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Bergeron J, Capo-Chichi JM, Tsui H, Mahe E, Berardi P, Minden MD, Brandwein JM, Schuh AC. The Clinical Utility of FLT3 Mutation Testing in Acute Leukemia: A Canadian Consensus. Curr Oncol 2023; 30:10410-10436. [PMID: 38132393 PMCID: PMC10742150 DOI: 10.3390/curroncol30120759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/02/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
FMS-like tyrosine kinase 3 (FLT3) mutations are detected in approximately 20-30% of patients with acute myeloid leukemia (AML), with the presence of a FLT3 internal tandem duplication (FLT3-ITD) mutation being associated with an inferior outcome. Assessment of FLT3 mutational status is now essential to define optimal upfront treatment in both newly diagnosed and relapsed AML, to support post-induction allogeneic hematopoietic stem cell transplantation (alloSCT) decision-making, and to evaluate treatment response via measurable (minimal) residual disease (MRD) evaluation. In view of its importance in AML diagnosis and management, the Canadian Leukemia Study Group/Groupe canadien d'étude sur la leucémie (CLSG/GCEL) undertook the development of a consensus statement on the clinical utility of FLT3 mutation testing, as members reported considerable inter-center variability across Canada with respect to testing availability and timing of use, methodology, and interpretation. The CLSG/GCEL panel identified key clinical and hematopathological questions, including: (1) which patients should be tested for FLT3 mutations, and when?; (2) which is the preferred method for FLT3 mutation testing?; (3) what is the clinical relevance of FLT3-ITD size, insertion site, and number of distinct FLT3-ITDs?; (4) is there a role for FLT3 analysis in MRD assessment?; (5) what is the clinical relevance of the FLT3-ITD allelic burden?; and (6) how should results of FLT3 mutation testing be reported? The panel followed an evidence-based approach, taken together with Canadian clinical and laboratory experience and expertise, to create a consensus document to facilitate a more uniform approach to AML diagnosis and treatment across Canada.
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Affiliation(s)
- Julie Bergeron
- CEMTL Installation Maisonneuve-Rosemont, Institut Universitaire d’Hématologie-Oncologie et de Thérapie Cellulaire, Université de Montréal, Montréal, QC H1T 2M4, Canada
| | - Jose-Mario Capo-Chichi
- Division of Clinical Laboratory Genetics, Department of Laboratory Medicine and Pathobiology, Laboratory Medicine Program, University Health Network, University of Toronto, Toronto, ON M5G 2C4, Canada;
| | - Hubert Tsui
- Division of Hematological Pathology, Department of Laboratory Medicine and Molecular Diagnostics, Precision Diagnostics and Therapeutics Program, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada;
- Department of Laboratory Medicine and Pathobiology, Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Etienne Mahe
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
- Division of Hematology and Hematological Malignancies, Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Philip Berardi
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital/Eastern Ontario Regional Laboratory Association, Ottawa, ON K1H 8M2, Canada;
- Department of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Mark D. Minden
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada; (M.D.M.); (A.C.S.)
- Department of Medicine, University of Toronto, Toronto, ON M5S 3H2, Canada
| | - Joseph M. Brandwein
- Division of Hematology, Department of Medicine, University of Alberta, Edmonton, AB T6G 2G3, Canada;
| | - Andre C. Schuh
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada; (M.D.M.); (A.C.S.)
