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Leung B, Aung H, Nandini A, Abdulrasool G, Lau C, Seymour L. Analytical Validation of a 37-Gene Next-Generation Sequencing Panel for Myeloid Malignancies and Review of Initial Findings Incorporating Updated 2022 Diagnostic and Prognostic Guidelines. J Mol Diagn 2024; 26:399-412. [PMID: 38367765 DOI: 10.1016/j.jmoldx.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 10/23/2023] [Accepted: 01/16/2024] [Indexed: 02/19/2024] Open
Abstract
Myeloid neoplasms are clonal disorders that arise via acquisition of genetic mutations leading to excessive proliferation and defective differentiation. Mutational profiling is vital as it has implications for diagnosis, prognosis, and therapeutic decision-making. Next-generation sequencing (NGS) has become a mainstay in the evaluation of myeloid malignancies, as it enables efficient characterization of multiple genetic changes. Herein, the analytical validation of the 37-gene Archer VariantPlex Core Myeloid panel is reported, using 58 DNA specimens with 87 single-nucleotide variants and 23 insertions/deletions. The panel achieved good depth of coverage, 100% analytical sensitivity and specificity for single-nucleotide variants and insertions/deletions ≤21 bp, and 100% reproducibility, with a reportable limit of detection determined as 5%. The Archer NGS panel can accurately and reproducibly detect variants of clinical significance in myeloid neoplasms. A retrospective analysis of 535 clinical specimens tested with the Archer NGS panel showed a frequency and pattern of mutations across myeloid malignancies that were similar to other published studies. A review of the diagnostic classification of patients with acute myeloid leukemia and myelodysplastic syndrome using the World Health Organization 2017/2022 and International Consensus Classification 2022 guidelines, in addition to European LeukemiaNet 2017/2022 risk stratification of patients with acute myeloid leukemia, was also performed to assess the utility of the molecular information provided by the Archer NGS panel.
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Affiliation(s)
- Becky Leung
- Department of Haematology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia; School of Medicine, Griffith University, Gold Coast, Queensland, Australia.
| | - Hnin Aung
- Department of Haematology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Adayapalam Nandini
- Department of Haematology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Ghusoon Abdulrasool
- Department of Haematology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia; School of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Chiyan Lau
- Department of Haematology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia; School of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Louise Seymour
- Department of Haematology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia; School of Medicine, University of Queensland, Brisbane, Queensland, Australia
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Gudmundsson S, Carlston CM, O'Donnell-Luria A. Interpreting variants in genes affected by clonal hematopoiesis in population data. Hum Genet 2024; 143:545-549. [PMID: 36739343 PMCID: PMC10400727 DOI: 10.1007/s00439-023-02526-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 01/18/2023] [Indexed: 02/05/2023]
Abstract
Reference population databases like the Genome Aggregation Database (gnomAD) have improved our ability to interpret the human genome. Variant frequencies and frequency-derived tools (such as depletion scores) have become fundamental to variant interpretation and the assessment of variant-gene-disease relationships. Clonal hematopoiesis (CH) obstructs variant interpretation as somatic variants that provide proliferative advantage will affect variant frequencies, depletion scores, and downstream filtering. Further, default filtering of variants or genes associated with CH risks filtering bona fide germline variants as variants associated with CH can also cause Mendelian conditions. Here, we provide our insights on interpreting population variant data in genes affected by clonal hematopoiesis, as well as recommendations for careful review of 36 established CH genes associated with neurodevelopmental conditions.
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Affiliation(s)
- Sanna Gudmundsson
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Colleen M Carlston
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Anne O'Donnell-Luria
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
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3
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Yang L, Wei X, Gong Y. Prognosis and risk factors for ASXL1 mutations in patients with newly diagnosed acute myeloid leukemia and myelodysplastic syndrome. Cancer Med 2023; 13:e6871. [PMID: 38146893 PMCID: PMC10807681 DOI: 10.1002/cam4.6871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/29/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023] Open
Abstract
OBJECTIVE The objective of the study was to determine the prognosis and risk factors for additional sex combs like 1 (ASXL1) mutations in patients with acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). POPULATION AND METHODS This retrospective study enrolled 219 adult patients with newly diagnosed AML and MDS, who were treated in West China Hospital from October 2018 to January 2022. The primary clinical outcome was evaluated by overall survival (OS) followed up to January 2023. Kaplan-Meier analysis and Cox multivariate regression analysis were performed to identify potential prognostic parameters in patients with ASXL1 mutations (mt). RESULTS A total of 34 (15.53%) ASXL1mt were detected, which occurred more frequently in the elderly and MDS cohorts (p < 0.001). Significantly lower blasts% (p < 0.001) and higher frequencies of mutant RUNX1, SRSF2, STAG2, EZH2, and SETBP1 (p < 0.02) were observed in the ASXL1mt cohort. Patients with ASXL1mt manifested with a worse complete remission rate (p = 0.011), and an inferior OS was shown in subgroups with MDS, co-mutations of RUNX1, SRSF2, or NRAS, as well as mutations in G646W (p < 0.05). Multivariate analysis considering age, diagnosis, co-mutations, and mutation site confirmed an independently adverse prognosis of mutations in G646W (HR = 4.302, 95% CI: 1.150-16.097) or RUNX1 co-mutations (HR = 4.620, 95% CI: 1.385-15.414) in the ASXL1mt cohort. CONCLUSION Our study indicated that mutations in G646W or RUNX1 co-mutations are closely associated with a dismal clinical outcome in patients with AML and MDS harboring ASXL1mt . Considering the poor prognosis and risk factors in patients with ASXL1mt , more available treatments should be pursued.
