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Lang W, Luo Y, Wang L, Zhang Y, Hu C, Wang H, Tong H. The der(1;7)(q10;p10) defining a distinct profile from -7/del(7q) in myelodysplastic syndromes: A systematic review and meta-analysis. Cancer Med 2024; 13:e6890. [PMID: 38164059 PMCID: PMC10807610 DOI: 10.1002/cam4.6890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/03/2023] [Accepted: 12/17/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND AND OBJECTIVE Myelodysplastic syndromes (MDS) are myeloid neoplasms characterized by ineffective hematopoiesis due to stem cell abnormalities. Monosomy 7q aberrations are a common cytogenetic abnormality in MDS. Specifically, an unbalanced translocation der(1;7)(q10;p10) [der(1;7)] has been identified in MDS patients, which is a monosomy 7q aberration variant like -7/del(7q). However, knowledge of der(1;7)'s features remains limited. Existing studies have compared the clinical and genetic characteristics of der(1;7) to those of -7/del(7q) but yielded inconsistent findings. Accordingly, we conducted meta-analyses comparing der(1;7) to -7/del(7q). METHODS Publications were searched from the following databases up to January 10, 2023: Pubmed, Web of Science, Embase, Cochrane, and ClinicalTrials.gov. Eligible studies were assessed for risks of bias. Relevant data were extracted from included studies and analyzed using random-effects models. Publication bias was evaluated and sensitivity analyses were performed. RESULTS The comparative meta-analyses included 405 MDS patients with der(1;7) from nine studies. The analysis revealed that der(1;7) was associated with a greater male preponderance (86.1% vs. 68.3%, Odds Ratios (ORs) 2.007, p < 0.01) than -7/del(7q), lower platelets counts compared to del(7q), higher hemoglobin levels than -7, lower absolute neutrophil counts, and higher percentage of patients with non-excess blasts (66.9% vs. 41.3%, ORs 2.374, p = 0.01) in comparison with -7/del(7q). The der(1;7) existed more as a sole karyotype aberration (55.6% vs. 37.0%, ORs 2.902, p = 0.02), co-occurred more often with +8 (22.7% vs. 4.2%, ORs 5.714, p = 0.04) whereas less -5/del(5q) (1.5% vs. 41.3%, ORs 0.040, p < 0.01) and complex karyotype (7.3% vs. 54.8%, OR 0.085, p < 0.01). The der(1;7) was associated with higher frequencies of RUNX1 (40.8% vs. 12.3%, ORs 4.764, p < 0.01), ETNK1 (28.1% vs. 2.5%, ORs 42.106, p < 0.01) and EZH2 (24.8% vs. 6.9%, ORs 3.767, p = 0.02) mutations, but less TP53 mutation (2.4% vs. 45.3%, ORs 0.043, p < 0.01). Moreover, der(1;7) patients had longer time to progression (Hazard Ratios (HRs) 0.331, p = 0.02), better overall survival (OS) than -7 patients (HRs 0.557, p < 0.01), but similar OS with del(7q) patients (HRs 0.837, p = 0.37). CONCLUSION The findings revealed distinct clinical, cytogenetic, and molecular characteristics distinguishing der(1;7) from -7/del(7q), indicating der(1;7) defines a unique subtype within MDS with monosomy 7q. These findings support classifying der(1;7) as a separate MDS entity in future.
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Affiliation(s)
- Wei Lang
- Department of HematologyThe First Affiliated Hospital of Zhejiang UniversityHangzhouChina
| | - Yingwan Luo
- Department of HematologyThe First Affiliated Hospital of Zhejiang UniversityHangzhouChina
| | - Lu Wang
- Department of HematologyThe First Affiliated Hospital of Zhejiang UniversityHangzhouChina
| | - Yudi Zhang
- Department of HematologyThe First Affiliated Hospital of Zhejiang UniversityHangzhouChina
| | - Chao Hu
- Department of HematologyThe First Affiliated Hospital of Zhejiang UniversityHangzhouChina
| | - Huanping Wang
- Department of HematologyThe First Affiliated Hospital of Zhejiang UniversityHangzhouChina
| | - Hongyan Tong
- Department of HematologyThe First Affiliated Hospital of Zhejiang UniversityHangzhouChina
- Zhejiang Provincial Key Laboratory of Hematopoietic MalignancyZhejiang UniversityHangzhouChina
- Zhejiang Provincial Clinical Research Center for Hematological disordersHangzhouChina
- Zhejiang University Cancer CenterHangzhouChina
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Scarpelli I, Stalder VB, Tsilimidos G, Rapakko K, Costanza M, Blum S, Schoumans J. Refined cytogenetic IPSS-R evaluation by the use of SNP array in a cohort of 290 MDS patients. Genes Chromosomes Cancer 2023; 62:721-731. [PMID: 37449676 DOI: 10.1002/gcc.23191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
Genetic testing plays a central role in myelodysplastic neoplasms (MDS) diagnosis, prognosis, and therapeutic decisions. The widely applied cytogenetic revised international prognostic scoring system (IPSS-R) was based on chromosome banding analysis (CBA). However, subsequently developed genetic methodologies, such as single nucleotide polymorphism (SNP) array, demonstrated to be a valid alternative test for MDS. SNP array is, in fact, able to detect the majority of MDS-associated cytogenetic aberrations, by providing further genomic information due to its higher resolution. In this study, 290 samples from individuals with a confirmed or suspected diagnosis of MDS were tested by both CBA and SNP array, in order to evaluate and compare their cytogenetic IPSS-R score in the largest MDS cohort reported so far. A concordant or better refined cytogenetic IPSS-R array-based score was obtained for 95% of cases (277). Therefore, this study confirms the effective applicability of SNP array toward the cytogenetic IPSS-R evaluation and consequently, toward the molecular international prognostic scoring system for MDS (IPSS-M) assessment, which ensures an improved MDS risk stratification refinement. Considering the advent of additional genetic technologies interrogating the whole genome with increased resolutions, counting cytogenetic abnormalities based on their size may result in a simplistic approach. On the contrary, assessing overall genomic complexity may provide additional crucial information. Independently of the technology used, genetic results should indeed aim at ensuring a highly refined stratification for MDS patients.
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Affiliation(s)
- Ilaria Scarpelli
- Oncogenomic laboratory, Hematology Service, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Valérie Beyer Stalder
- Oncogenomic laboratory, Hematology Service, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gerasimos Tsilimidos
- Hematology Service and Central Laboratory of Hematology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Katrin Rapakko
- Oncogenomic laboratory, Hematology Service, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Mariangela Costanza
- Hematology Service, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Sabine Blum
- Hematology Service, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Jacqueline Schoumans
- Oncogenomic laboratory, Hematology Service, University Hospital and University of Lausanne, Lausanne, Switzerland
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Qin Y, Zhang H, Feng L, Wei H, Wu Y, Jiang C, Xu Z, Zhu H, Liu T. Combining metaphase cytogenetics with single nucleotide polymorphism arrays can improve the diagnostic yield and identify prognosis more precisely in myelodysplastic syndromes. Ann Med 2022; 54:2627-2636. [PMID: 36148999 PMCID: PMC9518301 DOI: 10.1080/07853890.2022.2125173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Myelodysplastic syndromes (MDS) encompass a group of heterogeneous haematopoietic stem cell malignancies characterised by ineffective haematopoiesis, cytological aberrations, and a propensity for progression to acute myeloid leukaemia. Diagnosis and disease prognostic stratification are much based on genomic abnormalities. The traditional metaphase cytogenetics analysis (MC) can detect about 40-60% aberrations. Single-nucleotide polymorphism arrays (SNP-A) karyotyping can detect copy number variations with a higher resolution and has a unique advantage in detection of copy number neutral loss of heterozygosity (CN-LOH). Combining these two methods may improve the diagnostic efficiency and accuracy for MDS. METHODS We retrospectively analysed the data of 110 MDS patients diagnosed from January 2012 to December 2019 to compare the detection yield of chromosomal abnormalities by MC with by SNP-A, and the relationship between chromosomal abnormalities and prognosis. RESULTS Our results showed that SNP-A improved the detection yield of chromosomal aberrations compared with MC (74.5 vs. 55.5%, p < .001). In addition, the positive yield could be further improved by combining MC with SNP-A to 77.3%, compared with MC alone. Univariate analysis showed that age >65 years, bone marrow blasts ≥5%, with acquired CN-LOH, new aberrations detected by SNP-A, TGA value > the median (81.435 Mb), higher risk by IPSS-R-MC, higher risk by IPSS-R-SNP-A all had poorer prognosis. More critically, multivariable analysis showed that age >65 years and higher risk by IPSS-R-SNP-A were independent predictors of inferior OS in MDS patients. CONCLUSION The combination of MC and SNP-A based karyotyping can further improve the diagnostic yield and provide more precise prognostic stratification in MDS patients. However, SNP-A may not completely replace MC because of its inability to detect balanced translocation and to detect different clones. From a practical point of view, we recommend the concurrent use of SNP-A and MC in the initial karyotypic evaluation for MDS patients on diagnosis and prognosis stratification.KEY MESSAGESSNP-A based karyotyping can further improve the MDS diagnostic yield and provide more precise prognostic stratification in MDS patients.Acquired CN-LOH is a characteristic chromosomal aberration of MDS, which should be integrated to the diagnostic project of MDS.The concurrent use of SNP-A and MC in the initial karyotypic evaluation for MDS patients can be recommended.