- Department of Medicine, University of Toronto, Toronto, ON M5S 3H2, Canada
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2
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da Rosa SEA, de Lima LB, Silveira CN, Cortes LGF, de Oliveira Filho JB, de Souza Reis R, Cervato MC, Rodrigues PHS, de Oliveira Pelegrino K, Petroni RC, da Silva Araujo E, Campregher PV. Real-world genomic profiling of acute myeloid leukemia and the impact of European LeukemiaNet risk stratification 2022 update. Clin Transl Oncol 2023; 25:3431-3436. [PMID: 37165281 DOI: 10.1007/s12094-023-03195-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/07/2023] [Indexed: 05/12/2023]
Abstract
BACKGROUND Acute myeloid leukemia (AML) is a myeloid neoplasm associated with a high morbidity and mortality. The diagnosis, risk stratification and therapy selection in AML have changed substantially in the last decade with the progressive incorporation of clinically relevant molecular markers. METHODS In this work, our aim was to describe a real-world genomic profiling experience in AML and to demonstrate the impact of the European Leukemia Net 2022 update on risk stratification in AML. RESULTS AND DISCUSSION One hundred and forty-one patients were evaluated with an amplicon-based multi-gene next-generation sequencing (NGS) panel. The most commonly mutated genes were FLT3, DNMT3A, RUNX1, IDH2, NPM1, ASXL1, SRSF2, NRAS, TP53 and TET2. Detection of FLT3 ITD with NGS had a sensitivity of 96.3% when compared to capillary electrophoresis. According to ELN 2017, 26.6%, 20.1%, and 53.3% of patients were classified as having a good, moderate, or unfavorable risk. When ELN 2022 was used, 15.6%, 27.8%, and 56.6% of patients were classified as favorable, moderate, or unfavorable risk, respectively. When ELN 2022 was compared to ELN 2017, thirteen patients (14.4%) exhibited a different risk classification, with a significant decrease in the number of favorable risk patients, what has immediate clinical impact. CONCLUSIONS In conclusion, we have described a real-world genomic profiling experience in AML and the impact of the 2022 ELN update on risk stratification.
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3
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Koo M, Song IC, Kim J, Kwon GC, Kim SY. Prognostic value of the mutation types and dynamics of FLT3-ITD in acute myeloid leukemia. Eur J Haematol 2023; 111:562-572. [PMID: 37435718 DOI: 10.1111/ejh.14044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/03/2023] [Accepted: 07/03/2023] [Indexed: 07/13/2023]
Abstract
OBJECTIVE The prognostic value of the mutation types and dynamics of FLT3-ITD in acute myeloid leukemia (AML) and other known factors were studied. METHODS Initial and follow-up samples from 45 AML patients with FLT3-ITD mutations were analyzed by fragment length analysis, Sanger sequencing, and next-generation sequencing. RESULTS Some patients (13%) had multiple FLT3-ITD mutations, and many of them had acute promyelocytic leukemia (APL). FLT3-ITD mutations were classified according to mutation types, including duplication-only FLT3-ITD (52%) and FLT3-ITD with duplications and insertions (dup + ins) (48%). The dup + ins FLT3-ITD variant was independently associated with poor prognosis among non-APL patients (odds ratio, 2.92) in addition to FLT3-ITD with ≥50% variant allele frequency (VAF). The VAFs of FLT3-ITD were low (median 2.2%) when detected during morphologic complete remission (CR) after conventional chemotherapy; however, in two patients treated with gilteritinib after relapse, the VAFs of FLT3-ITD were much higher (>95% and 8.1%) in the morphologic CR state. CONCLUSIONS The type of FLT3-ITD mutation is important in prognosis, and the dup + ins type of FLT3-ITD can be an indicator of poor prognosis. In addition, the FLT3-ITD mutation status may unexpectedly not match the morphologic examination results after gilteritinib treatment.