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Affiliation(s)
- Liqing Yang
- Department of Hematology, West China HospitalSichuan UniversityChengduSichuanChina
- Department of HematologyFujian Medical University Union Hospital, Fujian Medical UniversityFuzhouFujianChina
| | - Xiaoyu Wei
- Department of Hematology, West China HospitalSichuan UniversityChengduSichuanChina
| | - Yuping Gong
- Department of Hematology, West China HospitalSichuan UniversityChengduSichuanChina
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Cross NCP, Ernst T, Branford S, Cayuela JM, Deininger M, Fabarius A, Kim DDH, Machova Polakova K, Radich JP, Hehlmann R, Hochhaus A, Apperley JF, Soverini S. European LeukemiaNet laboratory recommendations for the diagnosis and management of chronic myeloid leukemia. Leukemia 2023; 37:2150-2167. [PMID: 37794101 PMCID: PMC10624636 DOI: 10.1038/s41375-023-02048-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023]
Abstract
From the laboratory perspective, effective management of patients with chronic myeloid leukemia (CML) requires accurate diagnosis, assessment of prognostic markers, sequential assessment of levels of residual disease and investigation of possible reasons for resistance, relapse or progression. Our scientific and clinical knowledge underpinning these requirements continues to evolve, as do laboratory methods and technologies. The European LeukemiaNet convened an expert panel to critically consider the current status of genetic laboratory approaches to help diagnose and manage CML patients. Our recommendations focus on current best practice and highlight the strengths and pitfalls of commonly used laboratory tests.
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Affiliation(s)
| | - Thomas Ernst
- Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | - Susan Branford
- Centre for Cancer Biology and SA Pathology, Adelaide, SA, Australia
| | - Jean-Michel Cayuela
- Laboratory of Hematology, University Hospital Saint-Louis, AP-HP and EA3518, Université Paris Cité, Paris, France
| | | | - Alice Fabarius
- III. Medizinische Klinik, Medizinische Fakultät Mannheim, Universität Heidelberg, Mannheim, Germany
| | - Dennis Dong Hwan Kim
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada
| | | | | | - Rüdiger Hehlmann
- III. Medizinische Klinik, Medizinische Fakultät Mannheim, Universität Heidelberg, Mannheim, Germany
- ELN Foundation, Weinheim, Germany
| | - Andreas Hochhaus
- Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | - Jane F Apperley
- Centre for Haematology, Imperial College London, London, UK
- Department of Clinical Haematology, Imperial College Healthcare NHS Trust, London, UK
| | - Simona Soverini
- Department of Medical and Surgical Sciences, Institute of Hematology "Lorenzo e Ariosto Seràgnoli", University of Bologna, Bologna, Italy
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Shanmuganathan N, Wadham C, Shahrin N, Feng J, Thomson D, Wang P, Saunders V, Kok CH, King RM, Kenyon RR, Lin M, Pagani IS, Ross DM, Yong ASM, Grigg AP, Mills AK, Schwarer AP, Braley J, Altamura H, Yeung DT, Scott HS, Schreiber AW, Hughes TP, Branford S. Impact of additional genetic abnormalities at diagnosis of chronic myeloid leukemia for first-line imatinib-treated patients receiving proactive treatment intervention. Haematologica 2023; 108:2380-2395. [PMID: 36951160 PMCID: PMC10483360 DOI: 10.3324/haematol.2022.282184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 03/16/2023] [Indexed: 03/24/2023] Open
Abstract
The BCR::ABL1 gene fusion initiates chronic myeloid leukemia (CML); however, evidence has accumulated from studies of highly selected cohorts that variants in other cancer-related genes are associated with treatment failure. Nevertheless, the true incidence and impact of additional genetic abnormalities (AGA) at diagnosis of chronic phase (CP)-CML is unknown. We sought to determine whether AGA at diagnosis in a consecutive imatinib-treated cohort of 210 patients enrolled in the TIDEL-II trial influenced outcome despite a highly proactive treatment intervention strategy. Survival outcomes including overall survival, progression-free survival, failure-free survival, and BCR::ABL1 kinase domain mutation acquisition were evaluated. Molecular outcomes were measured at a central laboratory and included major molecular response (MMR, BCR::ABL1 ≤0.1%IS), MR4 (BCR::ABL1 ≤0.01%IS), and MR4.5 (BCR::ABL1 ≤0.0032%IS). AGA included variants in known cancer genes and novel rearrangements involving the formation of the Philadelphia chromosome. Clinical outcomes and molecular response were assessed based on the patient's genetic profile and other baseline factors. AGA were identified in 31% of patients. Potentially pathogenic variants in cancer-related genes were detected in 16% of patients at diagnosis (including gene fusions and deletions) and structural rearrangements involving the Philadelphia chromosome (Ph-associated rearrangements) were detected in 18%. Multivariable analysis demonstrated that the combined genetic abnormalities plus the EUTOS long-term survival clinical risk score were independent predictors of lower molecular response rates and higher treatment failure. Despite a highly proactive treatment intervention strategy, first-line imatinib-treated patients with AGA had poorer response rates. These data provide evidence for the incorporation of genomically-based risk assessment for CML.