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Affiliation(s)
- Yao Qin
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Hang Zhang
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Lin Feng
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Haichen Wei
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Yuling Wu
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Chaoran Jiang
- Sichuan Hua Xi Kindstar Medical Diagnostic Centre, Chengdu, Sichuan, P. R. China
| | - Zhihong Xu
- Sichuan Hua Xi Kindstar Medical Diagnostic Centre, Chengdu, Sichuan, P. R. China
| | - Huanling Zhu
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Ting Liu
- Department of Hematology, Institute of Hematology, West China Hospital, Sichuan University, Chengdu, P. R. China
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Xie Z, Chen EC, Stahl M, Zeidan AM. Prognostication in myelodysplastic syndromes (neoplasms): Molecular risk stratification finally coming of age. Blood Rev 2022; 59:101033. [PMID: 36357283 DOI: 10.1016/j.blre.2022.101033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022]
Abstract
Accurate risk prognostication is central to the management of myelodysplastic syndromes, given the widely heterogeneous clinical outcomes of these bone marrow failure disorders. Over the past decade, the rapidly expanding compendium of molecular lesions in myelodysplastic syndrome (MDS) has offered unprecedented insight into MDS pathobiology. Recently, molecular prognostic models such as the Molecular International Prognostic Scoring System (IPSS-M) have leveraged the wellspring of genetic data to improve upon traditional risk models such as the Revised IPSS (IPSS-R), but also added substantial complexity. In this review, we highlight early MDS prognostic models, the significant advancements in MDS genomics since then, and the recent advent of molecular based prognostic models. We conclude by discussing important opportunities and challenges in the management of MDS as we arrive at the molecular frontier.
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Myeloid-Derived Suppressor Cells: New Insights into the Pathogenesis and Therapy of MDS. J Clin Med 2022; 11:jcm11164908. [PMID: 36013147 PMCID: PMC9410159 DOI: 10.3390/jcm11164908] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/15/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are hematopoietic malignancies characterized by the clonal expansion of hematopoietic stem cells, bone marrow failure manifested by cytopenias, and increased risk for evolving to acute myeloid leukemia. Despite the fact that the acquisition of somatic mutations is considered key for the initiation of the disease, the bone marrow microenvironment also plays significant roles in MDS by providing the right niche and even shaping the malignant clone. Aberrant immune responses are frequent in MDS and are implicated in many aspects of MDS pathogenesis. Recently, myeloid-derived suppressor cells (MDSCs) have gained attention for their possible implication in the immune dysregulation associated with MDS. Here, we summarize the key findings regarding the expansion of MDSCs in MDS, their role in MDS pathogenesis and immune dysregulation, as well their potential as a new therapeutic target for MDS.
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Nguyen-Khac F, Bidet A, Daudignon A, Lafage-Pochitaloff M, Ameye G, Bilhou-Nabéra C, Chapiro E, Collonge-Rame MA, Cuccuini W, Douet-Guilbert N, Eclache V, Luquet I, Michaux L, Nadal N, Penther D, Quilichini B, Terre C, Lefebvre C, Troadec MB, Véronèse L. The complex karyotype in hematological malignancies: a comprehensive overview by the Francophone Group of Hematological Cytogenetics (GFCH). Leukemia 2022; 36:1451-1466. [DOI: 10.1038/s41375-022-01561-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 12/16/2022]
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Nagarjun BR, Kalaharaghini R, Sawhney J, Trivedi PJ, Dhandapani K, Parikh B. Should We Look beyond Revised International Prognostic Scoring System: A Retrospective Observational Study of Progression of Myelodysplastic Syndrome to Acute Leukemia. Indian J Med Paediatr Oncol 2021. [DOI: 10.1055/s-0041-1736175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Abstract
Introduction Myelodysplastic syndrome (MDS) is a clonal stem cell disorder and heterogeneous condition resulting in peripheral cytopenias with marrow dysplasia due to ineffective hematopoiesis. The revised International Prognostic Scoring System (IPSS-R) predicts the risk of progression to acute leukemia (AL). Indian data on MDS and its progression to AL are limited. Additionally, the cytogenetic findings are dictated by patients' racial background. Study intended to analyze the cytogenetic profile of the patients with MDS.
Objectives This study aimed to (1) evaluate the clinicohematologic and morphologic spectrum of newly diagnosed MDS cases, (2) evaluate the cytogenetic profile of these cases, and (3) study the cases progressed to AL.
Materials and Methods MDS cases diagnosed and followed-up during a 5-year study period, from January 2015 to December 2019, were included in the study and the study was conducted at regional cancer center in Western India. De novo diagnosed MDS cases with complete workup were considered and MDS due to secondary causes were excluded. Baseline clinical, hematologic findings were tabulated along with cytogenetics and risk stratified as per IPSS-R, and their progression was studied.
Results A total of 63 cases of de novo MDS were diagnosed over a period of 5 years with 45 cases on follow-up and 15 cases (33.3%) progressed to AL. Maximum number of cases belonged to MDS-excess blast (EB) category accounting to 48 cases (76.1%). Apparently normal karyotyping was the commonest cytogenetic finding in 33 MDS cases (61.2%) and in 8 cases that progressed to AL (53.4%).
Conclusion MDS cases diagnosed at relatively early age were at higher risk of progression to AL. Majority of the cases that progressed to AL were risk stratified in high and very high risk groups and 10 cases which progressed to AL belonged to good category, interestingly apparent normal karyotyping was the commonest cytogenetic finding in more than 50% of the cases progressed to AL. Molecular mutations could only explain this progression and studies integrating molecular mutations with present IPSS-R scoring system should be conducted, as it could translate into better risk stratification and help in early identification and better management of cases at risk in progression to AL.
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Affiliation(s)
| | | | - Jyoti Sawhney
- Department of OncoPathology, The Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Pina J. Trivedi
- Department of OncoPathology, The Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Karthik Dhandapani
- Department of OncoPathology, The Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Biren Parikh
- Department of OncoPathology, The Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
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Sutandyo N, Rinaldi I, Mulya Sari R, Susanto Kosasih A, Setiawan L, Winston K. Rare Case of Multiple Lineage Dysplasia Myelodysplastic Syndrome Presenting with Only Anemia: A Case Report. Open Access Maced J Med Sci 2021. [DOI: 10.3889/oamjms.2021.6969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND: Myelodysplastic syndrome (MDS) is a heterogeneous group of hematopoietic stem cell disorders which is characterized by ineffective hematopoiesis and risk of progression into acute myeloid leukemia. The diagnosis and classification of MDS are determined from the findings of dysplasia in one or more cell lineage and the percentage of blast cell on bone marrow examination. However, it should be noted that an abnormality in one marrow cell lineage does not necessarily translate to the corresponding clinical phenotype. Here, we present a case of MDS with multilineage dysplasia (MLD) (erythrocyte, leukocyte, and thrombocyte) from bone marrow aspiration, but with anemia as the sole clinical manifestation (single cytopenia).
CASE REPORT: A 78-year-old male patient came to our clinic on July 10, 2020, with chief complaint of worsening fatigue which started approximately 1 year before visit. His vital signs during the visit were stable and no other abnormalities observed other than pale conjunctivae. Complete blood count showed macrocytic anemia with no abnormalities in leukocyte count and thrombocyte count, which suggested a single cytopenia. Peripheral blood smear was negative for megaloblasts and hypersegmented neutrophils. The patient’s bone marrow examination showed MDS with MLD. This result was in contrast to complete blood count examination which only showed anemia (single cytopenia).
CONCLUSION: This case showed that there could be discrepancy between clinical manifestations of the cytopenia with bone marrow dysplasia, which highlighted the importance of conducting bone marrow examination to properly classify MDS type.
