleveland, Ohio.
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Kojabad AA, Chegeni R, Rostami S, Zaker F, Safa M. Ultrasensitive quantitation of FLT3-ITD mutation in patients with acute myeloid leukemia using ddPCR. Mol Biol Rep 2023:10.1007/s11033-023-08534-x. [PMID: 37300744 DOI: 10.1007/s11033-023-08534-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 05/17/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND FLT3-ITD mutations occur in 45-50% of cytogenetically normal AML patients. Conventional fragment analysis using capillary electrophoresis is routinely used to quantitate FLT3-ITD mutations. Fragment analysis however has limited sensitivity. METHODS AND RESULTS Here, FLT3-ITD was quantified in AML patients using an in-house developed ultra-sensitive droplet digital polymerase chain reaction assay (ddPCR). The allelic ratio of FLT3-ITD was also absolutely measured by both Fragment analysis and ddPCR. The sensitivity of ddPCR in quantitation of FLT3-ITD mutation was superior to Fragment analysis. CONCLUSION This study demonstrates the feasibility of using the described in-house ddPCR method to quantify the FLT3-ITD mutation and measure FLT3-ITD AR in AML patients.
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Affiliation(s)
- Amir Asri Kojabad
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Rouzbeh Chegeni
- Medical Laboratory Sciences Program, College of Health and Human Sciences, Northern Illinois University, DeKalb, IL, USA
| | - Shaharbano Rostami
- Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Farhad Zaker
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Safa
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran.
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3
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Yokoyama S, Onozawa M, Yoshida S, Miyashita N, Kimura H, Takahashi S, Matsukawa T, Goto H, Fujisawa S, Miki K, Hidaka D, Hashiguchi J, Wakasa K, Ibata M, Takeda Y, Shigematsu A, Fujimoto K, Tsutsumi Y, Mori A, Ishihara T, Kakinoki Y, Kondo T, Hashimoto D, Teshima T. Subclinical minute FLT3-ITD clone can be detected in clinically FLT3-ITD-negative acute myeloid leukaemia at diagnosis. Br J Haematol 2023. [PMID: 37067758 DOI: 10.1111/bjh.18800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/18/2023]
Abstract
Recent advances in next-generation sequencing (NGS) have enabled the detection of subclinical minute FLT3-ITD. We selected 74 newly diagnosed, cytogenetically normal acute myeloid leukaemia (AML) samples in which FLT3-ITD was not detected by gel electrophoresis. We sequenced them using NGS and found minute FLT3-ITDs in 19 cases. We compared cases with clinically relevant FLT3-ITD (n = 37), cases with minute FLT3-ITD (n = 19) and cases without detectable FLT3-ITD (n = 55). Molecular characteristics (location and length) of minute FLT3-ITD were similar to those of clinically relevant FLT3-ITD. Survival of cases with minute FLT3-ITD was similar to that of cases without detectable FLT3-ITD, whereas the relapse rate within 1 year after onset was significantly higher in cases with minute FLT3-ITD. We followed 18 relapsed samples of cases with clinically FLT3-ITD-negative at diagnosis. Two of 3 cases with minute FLT3-ITD relapsed with progression to clinically relevant FLT3-ITD. Two of 15 cases in which FLT3-ITD was not detected by NGS relapsed with the emergence of minute FLT3-ITD, and one of them showed progression to clinically relevant FLT3-ITD at the second relapse. We revealed the clonal dynamics of subclinical minute FLT3-ITD in clinically FLT3-ITD-negative AML. Minute FLT3-ITD at the initial AML can expand to become a dominant clone at relapse.
