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Zbieranski N, Insuasti-Beltran G. Analytical Validation of an Automated Semiconductor-Based Next-Generation Sequencing Assay for Detection of DNA and RNA Alterations in Myeloid Neoplasms. J Mol Diagn 2024; 26:29-36. [PMID: 37879438 DOI: 10.1016/j.jmoldx.2023.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/23/2023] [Accepted: 09/20/2023] [Indexed: 10/27/2023] Open
Abstract
Myeloid neoplasms are heterogeneous tumors derived from early hematopoietic progenitors. Most international guidelines, including the European LeukemiaNet 2022 update, recommend testing a comprehensive set of genes, most within a 3- to 5-day period for optimal treatment decisions. Next-generation sequencing gene panels are essential for identifying genetic alterations, risk stratification, and determining targeted therapies for myeloid malignancies. This study describes the analytical validation of the Oncomine Myeloid Assay GX v2 (Myeloid GX v2) in combination with the Ion Torrent Genexus System using commercial controls, 16 variant-negative samples, and 130 clinical samples of myeloid neoplasms. The Myeloid GX v2 panel detected single nucleotide variants (SNVs), insertions/deletions (indels) (allele frequency >5%), and gene fusions (minimum 11 fusion copies/μL) in synthetic controls with a sensitivity of 100%. Specificity for detection of SNVs, indels, or fusions in 16 variant-negative samples was 100%. Sensitivity for detection of SNVs, indels, and gene fusions in 130 clinical samples was 99%, 97%, and 100%, respectively. Overall precision was 100% for SNVs, 96% for indels, and 100% for fusions. The average turnaround time from nucleic acid extraction to results was 2 days. The Myeloid GX v2 panel is highly accurate and reproducible for the detection of SNVs, indels, and gene fusions in myeloid neoplasms. The ability to deliver clinically relevant results in a short time is key to providing personalized treatments.
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Affiliation(s)
- Nora Zbieranski
- Department of Pathology, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina
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Biernacki MA, Lok J, Black RG, Foster KA, Cummings C, Woodward KB, Monahan T, Oehler VG, Stirewalt DL, Wu D, Rongvaux A, Deeg HJ, Bleakley M. Discovery of U2AF1 neoantigens in myeloid neoplasms. J Immunother Cancer 2023; 11:e007490. [PMID: 38164756 PMCID: PMC10729103 DOI: 10.1136/jitc-2023-007490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND Myelodysplastic syndromes (MDS) arise from somatic mutations acquired in hematopoietic stem and progenitor cells, causing cytopenias and predisposing to transformation into secondary acute myeloid leukemia (sAML). Recurrent mutations in spliceosome genes, including U2AF1, are attractive therapeutic targets as they are prevalent in MDS and sAML, arise early in neoplastic cells, and are generally absent from normal cells, including normal hematopoietic cells. MDS and sAML are susceptible to T cell-mediated killing, and thus engineered T-cell immunotherapies hold promise for their treatment. We hypothesized that targeting spliceosome mutation-derived neoantigens with transgenic T-cell receptor (TCR) T cells would selectively eradicate malignant cells in MDS and sAML. METHODS We identified candidate neoantigen epitopes from recurrent protein-coding mutations in the spliceosome genes SRSF2 and U2AF1 using a multistep in silico process. Candidate epitopes predicted to bind human leukocyte antigen (HLA) class I, be processed and presented from the parent protein, and not to be subject to tolerance then underwent in vitro immunogenicity screening. CD8+ T cells recognizing immunogenic neoantigen epitopes were evaluated in in vitro assays to assess functional avidity, confirm the predicted HLA restriction, the potential for recognition of similar peptides, and the ability to kill neoplastic cells in an antigen-specific manner. Neoantigen-specific TCR were sequenced, cloned into lentiviral vectors, and transduced into third-party T cells after knock-out of endogenous TCR, then tested in vitro for specificity and ability to kill neoplastic myeloid cells presenting the neoantigen. The efficacy of neoantigen-specific T cells was evaluated in vivo in a murine cell line-derived xenograft model. RESULTS We identified two neoantigens created from a recurrent mutation in U2AF1, isolated CD8+ T cells specific for the neoantigens, and demonstrated that transferring their TCR to third-party CD8+ T cells is feasible and confers specificity for the U2AF1 neoantigens. Finally, we showed that these neoantigen-specific TCR-T cells do not recognize normal hematopoietic cells but efficiently kill malignant myeloid cells bearing the specific U2AF1 mutation, including primary cells, in vitro and in vivo. CONCLUSIONS These data serve as proof-of-concept for developing precision medicine approaches that use neoantigen-directed T-cell receptor-transduced T cells to treat MDS and sAML.
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MESH Headings
- Humans
- Mice
- Animals
- CD8-Positive T-Lymphocytes
- Splicing Factor U2AF/genetics
- Splicing Factor U2AF/metabolism
- Antigens, Neoplasm
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/therapy
- Leukemia, Myeloid, Acute/metabolism
- Epitopes/metabolism
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Affiliation(s)
- Melinda Ann Biernacki
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jessica Lok
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Ralph Graeme Black
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Kimberly A Foster
- Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Carrie Cummings
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Kyle B Woodward
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Tim Monahan
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Vivian G Oehler
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Derek L Stirewalt
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - David Wu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Anthony Rongvaux
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Hans Joachim Deeg
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Marie Bleakley
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
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Badar T, Vanegas YAM, Nanaa A, Foran JM, Al-Kali A, Mangaonkar A, Murthy H, Alkhateeb HB, Viswanatha D, He R, Shah M, Yi CA, Litzow MR, Gangat N, Tefferi A, Patnaik MM. U2AF1 pathogenic variants in myeloid neoplasms and precursor states: distribution of co-mutations and prognostic heterogeneity. Blood Cancer J 2023; 13:149. [PMID: 37735430 PMCID: PMC10514309 DOI: 10.1038/s41408-023-00922-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/22/2023] [Accepted: 09/06/2023] [Indexed: 09/23/2023] Open
Abstract
We have previously recognized the genotypic and prognostic heterogeneity of U2AF1 mutations (MT) in myelofibrosis (MF) and myelodysplastic syndromes (MDS). In the current study, we considered 179 U2AF1-mutated patients with clonal cytopenia of undetermined significance (CCUS; n = 22), MDS (n = 108), MDS/acute myeloid leukemia (AML; n = 18) and AML (n = 31). U2AF1 variants included S34 (60%), Q157 (35%), and others (5%): corresponding mutational frequencies were 45%, 55%, and 0% in CCUS; 57%, 39%, and 4% in MDS; 61%, 33%, and 6% in MDS/AML; and 55%, 35% and 10% in AML (P = 0.17, 0.36 and 0.09), respectively. Concurrent mutations included ASXL1 (37%), BCOR (19%), RUNX1 (14%), TET2 (15%), DNMT3A (10%), NRAS/KRAS (8%), TP53 (8%), JAK2 (5.5%) and SETBP1 (5%). The two most frequent U2AF1 MT were S34F (n = 97) and Q157P (n = 46); concurrent MT were more likely to be seen with the latter (91% vs 74%; P = 0.01) and abnormal karyotype with the former (70% vs 62%; P = 0.05). U2AF1 S34F MT clustered with BCOR (P = 0.04) and Q157P MT with ASXL1 (P = 0.01) and TP53 (P = 0.03). The median overall survival (OS) in months was significantly worse in AML (14.2) vs MDS/AML (27.3) vs MDS (33.7; P = 0.001); the latter had similar OS with CCUS (30.0). In morphologically high-risk disease (n = 49), defined by ≥10% blood or bone marrow blasts (i.e., AML or MDS/AML), median OS was 14.2 with Q157P vs 37.1 months in the presence of S34F (P = 0.008); transplant-adjusted multivariable analysis confirmed the detrimental impact of Q157P (P = 0.01) on survival and also identified JAK2 MT as an additional risk factor (P = 0.02). OS was favorably affected by allogeneic hematopoietic stem cell transplantation (HR: 0.16, 95% CI; 0.04-0.61, P = 0.007). The current study defines the prevalence and co-mutational profiles of U2AF1 pathogenic variants in AML, MDS/AML, MDS, and CCUS, and suggests prognostic heterogeneity in patients with ≥10% blasts.
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Affiliation(s)
- Talha Badar
- Division of Hematology-Oncology and Bone Marrow Transplant Program, Mayo Clinic, Jacksonville, FL, 32224, USA.
| | - Yenny A Moreno Vanegas
- Division of Hematology-Oncology and Bone Marrow Transplant Program, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Ahmad Nanaa
- Division of Hematology, Mayo Clinic, Rochester, MN, 55905, USA
- John H. Stroger, Jr. Hospital of Cook County, Chicago, IL, 60612, USA
| | - James M Foran
- Division of Hematology-Oncology and Bone Marrow Transplant Program, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Aref Al-Kali
- Division of Hematology, Mayo Clinic, Rochester, MN, 55905, USA
| | | | - Hemant Murthy
- Division of Hematology-Oncology and Bone Marrow Transplant Program, Mayo Clinic, Jacksonville, FL, 32224, USA
| | | | - David Viswanatha
- Division of Hematopathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Rong He
- Division of Hematopathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Mithun Shah
- Division of Hematology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Cecilia Arana Yi
- Department of Hematology Oncology, Mayo Clinic, Phoenix, AZ, USA
| | - Mark R Litzow
- Division of Hematology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Naseema Gangat
- Division of Hematology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Ayalew Tefferi
- Division of Hematology, Mayo Clinic, Rochester, MN, 55905, USA
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Li Y, Solis-Ruiz J, Yang F, Long N, Tong CH, Lacbawan FL, Racke FK, Press RD. NGS-defined measurable residual disease (MRD) after initial chemotherapy as a prognostic biomarker for acute myeloid leukemia. Blood Cancer J 2023; 13:59. [PMID: 37088803 PMCID: PMC10123056 DOI: 10.1038/s41408-023-00833-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/28/2023] [Accepted: 04/11/2023] [Indexed: 04/25/2023] Open
Abstract
Treated AML patients often have measurable residual disease (MRD) due to persisting low-level clones. This study assessed whether residual post-treatment somatic mutations, detected by NGS, were significantly prognostic for subsequent clinical outcomes. AML patients (n = 128) underwent both pre-and post-treatment testing with the same 42-gene MRD-validated NGS assay. After induction, 59 (46%) patients were mutation-negative (0.0024 VAF detection limit) and 69 (54%) had ≥1 persisting NGS-detectable mutation. Compared with NGS-negative patients, NGS-positive patients had shorter overall survival (17 months versus median not reached; P = 0.004; hazard ratio = 2.2 [95% CI: 1.3-3.7]) and a shorter time to relapse (14 months versus median not reached; P = 0.014; HR = 1.9 [95% CI: 1.1-3.1]). Among 95 patients with a complete morphologic remission (CR), 43 (45%) were MRD-positive by NGS and 52 (55%) were MRD-negative. These MRD-positive CR patients had a shorter overall survival (16.8 months versus median not reached; P = 0.013; HR = 2.1 [95% CI: 1.2-3.9]) than did the MRD-negative CR patients. Post-treatment persisting MRD positivity, defined by the same NGS-based test used at diagnosis, is thus a more sensitive biomarker for low-level leukemic clones compared to traditional non-molecular methods and is prognostic of subsequent relapse and death.