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Killick SB, Wiseman DH, Quek L, Cargo C, Culligan D, Enright H, Green S, Ingram W, Jones GL, Kell J, Krishnamurthy P, Kulasekararaj A, Mills J, Mufti G, Payne EM, Raghavan M, Stanworth SJ, Sternberg A, Bowen D. British Society for Haematology guidelines for the diagnosis and evaluation of prognosis of Adult Myelodysplastic Syndromes. Br J Haematol 2021; 194:282-293. [PMID: 34137023 DOI: 10.1111/bjh.17621] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 12/20/2022]
Affiliation(s)
- Sally B Killick
- University Hospitals Dorset NHS Foundation Trust, The Royal Bournemouth Hospital, Bournemouth, UK
| | | | - Lynn Quek
- Kings College Hospital NHS Foundation Trust, London, UK
| | - Catherine Cargo
- St. James's Institute of Oncology, Leeds Teaching Hospitals, Leeds, UK
| | | | - Helen Enright
- Tallaght University Hospital, Trinity College Medical School, Dublin, Ireland
| | - Simone Green
- Hull and East Yorkshire Hospitals NHS Trust, Hull, UK
| | | | - Gail L Jones
- Newcastle Hospitals NHS Foundation Trust, Newcastle, UK
| | | | | | | | - Juliet Mills
- Worcestershire Acute Hospitals NHS Trust and Birmingham NHS Foundation Trust, Worcester, UK
| | - Ghulam Mufti
- Kings College Hospital NHS Foundation Trust, London, UK
| | | | - Manoj Raghavan
- University Hospitals Birmingham NHS foundation Trust, Birmingham, UK
| | - Simon J Stanworth
- Oxford University and Oxford University Hospitals NHS Trust & NHS Blood and Transplant, Oxford, UK
| | - Alex Sternberg
- Great Western Hospitals NHS Foundation Trust, Swindon, UK
| | - David Bowen
- St. James's Institute of Oncology, Leeds Teaching Hospitals, Leeds, UK
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Palomo L, Acha P, Solé F. Genetic Aspects of Myelodysplastic/Myeloproliferative Neoplasms. Cancers (Basel) 2021; 13:cancers13092120. [PMID: 33925681 PMCID: PMC8124412 DOI: 10.3390/cancers13092120] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary Myelodysplastic/myeloproliferative neoplasms (MDS/MPN) are clonal myeloid neoplasms characterized, at the time of their presentation, by the simultaneous presence of both myelodysplastic and myeloproliferative features. In MDS/MPN, the karyotype is often normal but mutations in genes that are common across myeloid neoplasms can be detected in a high proportion of cases by targeted sequencing. In this review, we intend to summarize the main genetic findings across all MDS/MPN overlap syndromes and discuss their relevance in the management of patients. Abstract Myelodysplastic/myeloproliferative neoplasms (MDS/MPN) are myeloid neoplasms characterized by the presentation of overlapping features from both myelodysplastic syndromes and myeloproliferative neoplasms. Although the classification of MDS/MPN relies largely on clinical features and peripheral blood and bone marrow morphology, studies have demonstrated that a large proportion of patients (~90%) with this disease harbor somatic mutations in a group of genes that are common across myeloid neoplasms. These mutations play a role in the clinical heterogeneity of these diseases and their clinical evolution. Nevertheless, none of them is specific to MDS/MPN and current diagnostic criteria do not include molecular data. Even when such alterations can be helpful for differential diagnosis, they should not be used alone as proof of neoplasia because some of these mutations may also occur in healthy older people. Here, we intend to review the main genetic findings across all MDS/MPN overlap syndromes and discuss their relevance in the management of the patients.
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Affiliation(s)
- Laura Palomo
- MDS Group, Institut de Recerca Contra la Leucèmia Josep Carreras, ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (L.P.); (P.A.)
- Experimental Hematology, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Pamela Acha
- MDS Group, Institut de Recerca Contra la Leucèmia Josep Carreras, ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (L.P.); (P.A.)
| | - Francesc Solé
- MDS Group, Institut de Recerca Contra la Leucèmia Josep Carreras, ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (L.P.); (P.A.)
- Correspondence: ; Tel.: +34-93-557-2806
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Ou Y, Yang Y, Yu H, Zhang X, Liu M, Wu Y. The prognostic significance of single-nucleotide polymorphism array-based whole-genome analysis and uniparental disomy in myelodysplastic syndrome. Int J Lab Hematol 2021; 43:1062-1069. [PMID: 33650312 PMCID: PMC8518839 DOI: 10.1111/ijlh.13502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/03/2021] [Accepted: 02/09/2021] [Indexed: 02/05/2023]
Abstract
Introduction Myelodysplastic syndrome (MDS) is a group of heterogeneous hematological diseases characterized by ineffective hematopoiesis and dysplastic morphology. Single nucleotide polymorphism array (SNP‐A)‐based whole genome analysis has a much higher resolution for chromosomal alterations when compared with conventional cytogenetic tools. In the present study, we evaluated the diagnostic value and prognostic significance of SNP‐A in MDS patients with normal karyotypes. Methods A total of 127 patients with MDS and myeloproliferative neoplasms or acute myeloid leukemia with myelodysplasia‐related changes were included in our study. The advantages and disadvantages of SNP‐A were compared with those of traditional metaphase cytogenetic analysis (MC). The Kaplan‐Meier analysis and COX regression analysis were used to investigate the prognostic value of SNP‐A and uniparental disomy (UPD) in MDS patients with normal karyotype. Furthermore, the chromosomal abnormalities detected by SNP‐A in patients with specific gene mutations were explored. Results SNP‐A was more sensitive toward meaningful chromosomal aberrations (58.2% vs 36.9%; P < .05) than MC. Among the patients with normal karyotype, those who were detected with new chromosomal abnormalities via SNP‐A presented with inferior survival compared with those without the abnormalities (P = .003). Additionally, the presence of UPD was an independent prognostic factor in patients with normal karyotype (P = .01). TP53 and RUNX1 mutations often occurred with abnormalities in chromosomes 17p and 21q, respectively. Conclusions Compared with MC, SNP‐A capable of detecting UPD can offer more diagnostic and prognostic information; TP53 and RUNX1 gene mutations are often accompanied by abnormalities in their chromosomes (17p, 22q).
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Affiliation(s)
- Yang Ou
- Department of Hematology and Hematology Research Laboratory, West China Hospital, Sichuan University, Chengdu, China
| | - Yan Yang
- Department of Hematology and Hematology Research Laboratory, West China Hospital, Sichuan University, Chengdu, China
| | - Hongbin Yu
- Department of Hematology and Hematology Research Laboratory, West China Hospital, Sichuan University, Chengdu, China
| | - Xin Zhang
- Department of Hematology and Hematology Research Laboratory, West China Hospital, Sichuan University, Chengdu, China
| | - Min Liu
- Department of Hematology and Hematology Research Laboratory, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Wu
- Department of Hematology and Hematology Research Laboratory, West China Hospital, Sichuan University, Chengdu, China
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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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Ronaghy A, Yang RK, Khoury JD, Kanagal-Shamanna R. Clinical Applications of Chromosomal Microarray Testing in Myeloid Malignancies. Curr Hematol Malig Rep 2020; 15:194-202. [PMID: 32382988 DOI: 10.1007/s11899-020-00578-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
PURPOSE OF REVIEW Knowledge of both somatic mutations and copy number aberrations are important for the understanding of cancer pathogenesis and management of myeloid neoplasms. The currently available standard of care technologies for copy number assessment such as conventional karyotype and FISH are either limited by low resolution or restriction to targeted assessment. RECENT FINDINGS Chromosomal microarray (CMA) is effective in characterization of chromosomal and gene aberrations of diagnostic, prognostic, and therapeutic significance at a higher resolution than conventional karyotyping. These results are complementary to NGS mutation studies. Copy-neutral loss of heterozygosity (CN-LOH), which is prognostic in AML, is currently only identified by CMA. Yet, despite the widespread availability, CMA testing is not routinely performed in diagnostic laboratories due to lack of knowledge on best-testing practices for clinical work-up of myeloid neoplasms. In this review, we provide an overview of the clinical significance of CMA in acute myeloid leukemia (AML), myelodysplastic syndromes (MDS), and myelodysplastic/myeloproliferative neoplasms (MDS/MPN). We will also elaborate the specific clinical scenarios where CMA can provide additional information essential for management and could potentially alter treatment. Chromosomal microarray (CMA) is an effective technology for characterizing chromosomal copy number changes and copy-neutral loss of heterozygosity of diagnostic, prognostic, and therapeutic significance at a high resolution in myeloid malignancies.