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Affiliation(s)
- Shota Yokoyama
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Masahiro Onozawa
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Shota Yoshida
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Naoki Miyashita
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Hiroyuki Kimura
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Shogo Takahashi
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Toshihiro Matsukawa
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Hideki Goto
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan
| | - Shinichi Fujisawa
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan
| | - Kosuke Miki
- Department of Hematology, Teine Keijinkai Hospital, Sapporo, Japan
| | - Daisuke Hidaka
- Department of Hematology, Sapporo Hokuyu Hospital, Sapporo, Japan
| | | | - Kentaro Wakasa
- Division of Hematology, Obihiro-Kosei General Hospital, Obihiro, Japan
| | - Makoto Ibata
- Department of Hematology, Sapporo-Kosei General Hospital, Sapporo, Japan
| | - Yukari Takeda
- Department of Hematology, Tonan Hospital, Sapporo, Japan
| | - Akio Shigematsu
- Department of Hematology, Kushiro Rosai Hospital, Kushiro, Japan
| | - Katsuya Fujimoto
- Department of Hematology, National Hospital Organization Hokkaido Cancer Center, Sapporo, Japan
| | - Yutaka Tsutsumi
- Department of Hematology, Hakodate Municipal Hospital, Hakodate, Japan
| | - Akio Mori
- Blood Disorders Center, Aiiku Hospital, Sapporo, Japan
| | | | | | - Takeshi Kondo
- Blood Disorders Center, Aiiku Hospital, Sapporo, Japan
| | - Daigo Hashimoto
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Takanori Teshima
- Department of Hematology, Hokkaido University Faculty of Medicine, Sapporo, Japan
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan
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TERT genetic variability and telomere length as factors affecting survival and risk in acute myeloid leukaemia. Sci Rep 2021; 11:23301. [PMID: 34857839 PMCID: PMC8640063 DOI: 10.1038/s41598-021-02767-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/22/2021] [Indexed: 11/16/2022] Open
Abstract
Acute myeloid leukaemia (AML) is a neoplasm of immature myeloid cells characterized by various cytogenetic alterations. The present study showed that in addition to the FLT3-ITD and NPM1 mutation status, telomere length (TL) and telomerase reverse transcriptase (TERT) gene polymorphisms may affect risk and overall survival (OS) in AML. TL was longer in healthy controls than in AML patients and positively correlated with age in the patients, but not in healthy subjects. TL was found to be independently affected by the presence of the FLT3-ITD mutation. As for the TERT gene polymorphism, AML patients with the TERT rs2853669 CC genotype were characterized by significantly shorter OS than patients carrying the T allele. Another observation in our study is the difference in TL and OS in patients belonging to various risk stratification groups related to the FLT3-ITD and NPM1 mutation status. Patients with adverse risk classification (mutation in FLT3-ITD and lack of mutation in NPM1) presented with the shortest telomeres and significantly worse OS. In conclusion, OS of AML patients appears to be affected by TERT gene variability and TL in addition to other well-established factors such as age, WBC count, or FLT3-ITD and NPM1 mutation status.
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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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6
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Freeman SD, Hourigan CS. MRD evaluation of AML in clinical practice: are we there yet? HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2019; 2019:557-569. [PMID: 31808906 PMCID: PMC6913462 DOI: 10.1182/hematology.2019000060] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
MRD technologies increase our ability to measure response in acute myeloid leukemia (AML) beyond the limitations of morphology. When applied in clinical trials, molecular and immunophenotypic MRD assays have improved prognostic precision, providing a strong rationale for their use to guide treatment, as well as to measure its effectiveness. Initiatives such as those from the European Leukemia Network now provide a collaborative knowledge-based framework for selection and implementation of MRD assays most appropriate for defined genetic subgroups. For patients with mutated-NPM1 AML, quantitative polymerase chain reaction (qPCR) monitoring of mutated-NPM1 transcripts postinduction and sequentially after treatment has emerged as a highly sensitive and specific tool to predict relapse and potential benefit from allogeneic transplant. Flow cytometric MRD after induction is prognostic across genetic risk groups and can identify those patients in the wild-type NPM1 intermediate AML subgroup with a very high risk for relapse. In parallel with these data, advances in genetic profiling have extended understanding of the etiology and the complex dynamic clonal nature of AML, as well as created the opportunity for MRD monitoring using next-generation sequencing (NGS). NGS AML MRD detection can stratify outcomes and has potential utility in the peri-allogeneic transplant setting. However, there remain challenges inherent in the NGS approach of multiplex quantification of mutations to track AML MRD. Although further development of this methodology, together with orthogonal testing, will clarify its relevance for routine clinical use, particularly for patients lacking a qPCR genetic target, established validated MRD assays can already provide information to direct clinical practice.