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MESH Headings
- Humans
- Imatinib Mesylate/therapeutic use
- Antineoplastic Agents/therapeutic use
- Philadelphia Chromosome
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/diagnosis
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myeloid, Chronic-Phase/drug therapy
- Protein Kinase Inhibitors/therapeutic use
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Affiliation(s)
- Naranie Shanmuganathan
- Department of Hematology, Royal Adelaide Hospital and SA Pathology, Adelaide, Australia; Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia; Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide, Australia; Australasian Leukemia and Lymphoma Group (ALLG).
| | - Carol Wadham
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia; Clinical and Health Sciences, University of South Australia, Adelaide
| | - NurHezrin Shahrin
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide
| | - Jinghua Feng
- Clinical and Health Sciences, University of South Australia, Adelaide, Australia; Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide
| | - Daniel Thomson
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide
| | - Paul Wang
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia; Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide
| | - Verity Saunders
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide
| | - Chung Hoow Kok
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide
| | - Rob M King
- Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide
| | - Rosalie R Kenyon
- Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide
| | - Ming Lin
- Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide
| | - Ilaria S Pagani
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide, Australia; Australasian Leukemia and Lymphoma Group (ALLG)
| | - David M Ross
- Department of Hematology, Royal Adelaide Hospital and SA Pathology, Adelaide, Australia; Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia; Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Australasian Leukemia and Lymphoma Group (ALLG); Department of Hematology, Flinders University and Medical Centre, Adelaide
| | - Agnes S M Yong
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide, Australia; Australasian Leukemia and Lymphoma Group (ALLG); The University of Western Australia Medical School, Western Australia
| | - Andrew P Grigg
- Australasian Leukemia and Lymphoma Group (ALLG); Department of Clinical Hematology, Austin Hospital and University of Melbourne, Melbourne
| | - Anthony K Mills
- Australasian Leukemia and Lymphoma Group (ALLG); Department of Hematology, Princess Alexandra Hospital, Brisbane
| | - Anthony P Schwarer
- Australasian Leukemia and Lymphoma Group (ALLG); Department of Hematology, Box Hill Hospital, Melbourne
| | - Jodi Braley
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide
| | - Haley Altamura
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide
| | - David T Yeung
- Department of Hematology, Royal Adelaide Hospital and SA Pathology, Adelaide, Australia; Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide, Australia; Australasian Leukemia and Lymphoma Group (ALLG)
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide, Australia; Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide
| | - Andreas W Schreiber
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia; Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia; School of Biological Sciences, University of Adelaide, Adelaide
| | - Timothy P Hughes
- Department of Hematology, Royal Adelaide Hospital and SA Pathology, Adelaide, Australia; Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide, Australia; Australasian Leukemia and Lymphoma Group (ALLG)
| | - Susan Branford
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia; Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, Australia; Adelaide Medical School, University of Adelaide, Adelaide
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Sobieralski P, Wasąg B, Leszczyńska A, Żuk M, Bieniaszewska M. The molecular profile in patients with polycythemia vera and essential thrombocythemia is dynamic and correlates with disease's phenotype. Front Oncol 2023; 13:1224590. [PMID: 37671053 PMCID: PMC10475996 DOI: 10.3389/fonc.2023.1224590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/02/2023] [Indexed: 09/07/2023] Open
Abstract
Introduction Polycythemia vera (PV) and essential thrombocythemia (ET) are diseases driven by canonical mutations in JAK2, CALR, or MPL gene. Previous studies revealed that in addition to driver mutations, patients with PV and ET can harbor other mutations in various genes, with no established impact on disease phenotype. We hypothesized that the molecular profile of patients with PV and ET is dynamic throughout the disease. Methods In this study, we performed a 37-gene targeted next-generation sequencing panel on the DNA samples collected from 49 study participants in two-time points, separated by 78-141 months. We identified 78 variants across 37 analyzed genes in the study population. Results By analyzing the change in variant allele frequencies and revealing the acquisition of new mutations during the disease, we confirmed the dynamic nature of the molecular profile of patients with PV and ET. We found connections between specific variants with the development of secondary myelofibrosis, thrombotic events, and response to treatment. We confronted our results with existing conventional and mutation-enhanced prognostic systems, showing the limited utility of available prognostic tools. Discussion The results of this study underline the significance of repeated molecular testing in patients with PV and ET and indicate the need for further research within this field to better understand the disease and improve available prognostic tools.