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Affiliation(s)
- Yonghong Li
- Quest Diagnostics, San Juan Capistrano, CA, USA
| | - Jose Solis-Ruiz
- Department of Pathology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Fei Yang
- Department of Pathology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Nicola Long
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | | | | | | | - Richard D Press
- Department of Pathology, Oregon Health & Science University, Portland, OR, USA.
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
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Jansko-Gadermeir B, Leisch M, Gassner FJ, Zaborsky N, Dillinger T, Hutter S, Risch A, Melchardt T, Egle A, Drost M, Larcher-Senn J, Greil R, Pleyer L. Myeloid NGS Analyses of Paired Samples from Bone Marrow and Peripheral Blood Yield Concordant Results: A Prospective Cohort Analysis of the AGMT Study Group. Cancers (Basel) 2023; 15:cancers15082305. [PMID: 37190237 DOI: 10.3390/cancers15082305] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Background: Next generation sequencing (NGS) has become indispensable for diagnosis, risk stratification, prognostication, and monitoring of response in patients with myeloid neoplasias. Guidelines require bone marrow evaluations for the above, which are often not performed outside of clinical trials, indicating a need for surrogate samples. Methods: Myeloid NGS analyses (40 genes and 29 fusion drivers) of 240 consecutive, non-selected, prospectively collected, paired bone marrow/peripheral blood samples were compared. Findings: Very strong correlation (r = 0.91, p < 0.0001), high concordance (99.6%), sensitivity (98.8%), specificity (99.9%), positive predictive value (99.8%), and negative predictive value (99.6%) between NGS analyses of paired samples was observed. A total of 9/1321 (0.68%) detected mutations were discordant, 8 of which had a variant allele frequency (VAF) ≤ 3.7%. VAFs between peripheral blood and bone marrow samples were very strongly correlated in the total cohort (r = 0.93, p = 0.0001) and in subgroups without circulating blasts (r = 0.92, p < 0.0001) or with neutropenia (r = 0.88, p < 0.0001). There was a weak correlation between the VAF of a detected mutation and the blast count in either the peripheral blood (r = 0.19) or the bone marrow (r = 0.11). Interpretation: Peripheral blood samples can be used to molecularly classify and monitor myeloid neoplasms via NGS without loss of sensitivity/specificity, even in the absence of circulating blasts or in neutropenic patients.
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Affiliation(s)
- Bettina Jansko-Gadermeir
- Salzburg Cancer Research Institute (SCRI), Center for Clinical Cancer and Immunology Trials (CCCIT), 5020 Salzburg, Austria
- 3rd Medical Department with Hematology, Medical Oncology, Hemostaseology, Rheumatology and Infectiology, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- Laboratory of Immunological and Molecular Cancer Research (LIMCR), 5020 Salzburg, Austria
- Laboratory for Molecular Cytology (MZL), 5020 Salzburg, Austria
- Department of Biosciences and Medical Biology, Allergy-Cancer-BioNano Research Centre, University of Salzburg, 5020 Salzburg, Austria
| | - Michael Leisch
- Salzburg Cancer Research Institute (SCRI), Center for Clinical Cancer and Immunology Trials (CCCIT), 5020 Salzburg, Austria
- 3rd Medical Department with Hematology, Medical Oncology, Hemostaseology, Rheumatology and Infectiology, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- Austrian Group for Medical Tumor Therapy (AGMT) Study Group, 1180 Vienna, Austria
| | - Franz J Gassner
- Salzburg Cancer Research Institute (SCRI), Center for Clinical Cancer and Immunology Trials (CCCIT), 5020 Salzburg, Austria
- 3rd Medical Department with Hematology, Medical Oncology, Hemostaseology, Rheumatology and Infectiology, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- Laboratory of Immunological and Molecular Cancer Research (LIMCR), 5020 Salzburg, Austria
| | - Nadja Zaborsky
- Salzburg Cancer Research Institute (SCRI), Center for Clinical Cancer and Immunology Trials (CCCIT), 5020 Salzburg, Austria
- 3rd Medical Department with Hematology, Medical Oncology, Hemostaseology, Rheumatology and Infectiology, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- Laboratory of Immunological and Molecular Cancer Research (LIMCR), 5020 Salzburg, Austria
| | - Thomas Dillinger
- 3rd Medical Department with Hematology, Medical Oncology, Hemostaseology, Rheumatology and Infectiology, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Laboratory for Molecular Cytology (MZL), 5020 Salzburg, Austria
| | - Sonja Hutter
- 3rd Medical Department with Hematology, Medical Oncology, Hemostaseology, Rheumatology and Infectiology, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Laboratory for Molecular Cytology (MZL), 5020 Salzburg, Austria
| | - Angela Risch
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- Department of Biosciences and Medical Biology, Allergy-Cancer-BioNano Research Centre, University of Salzburg, 5020 Salzburg, Austria
| | - Thomas Melchardt
- Salzburg Cancer Research Institute (SCRI), Center for Clinical Cancer and Immunology Trials (CCCIT), 5020 Salzburg, Austria
- 3rd Medical Department with Hematology, Medical Oncology, Hemostaseology, Rheumatology and Infectiology, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- Austrian Group for Medical Tumor Therapy (AGMT) Study Group, 1180 Vienna, Austria
| | - Alexander Egle
- Salzburg Cancer Research Institute (SCRI), Center for Clinical Cancer and Immunology Trials (CCCIT), 5020 Salzburg, Austria
- 3rd Medical Department with Hematology, Medical Oncology, Hemostaseology, Rheumatology and Infectiology, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- Laboratory of Immunological and Molecular Cancer Research (LIMCR), 5020 Salzburg, Austria
- Austrian Group for Medical Tumor Therapy (AGMT) Study Group, 1180 Vienna, Austria
| | - Manuel Drost
- Assign Data Management and Biostatistics GmbH, 6020 Innsbruck, Austria
| | | | - Richard Greil
- Salzburg Cancer Research Institute (SCRI), Center for Clinical Cancer and Immunology Trials (CCCIT), 5020 Salzburg, Austria
- 3rd Medical Department with Hematology, Medical Oncology, Hemostaseology, Rheumatology and Infectiology, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- Laboratory of Immunological and Molecular Cancer Research (LIMCR), 5020 Salzburg, Austria
- Laboratory for Molecular Cytology (MZL), 5020 Salzburg, Austria
- Austrian Group for Medical Tumor Therapy (AGMT) Study Group, 1180 Vienna, Austria
| | - Lisa Pleyer
- Salzburg Cancer Research Institute (SCRI), Center for Clinical Cancer and Immunology Trials (CCCIT), 5020 Salzburg, Austria
- 3rd Medical Department with Hematology, Medical Oncology, Hemostaseology, Rheumatology and Infectiology, Oncologic Center, Paracelsus Medical University, 5020 Salzburg, Austria
- Cancer Cluster Salzburg (CCS), 5020 Salzburg, Austria
- Laboratory of Immunological and Molecular Cancer Research (LIMCR), 5020 Salzburg, Austria
- Laboratory for Molecular Cytology (MZL), 5020 Salzburg, Austria
- Austrian Group for Medical Tumor Therapy (AGMT) Study Group, 1180 Vienna, Austria
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Yang F, Akkari Y, Fan G, Olson S, Moore S. A novel heptasomy 21 associated with complete loss of heterozygosity and loss of function RUNX1 mutation in acute myeloid leukemia. Cancer Genet 2022; 266-267:69-73. [DOI: 10.1016/j.cancergen.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 06/07/2022] [Accepted: 07/01/2022] [Indexed: 11/17/2022]
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Newell LF, Dunlap J, Gatter K, Bagby GC, Press RD, Cook RJ, Fletcher L, Leonard JT, Leong KM, Bubalo JS, Olyaei A, Deloughery TG, Maziarz RT, Maynard E, Orloff SL, Enestvedt CK. Graft-versus-host disease after liver transplantation is associated with bone marrow failure, hemophagocytosis, and DNMT3A mutations. Am J Transplant 2021; 21:3894-3906. [PMID: 33961341 DOI: 10.1111/ajt.16635] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/16/2021] [Accepted: 04/30/2021] [Indexed: 01/25/2023]
Abstract
Graft-versus-host disease after liver transplantation (LT-GVHD) is rare, frequently fatal, and associated with bone marrow failure (BMF), cytopenias, and hyperferritinemia. Given hyperferritinemia and cytopenias are present in hemophagocytic lymphohistiocytosis (HLH), and somatic mutations in hematopoietic cells are associated with hyperinflammatory responses (clonal hematopoiesis of indeterminate potential, CHIP), we identified the frequency of hemophagocytosis and CHIP mutations in LT-GVHD. We reviewed bone marrow aspirates and biopsies, quantified blood/marrow chimerism, and performed next-generation sequencing (NGS) with a targeted panel of genes relevant to myeloid malignancies, CHIP, and BMF. In all, 12 marrows were reviewed from 9 LT-GVHD patients. In all, 10 aspirates were evaluable for hemophagocytosis; 7 had adequate DNA for NGS. NGS was also performed on marrow from an LT cohort (n = 6) without GVHD. Nine of 10 aspirates in LT-GVHD patients showed increased hemophagocytosis. Five (71%) of 7 with LT-GVHD had DNMT3A mutations; only 1 of 6 in the non-GVHD LT cohort demonstrated DNMT3A mutation (p = .04). Only 1 LT-GVHD patient survived. BMF with HLH features was associated with poor hematopoietic recovery, and DNMT3A mutations were over-represented, in LT-GVHD patients. Identification of HLH features may guide prognosis and therapeutics. Further studies are needed to clarify the origin and impact of CHIP mutations on the hyperinflammatory state.