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Affiliation(s)
- Sylvie D Freeman
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom; and
| | - Christopher S Hourigan
- Laboratory of Myeloid Malignancies, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
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A DNA pool of FLT3-ITD positive DNA samples can be used efficiently for analytical evaluation of NGS-based FLT3-ITD quantitation - Testing several different ITD sequences and rates, simultaneously. J Biotechnol 2019; 303:25-29. [PMID: 31302157 DOI: 10.1016/j.jbiotec.2019.06.305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/31/2019] [Accepted: 06/03/2019] [Indexed: 12/16/2022]
Abstract
Internal tandem duplication (ITD) in the fms-like tyrosine kinase 3 (FLT3) gene is one of the most frequent genetic alteration in acute myeloid leukemia (AML), and it is associated with worse clinical outcome. Not only the presence but also the size, localization and the rate of this variant or the presence of multiple ITDs has prognostic information. The traditional PCR based diagnostic methods cannot provide information about all of these parameters in one assay, however the application of next generation sequencing (NGS) technique can be a reliable solution for this diagnostic problem. In order to evaluate the analytical properties of an NGS-based FLT3-ITD detection assay a quality control sample was prepared from DNA of AML patients containing 19 different FLT3-ITD variants identified by NGS. The higher the total read count was in a certain sample of the NGS run, the more ITD variant types could be detected. The maximal sensitivity of FLT3-ITD detection by NGS technique was as low as 0.007% FLT3-ITD/total allele rate, however, below 0.1% rate, the reproducibility of the quantitation was poor (CV > 25%). DNA pools with several FLT3-ITDs can be used efficiently for analytical evaluation of NGS-based FLT3-ITD quantitation testing several different ITD sequences and rates, simultaneously.
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8
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FLT3-ITD and CEBPA Mutations Predict Prognosis in Acute Myelogenous Leukemia Irrespective of Hematopoietic Stem Cell Transplantation. Biol Blood Marrow Transplant 2019; 25:941-948. [DOI: 10.1016/j.bbmt.2018.11.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/26/2018] [Indexed: 01/06/2023]
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9
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Ferrall-Fairbanks MC, Ball M, Padron E, Altrock PM. Leveraging Single-Cell RNA Sequencing Experiments to Model Intratumor Heterogeneity. JCO Clin Cancer Inform 2019; 3:1-10. [PMID: 30995123 PMCID: PMC6873939 DOI: 10.1200/cci.18.00074] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
PURPOSE Many cancers can be treated with targeted therapy. Almost inevitably, tumors develop resistance to targeted therapy, either from pre-existence or by evolving new genotypes and traits. Intratumor heterogeneity serves as a reservoir for resistance, which often occurs as a result of the selection of minor cellular subclones. On the level of gene expression, clonal heterogeneity can only be revealed using high-dimensional single-cell methods. We propose using a general diversity index (GDI) to quantify heterogeneity on multiple scales and relate it to disease evolution. MATERIALS AND METHODS We focused on individual patient samples that were probed with single-cell RNA (scRNA) sequencing to describe heterogeneity. We developed a pipeline to analyze single-cell data via sample normalization, clustering, and mathematical interpretation using a generalized diversity measure, as well as to exemplify the utility of this platform using single-cell data. RESULTS We focused on three sources of patient scRNA sequencing data: two healthy bone marrow (BM) donors, two patients with acute myeloid leukemia-each sampled before and after BM transplantation, four samples of presorted lineages-and six patients with lung carcinoma with multiregion sampling. While healthy/normal samples scored low in diversity overall, GDI further quantified the ways in which these samples differed. Whereas a widely used Shannon diversity index sometimes reveals fewer differences, GDI exhibits differences in the number of potential key drivers or clonal richness. Comparison of pre- and post-BM transplantation acute myeloid leukemia samples did not reveal differences in heterogeneity, although biological differences can exist. CONCLUSION GDI can quantify cellular heterogeneity changes across a wide spectrum, even when standard measures, such as the Shannon index, do not. Our approach can be widely applied to quantify heterogeneity across samples and conditions.