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Affiliation(s)
- Patryk Sobieralski
- Department of Hematology and Transplantology, Medical University of Gdansk, Gdansk, Poland
| | - Bartosz Wasąg
- Department of Biology and Medical Genetics, Faculty of Medicine, Medical University of Gdańsk, Gdansk, Poland
- Laboratory of Clinical Genetics, University Clinical Centre, Gdansk, Poland
| | - Aleksandra Leszczyńska
- Department of Hematology and Transplantology, Medical University of Gdansk, Gdansk, Poland
| | - Monika Żuk
- Department of Biology and Medical Genetics, Faculty of Medicine, Medical University of Gdańsk, Gdansk, Poland
- Laboratory of Clinical Genetics, University Clinical Centre, Gdansk, Poland
| | - Maria Bieniaszewska
- Department of Hematology and Transplantology, Medical University of Gdansk, Gdansk, Poland
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Gondek LP. Refining CHIP in population data sets. Blood 2023; 141:2163-2164. [PMID: 37140953 DOI: 10.1182/blood.2023019801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
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Vlasschaert C, Mack T, Heimlich JB, Niroula A, Uddin MM, Weinstock J, Sharber B, Silver AJ, Xu Y, Savona M, Gibson C, Lanktree MB, Rauh MJ, Ebert BL, Natarajan P, Jaiswal S, Bick AG. A practical approach to curate clonal hematopoiesis of indeterminate potential in human genetic data sets. Blood 2023; 141:2214-2223. [PMID: 36652671 PMCID: PMC10273159 DOI: 10.1182/blood.2022018825] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/03/2023] [Accepted: 01/17/2023] [Indexed: 01/19/2023] Open
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) is a common form of age-related somatic mosaicism that is associated with significant morbidity and mortality. CHIP mutations can be identified in peripheral blood samples that are sequenced using approaches that cover the whole genome, the whole exome, or targeted genetic regions; however, differentiating true CHIP mutations from sequencing artifacts and germ line variants is a considerable bioinformatic challenge. We present a stepwise method that combines filtering based on sequencing metrics, variant annotation, and population-based associations to increase the accuracy of CHIP calls. We apply this approach to ascertain CHIP in ∼550 000 individuals in the UK Biobank complete whole exome cohort and the All of Us Research Program initial whole genome release cohort. CHIP ascertainment on this scale unmasks recurrent artifactual variants and highlights the importance of specialized filtering approaches for several genes, including TET2 and ASXL1. We show how small changes in filtering parameters can considerably increase CHIP misclassification and reduce the effect size of epidemiological associations. Our high-fidelity call set refines previous population-based associations of CHIP with incident outcomes. For example, the annualized incidence of myeloid malignancy in individuals with small CHIP clones is 0.03% per year, which increases to 0.5% per year among individuals with very large CHIP clones. We also find a significantly lower prevalence of CHIP in individuals of self-reported Latino or Hispanic ethnicity in All of Us, highlighting the importance of including diverse populations. The standardization of CHIP calling will increase the fidelity of CHIP epidemiological work and is required for clinical CHIP diagnostic assays.
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Affiliation(s)
| | - Taralynn Mack
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - J. Brett Heimlich
- Division of Cardiology, Vanderbilt University Medical Center, Nashville, TN
| | - Abhishek Niroula
- Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Md Mesbah Uddin
- Broad Institute of MIT and Harvard, Cambridge, MA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
| | - Joshua Weinstock
- Center for Statistical Genetics, Department of Biostatistics – University of Michigan School of Public Health, Ann Arbor, MI
| | - Brian Sharber
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Alexander J. Silver
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN
| | - Yaomin Xu
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN
| | - Michael Savona
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN
- Division of Hematology/Oncology, Vanderbilt University School of Medicine, Nashville, TN
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN
- Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, TN
| | - Christopher Gibson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Matthew B. Lanktree
- Division of Nephrology, St. Joseph’s Healthcare Hamilton, Hamilton, ON, Canada
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, ON, Canada
| | - Michael J. Rauh
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON, Canada
| | - Benjamin L. Ebert
- Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Howard Hughes Medical Institute, Boston, MA
| | - Pradeep Natarajan
- Broad Institute of MIT and Harvard, Cambridge, MA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | | | - Alexander G. Bick
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN
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9
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Yang FC, Agosto-Peña J. Epigenetic regulation by ASXL1 in myeloid malignancies. Int J Hematol 2023; 117:791-806. [PMID: 37062051 DOI: 10.1007/s12185-023-03586-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/02/2023] [Accepted: 03/22/2023] [Indexed: 04/17/2023]
Abstract
Myeloid malignancies are clonal hematopoietic disorders that are comprised of a spectrum of genetically heterogeneous disorders, including myelodysplastic syndromes (MDS), myeloproliferative neoplasms (MPN), chronic myelomonocytic leukemia (CMML), and acute myeloid leukemia (AML). Myeloid malignancies are characterized by excessive proliferation, abnormal self-renewal, and/or differentiation defects of hematopoietic stem cells (HSCs) and myeloid progenitor cells hematopoietic stem/progenitor cells (HSPCs). Myeloid malignancies can be caused by genetic and epigenetic alterations that provoke key cellular functions, such as self-renewal, proliferation, biased lineage commitment, and differentiation. Advances in next-generation sequencing led to the identification of multiple mutations in myeloid neoplasms, and many new gene mutations were identified as key factors in driving the pathogenesis of myeloid malignancies. The polycomb protein ASXL1 was identified to be frequently mutated in all forms of myeloid malignancies, with mutational frequencies of 20%, 43%, 10%, and 20% in MDS, CMML, MPN, and AML, respectively. Significantly, ASXL1 mutations are associated with a poor prognosis in all forms of myeloid malignancies. The fact that ASXL1 mutations are associated with poor prognosis in patients with CMML, MDS, and AML, points to the possibility that ASXL1 mutation is a key factor in the development of myeloid malignancies. This review summarizes the recent advances in understanding myeloid malignancies with a specific focus on ASXL1 mutations.