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Affiliation(s)
- Mosae Koo
- Department of Laboratory Medicine, Chungnam National University College of Medicine, Chungnam National University Hospital, Daejeon, Republic of Korea
| | - Ik-Chan Song
- Division of Hematology/Oncology, Department of Internal Medicine, Chungnam National University College of Medicine, Chungnam National University Hospital, Daejeon, Republic of Korea
| | - Jimyung Kim
- Department of Laboratory Medicine, Chungnam National University College of Medicine, Chungnam National University Hospital, Daejeon, Republic of Korea
| | - Gye Cheol Kwon
- Department of Laboratory Medicine, Chungnam National University College of Medicine, Chungnam National University Hospital, Daejeon, Republic of Korea
| | - Seon Young Kim
- Department of Laboratory Medicine, Chungnam National University College of Medicine, Chungnam National University Hospital, Daejeon, Republic of Korea
- Cancer Research Institute, Chungnam National University School of Medicine, Daejeon, Republic of Korea
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4
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DiNardo CD, Erba HP, Freeman SD, Wei AH. Acute myeloid leukaemia. Lancet 2023; 401:2073-2086. [PMID: 37068505 DOI: 10.1016/s0140-6736(23)00108-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/09/2022] [Accepted: 01/12/2023] [Indexed: 04/19/2023]
Abstract
Progress in acute myeloid leukaemia treatment is occurring at an unprecedented pace. The past decade has witnessed an increasingly improved scientific understanding of the underlying biology of acute myeloid leukaemia, leading to enhanced prognostication tools and refined risk assessments, and most especially incorporating measurable residual disease (MRD) into longitudinal risk assessments. The classification of acute myeloid leukaemia has recently been updated by WHO and the International Consensus Classification (ICC). Recommendations for prognostic stratification, response assessment, and MRD determination have also been updated by the European LeukemiaNet. Treatment options have evolved substantially in the last 5 years for patients with newly diagnosed acute myeloid leukaemia, leading to improved outcomes in intensively treated patients and those more appropriate for non-intensive chemotherapy. More effective targeted treatment options in the relapsed setting are also available, further advancing the treatment armamentarium and improving patient outcomes.
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Affiliation(s)
| | - Harry P Erba
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Sylvie D Freeman
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Andrew H Wei
- Department of Haematology, Peter MacCallum Cancer Centre, Royal Melbourne Hospital, University of Melbourne and Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
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5
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Tiong IS, Loo S. Targeting Measurable Residual Disease (MRD) in Acute Myeloid Leukemia (AML): Moving beyond Prognostication. Int J Mol Sci 2023; 24:4790. [PMID: 36902217 PMCID: PMC10003715 DOI: 10.3390/ijms24054790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 03/06/2023] Open
Abstract
Measurable residual disease (MRD) assessment in acute myeloid leukemia (AML) has an established role in disease prognostication, particularly in guiding decisions for hematopoietic cell transplantation in first remission. Serial MRD assessment is now routinely recommended in the evaluation of treatment response and monitoring in AML by the European LeukemiaNet. The key question remains, however, if MRD in AML is clinically actionable or "does MRD merely portend fate"? With a series of new drug approvals since 2017, we now have more targeted and less toxic therapeutic options for the potential application of MRD-directed therapy. Recent approval of NPM1 MRD as a regulatory endpoint is also foreseen to drastically transform the clinical trial landscape such as biomarker-driven adaptive design. In this article, we will review (1) the emerging molecular MRD markers (such as non-DTA mutations, IDH1/2, and FLT3-ITD); (2) the impact of novel therapeutics on MRD endpoints; and (3) how MRD might be used as a predictive biomarker to guide therapy in AML beyond its prognostic role, which is the focus of two large collaborative trials: AMLM26 INTERCEPT (ACTRN12621000439842) and MyeloMATCH (NCT05564390).
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Affiliation(s)
- Ing S. Tiong
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- The Alfred Hospital, Melbourne, VIC 3004, Australia
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC 3004, Australia
| | - Sun Loo
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- The Northern Hospital, Epping, VIC 3076, Australia
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6
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Lee S, Sun CH, Jang H, Kim D, Yoon SS, Koh Y, Na SC, Cho SI, Kim MJ, Seong MW, Byun JM, Yun H. ITDetect: a method to detect internal tandem duplication of FMS-like tyrosine kinase (FLT3) from next-generation sequencing data with high sensitivity and clinical application. BMC Bioinformatics 2023; 24:62. [PMID: 36823555 PMCID: PMC9951415 DOI: 10.1186/s12859-023-05173-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
Internal tandem duplication (ITD) of the FMS-like tyrosine kinase (FLT3) gene is associated with poor clinical outcomes in patients with acute myeloid leukemia. Although recent methods for detecting FLT3-ITD from next-generation sequencing (NGS) data have replaced traditional ITD detection approaches such as conventional PCR or fragment analysis, their use in the clinical field is still limited and requires further information. Here, we introduce ITDetect, an efficient FLT3-ITD detection approach that uses NGS data. Our proposed method allows for more precise detection and provides more detailed information than existing in silico methods. Further, it enables FLT3-ITD detection from exome sequencing or targeted panel sequencing data, thereby improving its clinical application. We validated the performance of ITDetect using NGS-based and experimental ITD detection methods and successfully demonstrated that ITDetect provides the highest concordance with the experimental methods. The program and data underlying this study are available in a public repository.