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Affiliation(s)
| | - Markus Ball
- All authors: Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Eric Padron
- All authors: Moffitt Cancer Center and Research Institute, Tampa, FL
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Next Generation Sequencing in AML-On the Way to Becoming a New Standard for Treatment Initiation and/or Modulation? Cancers (Basel) 2019; 11:cancers11020252. [PMID: 30795628 PMCID: PMC6406956 DOI: 10.3390/cancers11020252] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/08/2019] [Accepted: 02/12/2019] [Indexed: 12/19/2022] Open
Abstract
Acute myeloid leukemia (AML) is a clonal disease caused by genetic abberations occurring predominantly in the elderly. Next generation sequencing (NGS) analysis has led to a deeper genetic understanding of the pathogenesis and the role of recently discovered genetic precursor lesions (clonal hematopoiesis of indeterminate/oncogenic potential (CHIP/CHOP)) in the evolution of AML. These advances are reflected by the inclusion of certain mutations in the updated World Health Organization (WHO) 2016 classification and current treatment guidelines by the European Leukemia Net (ELN) and National Comprehensive Cancer Network (NCCN) and results of mutational testing are already influencing the choice and timing of (targeted) treatment. Genetic profiling and stratification of patients into molecularly defined subgroups are expected to gain ever more weight in daily clinical practice. Our aim is to provide a concise summary of current evidence regarding the relevance of NGS for the diagnosis, risk stratification, treatment planning and response assessment in AML, including minimal residual disease (MRD) guided approaches. We also summarize recently approved drugs targeting genetically defined patient populations with risk adapted- and individualized treatment strategies.
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Clonal heterogeneity of FLT3-ITD detected by high-throughput amplicon sequencing correlates with adverse prognosis in acute myeloid leukemia. Oncotarget 2018; 9:30128-30145. [PMID: 30046393 PMCID: PMC6059024 DOI: 10.18632/oncotarget.25729] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 06/19/2018] [Indexed: 12/14/2022] Open
Abstract
In acute myeloid leukemia (AML), internal tandem duplications (ITDs) of FLT3 are frequent mutations associated with unfavorable prognosis. At diagnosis, the FLT3-ITD status is routinely assessed by fragment analysis, providing information about the length but not the position and sequence of the ITD. To overcome this limitation, we performed cDNA-based high-throughput amplicon sequencing (HTAS) in 250 FLT3-ITD positive AML patients, treated on German AML Cooperative Group (AMLCG) trials. FLT3-ITD status determined by routine diagnostics was confirmed by HTAS in 242 out of 250 patients (97%). The total number of ITDs detected by HTAS was higher than in routine diagnostics (n = 312 vs. n = 274). In particular, HTAS detected a higher number of ITDs per patient compared to fragment analysis, indicating higher sensitivity for subclonal ITDs. Patients with more than one ITD according to HTAS had a significantly shorter overall and relapse free survival. There was a close correlation between FLT3-ITD mRNA levels in fragment analysis and variant allele frequency in HTAS. However, the abundance of long ITDs (≥75nt) was underestimated by HTAS, as the size of the ITD affected the mappability of the corresponding sequence reads. In summary, this study demonstrates that HTAS is a feasible approach for FLT3-ITD detection in AML patients, delivering length, position, sequence and mutational burden of this alteration in a single assay with high sensitivity. Our findings provide insights into the clonal architecture of FLT3-ITD positive AML and have clinical implications.
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13
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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: 26] [Impact Index Per Article: 3.7] [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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14
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Lagunas-Rangel FA, Chávez-Valencia V. FLT3–ITD and its current role in acute myeloid leukaemia. Med Oncol 2017; 34:114. [DOI: 10.1007/s12032-017-0970-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 04/25/2017] [Indexed: 01/20/2023]
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15
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Gaballa S, Saliba R, Oran B, Brammer JE, Chen J, Rondon G, Alousi AM, Kebriaei P, Marin D, Popat UR, Andersson BS, Shpall EJ, Jabbour E, Daver N, Andreeff M, Ravandi F, Cortes J, Patel K, Champlin RE, Ciurea SO. Relapse risk and survival in patients with FLT3 mutated acute myeloid leukemia undergoing stem cell transplantation. Am J Hematol 2017; 92:331-337. [PMID: 28052408 DOI: 10.1002/ajh.24632] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/15/2016] [Accepted: 12/19/2016] [Indexed: 01/13/2023]
Abstract
In patients with AML with FMS-like tyrosine kinase 3 (FLT3) mutations, the significance of minimal residual disease (MRD) detected by PCR before allogeneic stem cell transplantation (SCT) on outcomes after transplant remains unclear. We identified 200 patients with FLT3-AML who underwent SCT at our institution. Disease status at transplant was: first or second complete remission (CR1/CR2, n = 119), high-risk CR (third or subsequent CR, marrow hypoplasia, or incomplete count recovery) (CR-HR, n = 31), and morphological evidence of active disease (AD, n = 50). The median follow-up was 27 months, and the 2-year overall and progression-free survival were 43% and 41%, respectively. Relapse was highest in the AD group (85%) and the CR-HR FLT3 MRD positive group (72%), followed by CR-HR FLT3 MRD negative (58%), CR1/CR2 FLT3 MRD positive (39%), and lowest in the CR1/CR2 FLT3 MRD negative group (23%). On multivariate analysis, independent factors influencing the risk of relapse were detectable morphological disease and FLT3 MRD by PCR pre-transplant. Factors that did not influence the relapse risk included: age, graft type, graft source, type of FLT3 mutation, or conditioning intensity. Morphologic and molecular remission status at the time of transplant were key predictors of disease relapse and survival in patients with FLT3-AML.