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Affiliation(s)
- Feng-Chun Yang
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
| | - Joel Agosto-Peña
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
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10
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Medina EA, Delma CR, Yang FC. ASXL1/2 mutations and myeloid malignancies. J Hematol Oncol 2022; 15:127. [PMID: 36068610 PMCID: PMC9450349 DOI: 10.1186/s13045-022-01336-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/04/2022] [Indexed: 11/10/2022] Open
Abstract
Myeloid malignancies develop through the accumulation of genetic and epigenetic alterations that dysregulate hematopoietic stem cell (HSC) self-renewal, stimulate HSC proliferation and result in differentiation defects. The polycomb group (PcG) and trithorax group (TrxG) of epigenetic regulators act antagonistically to regulate the expression of genes key to stem cell functions. The genes encoding these proteins, and the proteins that interact with them or affect their occupancy at chromatin, are frequently mutated in myeloid malignancies. PcG and TrxG proteins are regulated by Enhancers of Trithorax and Polycomb (ETP) proteins. ASXL1 and ASXL2 are ETP proteins that assemble chromatin modification complexes and transcription factors. ASXL1 mutations frequently occur in myeloid malignancies and are associated with a poor prognosis, whereas ASXL2 mutations frequently occur in AML with t(8;21)/RUNX1-RUNX1T1 and less frequently in other subtypes of myeloid malignancies. Herein, we review the role of ASXL1 and ASXL2 in normal and malignant hematopoiesis by summarizing the findings of mouse model systems and discussing their underlying molecular mechanisms.
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Affiliation(s)
- Edward A Medina
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, Joe R. and Teresa Lozano Long School of Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA.
| | - Caroline R Delma
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, Joe R. and Teresa Lozano Long School of Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
| | - Feng-Chun Yang
- Department of Cell Systems and Anatomy, Joe R. and Teresa Lozano Long School of Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA.,Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
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11
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Chen L, Eriksson A, Weström S, Pandzic T, Lehmann S, Cavelier L, Landegren U. Ultra-sensitive monitoring of leukemia patients using superRCA mutation detection assays. Nat Commun 2022; 13:4033. [PMID: 35821208 PMCID: PMC9276831 DOI: 10.1038/s41467-022-31397-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 06/16/2022] [Indexed: 11/09/2022] Open
Abstract
Rare tumor-specific mutations in patient samples serve as excellent markers to monitor the course of malignant disease and responses to therapy in clinical routine, and improved assay techniques are needed for broad adoption. We describe herein a highly sensitive and selective molecule amplification technology - superRCA assays - for rapid and highly specific detection of DNA sequence variants present at very low frequencies in DNA samples. Using a standard flow cytometer we demonstrate precise, ultra-sensitive detection of single-nucleotide mutant sequences from malignant cells against up to a 100,000-fold excess of DNA from normal cells in either bone marrow or peripheral blood, to follow the course of patients treated for acute myeloid leukemia (AML). We also demonstrate that sequence variants located in a high-GC region may be sensitively detected, and we illustrate the potential of the technology for early detection of disease recurrence as a basis for prompt change of therapy.
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Affiliation(s)
- Lei Chen
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-752 37, Uppsala, Sweden. .,Rarity Bioscience AB, SE-752 37, Uppsala, Sweden.
| | - Anna Eriksson
- Department of Medical Sciences, Uppsala University, SE-751 05, Uppsala, Sweden
| | - Simone Weström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-752 37, Uppsala, Sweden
| | - Tatjana Pandzic
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-752 37, Uppsala, Sweden
| | - Sören Lehmann
- Department of Medical Sciences, Uppsala University, SE-751 05, Uppsala, Sweden
| | - Lucia Cavelier
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-752 37, Uppsala, Sweden
| | - Ulf Landegren
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-752 37, Uppsala, Sweden.