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MESH Headings
- Chromosome Aberrations
- Chromosomes, Human
- Comparative Genomic Hybridization
- DNA Copy Number Variations
- Genetic Predisposition to Disease
- High-Throughput Nucleotide Sequencing
- Humans
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myelomonocytic, Chronic/diagnosis
- Leukemia, Myelomonocytic, Chronic/genetics
- Loss of Heterozygosity
- Microarray Analysis
- Myelodysplastic Syndromes/diagnosis
- Myelodysplastic Syndromes/genetics
- Polymorphism, Single Nucleotide
- Predictive Value of Tests
- Prognosis
- Reproducibility of Results
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Affiliation(s)
- Arash Ronaghy
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 072, Houston, TX, 77030, USA
| | - Richard K Yang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 072, Houston, TX, 77030, USA
| | - Joseph D Khoury
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 072, Houston, TX, 77030, USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 072, Houston, TX, 77030, USA.
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14
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Awada H, Thapa B, Visconte V. The Genomics of Myelodysplastic Syndromes: Origins of Disease Evolution, Biological Pathways, and Prognostic Implications. Cells 2020; 9:E2512. [PMID: 33233642 PMCID: PMC7699752 DOI: 10.3390/cells9112512] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022] Open
Abstract
The molecular pathogenesis of myelodysplastic syndrome (MDS) is complex due to the high rate of genomic heterogeneity. Significant advances have been made in the last decade which elucidated the landscape of molecular alterations (cytogenetic abnormalities, gene mutations) in MDS. Seminal experimental studies have clarified the role of diverse gene mutations in the context of disease phenotypes, but the lack of faithful murine models and/or cell lines spontaneously carrying certain gene mutations have hampered the knowledge on how and why specific pathways are associated with MDS pathogenesis. Here, we summarize the genomics of MDS and provide an overview on the deregulation of pathways and the latest molecular targeted therapeutics.
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Affiliation(s)
- Hassan Awada
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44106, USA;
| | - Bicky Thapa
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI 53226, USA;
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44106, USA;
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15
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Cytogenetics in the genomic era. Best Pract Res Clin Haematol 2020; 33:101196. [DOI: 10.1016/j.beha.2020.101196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/30/2020] [Accepted: 05/27/2020] [Indexed: 02/06/2023]
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16
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Laurent AP, Kotecha RS, Malinge S. Gain of chromosome 21 in hematological malignancies: lessons from studying leukemia in children with Down syndrome. Leukemia 2020; 34:1984-1999. [PMID: 32433508 PMCID: PMC7387246 DOI: 10.1038/s41375-020-0854-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/22/2020] [Accepted: 04/28/2020] [Indexed: 12/31/2022]
Abstract
Structural and numerical alterations of chromosome 21 are extremely common in hematological malignancies. While the functional impact of chimeric transcripts from fused chromosome 21 genes such as TEL-AML1, AML1-ETO, or FUS-ERG have been extensively studied, the role of gain of chromosome 21 remains largely unknown. Gain of chromosome 21 is a frequently occurring aberration in several types of acute leukemia and can be found in up to 35% of cases. Children with Down syndrome (DS), who harbor constitutive trisomy 21, highlight the link between gain of chromosome 21 and leukemogenesis, with an increased risk of developing acute leukemia compared with other children. Clinical outcomes for DS-associated leukemia have improved over the years through the development of uniform treatment protocols facilitated by international cooperative groups. The genetic landscape has also recently been characterized, providing an insight into the molecular pathogenesis underlying DS-associated leukemia. These studies emphasize the key role of trisomy 21 in priming a developmental stage and cellular context susceptible to transformation, and have unveiled its cooperative function with additional genetic events that occur during leukemia progression. Here, using DS-leukemia as a paradigm, we aim to integrate our current understanding of the role of trisomy 21, of critical dosage-sensitive chromosome 21 genes, and of associated mechanisms underlying the development of hematological malignancies. This review will pave the way for future investigations on the broad impact of gain of chromosome 21 in hematological cancer, with a view to discovering new vulnerabilities and develop novel targeted therapies to improve long term outcomes for DS and non-DS patients.
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Affiliation(s)
- Anouchka P Laurent
- INSERM U1170, Gustave Roussy Institute, Université Paris Saclay, Villejuif, France
- Université Paris Diderot, Paris, France
| | - Rishi S Kotecha
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Western Australia, Australia
- Department of Clinical Haematology, Oncology and Bone Marrow Transplantation, Perth Children's Hospital, Perth, Western Australia, Australia
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Sébastien Malinge
- INSERM U1170, Gustave Roussy Institute, Université Paris Saclay, Villejuif, France.
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia.
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17
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Xiao X, He X, Li Q, Zhang W, Zhu H, Yang W, Li Y, Geng L, Liu H, Li L, Wang H, Fu R, Zhao M, Chen Z, Shao Z. Single-Nucleotide Polymorphism Array Technique Generating Valuable Risk-Stratification Information for Patients With Myelodysplastic Syndromes. Front Oncol 2020; 10:962. [PMID: 32733790 PMCID: PMC7358551 DOI: 10.3389/fonc.2020.00962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 05/15/2020] [Indexed: 11/13/2022] Open
Abstract
Background: Chromosomal abnormalities play an important role in the diagnosis and prognosis of patients with myelodysplastic syndromes (MDSs). The single-nucleotide polymorphism array (SNP-A) technique has gained popularity due to its improved resolution compared to that of metaphase cytogenetic (MC) analysis. Methods: A total of 376 individuals were recruited from two medical centers in China, including 350 patients and 26 healthy individuals. Among these patients, 200 were diagnosed with de novo MDS, 25 with myeloproliferative neoplasm (MPN), 63 with primary acute myeloid leukemia (AML), and 62 with idiopathic cytopenia of undetermined significance (ICUS). We evaluated the significance of abnormal chromosomes detected by SNP-A in the diagnosis and prognosis of MDS-related disorders. Results: (1) When certain chromosomal abnormalities could not be detected by conventional MC methods, these abnormalities could be detected more efficiently by the SNP-A method. With SNP-A, the detection rates of submicroscopic or cryptic aberrations in the MDS, MPN, and AML patients with normal MC findings were 32.8, 30.8, and 30%, respectively. (2) The chromosomal abnormalities detected by SNP-A had a very important value for the prognosis of patients with MDSs, especially in the low-risk group. The survival of patients with abnormal chromosomes detected by SNP-A was significantly lower than that of patients with no detected chromosomal abnormalities; this difference was observed in overall survival (OS) (P = 0.001) and progression-free survival (PFS) [24 months vs. not reach (NR); P = 0.008]. The patients with multiple chromosomal abnormalities detected by SNP-A had an inferior prognosis, and SNP-A abnormalities (≥3 per patient) were found to be an independent predictor of poor prognosis in patients with MDSs [hazard ratio (HR) = 2.40, P = 0.002]. (3) Patients with ICUS may progress to myeloid malignancies, but most patients often maintain a stable ICUS status for many years without progression. An ICUS patient found to have an MDS-related karyotype would be rediagnosed with MDS. SNP-A can efficiently detect chromosomal abnormalities, which would be important for assessing the evolution of ICUS. In our study, 17 ICUS patients with SNP-A-detected abnormalities developed typical MDSs. Conclusions: SNP-A can help evaluate the prognosis of patients with MDSs and better assess the risk of disease progression for patients with ICUS.