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Affiliation(s)
- Sungyoung Lee
- grid.412484.f0000 0001 0302 820XDepartment of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea ,grid.412484.f0000 0001 0302 820XCenter for Precision Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Choong-Hyun Sun
- GenomeOpinion Inc., 117-3 Hoegiro, Dongdaemoon-gu, Seoul, Republic of Korea
| | - Heejun Jang
- grid.31501.360000 0004 0470 5905Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Daeyoon Kim
- grid.31501.360000 0004 0470 5905Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung-Soo Yoon
- grid.31501.360000 0004 0470 5905Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea ,grid.412484.f0000 0001 0302 820XDepartment of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Youngil Koh
- grid.31501.360000 0004 0470 5905Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea ,grid.412484.f0000 0001 0302 820XDepartment of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seung Chan Na
- grid.412484.f0000 0001 0302 820XDepartment of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sung Im Cho
- grid.412484.f0000 0001 0302 820XDepartment of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Man Jin Kim
- grid.412484.f0000 0001 0302 820XDepartment of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Moon-Woo Seong
- grid.412484.f0000 0001 0302 820XDepartment of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Ja Min Byun
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea. .,Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Hongseok Yun
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea. .,Center for Precision Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
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7
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Tefferi A, Singh A, Gangat N, Al-Kali A, Alkhateeb H, Shah M, Patnaik MS, Elliott MA, Hogan WJ, Litzow MR, Wolanskyj-Spinner A, Hook CC, Mangaonkar A, Viswanatha D, Chen D, Pardanani A, Begna KH, Ketterling RP. Adverse karyotype subcategories in acute myeloid leukemia display significant differences in mutation composition and transplant-augmented survival. Haematologica 2022; 108:245-249. [PMID: 36073516 PMCID: PMC9827171 DOI: 10.3324/haematol.2022.281495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Indexed: 02/05/2023] Open
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - David Viswanatha
- Division of Hematopathology, Departments of Medicine and Laboratory Medicine, Mayo Clinic, Rochester, MN, USA
| | - Dong Chen
- Division of Hematopathology, Departments of Medicine and Laboratory Medicine, Mayo Clinic, Rochester, MN, USA
| | | | | | - Rhett P. Ketterling
- Division of Hematopathology, Departments of Medicine and Laboratory Medicine, Mayo Clinic, Rochester, MN, USA,R. P. KETTERLING -
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8
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Jevremovic D, Nanaa A, Geyer SM, Timm M, Azouz H, Hengel C, Reberg A, He R, Viswanatha D, Salama ME, Shi M, Olteanu H, Horna P, Otteson G, Greipp PT, Xie Z, Alkhateeb HB, Hogan W, Litzow M, Patnaik MM, Shah M, Al-Kali A, Nguyen PL. Abnormal CD13/HLA-DR Expression Pattern on Myeloblasts Predicts Development of Myeloid Neoplasia in Patients With Clonal Cytopenia of Undetermined Significance. Am J Clin Pathol 2022; 158:530-536. [PMID: 35938646 PMCID: PMC9535519 DOI: 10.1093/ajcp/aqac083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/09/2022] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES Patients with clonal cytopenia of undetermined significance (CCUS) are at increased risk of developing myeloid neoplasia (MN). We evaluated whether a simple flow cytometry immunophenotyping (FCIP) assay could differentiate the risk of development of MN in patients with CCUS. METHODS Bone marrow aspirates were assessed by FCIP panel in a cohort of 80 patients identified as having CCUS based on next-generation sequencing or cytogenetics from March 2015 to May 2020, with available samples. Flow cytometric assay included CD13/HLA-DR expression pattern on CD34-positive myeloblasts; CD13/CD16 pattern on maturing granulocytic precursors; and aberrant expression of CD2, CD7, or CD56 on CD34-positive myeloblasts. Relevant demographic, comorbidity, and clinical and laboratory data, including the type and extent of genetic abnormalities, were extracted from the electronic health record. RESULTS In total, 17 (21%) patients with CCUS developed MN over the follow-up period (median survival follow-up, 28 months [95% confidence interval, 19-31]). Flow cytometry immunophenotyping abnormalities, including the aberrant pattern of CD13/HLA-DR expression, as detected at the time of the diagnosis of CCUS, were significantly associated with risk of developing MN (hazard ratio, 2.97; P = .006). Additional FCIP parameters associated with the development of MN included abnormal expression of CD7 on myeloblasts and the presence vs absence of any FCIP abnormality. CONCLUSIONS A simple FCIP approach that includes assessment of CD13/HLA-DR pattern on CD34-positive myeloblasts can be useful in identifying patients with CCUS at higher risk of developing MN.