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Affiliation(s)
- Laura F Newell
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon, USA
| | - Jennifer Dunlap
- Department of Pathology, Oregon Health & Science University, Portland, Oregon, USA
| | - Ken Gatter
- Department of Pathology, Oregon Health & Science University, Portland, Oregon, USA
| | - Grover C Bagby
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon, USA
| | - Richard D Press
- Department of Pathology, Oregon Health & Science University, Portland, Oregon, USA
| | - Rachel J Cook
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon, USA
| | - Luke Fletcher
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon, USA
| | - Jessica T Leonard
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon, USA
| | - Kelli M Leong
- Department of Pharmacy, Oregon Health & Science University, Portland, Oregon, USA
| | - Joseph S Bubalo
- Department of Pharmacy, Oregon Health & Science University, Portland, Oregon, USA
| | - Ali Olyaei
- Division of Nephrology and Hypertension, Oregon Health & Science University, Portland, Oregon, USA
| | - Thomas G Deloughery
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon, USA
| | - Richard T Maziarz
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon, USA
| | - Erin Maynard
- Department of Surgery, Division of Abdominal Organ Transplantation, Oregon Health & Science University, Portland, Oregon, USA
| | - Susan L Orloff
- Department of Surgery, Division of Abdominal Organ Transplantation, Oregon Health & Science University, Portland, Oregon, USA
| | - C Kristian Enestvedt
- Department of Surgery, Division of Abdominal Organ Transplantation, Oregon Health & Science University, Portland, Oregon, USA
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8
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Park J, Kim HS, Lee JM, Jung J, Kang D, Choi H, Lee GD, Son J, Park S, Cho BS, Kim HJ, Kim S, Lee JW, Chung NG, Cho B, Zhang H, Khazanov NA, Choi J, Jung JW, Kim Y, Kim M. Analytical and Potential Clinical Performance of Oncomine Myeloid Research Assay for Myeloid Neoplasms. Mol Diagn Ther 2021; 24:579-592. [PMID: 32676933 DOI: 10.1007/s40291-020-00484-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Next-generation sequencing (NGS) panels have recently been introduced to efficiently detect genetic variations in hematologic malignancies. OBJECTIVES Our aim was to evaluate the performance of the commercialized Oncomine™ myeloid research assay (OMA) for myeloid neoplasms. METHODS Certified reference materials and clinical research samples were used, including 60 genomic DNA and 56 RNA samples. NGS was performed using OMA, which enables the interrogation of 40 target genes, 29 gene fusions, and five expression target genes with five expression control genes by the Ion S5 XL Sequencer. The analyzed data were compared with clinical data using karyotyping, reverse transcription polymerase chain reaction (PCR), fluorescence in situ hybridization, Sanger sequencing, customized NGS panel, and fragment analysis. RESULTS All targets of reference materials were detected except three (two ASXL1 and one CEBPA) mutations, which we had not expected OMA to detect. In clinical search samples, OMA satisfactorily identified DNA variants, including 90 single nucleotide variants (SNVs), 48 small insertions and deletions (indels), and eight FLT3 internal tandem duplications (ITDs) (Kappa agreement 0.938). The variant allele frequencies of SNVs and indels measured by OMA correlated well with clinical data, whereas those of FLT3-ITDs were significantly lower than with fragment analysis (P = 0.008). Together, OMA showed strong ability to identify RNA gene fusions (Kappa agreement 0.961), except one RUNX1-MECOM. The MECOM gene was highly expressed in all five samples with MECOM-associated rearrangements, including inv(3), t(3;3), and t(3;21). CONCLUSION OMA revealed excellent analytical and potential clinical performance and could be a good replacement for conventional molecular tests.
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Affiliation(s)
- Joonhong Park
- Department of Laboratory Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hoon Seok Kim
- Department of Laboratory Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jong-Mi Lee
- Department of Laboratory Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jin Jung
- Department of Laboratory Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Dain Kang
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hayoung Choi
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Gun Dong Lee
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jungok Son
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Silvia Park
- Division of Acute Leukemia, Department of Hematology, Catholic Hematology Hospital, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Byung-Sik Cho
- Division of Acute Leukemia, Department of Hematology, Catholic Hematology Hospital, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hee-Je Kim
- Division of Acute Leukemia, Department of Hematology, Catholic Hematology Hospital, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seongkoo Kim
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jae Wook Lee
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Nack-Gyun Chung
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Bin Cho
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hua Zhang
- Thermo Fisher Scientific, Waltham, MA, USA
| | | | - Jongpill Choi
- Thermo Fisher Scientific Solutions, Seoul, Republic of Korea
| | - Jae-Won Jung
- Thermo Fisher Scientific Solutions, Seoul, Republic of Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea.
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
| | - Myungshin Kim
- Department of Laboratory Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea.
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
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9
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Ibrar W, Zhang W, Cox JL, Cushman-Vokoun A, Fu K, Greiner TC, Yuan J. The utility of a myeloid mutation panel for the diagnosis of myelodysplastic syndrome and myelodysplastic/myeloproliferative neoplasm. Int J Lab Hematol 2021; 43:1501-1509. [PMID: 34270867 DOI: 10.1111/ijlh.13659] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/03/2021] [Accepted: 06/29/2021] [Indexed: 11/29/2022]
Abstract
INTRODUCTION The diagnosis of myelodysplastic syndromes (MDS) and myelodysplastic/myeloproliferative neoplasms (MDS/MPN) is based on morphology and cytogenetics/FISH findings per 2017 WHO classification. With rare exceptions, somatic mutations have not been incorporated as the diagnostic criteria. METHODS We analyzed the utility of mutational analysis with a targeted 54-gene or 40-gene next-generation sequencing (NGS) panel in the diagnosis of MDS and MDS/MPN. RESULTS We retrospectively collected 92 patients who presented with unexplained cytopenia with or without cytosis, including 32 low-grade MDS (MDS-L), 18 high-grade MDS (MDS-H), 5 therapy-related MDS (MDS-TR), 19 MDS/MPN, and 18 negative cases. Of 92 patients, 197 somatic mutations involving 38 genes were detected and had variant allele frequency (VAF) ranging from 3% to 99%. The most common mutated genes were TET2, ASXL1, RUNX1, TP53, SRSF2, and SF3B1. MDS-L, MDS-H, MDS-TR, and MDS/MPN showed an average number of somatic mutations with a mean VAF of 1.9/33%, 2.6/30%, 2/36%, and 4/41%, respectively. SF3B1 mutations were exclusively observed in MDS-L and MDS/MPN. TP53 gene mutations were more frequently seen in MDS-H and MDS-TR. Among 34 patients with a diagnosis of MDS or MDS/MPN with normal cytogenetics, 31 patients (91%) had at least 1 mutation and 24 patients (71%) had ≥2 mutations with ≥10% VAF. CONCLUSION A myeloid mutational panel provides additional evidence of clonality besides cytogenetics/FISH studies in the diagnosis of cytopenia with or without cytosis. Two or more mutations with ≥10% VAF highly predicts MDS and MDS/MPN with a positive predictive value of 100%.
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Affiliation(s)
- Warda Ibrar
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Weiwei Zhang
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Jesse Lee Cox
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Allison Cushman-Vokoun
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Kai Fu
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Timothy C Greiner
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ji Yuan
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
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Chia YC, Islam MA, Hider P, Woon PY, Johan MF, Hassan R, Ramli M. The Prevalence of TET2 Gene Mutations in Patients with BCR- ABL-Negative Myeloproliferative Neoplasms (MPN): A Systematic Review and Meta-Analysis. Cancers (Basel) 2021; 13:3078. [PMID: 34203097 PMCID: PMC8235080 DOI: 10.3390/cancers13123078] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/13/2021] [Accepted: 06/17/2021] [Indexed: 12/19/2022] Open
Abstract
Multiple recurrent somatic mutations have recently been identified in association with myeloproliferative neoplasms (MPN). This meta-analysis aims to assess the pooled prevalence of TET2 gene mutations among patients with MPN. Six databases (PubMed, Scopus, ScienceDirect, Google Scholar, Web of Science and Embase) were searched for relevant studies from inception till September 2020, without language restrictions. The eligibility criteria included BCR-ABL-negative MPN adults with TET2 gene mutations. A random-effects model was used to estimate the pooled prevalence with 95% confidence intervals (CIs). Subgroup analyses explored results among different continents and countries, WHO diagnostic criteria, screening methods and types of MF. Quality assessment was undertaken using the Joanna Briggs Institute critical appraisal tool. The study was registered with PROSPERO (CRD42020212223). Thirty-five studies were included (n = 5121, 47.1% female). Overall, the pooled prevalence of TET2 gene mutations in MPN patients was 15.5% (95% CI: 12.1-19.0%, I2 = 94%). Regional differences explained a substantial amount of heterogeneity. The prevalence of TET2 gene mutations among the three subtypes PV, ET and MF were 16.8%, 9.8% and 15.7%, respectively. The quality of the included studies was determined to be moderate-high among 83% of the included studies. Among patients with BCR-ABL-negative MPN, the overall prevalence of TET2 gene mutations was 15.5%.
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Affiliation(s)
- Yuh Cai Chia
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (Y.C.C.); (M.F.J.); (R.H.)
| | - Md Asiful Islam
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (Y.C.C.); (M.F.J.); (R.H.)
| | - Phil Hider
- Department of Population Health, University of Otago, Christchurch 8140, New Zealand;
| | - Peng Yeong Woon
- Department of Molecular Biology and Human Genetics, Tzu Chi University, Hualien 97004, Taiwan;
| | - Muhammad Farid Johan
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (Y.C.C.); (M.F.J.); (R.H.)
| | - Rosline Hassan
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (Y.C.C.); (M.F.J.); (R.H.)
| | - Marini Ramli
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (Y.C.C.); (M.F.J.); (R.H.)