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Affiliation(s)
- Xia Xiao
- Department of Hematology, Tianjin First Central Hospital, Tianjin, China
| | - Xiaoyuan He
- Department of Clinical Medicine, Nankai University School of Medicine, Tianjin, China
| | - Qing Li
- Department of Hematology, Tianjin First Central Hospital, Tianjin, China
| | - Wei Zhang
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Haibo Zhu
- Department of Hematology, Tianjin First Central Hospital, Tianjin, China
| | - Weihong Yang
- Wuhan Kindstar Diagnostics Co./Kindstar Global Gene (Beijing) Technology, Inc., Wuhan, China
| | - Yuming Li
- Department of Hematology, Tianjin First Central Hospital, Tianjin, China
| | - Li Geng
- Department of Hematology, Tianjin First Central Hospital, Tianjin, China
| | - Hui Liu
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Lijuan Li
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Huaquan Wang
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Rong Fu
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Mingfeng Zhao
- Department of Hematology, Tianjin First Central Hospital, Tianjin, China.,Department of Clinical Medicine, Nankai University School of Medicine, Tianjin, China
| | - Zhong Chen
- Wuhan Kindstar Diagnostics Co./Kindstar Global Gene (Beijing) Technology, Inc., Wuhan, China
| | - Zonghong Shao
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
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18
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Svobodova K, Lhotska H, Hodanova L, Pavlistova L, Vesela D, Belickova M, Vesela J, Brezinova J, Sarova I, Izakova S, Lizcova L, Siskova M, Jonasova A, Cermak J, Michalova K, Zemanova Z. Cryptic aberrations may allow more accurate prognostic classification of patients with myelodysplastic syndromes and clonal evolution. Genes Chromosomes Cancer 2020; 59:396-405. [PMID: 32170980 DOI: 10.1002/gcc.22841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/03/2020] [Accepted: 02/29/2020] [Indexed: 11/05/2022] Open
Abstract
The karyotype of bone-marrow cells at the time of diagnosis is one of the most important prognostic factors in patients with myelodysplastic syndromes (MDS). In some cases, the acquisition of additional genetic aberrations (clonal evolution [CE]) associated with clinical progression may occur during the disease. We analyzed a cohort of 469 MDS patients using a combination of molecular cytogenomic methods to identify cryptic aberrations and to assess their potential role in CE. We confirmed CE in 36 (8%) patients. The analysis of bone-marrow samples with a combination of cytogenomic methods at diagnosis and after CE identified 214 chromosomal aberrations. The early genetic changes in the diagnostic samples were frequently MDS specific (17 MDS-specific/57 early changes). Most progression-related aberrations identified after CE were not MDS specific (131 non-MDS-specific/155 progression-related changes). Copy number neutral loss of heterozygosity (CN-LOH) was detected in 19% of patients. MDS-specific CN-LOH (4q, 17p) was identified in three patients, and probably pathogenic homozygous mutations were found in TET2 (4q24) and TP53 (17p13.1) genes. We observed a statistically significant difference in overall survival (OS) between the groups of patients divided according to their diagnostic cytogenomic findings, with worse OS in the group with complex karyotypes (P = .021). A combination of cytogenomic methods allowed us to detect many cryptic genomic changes and identify genes and genomic regions that may represent therapeutic targets in patients with progressive MDS.
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Affiliation(s)
- Karla Svobodova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic.,First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Halka Lhotska
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Lucie Hodanova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Lenka Pavlistova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Denisa Vesela
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Monika Belickova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Jitka Vesela
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Jana Brezinova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Iveta Sarova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic.,Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Silvia Izakova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Libuse Lizcova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Magda Siskova
- First Medical Department, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Anna Jonasova
- First Medical Department, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Jaroslav Cermak
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Kyra Michalova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Zuzana Zemanova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic.,First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
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19
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Durrani J, Maciejewski JP. Idiopathic aplastic anemia vs hypocellular myelodysplastic syndrome. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2019; 2019:97-104. [PMID: 31808900 PMCID: PMC6913491 DOI: 10.1182/hematology.2019000019] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Proper diagnostic distinction of bone marrow failure syndromes can often be challenging. In particular, for older patients with idiopathic aplastic anemia (AA), differential diagnosis includes myelodysplastic syndrome (MDS), which can atypically present in a hypocellular form. In addition to blasts and overt dysplasia, the presence of chromosomal abnormalities and a spectrum of somatic mutations may be revealing. Both clonal cytogenetic aberrations and somatic mutations most typically correspond to a clonal myelodysplasia, but clonal somatic mutations have also recently been found in AA. True driver myeloid mutations are uncommon in AA. Marrow hypocellularity in AA and occasionally in MDS patients points toward a similar immune mechanism responsible for deficient blood cell production and indicates that cytopenias in early hypocellular MDS might be treated with immunosuppressive modalities. Primary hypocellular MDS has to be distinguished from post-AA secondary MDS, most commonly associated with del7/7q. Post-AA MDS evolves at the rate of about 10% in 10 years, but recent observations suggest that widespread use of eltrombopag may influence the risk of progression to MDS. This complication likely represents a clonal escape, with founder hits occurring early on in the course of AA. A similar mechanism operates in the evolution of paroxysmal nocturnal hemoglobinuria (PNH) in AA patients, but PNH clones are rarely encountered in primary MDS.
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Affiliation(s)
- Jibran Durrani
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
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20
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Tuna M, Liu W, Amos CI, Mills GB. Genome-Wide Profiling of Acquired Uniparental Disomy Reveals Prognostic Factors in Head and Neck Squamous Cell Carcinoma. Neoplasia 2019; 21:1102-1109. [PMID: 31734631 PMCID: PMC6889229 DOI: 10.1016/j.neo.2019.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 08/22/2019] [Accepted: 08/26/2019] [Indexed: 01/04/2023] Open
Abstract
Acquired uniparental disomy (aUPD) leads to homozygosity facilitating identification of monoallelically expressed genes. We analyzed single-nucleotide polymorphism array-based genotyping data of 448 head and neck squamous cell carcinoma (HNSCC) samples from The Cancer Genome Atlas to determine the frequency and distribution of aUPD regions and their association with survival, as well as to gain a better understanding of their influence on the tumor genome. We used expression data from the same dataset to identify differentially expressed genes between groups with and without aUPD. Univariate and multivariable Cox proportional hazards models were performed for survival analysis. We found that 82.14% of HNSCC samples carried aUPD; the most common regions were in chromosome 17p (31.25%), 9p (30.13%), and 9q (27.46%). In univariate analysis, five independent aUPD regions at chromosome 9p, two regions at chromosome 9q, and the CDKN2A region were associated with poor overall survival in all groups, including training and test sets and human papillomavirus (HPV)-negative samples. Forty-three genes in areas of aUPD including PD-L1 and CDKN2A were differentially expressed in samples with aUPD compared to samples without aUPD. In multivariable analysis, aUPD at the CDKN2A region was a significant predictor of overall survival in the whole cohort and in patients with HPV-negative HNSCC. aUPD at specific regions in the genome influences clinical outcomes of HNSCC and may be beneficial for selection of personalized therapy to prolong survival in patients with this disease.
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Affiliation(s)
- Musaffe Tuna
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Medicine, Baylor College of Medicine, Houston, TX.
| | - Wenbin Liu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Cell, Developmental & Cancer Biology, School of Medicine, Oregon Health Science University, Portland, OR; Precision Oncology, Knight Cancer Institute, Portland, OR
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21
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Li J, Li J, Li J, Yao H, Liu F, Gusella JF, Shi X, Chen X. A rare case of acquired immunodeficiency associated with myelodysplastic syndrome. Mol Genet Genomic Med 2019; 7:e923. [PMID: 31503426 PMCID: PMC6825869 DOI: 10.1002/mgg3.923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/13/2019] [Accepted: 07/17/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Pediatric myelodysplastic syndromes (MDS) display clonal genomic instability that can lead to acquisition of other hematological disorders, usually by loss of heterozygosity. Immunodeficiency caused by uniparental disomy (UPD) has not previously been reported. METHODS We investigated a 13-year-old boy who suffered from recurrent infections and pancytopenia for 1 year. Both the comet assay and chromosome breakage analysis were normal, but the bone marrow showed evidence of dysplasia characteristic of MDS. With his normal sister as donor, he underwent failed hematopoietic stem cell transplantation (HSCT) with reduced intensity conditioning (RIC) followed by successful HSCT with myeloablative conditioning (MAC). We used single nucleotide polymorphism (SNP) array, targeted gene panel, and whole exome sequencing to investigate the etiology of his disease. RESULTS The molecular analyses revealed multiple regions of homozygosity, one region encompassing a homozygous missense variant of recombination activating gene 1 (RAG1) which was previously associated with severe immunodeficiency in infancy. This RAG1 mutation was heterozygous in the proband's fingernail DNA, but was changed to homozygous in the proband's marrow by somatic acquisition of UPD event. No other pathogenic driver mutation for MDS-related genes was identified. CONCLUSION The hematological phenotype, somatic genomic instability, and response to HSCT MAC but not HSCT RIC deduced to a diagnosis of MDS type refractory cytopenia of children in this patient. His immunodeficiency was secondary to MDS due to somatic acquisition of homozygosity for known pathogenic RAG1 mutation.