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Affiliation(s)
| | - Ahmad Nanaa
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Susan M Geyer
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Michael Timm
- Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | - Haya Azouz
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Cynthia Hengel
- Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | | | - Rong He
- Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Min Shi
- Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | - Horatiu Olteanu
- Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | - Pedro Horna
- Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | - Gregory Otteson
- Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | - Patricia T Greipp
- Division of Hematopathology, Mayo Clinic, Rochester, MN, USA.,Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Zhuoer Xie
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | - William Hogan
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Mark Litzow
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | - Mithun Shah
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Aref Al-Kali
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Phuong L Nguyen
- Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
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9
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Akkari YM, Baughn LB, Dubuc AM, Smith AC, Mallo M, Dal Cin P, Diez Campelo M, Gallego MS, Granada Font I, Haase DT, Schlegelberger B, Slavutsky I, Mecucci C, Levine RL, Hasserjian RP, Solé F, Levy B, Xu X. Guiding the global evolution of cytogenetic testing for hematologic malignancies. Blood 2022; 139:2273-2284. [PMID: 35167654 PMCID: PMC9710485 DOI: 10.1182/blood.2021014309] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 02/03/2022] [Indexed: 12/15/2022] Open
Abstract
Cytogenetics has long represented a critical component in the clinical evaluation of hematologic malignancies. Chromosome banding studies provide a simultaneous snapshot of genome-wide copy number and structural variation, which have been shown to drive tumorigenesis, define diseases, and guide treatment. Technological innovations in sequencing have ushered in our present-day clinical genomics era. With recent publications highlighting novel sequencing technologies as alternatives to conventional cytogenetic approaches, we, an international consortium of laboratory geneticists, pathologists, and oncologists, describe herein the advantages and limitations of both conventional chromosome banding and novel sequencing technologies and share our considerations on crucial next steps to implement these novel technologies in the global clinical setting for a more accurate cytogenetic evaluation, which may provide improved diagnosis and treatment management. Considering the clinical, logistic, technical, and financial implications, we provide points to consider for the global evolution of cytogenetic testing.
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Affiliation(s)
- Yassmine M.N. Akkari
- Departments of Cytogenetics and Molecular Pathology, Legacy Health, Portland, OR
| | - Linda B. Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Adrian M. Dubuc
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Adam C. Smith
- Laboratory Medicine Program, University Health Network and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Mar Mallo
- MDS Group, Microarrays Unit, Josep Carreras Leukaemia Research Institute, Barcelona, Spain
| | - Paola Dal Cin
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Maria Diez Campelo
- Hematology Department University Hospital of Salamanca, IBSAL, Salamanca, Spain
| | - Marta S. Gallego
- Laboratory of Cytogenetics and Molecular Cytogenetics, Department of Clinical Pathology, Italian Hospital, Buenos Aires, Argentina
| | - Isabel Granada Font
- Hematology Laboratory, Germans Trias i Pujol University Hospital–Catalan Institute of Oncology, Josep Carreras Leukemia Research Institute, Barcelona, Spain
| | - Detlef T. Haase
- Clinics of Hematology and Medical Oncology, University Medical Center Göttingen, Göttingen, Germany
| | | | - Irma Slavutsky
- Laboratory Genetics of Lymphoid Malignancies, Institute of Experimental Medicine, Buenos Aires, Argentina
| | - Cristina Mecucci
- Laboratory of Cytogenetics and Molecular Medicine, Hematology University of Perugia, Perugia, Italy
| | - Ross L. Levine
- Department of Medicine, Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Francesc Solé
- MDS Group, Microarrays Unit, Josep Carreras Leukaemia Research Institute, Barcelona, Spain
| | - Brynn Levy
- College of Physicians and Surgeons, Columbia University Medical Center and the New York Presbyterian Hospital, New York, NY
| | - Xinjie Xu
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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10
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Oliveira JL, Greipp PT, Rangan A, Jatoi A, Nguyen PL. Myeloid malignancies in cancer patients treated with poly(ADP-ribose) polymerase (PARP) inhibitors: a case series. Blood Cancer J 2022; 12:11. [PMID: 35078980 PMCID: PMC8789926 DOI: 10.1038/s41408-022-00607-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/03/2021] [Indexed: 11/08/2022] Open
Affiliation(s)
| | - Patricia T Greipp
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Aruna Rangan
- Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | - Aminah Jatoi
- Division of Medical Oncology, Mayo Clinic, Rochester, MN, USA.