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11
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Lachowiez CA, Loghavi S, Furudate K, Montalban-Bravo G, Maiti A, Kadia T, Daver N, Borthakur G, Pemmaraju N, Sasaki K, Alvarado Y, Yilmaz M, Short NJ, Chien K, Ohanian M, Pierce S, Patel KP, Jabbour E, Ravandi F, Kantarjian HM, Garcia-Manero G, Takahashi K, Konopleva MY, DiNardo CD. Impact of splicing mutations in acute myeloid leukemia treated with hypomethylating agents combined with venetoclax. Blood Adv 2021; 5:2173-83. [PMID: 33885753 DOI: 10.1182/bloodadvances.2020004173] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/17/2021] [Indexed: 01/05/2023] Open
Abstract
Spliceosome mutations (SRSF2, SF3B1, U2AF1, ZRSR2), are encountered in ∼50% of secondary acute myeloid leukemia cases (sAML) and define a molecular subgroup with outcomes similar to sAML in de novo AML patients treated with intensive chemotherapy. Outcomes in patients with spliceosome mutations treated with hypomethylating agents in combination with venetoclax (HMA+VEN) remains unknown. The primary objective was to compare outcomes in patients with spliceosome mutations vs wild-type patients treated with HMA+VEN. Secondary objectives included analysis of the mutational landscape of the spliceosome cohort and assessing the impact of co-occurring mutations. We performed a retrospective cohort analysis of patients treated with HMA+VEN-based regimens at The University of Texas MD Anderson Cancer Center. A total of 119 patients (spliceosome mutated n = 39 [SRSF2, n = 24; SF3B1, n = 8; U2AF1, n = 7]; wild-type, n = 80) were included. Similar responses were observed between spliceosome and wild-type cohorts for composite complete response (CRc; 79% vs 75%, P = .65), and measurable residual disease-negative CRc (48% vs 60%, P = .34). Median overall survival for spliceosome vs wild-type patients was 35 vs 14 months (P = .58), and was not reached; 35 months and 8 months for patients with SRSF2, SF3B1, and U2AF1 mutations, respectively. IDH2 mutations were enriched in patients with SRSF2 mutations and associated with favorable outcomes (1- and 2-year overall survival [OS] of 100% and 88%). RAS mutations were enriched in patients with U2AF1 mutations and associated with inferior outcomes (median OS, 8 months). Comparable outcomes were observed between patients with vs without spliceosome mutations treated with HMA+VEN regimens, with specific co-mutation pairs demonstrating favorable outcomes.
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12
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Newell LF, Williams T, Liu J, Yu Y, Chen Y, Booth GC, Knight RJ, Goslee KR, Cook RJ, Leonard J, Meyers G, Traer E, Press RD, Fan G, Wang Y, Raess PW, Maziarz RT, Dunlap J. Engrafted Donor-Derived Clonal Hematopoiesis after Allogenic Hematopoietic Cell Transplantation is Associated with Chronic Graft-versus-Host Disease Requiring Immunosuppressive Therapy, but no Adverse Impact on Overall Survival or Relapse. Transplant Cell Ther 2021; 27:662.e1-662.e9. [PMID: 33901720 DOI: 10.1016/j.jtct.2021.04.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 11/19/2022]
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) is an age-associated condition defined by the presence of a somatic mutation in a leukemia-associated gene in individuals who otherwise have no evidence of a hematologic malignancy. In the allogeneic hematopoietic cell transplantation (HCT) setting, clonal hematopoiesis (CH) mutations present in donor stem cells can be transferred to recipients at the time of HCT. Given that the consequences of donor-derived CH in HCT recipients are not entirely clear, we sought to investigate clinical outcomes in patients with engrafted donor-derived CH using a matched cohort analysis of both related and unrelated donors. Of 209 patients with next-generation sequencing performed before and after HCT, donor-derived CH mutations were detected in 15 (5.2%). DNMT3A was the most commonly mutated gene (9 of 15; 60%); mutations in SF3B1, CSF3R, STAT3, CBLB, TET2, and ASXL1 were also identified. Donor-derived CH was not associated with delayed neutrophil or platelet engraftment, and there was no impact on conversion to full donor chimerism. No patients with donor-derived CH experienced relapse, in contrast to 15.6% (7 of 45) in the matched control cohort without CH (P = .176). Donor-derived CH was not associated with worse overall survival; however, patients with donor-derived CH were more likely to develop chronic graft-versus-host disease (GVHD) necessitating systemic immunosuppressive therapy (IST) (P = .045) and less likely to discontinue IST (P = .03) compared with controls without donor-derived CH. We conclude that donor-derived CH does not have an adverse impact on relapse, survival, or engraftment outcomes but may potentiate a graft-versus-leukemia effect, as reflected by increased chronic GVHD necessitating IST.
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Affiliation(s)
- Laura F Newell
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon
| | - Todd Williams
- Department of Pathology, Oregon Health & Science University, Portland, Oregon
| | - James Liu
- Department of Pathology, Oregon Health & Science University, Portland, Oregon
| | - Yun Yu
- Biostatistics Shared Resources, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Yiyi Chen
- Biostatistics Shared Resources, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Georgeann C Booth
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon
| | - Rebekah J Knight
- Cellular Therapy Laboratory, Hospital and Clinics, Oregon Health & Science University, Portland, Oregon
| | - Kelli R Goslee
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon
| | - Rachel J Cook
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon
| | - Jessica Leonard
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon
| | - Gabrielle Meyers
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon
| | - Elie Traer
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon
| | - Richard D Press
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon; Department of Pathology, Oregon Health & Science University, Portland, Oregon
| | - Guang Fan
- Department of Pathology, Oregon Health & Science University, Portland, Oregon
| | - Ying Wang
- Department of Pathology, Oregon Health & Science University, Portland, Oregon
| | - Philipp W Raess
- Department of Pathology, Oregon Health & Science University, Portland, Oregon
| | - Richard T Maziarz
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon
| | - Jennifer Dunlap
- Department of Pathology, Oregon Health & Science University, Portland, Oregon.
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13
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Atli EI, Gurkan H, Atli E, Kirkizlar HO, Yalcintepe S, Demir S, Demirci U, Eker D, Mail C, Kalkan R, Demir AM. The Importance of Targeted Next-Generation Sequencing Usage in Cytogenetically Normal Myeloid Malignancies. Mediterr J Hematol Infect Dis 2021; 13:e2021013. [PMID: 33489052 PMCID: PMC7813283 DOI: 10.4084/mjhid.2021.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/13/2020] [Indexed: 02/07/2023] Open
Abstract
Advanced diagnostic methods give an advantage for the identification of abnormalities in myeloid malignancies. Various researchers have shown the potential importance of genetic tests before the disease's onset and in remission. Large testing panels prevent false-negative results in myeloid malignancies. However, the critical question is how the results of conventional cytogenetic and molecular cytogenetic techniques can be merged with NGS technologies. In this paper, we drew an algorithm for the evaluation of myeloid malignancies. To evaluate genetic abnormalities, we performed cytogenetics, molecular cytogenetics, and NGS testing in myeloid malignancies. In this study, we analyzed 100 patients admitted to the Medical Genetics Laboratory with different myeloid malignancies. We highlighted the possible diagnostic algorithm for cytogenetically normal cases. We applied NGS 141 gene panel for cytogenetically normal patients, and we detected two or more pathogenic variations in 61 out of 100 patients (61%). NGS's pathogenic variation detection rate varies in disease groups: they were present in 85% of A.M.L. and 23% of M.D.S. Here, we identified 24 novel variations out of total pathogenic variations in myeloid malignancies. A total of 18 novel variations were identified in A.M.L., and 6 novel variations were identified in M.D.S. Despite long turnaround times, conventional techniques are still a golden standard for myeloid malignancies but sometimes cryptic gene fusions or complex abnormalities cannot be easily identified by conventional techniques. In these conditions, advanced technologies like NGS are highly recommended.
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Affiliation(s)
- Emine Ikbal Atli
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Hakan Gurkan
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Engin Atli
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Hakki Onur Kirkizlar
- Faculty of Medicine, Department of Hematology, Trakya University, Edirne, Turkey
| | - Sinem Yalcintepe
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Selma Demir
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Ufuk Demirci
- Faculty of Medicine, Department of Hematology, Trakya University, Edirne, Turkey
| | - Damla Eker
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Cisem Mail
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Rasime Kalkan
- Faculty of Medicine, Department of Medical Genetics, Near East University, Nicosia, Cyprus
| | - Ahmet Muzaffer Demir
- Faculty of Medicine, Department of Hematology, Trakya University, Edirne, Turkey
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Forghieri F, Nasillo V, Paolini A, Bettelli F, Pioli V, Giusti D, Gilioli A, Colasante C, Acquaviva G, Riva G, Barozzi P, Maffei R, Potenza L, Marasca R, Fozza C, Tagliafico E, Trenti T, Comoli P, Longo G, Luppi M. NPM1-Mutated Myeloid Neoplasms with <20% Blasts: A Really Distinct Clinico-Pathologic Entity? Int J Mol Sci 2020; 21:E8975. [PMID: 33255988 DOI: 10.3390/ijms21238975] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/19/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022] Open
Abstract
Nucleophosmin (NPM1) gene mutations rarely occur in non-acute myeloid neoplasms (MNs) with <20% blasts. Among nearly 10,000 patients investigated so far, molecular analyses documented NPM1 mutations in around 2% of myelodysplastic syndrome (MDS) cases, mainly belonging to MDS with excess of blasts, and 3% of myelodysplastic/myeloproliferative neoplasm (MDS/MPN) cases, prevalently classified as chronic myelomonocytic leukemia. These uncommon malignancies are associated with an aggressive clinical course, relatively rapid progression to overt acute myeloid leukemia (AML) and poor survival outcomes, raising controversies on their classification as distinct clinico-pathologic entities. Furthermore, fit patients with NPM1-mutated MNs with <20% blasts could benefit most from upfront intensive chemotherapy for AML rather than from moderate intensity MDS-directed therapies, although no firm conclusion can currently be drawn on best therapeutic approaches, due to the limited available data, obtained from small and mainly retrospective series. Caution is also suggested in definitely diagnosing NPM1-mutated MNs with blast count <20%, since NPM1-mutated AML cases frequently present dysplastic features and multilineage bone marrow cells showing abnormal cytoplasmic NPM1 protein delocalization by immunohistochemical staining, therefore belonging to NPM1-mutated clone regardless of blast morphology. Further prospective studies are warranted to definitely assess whether NPM1 mutations may become sufficient to diagnose AML, irrespective of blast percentage.
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Northrup V, Maybank A, Carson N, Rahmeh T. The Value of Next-Generation Sequencing in the Screening and Evaluation of Hematologic Neoplasms in Clinical Practice. Am J Clin Pathol 2020; 153:639-645. [PMID: 31875888 DOI: 10.1093/ajcp/aqz203] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVES The implementation of next-generation sequencing (NGS) in routine clinical hematology practice remains limited. We evaluate the clinical value of NGS in the screening, diagnosis, and follow-up in hematologic neoplasms. METHODS A targeted NGS panel was used to assess a total of 178 patients for questionable or previously diagnosed myeloid neoplasms. RESULTS Gene variants were identified in 53% of patients. Novel variants were identified in 29% of patients and variants of unknown significance in 34%. Bone marrow samples yielded a higher number of variants than in peripheral blood. NGS is a more sensitive test than conventional cytogenetics. In several cases, NGS played a key role in the screening, diagnostics, prognostic stratification, and the clinical follow-up of a wide variety of myeloid neoplasms. CONCLUSIONS NGS is an effective tool in the evaluation of suspected and confirmed hematologic neoplasms and could become part of the routine workup of patients.