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Affiliation(s)
- Juanjuan Li
- Department of HematologyAffiliated Children’s Hospital of Capital Institute of PediatricsBeijingChina
| | - Junhui Li
- Department of HematologyAffiliated Children’s Hospital of Capital Institute of PediatricsBeijingChina
| | - Jianguo Li
- Department of RheumatologyAffiliated Children’s Hospital of Capital Institute of PediatricsBeijingChina
| | - Hailan Yao
- Department of Molecular ImmunologyCapital Institute of PediatricsBeijingChina
| | - Fang Liu
- Department of Medical Genetics, Beijing Municipal Key Laboratory of Child Development and NutriomicsCapital Institute of PediatricsBeijingChina
| | - James F Gusella
- Molecular Neurogenetics Unit, Center for Genomic MedicineMassachusetts General HospitalBostonMassachusettsUSA
| | - Xiaodong Shi
- Department of HematologyAffiliated Children’s Hospital of Capital Institute of PediatricsBeijingChina
| | - Xiaoli Chen
- Department of Medical Genetics, Beijing Municipal Key Laboratory of Child Development and NutriomicsCapital Institute of PediatricsBeijingChina
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22
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Walker CJ, Kohlschmidt J, Eisfeld AK, Mrózek K, Liyanarachchi S, Song C, Nicolet D, Blachly JS, Bill M, Papaioannou D, Oakes CC, Giacopelli B, Genutis LK, Maharry SE, Orwick S, Archer KJ, Powell BL, Kolitz JE, Uy GL, Wang ES, Carroll AJ, Stone RM, Byrd JC, de la Chapelle A, Bloomfield CD. Genetic Characterization and Prognostic Relevance of Acquired Uniparental Disomies in Cytogenetically Normal Acute Myeloid Leukemia. Clin Cancer Res 2019; 25:6524-6531. [PMID: 31375516 DOI: 10.1158/1078-0432.ccr-19-0725] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/06/2019] [Accepted: 07/30/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Uniparental disomy (UPD) is a way cancer cells duplicate a mutated gene, causing loss of heterozygosity (LOH). Patients with cytogenetically normal acute myeloid leukemia (CN-AML) do not have microscopically detectable chromosome abnormalities, but can harbor UPDs. We examined the prognostic significance of UPDs and frequency of LOH in patients with CN-AML.Experimental Design: We examined the frequency and prognostic significance of UPDs in a set of 425 adult patients with de novo CN-AML who were previously sequenced for 81 genes typically mutated in cancer. Associations of UPDs with outcome were analyzed in the 315 patients with CN-AML younger than 60 years. RESULTS We detected 127 UPDs in 109 patients. Most UPDs were large and typically encompassed all or most of the affected chromosome arm. The most common UPDs occurred on chromosome arms 13q (7.5% of patients), 6p (2.8%), and 11p (2.8%). Many UPDs significantly cooccurred with mutations in genes they encompassed, including 13q UPD with FLT3-internal tandem duplication (FLT3-ITD; P < 0.001), and 11p UPD with WT1 mutations (P = 0.02). Among patients younger than 60 years, UPD of 11p was associated with longer overall survival (OS) and 13q UPD with shorter disease-free survival (DFS) and OS. In multivariable models that accounted for known prognostic markers, including FLT3-ITD and WT1 mutations, UPD of 13q maintained association with shorter DFS, and UPD of 11p maintained association with longer OS. CONCLUSIONS LOH mediated by UPD is a recurrent feature of CN-AML. Detection of UPDs of 13q and 11p might be useful for genetic risk stratification of patients with CN-AML.
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Affiliation(s)
| | - Jessica Kohlschmidt
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio.,Alliance Statistics and Data Center, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | | | - Krzysztof Mrózek
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | | | - Chi Song
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, Ohio
| | - Deedra Nicolet
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio.,Alliance Statistics and Data Center, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - James S Blachly
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Marius Bill
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | | | | | - Brian Giacopelli
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Luke K Genutis
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Sophia E Maharry
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Shelley Orwick
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Kellie J Archer
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio.,Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, Ohio
| | - Bayard L Powell
- Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, North Carolina
| | - Jonathan E Kolitz
- Monter Cancer Center, Zucker School of Medicine at Hofstra/Northwell, Lake Success, New York
| | - Geoffrey L Uy
- Washington University School of Medicine in St. Louis, Siteman Cancer Center, St. Louis, Missouri
| | - Eunice S Wang
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | | | | | - John C Byrd
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
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23
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Chen C, Heng EYH, Lim AST, Lau LC, Lim TH, Wong GC, Tien SL. Chromosomal microarray analysis is superior in identifying cryptic aberrations in patients with acute lymphoblastic leukemia at diagnosis/relapse as a single assay. Int J Lab Hematol 2019; 41:561-571. [PMID: 31112375 DOI: 10.1111/ijlh.13052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 04/23/2019] [Accepted: 04/27/2019] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Conventional cytogenetics (CC) is important in diagnosis, therapy, monitoring of post-transplant bone marrow, and prognosis assessment of acute lymphoblastic leukemia (ALL). However, due to the nature of ALL, CC often encounters difficulties of complex karyotype, poor chromosome morphology, low mitotic index, or normal cells dividing only. In contrast, chromosomal microarray analysis (CMA) showed a specificity >99% and a sensitivity of 100% in chronic lymphocytic leukemia (CLL) patients. Here, we report our experience with CMA on adult ALL patients. METHODS Thirty-three bone marrow/blood samples from ALL patients (aged 18-79 years, median 44) at diagnosis/relapse, analyzed by CC and/or fluorescence in situ hybridization (FISH), were recruited. Chromosomal microarray analysis results were compared with CC. Fluorescence in situ hybridization analysis, if available, was applied when there was a discrepancy. RESULTS Copy-neutral loss-of-heterozygosity (CN-LOH) was found in 8 cases (24.2%). Only CN-LOH at 9p was recurrent (3 cases, 9.1%). Copy number alterations (CNAs) were detected in 6 of 9 cases (66.7%) with normal karyotypes, in 3 of 5 cases (60.0%) with sole "balanced" translocations, and in 18 of 19 cases (94.7%) with complex karyotypes. Common CNAs involved CDKN2A/2B (30.3%), IKZF1 (27.3%), PAX5 (9.1%), RB1 (9.1%), BTG1 (6.7%), and ETV6 (6.7%), which regulate cell cycle, B lymphopoiesis, or act as tumor suppressors in ALL. Copy number alteration detection rate by CMA was 81.8% (27 of 33 cases) as compared to 57.6% (19 of 33 cases) by CC. CONCLUSION Incorporation of CMA as a routine clinical test at the time of diagnosis/relapse, in conjunction with CC and/or FISH, is highly recommended.
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Affiliation(s)
- Chuanfei Chen
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Evelyn Yee Hsieh Heng
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Alvin Soon Tiong Lim
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Lai Ching Lau
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Tse Hui Lim
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Gee Chuan Wong
- Department of Haematology, Singapore General Hospital, Singapore, Singapore
| | - Sim Leng Tien
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore.,Department of Haematology, Singapore General Hospital, Singapore, Singapore
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Genetic abnormalities and pathophysiology of MDS. Int J Clin Oncol 2019; 24:885-892. [DOI: 10.1007/s10147-019-01462-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 04/28/2019] [Indexed: 12/14/2022]
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25
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Walen KH. Genomic Instability in Cancer II: 4N-Skewed (90°) Reductive Division via Fragile Sites to Fitness Increase for Solid and Hematological Cancer Beginnings. ACTA ACUST UNITED AC 2019. [DOI: 10.4236/jct.2019.107045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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Assessing copy number abnormalities and copy-neutral loss-of-heterozygosity across the genome as best practice in diagnostic evaluation of acute myeloid leukemia: An evidence-based review from the cancer genomics consortium (CGC) myeloid neoplasms working group. Cancer Genet 2018; 228-229:218-235. [DOI: 10.1016/j.cancergen.2018.07.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/26/2018] [Accepted: 07/30/2018] [Indexed: 12/19/2022]
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27
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Kanagal-Shamanna R, Hodge JC, Tucker T, Shetty S, Yenamandra A, Dixon-McIver A, Bryke C, Huxley E, Lennon PA, Raca G, Xu X, Jeffries S, Quintero-Rivera F, Greipp PT, Slovak ML, Iqbal MA, Fang M. Assessing copy number aberrations and copy neutral loss of heterozygosity across the genome as best practice: An evidence based review of clinical utility from the cancer genomics consortium (CGC) working group for myelodysplastic syndrome, myelodysplastic/myeloproliferative and myeloproliferative neoplasms. Cancer Genet 2018; 228-229:197-217. [PMID: 30377088 DOI: 10.1016/j.cancergen.2018.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 07/27/2018] [Accepted: 07/30/2018] [Indexed: 12/16/2022]
Abstract
Multiple studies have demonstrated the utility of chromosomal microarray (CMA) testing to identify clinically significant copy number alterations (CNAs) and copy-neutral loss-of-heterozygosity (CN-LOH) in myeloid malignancies. However, guidelines for integrating CMA as a standard practice for diagnostic evaluation, assessment of prognosis and predicting treatment response are still lacking. CMA has not been recommended for clinical work-up of myeloid malignancies by the WHO 2016 or the NCCN 2017 guidelines but is a suggested test by the European LeukaemiaNet 2013 for the diagnosis of primary myelodysplastic syndrome (MDS). The Cancer Genomics Consortium (CGC) Working Group for Myeloid Neoplasms systematically reviewed peer-reviewed literature to determine the power of CMA in (1) improving diagnostic yield, (2) refining risk stratification, and (3) providing additional genomic information to guide therapy. In this manuscript, we summarize the evidence base for the clinical utility of array testing in the workup of MDS, myelodysplastic/myeloproliferative neoplasms (MDS/MPN) and myeloproliferative neoplasms (MPN). This review provides a list of recurrent CNAs and CN-LOH noted in this disease spectrum and describes the clinical significance of the aberrations and how they complement gene mutation findings by sequencing. Furthermore, for new or suspected diagnosis of MDS or MPN, we present suggestions for integrating genomic testing methods (CMA and mutation testing by next generation sequencing) into the current standard-of-care clinical laboratory testing (karyotype, FISH, morphology, and flow).