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12
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Tan J, Chow YP, Zainul Abidin N, Chang KM, Selvaratnam V, Tumian NR, Poh YM, Veerakumarasivam A, Laffan MA, Wong CL. Analysis of genetic variants in myeloproliferative neoplasms using a 22-gene next-generation sequencing panel. BMC Med Genomics 2022; 15:10. [PMID: 35033063 PMCID: PMC8760696 DOI: 10.1186/s12920-021-01145-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/06/2021] [Indexed: 12/18/2022] Open
Abstract
Background The Philadelphia (Ph)-negative myeloproliferative neoplasms (MPNs), namely essential thrombocythaemia (ET), polycythaemia vera (PV) and primary myelofibrosis (PMF), are a group of chronic clonal haematopoietic disorders that have the propensity to advance into bone marrow failure or acute myeloid leukaemia; often resulting in fatality. Although driver mutations have been identified in these MPNs, subtype-specific markers of the disease have yet to be discovered. Next-generation sequencing (NGS) technology can potentially improve the clinical management of MPNs by allowing for the simultaneous screening of many disease-associated genes. Methods The performance of a custom, in-house designed 22-gene NGS panel was technically validated using reference standards across two independent replicate runs. The panel was subsequently used to screen a total of 10 clinical MPN samples (ET n = 3, PV n = 3, PMF n = 4). The resulting NGS data was then analysed via a bioinformatics pipeline. Results The custom NGS panel had a detection limit of 1% variant allele frequency (VAF). A total of 20 unique variants with VAFs above 5% (4 of which were putatively novel variants with potential biological significance) and one pathogenic variant with a VAF of between 1 and 5% were identified across all of the clinical MPN samples. All single nucleotide variants with VAFs ≥ 15% were confirmed via Sanger sequencing. Conclusions The high fidelity of the NGS analysis and the identification of known and novel variants in this study cohort support its potential clinical utility in the management of MPNs. However, further optimisation is needed to avoid false negatives in regions with low sequencing coverage, especially for the detection of driver mutations in MPL. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01145-0.
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Affiliation(s)
- Jaymi Tan
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Petaling Jaya, Selangor, Malaysia
| | - Yock Ping Chow
- Clinical Research Centre, Sunway Medical Centre, Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - Norziha Zainul Abidin
- Molecular Diagnostics Laboratory, Sunway Medical Centre, Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - Kian Meng Chang
- Haematology Unit, Department of Medicine, Sunway Medical Centre, Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | | | - Nor Rafeah Tumian
- Haematology Unit, Department of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Yang Ming Poh
- School of Data Sciences, Perdana University, Serdang, Selangor, Malaysia
| | - Abhi Veerakumarasivam
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Petaling Jaya, Selangor, Malaysia
| | - Michael Arthur Laffan
- Centre for Haematology, Hammersmith Hospital, London, UK.,Faculty of Medicine, Imperial College London, London, UK
| | - Chieh Lee Wong
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Petaling Jaya, Selangor, Malaysia. .,Clinical Research Centre, Sunway Medical Centre, Petaling Jaya, Selangor Darul Ehsan, Malaysia. .,Molecular Diagnostics Laboratory, Sunway Medical Centre, Petaling Jaya, Selangor Darul Ehsan, Malaysia. .,Haematology Unit, Department of Medicine, Sunway Medical Centre, Petaling Jaya, Selangor Darul Ehsan, Malaysia. .,Centre for Haematology, Hammersmith Hospital, London, UK. .,Faculty of Medicine, Imperial College London, London, UK.
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13
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Lin YH, Wu PC, Tsai CY, Lin YH, Lo MY, Hsu SJ, Lin PH, Erdenechuluun J, Wu HP, Hsu CJ, Wu CC, Chen PL. Hearing Impairment with Monoallelic GJB2 Variants: A GJB2 Cause or Non-GJB2 Cause? J Mol Diagn 2021; 23:1279-1291. [PMID: 34325055 DOI: 10.1016/j.jmoldx.2021.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 03/23/2021] [Accepted: 07/07/2021] [Indexed: 12/26/2022] Open
Abstract
Recessive variants in GJB2 are the most common genetic cause of sensorineural hearing impairment. However, in many patients, only one variant in the GJB2 coding region is identified using conventional sequencing strategy (eg, Sanger sequencing), resulting in nonconfirmative diagnosis. Conceivably, there might be other unidentified pathogenic variants in the noncoding region of GJB2 or other deafness-causing genes in these patients. To address this, a next-generation sequencing-based diagnostic panel targeting the entire GJB2 gene and the coding regions of 158 other known deafness-causing genes was designed and applied to 95 patients with nonsyndromic sensorineural hearing impairment (including 81 Han Taiwanese and 14 Mongolian patients) in whom only a single GJB2 variant had been detected using conventional Sanger sequencing. The panel confirmed the genetic diagnosis in 24 patients (25.3%). Twenty-two of them had causative variants in several deafness-causing genes other than GJB2, including MYO15A, MYO7A, TECTA, POU4F3, KCNQ4, SLC26A4, OTOF, MT-RNR1, MITF, WFS1, and USH2A. The other two patients had causative variants in GJB2, including a Taiwanese patient with a mosaic maternal uniparental disomy c.235delC variant (approximately 69% mosaicism) and a Mongolian patient with compound heterozygous c.35dupG and c.35delG variants, which occurred at the same site. This study demonstrates the utility of next-generation sequencing in clarifying the genetic diagnosis of hearing-impaired patients with nonconfirmative GJB2 genotypes on conventional genetic examinations.