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Affiliation(s)
- Sameh Gaballa
- Department of Stem Cell Transplantation and Cellular Therapy; The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Rima Saliba
- Department of Stem Cell Transplantation and Cellular Therapy; The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Betul Oran
- Department of Stem Cell Transplantation and Cellular Therapy; The University of Texas MD Anderson Cancer Center; Houston Texas
- Transplant Myeloid Study Group; The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Jonathan E. Brammer
- Department of Stem Cell Transplantation and Cellular Therapy; The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Julianne Chen
- Department of Stem Cell Transplantation and Cellular Therapy; The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Gabriela Rondon
- Department of Stem Cell Transplantation and Cellular Therapy; The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Amin M. Alousi
- Department of Stem Cell Transplantation and Cellular Therapy; The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Partow Kebriaei
- Department of Stem Cell Transplantation and Cellular Therapy; The University of Texas MD Anderson Cancer Center; Houston Texas
- Transplant Myeloid Study Group; The University of Texas MD Anderson Cancer Center; Houston Texas
| | - David Marin
- Department of Stem Cell Transplantation and Cellular Therapy; The University of Texas MD Anderson Cancer Center; Houston Texas
- Transplant Myeloid Study Group; The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Uday R. Popat
- Department of Stem Cell Transplantation and Cellular Therapy; The University of Texas MD Anderson Cancer Center; Houston Texas
- Transplant Myeloid Study Group; The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Borje S. Andersson
- Department of Stem Cell Transplantation and Cellular Therapy; The University of Texas MD Anderson Cancer Center; Houston Texas
- Transplant Myeloid Study Group; The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Elizabeth J. Shpall
- Department of Stem Cell Transplantation and Cellular Therapy; The University of Texas MD Anderson Cancer Center; Houston Texas
- Transplant Myeloid Study Group; The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Elias Jabbour
- Department of Leukemia; The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Naval Daver
- Department of Leukemia; The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Michael Andreeff
- Department of Leukemia; The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Farhad Ravandi
- Department of Leukemia; The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Jorge Cortes
- Department of Leukemia; The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Keyur Patel
- Department of Hematopathology; The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Richard E. Champlin
- Department of Stem Cell Transplantation and Cellular Therapy; The University of Texas MD Anderson Cancer Center; Houston Texas
- Transplant Myeloid Study Group; The University of Texas MD Anderson Cancer Center; Houston Texas
| | - Stefan O. Ciurea
- Department of Stem Cell Transplantation and Cellular Therapy; The University of Texas MD Anderson Cancer Center; Houston Texas
- Transplant Myeloid Study Group; The University of Texas MD Anderson Cancer Center; Houston Texas
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16
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Minimal Residual Disease in Acute Myeloid Leukemia of Adults: Determination, Prognostic Impact and Clinical Applications. Mediterr J Hematol Infect Dis 2016; 8:e2016052. [PMID: 27872732 PMCID: PMC5111512 DOI: 10.4084/mjhid.2016.052] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 09/12/2016] [Indexed: 02/06/2023] Open
Abstract
Pretreatment assessment of cytogenetic/genetic signature of acute myeloid leukemia (AML) has been consistently shown to play a major prognostic role but also to fail at predicting outcome on individual basis, even in low-risk AML. Therefore, we are in need of further accurate methods to refine the patients’ risk allocation process, distinguishing more adequately those who are likely to recur from those who are not. In this view, there is now evidence that the submicroscopic amounts of leukemic cells (called minimal residual disease, MRD), measured during the course of treatment, indicate the quality of response to therapy. Therefore, MRD might serve as an independent, additional biomarker to help to identify patients at higher risk of relapse. Detection of MRD requires the use of highly sensitive ancillary techniques, such as polymerase chain reaction (PCR) and multiparametric flow cytometry(MPFC). In the present manuscript, we will review the current approaches to investigate MRD and its clinical applications in AML management.
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17
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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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