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Affiliation(s)
- Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston TX, USA.
| | - Jennelle C Hodge
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pediatrics, University of California Los Angeles, Los Angeles, CA, USA; Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tracy Tucker
- Department of Pathology and Laboratory Medicine, Cancer Genetics Laboratory, British Columbia Cancer Agency, Vancouver, BC Canada
| | - Shashi Shetty
- Department of Pathology, UHCMC, University Hospitals and Case Western Reserve University, Cleveland, OH, USA
| | - Ashwini Yenamandra
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Christine Bryke
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Emma Huxley
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | | | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA, USA
| | - Xinjie Xu
- ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | - Sally Jeffries
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA
| | - Patricia T Greipp
- Department of Laboratory Medicine and Pathology, Genomics Laboratory, Mayo Clinic, Rochester, MN, USA
| | - Marilyn L Slovak
- TriCore Reference Laboratories, University of New Mexico, Albuquerque, NM, USA
| | - M Anwar Iqbal
- University of Rochester Medical Center, Rochester, NY, USA
| | - Min Fang
- Fred Hutchinson Cancer Research Center and University of Washington, Seattle, WA, USA.
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28
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Chronic immune response dysregulation in MDS pathogenesis. Blood 2018; 132:1553-1560. [PMID: 30104218 DOI: 10.1182/blood-2018-03-784116] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/03/2018] [Indexed: 12/18/2022] Open
Abstract
Chronic innate immune signaling in hematopoietic cells is widely described in myelodysplastic syndromes (MDS), and innate immune pathway activation, predominantly via pattern recognition receptors, increases the risk of developing MDS. An inflammatory component to MDS has been reported for many years, but only recently has evidence supported a more direct role of chronic innate immune signaling and associated inflammatory pathways in the pathogenesis of MDS. Here we review recent findings and discuss relevant questions related to chronic immune response dysregulation in MDS.
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Diagnostic, Prognostic, and Predictive Utility of Recurrent Somatic Mutations in Myeloid Neoplasms. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2018; 17S:S62-S74. [PMID: 28760304 DOI: 10.1016/j.clml.2017.02.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 02/28/2017] [Indexed: 02/02/2023]
Abstract
The classification and risk stratification of myeloid neoplasms, including acute myeloid leukemia, myelodysplastic syndromes, myelodysplastic syndromes/myeloproliferative neoplasms, and myeloproliferative neoplasms, have increasingly been guided by molecular genetic abnormalities. Gene expression analysis and next-generation sequencing have led to the ever increasing discovery of somatic gene mutations in myeloid neoplasms. Mutations have been identified in genes involved in epigenetic modification, RNA splicing, transcription factors, DNA repair, and the cohesin complex. These new somatic/acquired gene mutations have refined the classification of myeloid neoplasms and have been incorporated into the 2016 update of the World Health Organization (WHO) classification and the National Comprehensive Cancer Network guidelines. They have also been helpful in the development of new targeted therapeutic agents. In the present review, we describe the clinical utility of recently identified, clinically important gene mutations in myeloid neoplasms, including those incorporated in the 2016 update of the WHO classification.
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Yeung C, McElhone S, Chen XY, Ng D, Storer B, Deeg HJ, Fang M. Impact of copy neutral loss of heterozygosity and total genome aberrations on survival in myelodysplastic syndrome. Mod Pathol 2018; 31:569-580. [PMID: 29243741 PMCID: PMC5906151 DOI: 10.1038/modpathol.2017.157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 12/17/2022]
Abstract
Myelodysplastic syndromes (MDS) are a heterogeneous group of diseases with varying genetic aberrations. Half of MDS patients have normal karyotype, obscuring the underlying condition indicating a need for new markers for improved diagnostics and prognosis. We performed a retrospective review of sequential MDS patients who underwent chromosomal genetic array testing (CGAT) between November 2008 and March 2014. Total Genomic Aberration (TGA) scores, with and without copy-neutral loss of heterozygosity (cnLOH), were compared to pathology and clinical data. Of 68 MDS participants, 50 patients (73%) had abnormal CGAT results. 32% showedcnLOH, 41% had no cnLOH but displayed copy number aberration (CNAs). Of 26 patients with normal cytogenetics, 46% had clonal abnormalities by CGAT. Abnormal CGAT results were associated with lower overall survival (P=0.04). Overall survival in patients with TGA above the median (68.6 Mb) was significantly inferior to those below the median (HR=2.9, 95% CI=1.3-6.8, P=0.01). Furthermore, there was an observed association between increased TGA and increased dysplastic lineages (Ptrend=0.003). CGAT studies provide important findings that extend beyond current standard testing. Clinical utility of CGAT includes improved diagnostic yield, correlation of extent of TGA and increased dysplastic features, and survival.
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Affiliation(s)
- Cecilia Yeung
- Fred Hutchinson Cancer Research Center, Seattle, WA
- University of Washington, Seattle, WA
- Seattle Cancer Care Alliance, Seattle, WA
| | | | | | | | - Barry Storer
- Fred Hutchinson Cancer Research Center, Seattle, WA
- University of Washington, Seattle, WA
| | - H. Joachim Deeg
- Fred Hutchinson Cancer Research Center, Seattle, WA
- University of Washington, Seattle, WA
| | - Min Fang
- Fred Hutchinson Cancer Research Center, Seattle, WA
- University of Washington, Seattle, WA
- Seattle Cancer Care Alliance, Seattle, WA
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31
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Rego de Paula Junior M, Nonino A, Minuncio Nascimento J, Bonadio RS, Pic-Taylor A, de Oliveira SF, Wellerson Pereira R, do Couto Mascarenhas C, Forte Mazzeu J. High Frequency of Copy-Neutral Loss of Heterozygosity in Patients with Myelofibrosis. Cytogenet Genome Res 2018; 154:62-70. [DOI: 10.1159/000487627] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2017] [Indexed: 12/16/2022] Open
Abstract
Myelofibrosis is the rarest and most severe type of Philadelphia-negative classical myeloproliferative neoplasms. Although mutually exclusive driver mutations in JAK2, MPL, or CALR that activate JAK-STAT pathway have been related to the pathogenesis of the disease, chromosome abnormalities have also been associated with the phenotype and prognosis of the disease. Here, we report the use of a chromosomal microarray platform consisting of both oligo and SNP probes to improve the detection of chromosome abnormalities in patients with myelofibrosis. Sixteen patients with myelofibrosis were tested, and the results were compared to karyotype analysis. Driver mutations in JAK2, MPL, or CALR were investigated by PCR and MLPA. Conventional cytogenetics revealed chromosome abnormalities in 3 out of 16 cases (18.7%), while chromosomal microarray analysis detected copy-number variations (CNV) or copy-neutral loss of heterozygosity (CN-LOH) alterations in 11 out of 16 (68.7%) patients. These included 43 CN-LOH, 14 deletions, 1 trisomy, and 1 duplication. Ten patients showed multiple chromosomal abnormalities, varying from 2 to 13 CNVs or CN-LOHs. Mutational status for JAK2, CALR, and MPL by MLPA revealed a total of 3/16 (18.7%) patients positive for the JAK2 V617F mutation, 9 with CALR deletion or insertion and 1 positive for MPL mutation. Considering that most of the CNVs identified were smaller than the karyotype resolution and the high frequency of CN-LOHs in our study, we propose that chromosomal microarray platforms that combine oligos and SNP should be used as a first-tier genetic test in patients with myelofibrosis.