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Affiliation(s)
- Yi-Hsin Lin
- Department of Otolaryngology, National Taiwan University Hospital, National Taiwan University Hospital, Taipei, Taiwan; Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ping-Che Wu
- College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Cheng-Yu Tsai
- Department of Otolaryngology, National Taiwan University Hospital, National Taiwan University Hospital, Taipei, Taiwan; Graduate Institutes of Medical Genomic, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yin-Hung Lin
- Department of Otolaryngology, National Taiwan University Hospital, National Taiwan University Hospital, Taipei, Taiwan; Graduate Institutes of Medical Genomic, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ming-Yu Lo
- Department of Otolaryngology, National Taiwan University Hospital, National Taiwan University Hospital, Taipei, Taiwan; Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Shu-Jui Hsu
- Graduate Institutes of Medical Genomic, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Pei-Hsuan Lin
- Department of Otolaryngology, National Taiwan University Hospital Yunlin Branch, Yunlin, Taiwan
| | - Jargalkhuu Erdenechuluun
- Department of Otolaryngology, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia; The EMJJ Otolaryngology Hospital, Ulaanbaatar, Mongolia
| | - Hung-Pin Wu
- Department of Otolaryngology Head and Neck Surgery, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, Taiwan; School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Chuan-Jen Hsu
- Department of Otolaryngology, National Taiwan University Hospital, National Taiwan University Hospital, Taipei, Taiwan; Department of Otolaryngology Head and Neck Surgery, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, Taiwan
| | - Chen-Chi Wu
- Department of Otolaryngology, National Taiwan University Hospital, National Taiwan University Hospital, Taipei, Taiwan; Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan.
| | - Pei-Lung Chen
- Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei, Taiwan; Graduate Institutes of Medical Genomic, National Taiwan University College of Medicine, Taipei, Taiwan; Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University Hospital, Taipei, Taiwan.
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14
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Schejbel L, Novotny GW, Breinholt MF, El Fassi D, Schöllkopf C, Hogdall E, Nørgaard P. Improved Variant Detection in Clinical Myeloid NGS Testing by Supplementing a Commercial Myeloid NGS Assay with Custom or Extended Data Filtering and Accessory Fragment Analysis. Mol Diagn Ther 2021; 25:251-266. [PMID: 33687704 DOI: 10.1007/s40291-021-00519-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND Commercial myeloid next-generation sequencing (NGS) panels may facilitate uniform generation of raw data between laboratories. However, different strategies for data filtering and variant annotation may contribute to differences in variant detection and reporting. Here, we present how custom data filtering or the use of Oncomine extended data filtering improve detection of clinically relevant mutations with the Oncomine Myeloid Research Assay. METHODS The study included all patient samples (n = 264) analyzed during the first-year, single-site, clinical use of the Ion Torrent Oncomine Myeloid Research Assay. In data analysis, the default analysis filter was supplemented with our own data filtering algorithm in order to detect additional clinically relevant mutations. In addition, we developed a sensitive supplementary test for the ASXL1 c.1934dupG p.Gly646fs mutation by fragment analysis. RESULTS Using our custom filter chain, we found 96 different reportable variants that were not detected by the default filter chain. Twenty-six of these were classified as variants of strong or potential clinical significance (tier I/tier II variants), and the custom filtering discovered otherwise undetected tier I/tier II variants in 25 of 132 patients with clinically relevant mutations (19%). The remaining 70 variants not detected by the default filter chain were classified as variants of unknown significance. Among these were several unique variants with possible pathogenic potential judged by bioinformatic predictions. The recently launched Oncomine 5.14 extended filter algorithm detects most but not all of the tier I/tier II variants that were not detected by the default filter. The supplementary fragment analysis for the ASXL1 c.1934dupG p.Gly646fs confidently detected a variant allele frequency of down to 4.8% (SD 0.83%). The assay also detected the ASXL1 c.1900_1922del23 mutation. CONCLUSION Detection of clinically relevant variants with the Oncomine Myeloid Research NGS assay can be significantly improved by supplementing the default filter chain with custom data filtering or the recently launched Oncomine 5.14 extended filter algorithm. Our accessory fragment analysis facilitates easy testing for frequent ASXL1 mutations that are poorly or not covered by the NGS assay.