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Affiliation(s)
- Victoria Northrup
- Dalhousie Medicine New Brunswick, Saint John, Canada
- Departments of Laboratory Medicine, Saint John Regional Hospital, Saint John, Canada
- Research Services, Saint John Regional Hospital, Saint John, Canada
| | | | - Nancy Carson
- Departments of Laboratory Medicine, Saint John Regional Hospital, Saint John, Canada
| | - Tarek Rahmeh
- Dalhousie Medicine New Brunswick, Saint John, Canada
- Departments of Laboratory Medicine, Saint John Regional Hospital, Saint John, Canada
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Chen QC, Chen YH. Mutational profiling of myeloid neoplasms, focusing on AML with myelodysplasia-related changes (MRC) in comparison with MDS and AML without MRC. Leuk Lymphoma 2020; 61:1269-1271. [PMID: 32228284 DOI: 10.1080/10428194.2020.1742911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Qing Ching Chen
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yi-Hua Chen
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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Huang X, Wu J, Deng X, Xu X, Zhang X, Ma W, Hu T, Yang J, Guan M, Tang G. Mutation profiles of classic myeloproliferative neoplasms detected by a customized next-generation sequencing-based 50-gene panel. Journal of Bio-X Research 2020; 3:13-20. [DOI: 10.1097/jbr.0000000000000061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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Izevbaye I, Liang LY, Mather C, El-hallani S, Maglantay R, Saini L. Clinical Validation of a Myeloid Next-Generation Sequencing Panel for Single-Nucleotide Variants, Insertions/Deletions, and Fusion Genes. J Mol Diagn 2020; 22:208-19. [DOI: 10.1016/j.jmoldx.2019.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/11/2019] [Accepted: 10/07/2019] [Indexed: 02/06/2023] Open
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Yu J, Li Y, Li T, Li Y, Xing H, Sun H, Sun L, Wan D, Liu Y, Xie X, Jiang Z. Gene mutational analysis by NGS and its clinical significance in patients with myelodysplastic syndrome and acute myeloid leukemia. Exp Hematol Oncol 2020; 9:2. [PMID: 31921515 DOI: 10.1186/s40164-019-0158-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/26/2019] [Indexed: 01/05/2023] Open
Abstract
Background In this study, we retrospectively summarized the differences of molecular gene mutations between MDS and AML patients, as well as the young and older age groups of MDS and AML patients. We also analyzed the response of newly diagnosed AML patients to standard DA or IA induction chemotherapy and the relationship between the chemotherapy outcome and the frequency of different gene mutation abnormalities. Methods NGS assay covering 43 genes was studied in 93 de novo MDS and 325 non-M3 AML patients. Bone marrow samples from all patients underwent gene mutational analysis by NGS. Results At least one non-synonymous gene mutation was detected in 279 AML patients (85.8%) and 85 MDS patients (91.4%). Contrary to 59 years and younger AML patients, there was a significantly higher incidence of gene mutation in 60 years and older AML patients (2.37 vs 1.94, p = 0.034). Gene mutation incidence in 60 years and older MDS patients increased, but no statistical significance was present (1.95 vs 1.64, p = 0.216). AML patients had a significantly higher gene mutation incidence compared with MDS-MLD patients (2.02 vs 1.63, p = 0.046). Gene mutation incidence was higher in patients with MDS-EB1/EB2 compared with patients with MDS-MLD but there was no statistical significance present (2.14 vs 1.63, p = 0.081). AML patients had significantly higher incidences of CEBPA, FLT3-ITD, DNMT3A, NPM1 and IDH1/2 gene mutations (p = 0.0043, 0.000, 0.030962, 0.002752, and 0.000628, respectively) and a lower incidence of TET2 and U2AF1 gene mutations (p = 0.000004 and 0.000, respectively) compared with MDS patients. Among the individual genes in different age groups, there were significantly higher incidences of RUNX1, IDH2, TP53 and SF3B1 gene mutations (p = 0.0478, 0.0028, 0.0024 and 0.005, respectively) as well as a trend of higher ASXL gene mutation (p = 0.057) in 60 years and older AML patients compared to 59 years and younger patients. There was no statistically significant difference in MDS patients with the different age groups and among the individual genes. Between AML patients and MDS patients among the different gene functional groups, AML patients had a significantly higher incidence of transcriptional deregulation (27.4% vs 15.1%, p = 0.014963), activated signalling (36.3% vs 10.8%, p = 0.000002) related gene mutations as well as a significantly lower incidence of RNA spliceosome (6.15% vs 60.1%, p = 0.000) related gene mutations. Furthermore, among the patients who received either IA or DA regimen for induction chemotherapy, patients with IA regimen had a significantly better CR rate than those with DA regimen (76.6% vs 57.1%, p = 0.0228). Conclusions Different gene mutations had been found in majority of MDS and AML patients. MDS and AML patients had different gene mutation patterns. AML patients with fewer or no gene mutations had a better chance of achieving CR when treated with IA and DA regimen induction chemotherapy.
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Werstein B, Dunlap J, Cascio MJ, Ohgami RS, Fan G, Press R, Raess PW. Molecular Discordance between Myeloid Sarcomas and Concurrent Bone Marrows Occurs in Actionable Genes and Is Associated with Worse Overall Survival. J Mol Diagn 2019; 22:338-345. [PMID: 31866570 DOI: 10.1016/j.jmoldx.2019.11.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/24/2019] [Accepted: 11/18/2019] [Indexed: 12/27/2022] Open
Abstract
Myeloid sarcoma is a rare, architecture-effacing proliferation of myeloid blasts localized to an extramedullary site, with or without concurrent bone marrow involvement. Clonal heterogeneity results from acquisition of somatic mutations within different subclones of leukemic cells. It was hypothesized that clonal heterogeneity between myeloid sarcomas and concurrent bone marrow biopsies might be present, given their differing biological features and microenvironment. High-throughput sequencing of the largest series (n = 24) of paired myeloid sarcomas and bone marrow biopsies was performed. One third of myeloid sarcomas (8/24) showed discordant molecular profiles, and 75% (n = 6) of these cases had discordant mutations in genes with prognostic significance or molecularly targeted therapies. Patients with molecularly discordant myeloid sarcoma had significantly worse overall survival (median survival, 195 days versus not reached, hazard ratio, 3.3, P < 0.05). Further investigation into molecular discordance between myeloid sarcoma and concurrent bone marrow biopsies may help in understanding clonal evolution of myeloid neoplasms and mechanisms regulating extramedullary blast localization.
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Affiliation(s)
- Brian Werstein
- Department of Pathology, Oregon Health & Science University, Portland, Oregon
| | - Jennifer Dunlap
- Department of Pathology, Oregon Health & Science University, Portland, Oregon
| | - Michael J Cascio
- Department of Pathology, Oregon Health & Science University, Portland, Oregon
| | - Robert S Ohgami
- Department of Pathology, Stanford University, Stanford, California
| | - Guang Fan
- Department of Pathology, Oregon Health & Science University, Portland, Oregon
| | - Richard Press
- Department of Pathology, Oregon Health & Science University, Portland, Oregon; Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Philipp W Raess
- Department of Pathology, Oregon Health & Science University, Portland, Oregon.
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21
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Zheng G, Chen P, Pallavajjalla A, Haley L, Gondek L, Dezern A, Ling H, De Marchi F, Lin MT, Gocke C. The diagnostic utility of targeted gene panel sequencing in discriminating etiologies of cytopenia. Am J Hematol 2019; 94:1141-1148. [PMID: 31350794 PMCID: PMC9162094 DOI: 10.1002/ajh.25592] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 07/15/2019] [Accepted: 07/19/2019] [Indexed: 01/03/2023]
Abstract
The diagnostic utility of somatic mutations in the context of cytopenias is unclear: clonal hematopoiesis can be found in healthy individuals, patients with aplastic anemia (AA), clonal cytopenia of undetermined significance (CCUS) and myelodysplastic syndrome (MDS). We examined a cohort of 207 well-characterized cytopenic patients with a 640-gene next generation sequencing (NGS) panel and compared its diagnostic utility with a "virtual" 41 gene panel. The TET2, SF3B1, ASXL1, and TP53 were the most commonly mutated genes (frequency > 10%). Mutations in the 640-gene panel show high sensitivity (98.3%) but low specificity (47.6%) for diagnosis of MDS. Notably, mutations of splicing factors and genes in the RAS pathway are relatively specific to MDS. Furthermore, high variant allele frequency (VAF) predicts MDS: when the VAF is set at 20%, the positive predictive value (PPV) for MDS is 95.9%, with a specificity of 95.3%. The presence of two or more somatic mutations with ≥10% VAF showed a PPV of 95.2%. While the "virtual" 41-gene panel showed a mild decrease in sensitivity (95.7% vs 98.3%), 100% specificity was observed when either VAF was set at ≥20% (100% vs 95.3%), or two or more somatic mutations had VAFs ≥ 10%. Our study shows targeted gene panel sequencing improves the diagnostic approach and accuracy for unexplained cytopenia, with its high sensitivity and high PPV for MDS when applying VAF cutoffs. Furthermore, a 41-gene panel was shown to have at least comparable performance characteristics to the large 640-gene panel.