| | - Phuong L Nguyen
- Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
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11
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FLT3 mutational analysis in acute myeloid leukemia: Advantages and pitfalls with different approaches. Blood Rev 2022; 54:100928. [DOI: 10.1016/j.blre.2022.100928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 12/17/2022]
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12
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Tung JK, Suarez CJ, Chiang T, Zehnder JL, Stehr H. Accurate Detection and Quantification of FLT3 Internal Tandem Duplications in Clinical Hybrid Capture Next-Generation Sequencing Data. J Mol Diagn 2021; 23:1404-1413. [PMID: 34363960 DOI: 10.1016/j.jmoldx.2021.07.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 07/09/2021] [Accepted: 07/16/2021] [Indexed: 01/13/2023] Open
Abstract
FLT3 internal tandem duplications (ITDs) are found in approximately one-third of patients with acute myeloid leukemia and have important prognostic and therapeutic implications that have supported their assessment in routine clinical practice. Conventional methods for assessing FLT3-ITD status and allele burden have been primarily limited to PCR fragment size analysis because of the inherent difficulty in detecting large ITD variants by next-generation sequencing (NGS). In this study, we assess the performance of publicly available bioinformatic tools for the detection and quantification of FLT3-ITDs in clinical hybridization-capture NGS data. We found that FLT3_ITD_ext had the highest overall accuracy for detecting FLT3-ITDs and was able to accurately quantify allele burden. Although all other tools evaluated were able to detect FLT3-ITDs reasonably well, allele burden was consistently underestimated. We were able to significantly improve quantification of FLT3-ITD allelic burden independent of the detection method by utilizing soft-clipped reads and/or ITD junctional sequences. In addition, we show that identifying mutant reads by previously identified junctional sequences further improves the sensitivity of detecting FLT3-ITDs in post-treatment samples. Our results demonstrate that FLT3-ITDs can be reliably detected in clinical NGS data using available bioinformatic tools. We further describe how accurate quantification of FLT3-ITD allele burden can be added on to existing clinical NGS pipelines for routine assessment of FLT3-ITD status in patients with acute myeloid leukemia.
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Affiliation(s)
- Jack K Tung
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Carlos J Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Tsoyu Chiang
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Henning Stehr
- Department of Pathology, Stanford University School of Medicine, Stanford, California.
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13
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Qin D. Molecular testing for acute myeloid leukemia. Cancer Biol Med 2021; 19:j.issn.2095-3941.2020.0734. [PMID: 34347394 PMCID: PMC8763005 DOI: 10.20892/j.issn.2095-3941.2020.0734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/02/2021] [Indexed: 11/11/2022] Open
Abstract
In the era of personalized medicine, information on molecular change at the gene level is important for patient care. Such information has been used for disease classification, diagnosis, prognosis, risk stratification, and treatment, which is especially important in cancer patient care. Many molecular tests exist and can be used to detect the molecular changes at gene level. These tests include, but are not limited to, karyotyping, endpoint polymerase chain reaction (PCR), real-time PCR, Sanger sequencing, pyrosequencing, next-generation sequencing, and so forth. How to use the right tests for the right patients at the right time is essential for optimal patient outcome. This review puts together some information on molecular testing for acute myeloid leukemia.