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Affiliation(s)
- Lone Schejbel
- Department of Pathology, Herlev and Gentofte Hospital, Borgmester Ib Juuls Vej 73, 2730, Herlev, Denmark.
| | - Guy Wayne Novotny
- Department of Pathology, Herlev and Gentofte Hospital, Borgmester Ib Juuls Vej 73, 2730, Herlev, Denmark
| | - Marie Fredslund Breinholt
- Department of Pathology, Herlev and Gentofte Hospital, Borgmester Ib Juuls Vej 73, 2730, Herlev, Denmark
| | - Daniel El Fassi
- Department of Hematology, Herlev and Gentofte Hospital, Herlev, Denmark
| | | | - Estrid Hogdall
- Department of Pathology, Herlev and Gentofte Hospital, Borgmester Ib Juuls Vej 73, 2730, Herlev, Denmark
| | - Peter Nørgaard
- Department of Pathology, Herlev and Gentofte Hospital, Borgmester Ib Juuls Vej 73, 2730, Herlev, Denmark
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15
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Genetics of progression from MDS to secondary leukemia. Blood 2021; 136:50-60. [PMID: 32430504 DOI: 10.1182/blood.2019000942] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/27/2019] [Indexed: 12/14/2022] Open
Abstract
Our understanding of the genetics of acute myeloid leukemia (AML) development from myelodysplastic syndrome (MDS) has advanced significantly as a result of next-generation sequencing technology. Although differences in cell biology and maturation exist between MDS and AML secondary to MDS, these 2 diseases are genetically related. MDS and secondary AML cells harbor mutations in many of the same genes and functional categories, including chromatin modification, DNA methylation, RNA splicing, cohesin complex, transcription factors, cell signaling, and DNA damage, confirming that they are a disease continuum. Differences in the frequency of mutated genes in MDS and secondary AML indicate that the order of mutation acquisition is not random during progression. In almost every case, disease progression is associated with clonal evolution, typically defined by the expansion or emergence of a subclone with a unique set of mutations. Monitoring tumor burden and clonal evolution using sequencing provides advantages over using the blast count, which underestimates tumor burden, and could allow for early detection of disease progression prior to clinical deterioration. In this review, we outline advances in the study of MDS to secondary AML progression, with a focus on the genetics of progression, and discuss the advantages of incorporating molecular genetic data in the diagnosis, classification, and monitoring of MDS to secondary AML progression. Because sequencing is becoming routine in the clinic, ongoing research is needed to define the optimal assay to use in different clinical situations and how the data can be used to improve outcomes for patients with MDS and secondary AML.
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16
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Morishita S, Ochiai T, Misawa K, Osaga S, Inano T, Fukuda Y, Edahiro Y, Ohsaka A, Araki M, Komatsu N. Clinical impacts of the mutational spectrum in Japanese patients with primary myelofibrosis. Int J Hematol 2021; 113:500-507. [PMID: 33389584 DOI: 10.1007/s12185-020-03054-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 11/26/2020] [Accepted: 11/26/2020] [Indexed: 11/26/2022]
Abstract
Patients with primary myelofibrosis (PMF) have a poorer prognosis than those with other subtypes of myeloproliferative neoplasms (MPNs). To investigate the relationship between gene mutations and the prognosis of Japanese PMF patients, we analyzed mutations in 72 regions located in 14 MPN-relevant genes (CSF3R, MPL, JAK2, CALR, DNMT3A, TET2, EZH2, ASXL1, IDH1/2, SRSF2, SF3B1, U2AF1, and TP53) utilizing a target resequencing platform. In our cohort, ASXL1 mutations were more frequently detected in both overt and prefibrotic PMF patients than other mutations. The frequency of ASXL1 mutations was slightly higher among overt PMF patients than among prefibrotic PMF patients (44.6% vs 25.0%, FDR = 0.472). Decision tree classification algorithms revealed that ASXL1, EZH2, and SRSF2 mutations were associated with a poor prognosis for overt PMF. Overall survival was significantly shorter in patients harboring ASXL1, EZH2, or SRSF2 mutations than in those without these mutations (p = 0.03). These results suggest that, as reported in Western countries, MIPSS70 is applicable to Japanese PMF patients and ASXL1, EZH2, and SRSF2 mutations may be utilized as surrogate markers of a poor prognosis.
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Affiliation(s)
- Soji Morishita
- Department of Transfusion Medicine and Stem Cell Regulation, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Tomonori Ochiai
- Department of Hematology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Kyohei Misawa
- Department of Hematology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Satoshi Osaga
- Clinical Research Management Center, Nagoya City University Hospital, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, Aichi, 467-8601, Japan
| | - Tadaaki Inano
- Department of Hematology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yasutaka Fukuda
- Department of Hematology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yoko Edahiro
- Department of Hematology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Akimichi Ohsaka
- Department of Transfusion Medicine and Stem Cell Regulation, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Marito Araki
- Department of Transfusion Medicine and Stem Cell Regulation, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Norio Komatsu
- Department of Hematology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
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Spectrum of ASXL1 mutations in primary myelofibrosis: prognostic impact of the ASXL1 p.G646Wfs*12 mutation. Blood 2019; 133:2802-2808. [PMID: 31076447 DOI: 10.1182/blood.2018879536] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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