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Affiliation(s)
- Gang Zheng
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pathology and Laboratory Medicine, Mayo Clinic, Rochester, Minnesota
| | - Ping Chen
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Hematology, Jinan Central Hospital, Shandong University, Jinan, China
| | - Aparna Pallavajjalla
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lisa Haley
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lukasz Gondek
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Amy Dezern
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hua Ling
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Federico De Marchi
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ming-Tseh Lin
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christopher Gocke
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
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22
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Press RD, Eickelberg G, Froman A, Yang F, Stentz A, Flatley EM, Fan G, Lim JY, Meyers G, Maziarz RT, Cook RJ. Next-generation sequencing-defined minimal residual disease before stem cell transplantation predicts acute myeloid leukemia relapse. Am J Hematol 2019; 94:902-912. [PMID: 31124175 DOI: 10.1002/ajh.25514] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/16/2019] [Accepted: 05/21/2019] [Indexed: 12/19/2022]
Abstract
In acute myeloid leukemia (AML), the assessment of post-treatment minimal residual disease (MRD) may inform a more effective management approach. We investigated the prognostic utility of next-generation sequencing (NGS)-based MRD detection undertaken before hematopoietic stem cell transplantation (HSCT). Forty-two AML subjects underwent serial disease monitoring both by standard methods, and a targeted 42-gene NGS assay, able to detect leukemia-specific mutant alleles (with >0.5% VAF) (mean 5.1 samples per subject). The prognostic relevance of any persisting diagnostic mutation before transplant (≤27 days) was assessed during 22.1 months (median) of post-transplant follow-up. The sensitivity of the NGS assay (27 MRD-positive subjects) exceeded that of the non-molecular methods (morphology, FISH, and flow cytometry) (11 positive subjects). Only one of the 13 subjects who relapsed after HSCT was NGS MRD-negative (92% assay sensitivity). The cumulative incidence of post-transplant leukemic relapse was significantly higher in the pre-transplant NGS MRD-positive (vs MRD-negative) subjects (P = .014). After adjusting for TP53 mutation and transplant conditioning regimen, NGS MRD-positivity retained independent prognostic significance for leukemic relapse (subdistribution hazard ratio = 7.3; P = .05). The pre-transplant NGS MRD-positive subjects also had significantly shortened progression-free survival (P = .038), and marginally shortened overall survival (P = .068). In patients with AML undergoing HSCT, the pre-transplant persistence of NGS-defined MRD imparts a significant, sensitive, strong, and independent increased risk for subsequent leukemic relapse and death. Given that NGS can simultaneously detect multiple leukemia-associated mutations, it can be used in the majority of AML patients to monitor disease burdens and inform treatment decisions.
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Affiliation(s)
- Richard D. Press
- Department of PathologyOregon Health & Science University Portand Oregon
- Knight Cancer InstituteOregon Health & Science University Portand Oregon
| | - Garrett Eickelberg
- Knight Cancer InstituteOregon Health & Science University Portand Oregon
| | - Allison Froman
- Knight Cancer InstituteOregon Health & Science University Portand Oregon
| | - Fei Yang
- Department of PathologyOregon Health & Science University Portand Oregon
- Knight Cancer InstituteOregon Health & Science University Portand Oregon
| | - Alex Stentz
- Knight Cancer InstituteOregon Health & Science University Portand Oregon
- Division of Hematology‐OncologyOregon Health & Science University Portand Oregon
| | - Ellen M. Flatley
- Department of PathologyOregon Health & Science University Portand Oregon
| | - Guang Fan
- Department of PathologyOregon Health & Science University Portand Oregon
| | - Jeong Y. Lim
- Knight Cancer InstituteOregon Health & Science University Portand Oregon
| | - Gabrielle Meyers
- Knight Cancer InstituteOregon Health & Science University Portand Oregon
- Division of Hematology‐OncologyOregon Health & Science University Portand Oregon
| | - Richard T. Maziarz
- Knight Cancer InstituteOregon Health & Science University Portand Oregon
- Division of Hematology‐OncologyOregon Health & Science University Portand Oregon
| | - Rachel J. Cook
- Knight Cancer InstituteOregon Health & Science University Portand Oregon
- Division of Hematology‐OncologyOregon Health & Science University Portand Oregon
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Dunlap JB, Leonard J, Rosenberg M, Cook R, Press R, Fan G, Raess PW, Druker BJ, Traer E. The combination of NPM1, DNMT3A, and IDH1/2 mutations leads to inferior overall survival in AML. Am J Hematol 2019; 94:913-920. [PMID: 31145495 PMCID: PMC6771683 DOI: 10.1002/ajh.25517] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 05/21/2019] [Indexed: 12/19/2022]
Abstract
Acute myeloid leukemia (AML) is a genetically heterogeneous disease with a clinical course predicted by recurrent cytogenetic abnormalities and/or gene mutations. The NPM1 insertion mutations define the largest distinct genetic subset, ∼30% of AML, and is considered a favorable risk marker if there is no (or low allelic ratio) FLT3 internal tandem duplication (FLT3 ITD) mutation. However, ∼40% of patients with mutated NPM1 without FLT3 ITD still relapse, and the factors that drive relapse are still not fully understood. We used a next-generation sequencing panel to examine mutations at diagnosis; clearance of mutations after therapy, and gain/loss of mutations at relapse to prioritize mutations that contribute to relapse. Triple mutation of NPM1, DNMT3A and IDH1/2 showed a trend towards inferior overall survival in our discovery dataset, and was significantly associated with reduced OS in a large independent validation cohort. Analysis of relative variant allele frequencies suggests that early mutation and expansion of DNMT3A and IDH1/2 prior to acquisition of NPM1 mutation leads to increased risk of relapse. This subset of patients may benefit from allogeneic stem cell transplant or clinical trials with IDH inhibitors.
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Affiliation(s)
- Jennifer B. Dunlap
- Department of PathologyOregon Health & Science University Portland Oregon
| | - Jessica Leonard
- Knight Cancer InstituteOregon Health & Science University Portland Oregon
- Division of Hematology and Medical OncologyOregon Health & Science University Portland Oregon
| | - Mara Rosenberg
- Knight Cancer InstituteOregon Health & Science University Portland Oregon
| | - Rachel Cook
- Knight Cancer InstituteOregon Health & Science University Portland Oregon
- Division of Hematology and Medical OncologyOregon Health & Science University Portland Oregon
| | - Richard Press
- Department of PathologyOregon Health & Science University Portland Oregon
- Knight Cancer InstituteOregon Health & Science University Portland Oregon
| | - Guang Fan
- Department of PathologyOregon Health & Science University Portland Oregon
| | - Philipp W. Raess
- Department of PathologyOregon Health & Science University Portland Oregon
| | - Brian J. Druker
- Knight Cancer InstituteOregon Health & Science University Portland Oregon
- Division of Hematology and Medical OncologyOregon Health & Science University Portland Oregon
- Howard Hughes Medical Institute Chevy Chase Maryland
| | - Elie Traer
- Knight Cancer InstituteOregon Health & Science University Portland Oregon
- Division of Hematology and Medical OncologyOregon Health & Science University Portland Oregon
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24
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Levy MA, Santos S, Kerkhof J, Stuart A, Aref‐Eshghi E, Guo F, Hedley B, Wong H, Rauh M, Feilotter H, Berardi P, Semenuk L, Yang P, Knoll J, Ainsworth P, McLachlin CM, Chin‐Yee I, Kovacs M, Deotare U, Lazo‐Langner A, Hsia C, Keeney M, Xenocostas A, Howlett C, Lin H, Sadikovic B. Implementation of an NGS‐based sequencing and gene fusion panel for clinical screening of patients with suspected hematologic malignancies. Eur J Haematol 2019; 103:178-189. [DOI: 10.1111/ejh.13272] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/27/2019] [Accepted: 06/03/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Michael A. Levy
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Stephanie Santos
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Alan Stuart
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Erfan Aref‐Eshghi
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Fen Guo
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Ben Hedley
- Pathology and Laboratory Medicine London Health Sciences Centre London Ontario Canada
| | - Henry Wong
- Clinical Laboratories Kingston Health Sciences Centre Kingston Ontario Canada
| | - Michael Rauh
- Department of Pathology and Molecular Medicine Queen's University Kingston Ontario Canada
| | - Harriet Feilotter
- Department of Pathology and Molecular Medicine Queen's University Kingston Ontario Canada
- Molecular Diagnostics Kingston Health Sciences Centre Kingston Ontario Canada
| | - Philip Berardi
- University of Ottawa Ottawa Ontario Canada
- Eastern Ontario Regional Laboratory Association (EORLA) The Ottawa Hospital Ottawa Ontario Canada
| | - Laura Semenuk
- DNA Diagnostics & Cytogenetics Laboratory Kingston Health Sciences Centre Kingston Ontario Canada
| | - Ping Yang
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Cytogenetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Joan Knoll
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Peter Ainsworth
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
- Department of Biochemistry Western University London Ontario Canada
| | | | - Ian Chin‐Yee
- Hematology Division London Health Sciences Centre London Ontario Canada
| | - Michael Kovacs
- Hematology Division London Health Sciences Centre London Ontario Canada
| | - Uday Deotare
- Hematology Division London Health Sciences Centre London Ontario Canada
- Schulich School of Medicine and Dentistry Western University London Ontario Canada
- Departments of Medicine and Oncology London Health Sciences Centre London Ontario Canada
| | - Alejandro Lazo‐Langner
- Hematology Division London Health Sciences Centre London Ontario Canada
- Department of Epidemiology and Biostatistics Western University London Ontario Canada
| | - Cyrus Hsia
- Hematology Division London Health Sciences Centre London Ontario Canada
| | - Mike Keeney
- Hematology Division London Health Sciences Centre London Ontario Canada
| | - Anargyros Xenocostas
- Hematology Division London Health Sciences Centre London Ontario Canada
- Schulich School of Medicine and Dentistry Western University London Ontario Canada
| | - Christopher Howlett
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Hanxin Lin
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
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25
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Valent P, Orazi A, Savona MR, Patnaik MM, Onida F, van de Loosdrecht AA, Haase D, Haferlach T, Elena C, Pleyer L, Kern W, Pemovska T, Vladimer GI, Schanz J, Keller A, Lübbert M, Lion T, Sotlar K, Reiter A, De Witte T, Pfeilstöcker M, Geissler K, Padron E, Deininger M, Orfao A, Horny HP, Greenberg PL, Arber DA, Malcovati L, Bennett JM. Proposed diagnostic criteria for classical chronic myelomonocytic leukemia (CMML), CMML variants and pre-CMML conditions. Haematologica 2019; 104:1935-1949. [PMID: 31048353 PMCID: PMC6886439 DOI: 10.3324/haematol.2019.222059] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 04/29/2019] [Indexed: 12/15/2022] Open
Abstract
Chronic myelomonocytic leukemia (CMML) is a myeloid neoplasm characterized by dysplasia, abnormal production and accumulation of monocytic cells and an elevated risk of transforming into acute leukemia. Over the past two decades, our knowledge about the pathogenesis and molecular mechanisms in CMML has increased substantially. In parallel, better diagnostic criteria and therapeutic strategies have been developed. However, many questions remain regarding prognostication and optimal therapy. In addition, there is a need to define potential pre-phases of CMML and special CMML variants, and to separate these entities from each other and from conditions mimicking CMML. To address these unmet needs, an international consensus group met in a Working Conference in August 2018 and discussed open questions and issues around CMML, its variants, and pre-CMML conditions. The outcomes of this meeting are summarized herein and include diag nostic criteria and a proposed classification of pre-CMML conditions as well as refined minimal diagnostic criteria for classical CMML and special CMML variants, including oligomonocytic CMML and CMML associated with systemic mastocytosis. Moreover, we propose diagnostic standards and tools to distinguish between 'normal', pre-CMML and CMML entities. These criteria and standards should facilitate diagnostic and prognostic evaluations in daily practice and clinical studies in applied hematology.