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Affiliation(s)
- Dahui Qin
- Moffitt Cancer Center, Tampa, FL 33612-9416, USA
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14
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Yuan D, He X, Han X, Yang C, Liu F, Zhang S, Luan H, Li R, He J, Duan X, Wang D, Zhou Q, Gao S, Niu B. Comprehensive review and evaluation of computational methods for identifying FLT3-internal tandem duplication in acute myeloid leukaemia. Brief Bioinform 2021; 22:6225087. [PMID: 33851200 DOI: 10.1093/bib/bbab099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/15/2021] [Accepted: 03/06/2021] [Indexed: 12/25/2022] Open
Abstract
Internal tandem duplication (ITD) of FMS-like tyrosine kinase 3 (FLT3-ITD) constitutes an independent indicator of poor prognosis in acute myeloid leukaemia (AML). AML with FLT3-ITD usually presents with poor treatment outcomes, high recurrence rate and short overall survival. Currently, polymerase chain reaction and capillary electrophoresis are widely adopted for the clinical detection of FLT3-ITD, whereas the length and mutation frequency of ITD are evaluated using fragment analysis. With the development of sequencing technology and the high incidence of FLT3-ITD mutations, a multitude of bioinformatics tools and pipelines have been developed to detect FLT3-ITD using next-generation sequencing data. However, systematic comparison and evaluation of the methods or software have not been performed. In this study, we provided a comprehensive review of the principles, functionality and limitations of the existing methods for detecting FLT3-ITD. We further compared the qualitative and quantitative detection capabilities of six representative tools using simulated and biological data. Our results will provide practical guidance for researchers and clinicians to select the appropriate FLT3-ITD detection tools and highlight the direction of future developments in this field. Availability: A Docker image with several programs pre-installed is available at https://github.com/niu-lab/docker-flt3-itd to facilitate the application of FLT3-ITD detection tools.
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Affiliation(s)
- Danyang Yuan
- Computer Network Information Center, Chinese Academy of Sciences. She is mainly engaged in leukaemia-related bioinformatics and cancer genomics research. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaoyu He
- Computer Network Information Center, Chinese Academy of Sciences. She is mainly engaged in research related to the cancer genome and construction of the Chinese Cancer Genome Database. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China
| | - Xinyin Han
- Computer Network Information Center, Chinese Academy of Sciences. He is mainly engaged in cancer genomics research focusing on the precise detection of tumour immunotherapy biomarkers. His affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China
| | - Chunyan Yang
- Vice Director of the Laboratory of ChosenMed Technology (Beijing) Co., Ltd. She is mainly engaged in research regarding solid tumours and haematologic malignancy using multiple approaches, including next-generation sequencing. Her affiliation is with ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Fei Liu
- bioinformatics analysis engineer of ChosenMed Technology (Beijing) Co., Ltd. She is mainly engaged in the collection of biological information and analysis of genomic and cancer data or other biological information. Her affiliation is with ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Shuying Zhang
- Computer Network Information Center, Chinese Academy of Sciences. Her research mainly focuses on the cancer genome and bioinformatics. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China
| | - Haijing Luan
- Computer Network Information Center, Chinese Academy of Sciences. She is mainly engaged in researching cancers of unknown primary sites (CUP) based on deep learning. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China
| | - Ruilin Li
- Computer Network Information Center, Chinese Academy of Sciences. Her research interests include high-performance computing and bioinformatics. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Jiayin He
- George Washington University. She is currently researching at the Computer Network Information Center, Chinese Academy of Sciences. Her research interests include biostatistics and computational statistics. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaohong Duan
- Laboratory of ChosenMed Technology (Beijing) Co., Ltd. She is mainly engaged in the research of solid tumours and haematologic malignancies using multiple approaches, including next-generation sequencing. Her affiliation is with ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Dongliang Wang
- Harbin Medical University. He is now the Chief Medical Officer of ChosenMed Technology (Beijing). His research mainly focuses on the mining and verification of molecular markers for tumour therapy. His affiliation is with ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Qiming Zhou