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Affiliation(s)
- Peter Valent
- Department of Internal Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Vienna, Austria .,Ludwig Boltzmann Institute for Hematology & Oncology, Vienna, Austria
| | - Attilio Orazi
- Department of Pathology, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - Michael R Savona
- Department of Medicine, Vanderbilt University School of Medicine, Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Mrinal M Patnaik
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Francesco Onida
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Arjan A van de Loosdrecht
- Department of Hematology, Amsterdam UMC, location VU University Medical Center, Cancer Center Amsterdam, the Netherlands
| | - Detlef Haase
- Clinic of Hematology and Medical Oncology, University Medical Center Göttingen, Göttingen, Germany
| | | | - Chiara Elena
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Lisa Pleyer
- 3 Medical Department with Hematology and Medical Oncology, Hemostaseology, Rheumatology and Infectious Diseases, Paracelsus Medical University, Salzburg, Austria
| | | | - Tea Pemovska
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Gregory I Vladimer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Julie Schanz
- Clinic of Hematology and Medical Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Alexandra Keller
- Department of Internal Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Michael Lübbert
- Department of Medicine I, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Thomas Lion
- Children's Cancer Research Institute and Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Karl Sotlar
- Institute of Pathology, Paracelsus Medical University, Salzburg, Austria
| | - Andreas Reiter
- Department of Hematology and Oncology, University Hospital Mannheim, University of Heidelberg, Mannheim, Germany
| | - Theo De Witte
- Department of Tumor Immunology-Nijmegen Center for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Michael Pfeilstöcker
- Ludwig Boltzmann Institute for Hematology & Oncology, Vienna, Austria.,3 Medical Department, Hanusch Hospital, Vienna, Vienna, Austria
| | | | - Eric Padron
- Malignant Hematology Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Michael Deininger
- Huntsman Cancer Institute & Division of Hematology and Hematologic Malignancies, University of Utah, Salt Lake City, UT, USA
| | - Alberto Orfao
- Servicio Central de Citometría, Centro de Investigación del Cáncer (IBMCC, CSIC-USAL), CIBERONC and IBSAL, Universidad de Salamanca, Salamanca, Spain
| | - Hans-Peter Horny
- Institute of Pathology, Ludwig-Maximilians University, Munich, Germany
| | | | - Daniel A Arber
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - John M Bennett
- Department of Pathology, Hematopathology Unit and James P Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
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Abstract
The Precision Medicine Initiative (PMI) aims to change the way diseases are diagnosed and treated by taking into account a patient's genome, lifestyle, and environment. This type of research also uncovers potential biomarkers that can lead to the development of novel targeted therapies. Next-generation sequencing (NGS) is a new technology that facilitates collection of this genetic information by processing large amounts of DNA in an efficient and cost-effective way. NGS is particularly useful in oncology and has already begun to transform cancer management.
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27
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Moon Y, Kim MH, Kim HR, Ahn JY, Huh J, Huh JY, Han JH, Park JS, Cho SR. The 2016 WHO versus 2008 WHO Criteria for the Diagnosis of Chronic Myelomonocytic Leukemia. Ann Lab Med 2018; 38:481-483. [PMID: 29797820 PMCID: PMC5973924 DOI: 10.3343/alm.2018.38.5.481] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 12/12/2017] [Accepted: 04/27/2018] [Indexed: 11/19/2022] Open
Abstract
The 2016 WHO diagnostic criteria for chronic myelomonocytic leukemia (CMML) require both absolute and relative monocytosis (≥1×109/L and ≥10% of white blood cell counts) in peripheral blood. Moreover, myeloproliferative neoplasm (MPN) features in bone marrow and/or MPN-associated mutations tend to support MPN with monocytosis rather than CMML. We assessed the impact of the 2016 WHO criteria on CMML diagnosis, compared with the 2008 WHO criteria, through a retrospective review of the medical records of 38 CMML patients diagnosed according to the 2008 WHO classification. Application of the 2016 WHO criteria resulted in the exclusion of three (8%) patients who did not fulfill the relative monocytosis criterion and eight (21%) patients with an MPN-associated mutation. These 11 patients formed the 2016 WHO others group; the remaining 27 formed the 2016 WHO CMML group. The significant difference in the platelet count and monocyte percentage between the two groups indicated that the 2016 WHO criteria lead to a more homogenous and improved definition of CMML compared with the 2008 WHO criteria, which may have led to over-diagnosis of CMML. More widespread use of molecular tests and more sophisticated clinical and morphological evaluations are necessary to diagnose CMML accurately.
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Affiliation(s)
- Yeonsook Moon
- Department of Laboratory Medicine, Inha University School of Medicine, Incheon, Korea
| | - Mi Hyang Kim
- Department of Laboratory Medicine, Kosin University College of Medicine, Busan, Korea
| | - Hye Ryoun Kim
- Department of Laboratory Medicine, Chung-Ang University College of Medicine, Seoul, Korea
| | - Jeong Yeal Ahn
- Department of Laboratory Medicine, Gachon University Gil Hospital, Incheon, Korea
| | - Jungwon Huh
- Department of Laboratory Medicine, College of Medicine, Ewha Womans University, Seoul, Korea
| | - Ji Young Huh
- Department of Laboratory Medicine, CHA Bundang Medical Center, CHA University, Seongnam, Korea
| | - Jae Ho Han
- Department of Pathology, Ajou University School of Medicine, Suwon, Korea
| | - Joon Seong Park
- Department of Hematology-Oncology, Ajou University School of Medicine, Suwon, Korea
| | - Sung Ran Cho
- Department of Laboratory Medicine, Ajou University School of Medicine, Suwon, Korea.
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28
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Ma J, Dunlap J, Paliga A, Traer E, Press R, Shen L, Fan G. DNMT3A co-mutation is required for FLT3-ITD as an adverse prognostic indicator in intermediate-risk cytogenetic group AML. Leuk Lymphoma 2017; 59:1938-1948. [PMID: 29165010 DOI: 10.1080/10428194.2017.1397659] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
This single institution cohort study of 132 AML patients investigated the clinical implications of co-mutations detected with a 42-gene NGS panel. In the intermediate-risk cytogenetic group, FLT3-ITD is an adverse prognostic indicator only in the presence of a DNMT3A co-mutation, regardless of NPM1 mutation status. In the absence of a concomitant DNMT3A mutation, there was no significant difference in overall survival between FLT3-ITD positive and FLT3-ITD negative patients. Furthermore, mutation analysis on post-induction specimens showed that residual FLT3-ITD and/or DNMT3A mutations were associated with a high frequency of therapy resistance or relapse in AML. While FLT3-ITD positive patients are currently considered high risk, incorporation of DNMT3A mutation status may be needed to refine prognostication and guide clinical management in AML. Multi-gene mutation testing is essential to provide novel insights related to diagnostic and prognostic information.
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Affiliation(s)
- Juan Ma
- a Department of Clinical Laboratory , Xinhua Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai , PR China
| | - Jennifer Dunlap
- b Department of Pathology and Laboratory Medicine , Oregon Health & Science University , Portland , OR , USA
| | | | - Elie Traer
- d Division of Hematology & Medical Oncology, Knight Cancer Institute , Oregon Health & Science University , Portland , OR , USA
| | - Richard Press
- b Department of Pathology and Laboratory Medicine , Oregon Health & Science University , Portland , OR , USA
| | - Lisong Shen
- a Department of Clinical Laboratory , Xinhua Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai , PR China
| | - Guang Fan
- b Department of Pathology and Laboratory Medicine , Oregon Health & Science University , Portland , OR , USA
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29
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Maes B, Willemse J, Broekmans A, Smets R, Cruys B, Put N, Madoe V, Janssen M, Soepenberg O, Bries G, Vrelust I, Achten R, Van Pelt K, Buvé K, Theunissen K, Peeters V, Froyen G. Targeted next-generation sequencing using a multigene panel in myeloid neoplasms: Implementation in clinical diagnostics. Int J Lab Hematol 2017; 39:604-612. [DOI: 10.1111/ijlh.12709] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/23/2017] [Indexed: 01/22/2023]
Affiliation(s)
- B. Maes
- Department of Clinical Biology; Jessa Ziekenhuis; Hasselt Belgium
| | - J. Willemse
- Department of Clinical Biology; Jessa Ziekenhuis; Hasselt Belgium
- Department of Clinical Biology; AZ Turnhout; Turnhout Belgium
| | - A. Broekmans
- Department of Clinical Biology; Jessa Ziekenhuis; Hasselt Belgium
| | - R. Smets
- Department of Clinical Biology; Jessa Ziekenhuis; Hasselt Belgium
| | - B. Cruys
- Department of Clinical Biology; Jessa Ziekenhuis; Hasselt Belgium
| | - N. Put
- Department of Hematology; Jessa Ziekenhuis; Hasselt Belgium
| | - V. Madoe
- Department of Hematology; Jessa Ziekenhuis; Hasselt Belgium
| | - M. Janssen
- Department of Hematology; Ziekenhuis Oost-Limburg; Genk Belgium
| | - O. Soepenberg
- Department of Hematology; Mariaziekenhuis Noord-Limburg; Overpelt Belgium
| | - G. Bries
- Department of Hematology; AZ Turnhout; Turnhout Belgium
| | - I. Vrelust
- Department of Hematology; AZ Turnhout; Turnhout Belgium
| | - R. Achten
- Department of Pathology; Jessa Ziekenhuis; Hasselt Belgium
| | - K. Van Pelt
- Department of Clinical Biology; Ziekenhuis Oost-Limburg; Genk Belgium
| | - K. Buvé
- Department of Hematology; Jessa Ziekenhuis; Hasselt Belgium
| | - K. Theunissen
- Department of Hematology; Jessa Ziekenhuis; Hasselt Belgium
| | - V. Peeters
- Department of Clinical Biology; Jessa Ziekenhuis; Hasselt Belgium
| | - G. Froyen
- Department of Clinical Biology; Jessa Ziekenhuis; Hasselt Belgium
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30
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Ng IK, Ng C, Low JJ, Chiu L, Seah E, Ng CH, Chng WJ, Yan B, Ban KHK. Identifying large indels in targeted next generation sequencing assays for myeloid neoplasms: a cautionary tale of the ZRSR1 pseudogene. J Clin Pathol 2017; 70:1069-1073. [PMID: 28676493 DOI: 10.1136/jclinpath-2017-204440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/26/2017] [Accepted: 04/27/2017] [Indexed: 11/04/2022]
Abstract
Targeted next generation sequencing platforms have been increasingly utilised for identification of novel mutations in myeloid neoplasms, such as acute myeloid leukaemia (AML), and hold great promise for use in routine clinical diagnostics. In this study, we evaluated the utility of an open source variant caller in detecting large indels in a targeted sequencing of AML samples. While we found that this bioinformatics pipeline has the potential to accurately capture large indels (>20 bp) in patient samples, we highlighted the pitfall of a confounding ZRSR1 pseudogene that led to an erroneous ZRSR2 variant call. We further discuss possible clinical implications of the ZRSR1 pseudogene in myeloid neoplasms based on its molecular features. Knowledge of the confounding ZRSR1 pseudogene in ZRSR2 sequencing assays could be particularly important in AML diagnostics because the detection of ZRSR2 in AML patients is highly specific for an s-AML diagnosis.