- CTO of ChosenMed Technology (Beijing) Co., Ltd. He is mainly engaged in the development of new molecular diagnostics technologies in genetic testing. His affiliation is with ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Sujun Gao
- Department of Haematology, The First Hospital of Jilin University. Her research mainly focuses on the experimental and clinical research of malignant haematological disorders and haematopoietic stem cell transplantation. Her affiliation is with Department of Haematology, The First Hospital of Jilin University, Changchun 130021, China
| | - Beifang Niu
- Computer Network Information Center, Chinese Academy of Sciences. His research interests include cancer genomics, metagenomics, and the development of computational tools for working with data from next-generation sequencing technologies. His affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China, ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
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15
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Xie Z, Nanaa A, Saliba AN, He R, Viswanatha D, Nguyen P, Jevremovic D, Greipp P, Salama ME, Gangat N, Alkhateeb HB, Tefferi A, Litzow M, Patnaik M, Shah M, Al-Kali A. Treatment outcome of clonal cytopenias of undetermined significance: a single-institution retrospective study. Blood Cancer J 2021; 11:43. [PMID: 33649321 PMCID: PMC7921651 DOI: 10.1038/s41408-021-00439-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 12/20/2022] Open
Affiliation(s)
- Zhuoer Xie
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Ahmad Nanaa
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | - Rong He
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Phuong Nguyen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Patricia Greipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Mohamad E Salama
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Mark Litzow
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | - Mithun Shah
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Aref Al-Kali
- Division of Hematology, Mayo Clinic, Rochester, MN, USA.
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16
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Tsai HK, Brackett DG, Szeto D, Frazier R, MacLeay A, Davineni P, Manning DK, Garcia E, Lindeman NI, Le LP, Lennerz JK, Gibson CJ, Lindsley RC, Kim AS, Nardi V. Targeted Informatics for Optimal Detection, Characterization, and Quantification of FLT3 Internal Tandem Duplications Across Multiple Next-Generation Sequencing Platforms. J Mol Diagn 2020; 22:1162-1178. [PMID: 32603763 PMCID: PMC7479488 DOI: 10.1016/j.jmoldx.2020.06.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/27/2020] [Accepted: 06/08/2020] [Indexed: 01/09/2023] Open
Abstract
Assessment of internal tandem duplications in FLT3 (FLT3-ITDs) and their allelic ratio (AR) is recommended by clinical guidelines for diagnostic workup of acute myeloid leukemia and traditionally performed through capillary electrophoresis (CE). Although significant progress has been made integrating FLT3-ITD detection within contemporary next-generation sequencing (NGS) panels, AR estimation is not routinely part of clinical NGS practice because of inherent biases and challenges. In this study, data from multiple NGS platforms—anchored multiplex PCR (AMP), amplicon [TruSeq Custom Amplicon (TSCA)], and hybrid-capture—were analyzed through a custom algorithm, including platform-specific measures of AR. Sensitivity and specificity of NGS for FLT3-ITD status relative to CE were 100% (42/42) and 99.4% (1076/1083), respectively, by AMP on an unselected cohort and 98.1% (53/54) and 100% (48/48), respectively, by TSCA on a selected cohort. Primer analysis identified criteria for ITDs to escape detection by TSCA, estimated to occur in approximately 9% of unselected ITDs. Allelic fractions under AMP or TSCA were highly correlated to CE, with linear regression slopes near 1 for ITDs not duplicating primers, and systematically underestimated for ITDs duplicating a primer. Bias was alleviated in AMP through simple adjustments. This article provides an approach for targeted computational FLT3-ITD analysis for NGS data from multiple platforms; AMP was found capable of near perfect sensitivity and specificity with relatively accurate estimates of ARs.
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Affiliation(s)
- Harrison K Tsai
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Diane G Brackett
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - David Szeto
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Ryan Frazier
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Allison MacLeay
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Phani Davineni
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Danielle K Manning
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Elizabeth Garcia
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Long P Le
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Christopher J Gibson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - R Coleman Lindsley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts.
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