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Affiliation(s)
- Isaac Ks Ng
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Christopher Ng
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore
| | - Jia Jin Low
- Department of Statistics, National University of Singapore, Singapore
| | - Lily Chiu
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore
| | - Elaine Seah
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore
| | - Chin Hin Ng
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore
| | - Wee-Joo Chng
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore.,Cancer Science Institute, National University of Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Benedict Yan
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore
| | - Kenneth H K Ban
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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31
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Valent P, Orazi A, Steensma DP, Ebert BL, Haase D, Malcovati L, van de Loosdrecht AA, Haferlach T, Westers TM, Wells DA, Giagounidis A, Loken M, Orfao A, Lübbert M, Ganser A, Hofmann WK, Ogata K, Schanz J, Béné MC, Hoermann G, Sperr WR, Sotlar K, Bettelheim P, Stauder R, Pfeilstöcker M, Horny HP, Germing U, Greenberg P, Bennett JM. Proposed minimal diagnostic criteria for myelodysplastic syndromes (MDS) and potential pre-MDS conditions. Oncotarget 2017; 8:73483-73500. [PMID: 29088721 PMCID: PMC5650276 DOI: 10.18632/oncotarget.19008] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 06/26/2017] [Indexed: 12/13/2022] Open
Abstract
Myelodysplastic syndromes (MDS) comprise a heterogeneous group of myeloid neoplasms characterized by peripheral cytopenia, dysplasia, and a variable clinical course with about 30% risk to transform to secondary acute myeloid leukemia (AML). In the past 15 years, diagnostic evaluations, prognostication, and treatment of MDS have improved substantially. However, with the discovery of molecular markers and advent of novel targeted therapies, new challenges have emerged in the complex field of MDS. For example, MDS-related molecular lesions may be detectable in healthy individuals and increase in prevalence with age. Other patients exhibit persistent cytopenia of unknown etiology without dysplasia. Although these conditions are potential pre-phases of MDS they may also transform into other bone marrow neoplasms. Recently identified molecular, cytogenetic, and flow-based parameters may add in the delineation and prognostication of these conditions. However, no generally accepted integrated classification and no related criteria are as yet available. In an attempt to address this challenge, an international consensus group discussed these issues in a working conference in July 2016. The outcomes of this conference are summarized in the present article which includes criteria and a proposal for the classification of pre-MDS conditions as well as updated minimal diagnostic criteria of MDS. Moreover, we propose diagnostic standards to delineate between ´normal´, pre-MDS, and MDS. These standards and criteria should facilitate diagnostic and prognostic evaluations in clinical studies as well as in clinical practice.
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Affiliation(s)
- Peter Valent
- Department of Internal Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Vienna, Austria.,Ludwig Boltzmann Cluster Oncology, Medical University of Vienna, Vienna, Austria
| | - Attilio Orazi
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
| | - David P Steensma
- Division of Hematological Malignancies, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Benjamin L Ebert
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Detlef Haase
- Clinic of Hematology and Medical Oncology, Universitymedicine Göttingen, Göttingen, Germany
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Arjan A van de Loosdrecht
- Department of Hematology Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Theresia M Westers
- Department of Hematology Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | | | | | | | - Alberto Orfao
- Servicio Central de Citometría, Centro de Investigación del Cáncer (IBMCC, CSIC-USAL) and IBSAL, Universidad de Salamanca, Salamanca, Spain
| | - Michael Lübbert
- Department of Medicine I, Medical Center-University of Freiburg, Freiburg, Germany
| | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Wolf-Karsten Hofmann
- Department of Hematology and Oncology, University Hospital Mannheim, Medical Faculty Mannheim of the University of Heidelberg, Mannheim, Germany
| | - Kiyoyuki Ogata
- Metropolitan Research and Treatment Center for Blood Disorders (MRTC Japan), Tokyo, Japan
| | - Julie Schanz
- Clinic of Hematology and Medical Oncology, Universitymedicine Göttingen, Göttingen, Germany
| | - Marie C Béné
- Laboratoire d'Hématologie CHU de Nantes, Nantes, France
| | - Gregor Hoermann
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Wolfgang R Sperr
- Department of Internal Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Vienna, Austria.,Ludwig Boltzmann Cluster Oncology, Medical University of Vienna, Vienna, Austria
| | - Karl Sotlar
- Institute of Pathology, Paracelsus Medical University Salzburg, Salzburg, Austria
| | | | - Reinhard Stauder
- Department of Internal Medicine V (Haematology and Oncology) Innsbruck Medical University, Innsbruck, Austria
| | | | - Hans-Peter Horny
- Institute of Pathology, Ludwig-Maximilians University, Munich, Germany
| | - Ulrich Germing
- Department of Hematology, Oncology, and Clinical Immunology, Heinrich-Heine-University, Düsseldorf, Germany
| | | | - John M Bennett
- Department of Pathology, Hematopathology Unit and James P Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York, USA
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32
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Arulogun SO, Choong HL, Taylor D, Ambrosoli P, Magor G, Irving IM, Keng TB, Perkins AC. JAK1 somatic mutation in a myeloproliferative neoplasm. Haematologica 2017; 102:e324-e327. [PMID: 28550193 DOI: 10.3324/haematol.2017.170266] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
| | | | | | | | - Graham Magor
- Mater Research, Translational Research Institute, University of Queensland, Woolloongabba, Australia
| | - Ian M Irving
- Townsville Hospital, South Brisbane, Australia.,ICON Cancer Care, South Brisbane, Australia
| | | | - Andrew C Perkins
- Mater Pathology, South Brisbane, Australia .,Mater Research, Translational Research Institute, University of Queensland, Woolloongabba, Australia.,ICON Cancer Care, South Brisbane, Australia
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33
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Raess PW, Cascio MJ, Fan G, Press R, Druker BJ, Brewer D, Spurgeon SE. Concurrent STAT3, DNMT3A, and TET2 mutations in T-LGL leukemia with molecularly distinct clonal hematopoiesis of indeterminate potential. Am J Hematol 2017; 92:E6-E8. [PMID: 27761930 DOI: 10.1002/ajh.24586] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/10/2016] [Accepted: 10/17/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Philipp W. Raess
- Department of Pathology; Oregon Health and Science University; Portland Oregon
| | - Michael J. Cascio
- Department of Pathology; Oregon Health and Science University; Portland Oregon
| | - Guang Fan
- Department of Pathology; Oregon Health and Science University; Portland Oregon
| | - Richard Press
- Department of Pathology; Oregon Health and Science University; Portland Oregon
- Knight Cancer Institute, Oregon Health and Science University; Portland Oregon
| | - Brian J. Druker
- Knight Cancer Institute, Oregon Health and Science University; Portland Oregon
| | - Diana Brewer
- Knight Cancer Institute, Oregon Health and Science University; Portland Oregon
| | - Stephen E. Spurgeon
- Knight Cancer Institute, Oregon Health and Science University; Portland Oregon
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34
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Traer E, Martinez J, Javidi-Sharifi N, Agarwal A, Dunlap J, English I, Kovacsovics T, Tyner JW, Wong M, Druker BJ. FGF2 from Marrow Microenvironment Promotes Resistance to FLT3 Inhibitors in Acute Myeloid Leukemia. Cancer Res 2016; 76:6471-6482. [PMID: 27671675 DOI: 10.1158/0008-5472.can-15-3569] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 09/14/2016] [Accepted: 09/14/2016] [Indexed: 12/16/2022]
Abstract
Potent FLT3 inhibitors, such as quizartinib (AC220), have shown promise in treating acute myeloid leukemia (AML) containing FLT3 internal tandem duplication (ITD) mutations. However, responses are not durable and resistance develops within months. In this study, we outline a two-step model of resistance whereby extrinsic microenvironmental proteins FLT3 ligand (FL) and fibroblast growth factor 2 (FGF2) protect FLT3-ITD+ MOLM14 cells from AC220, providing time for subsequent accumulation of ligand-independent resistance mechanisms. FL directly attenuated AC220 inhibition of FLT3, consistent with previous reports. Conversely, FGF2 promoted resistance through activation of FGFR1 and downstream MAPK effectors; these resistant cells responded synergistically to combinatorial inhibition of FGFR1 and FLT3. Removing FL or FGF2 from ligand-dependent resistant cultures transiently restored sensitivity to AC220, but accelerated acquisition of secondary resistance via reactivation of FLT3 and RAS/MAPK signaling. FLT3-ITD AML patients treated with AC220 developed increased FGF2 expression in marrow stromal cells, which peaked prior to overt clinical relapse and detection of resistance mutations. Overall, these results support a strategy of early combination therapy to target early survival signals from the bone marrow microenvironment, in particular FGF2, to improve the depth of response in FLT3-ITD AML. Cancer Res; 76(22); 6471-82. ©2016 AACR.
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Affiliation(s)
- Elie Traer
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon. .,Division of Hematology and Medical Oncology, Oregon Health and Science University, Portland, Oregon
| | - Jacqueline Martinez
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | | | - Anupriya Agarwal
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon.,Division of Hematology and Medical Oncology, Oregon Health and Science University, Portland, Oregon
| | - Jennifer Dunlap
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon.,Department of Anatomic Pathology, Oregon Health and Science University, Portland, Oregon
| | - Isabel English
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Tibor Kovacsovics
- BMT, Blood and Marrow Transplant, Huntsman Cancer Institute, Salt Lake City, Utah
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon.,Department of Cell, Developmental, and Cancer Biology, Oregon Health and Science University, Portland, Oregon
| | - Melissa Wong
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon.,Department of Cell, Developmental, and Cancer Biology, Oregon Health and Science University, Portland, Oregon
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon.,Division of Hematology and Medical Oncology, Oregon Health and Science University, Portland, Oregon.,Howard Hughes Medical Institute, Chevy Chase, Maryland
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