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33
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Grygalewicz B, Woroniecka R, Rymkiewicz G, Rygier J, Borkowska K, Kotyl A, Blachnio K, Bystydzienski Z, Nowakowska B, Pienkowska-Grela B. The 11q-Gain/Loss Aberration Occurs Recurrently in MYC-Negative Burkitt-like Lymphoma With 11q Aberration, as Well as MYC-Positive Burkitt Lymphoma and MYC-Positive High-Grade B-Cell Lymphoma, NOS. Am J Clin Pathol 2017; 149:17-28. [PMID: 29272887 PMCID: PMC5848380 DOI: 10.1093/ajcp/aqx139] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Objectives The latest revision of lymphoma’s World Health Organization classification describes the new provisional entity “Burkitt-like lymphoma with 11q aberration” (BLL, 11q) as lacking MYC rearrangement, but harboring the specific11q-gain/loss aberration. We report genetic characteristics of 11 lymphoma cases with this aberration. Methods Classical cytogenetics, fluorescence in situ hybridization (FISH), and single nucleotide polymorphism/array comparative genomic hybridization. Results The 11q aberrations were described as duplication, inversion, and deletion. Array comparative genomic hybridization showed two types of duplication: bigger than 50 megabase pairs (Mbp) and smaller than 20 Mbp, which were associated with bulky tumor larger than 20 cm and amplification of the 11q23.3 region, including KMT2A. Six cases revealed a normal FISH status of MYC and were diagnosed as BLL,11q. Five cases showed MYC rearrangement and were diagnosed as Burkitt lymphoma (BL) or high-grade B-cell lymphoma, not otherwise specified (HGBL, NOS). Conclusions The 11q-gain/loss is not specific for BLL, 11q, but occurs recurrently in MYC-positive BL and MYC-positive HGBL.
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Affiliation(s)
- Beata Grygalewicz
- Cytogenetic Laboratory, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Renata Woroniecka
- Cytogenetic Laboratory, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Grzegorz Rymkiewicz
- Cytogenetic Laboratory, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
- Flow Cytometry Laboratory, Pathology and Laboratory Diagnostics Department, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Jolanta Rygier
- Cytogenetic Laboratory, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Klaudia Borkowska
- Cytogenetic Laboratory, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Aleksandra Kotyl
- Cytogenetic Laboratory, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Katarzyna Blachnio
- Flow Cytometry Laboratory, Pathology and Laboratory Diagnostics Department, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Zbigniew Bystydzienski
- Flow Cytometry Laboratory, Pathology and Laboratory Diagnostics Department, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Beata Nowakowska
- Department of Medical Genetics, Mother and Child Institute, Warsaw, Poland
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Shen W, Paxton CN, Szankasi P, Longhurst M, Schumacher JA, Frizzell KA, Sorrells SM, Clayton AL, Jattani RP, Patel JL, Toydemir R, Kelley TW, Xu X. Detection of genome-wide copy number variants in myeloid malignancies using next-generation sequencing. J Clin Pathol 2017; 71:372-378. [PMID: 29197855 DOI: 10.1136/jclinpath-2017-204823] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/01/2017] [Accepted: 11/16/2017] [Indexed: 12/22/2022]
Abstract
AIMS Genetic abnormalities, including copy number variants (CNV), copy number neutral loss of heterozygosity (CN-LOH) and gene mutations, underlie the pathogenesis of myeloid malignancies and serve as important diagnostic, prognostic and/or therapeutic markers. Currently, multiple testing strategies are required for comprehensive genetic testing in myeloid malignancies. The aim of this proof-of-principle study was to investigate the feasibility of combining detection of genome-wide large CNVs, CN-LOH and targeted gene mutations into a single assay using next-generation sequencing (NGS). METHODS For genome-wide CNV detection, we designed a single nucleotide polymorphism (SNP) sequencing backbone with 22 762 SNP regions evenly distributed across the entire genome. For targeted mutation detection, 62 frequently mutated genes in myeloid malignancies were targeted. We combined this SNP sequencing backbone with a targeted mutation panel, and sequenced 9 healthy individuals and 16 patients with myeloid malignancies using NGS. RESULTS We detected 52 somatic CNVs, 11 instances of CN-LOH and 39 oncogenic mutations in the 16 patients with myeloid malignancies, and none in the 9 healthy individuals. All CNVs and CN-LOH were confirmed by SNP microarray analysis. CONCLUSIONS We describe a genome-wide SNP sequencing backbone which allows for sensitive detection of genome-wide CNVs and CN-LOH using NGS. This proof-of-principle study has demonstrated that this strategy can provide more comprehensive genetic profiling for patients with myeloid malignancies using a single assay.
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Affiliation(s)
- Wei Shen
- ARUP Laboratories, Salt Lake City, Utah, USA.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | | | | | | | | | | | | | | | | | - Jay L Patel
- ARUP Laboratories, Salt Lake City, Utah, USA.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Reha Toydemir
- ARUP Laboratories, Salt Lake City, Utah, USA.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Todd W Kelley
- ARUP Laboratories, Salt Lake City, Utah, USA.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Xinjie Xu
- ARUP Laboratories, Salt Lake City, Utah, USA.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
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Song Q, Chu Y, Yao Y, Peng M, Yang W, Li X, Huang S. Identify latent chromosomal aberrations relevant to myelodysplastic syndromes. Sci Rep 2017; 7:10354. [PMID: 28871208 PMCID: PMC5583229 DOI: 10.1038/s41598-017-10551-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 08/11/2017] [Indexed: 12/02/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are a group of heterogeneous hematologic malignancies. This study aims to identify latent chromosomal abnormalities relevant to MDS, which may optimize the current diagnosis of MDS. Affymetrix CytoScan 750 K microarray platform was utilized to perform a genome-wide detection of chromosomal aberrations in the bone marrow cells of the patients. The findings were compared with the results from traditional karyotypic analysis and FISH to reveal latent chromosomal aberrations. Chromosomal gain, loss, and UPD, and complex karyotypes were identified in those samples. In addition to established cytogenetic aberrations detected by karyotypic analysis, CytoScan 750 K microarray also detected cryptic chromosomal lesions in MDS. Those latent defects underlying multiple gene mutations may construe the clinical variability of MDS. In Conclusion, Affymetrix CytoScan 750 K microarray is efficient in identifying latent chromosomal aberrations in MDS.
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Affiliation(s)
- Qibin Song
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China.
| | - Yuxin Chu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yi Yao
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Min Peng
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Weihong Yang
- Molecular department, Kindstar global, Wuhan, China
| | - Xiaoqing Li
- Molecular department, Kindstar global, Wuhan, China
| | - Shiang Huang
- Molecular department, Kindstar global, Wuhan, China
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Cargo C, Bowen D. Individual risk assessment in MDS in the era of genomic medicine. Semin Hematol 2017; 54:133-140. [PMID: 28958286 DOI: 10.1053/j.seminhematol.2017.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/10/2017] [Indexed: 02/06/2023]
Abstract
Assessment of risk for patients with myelodysplastic syndromes has evolved from pure morphological bone marrow assessment to a series of validated prognostic scoring systems whose 'risk' assessment is of death (overall survival) or disease progression (AML transformation). The revised International Prognostic Scoring System (2012) improved the precision for prognosis but did not consider patient-specific factors such as comorbidity and performance status, which have a clear impact on outcome, particularly in lower-risk MDS. The improved understanding of MDS biology predominantly through genomic mutational analysis, flow cytometry and gene expression profiling poses a question regarding incorporation of these parameters into the existing scoring systems. Although some gene mutations have clear prognostic significance (e.g. SF3B1, TP53), there is no definitive and reproducible evidence that this additional knowledge will change management. Although incorporation of some of these novel data into risk assessment may be imminent, the IPSS-R remains the gold standard tool for everyday practice.
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Affiliation(s)
- Catherine Cargo
- Haematological Malignancies Diagnostic Service and Department of Haematology, Leeds Teaching Hospitals, St. James's Institute of Oncology, Beckett Street, Leeds UK
| | - David Bowen
- Department of Haematology, Leeds Teaching Hospitals, St. James's Institute of Oncology, Beckett Street, Leeds UK
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Pawlina-Tyszko K, Gurgul A, Szmatoła T, Ropka-Molik K, Semik-Gurgul E, Klukowska-Rötzler J, Koch C, Mählmann K, Bugno-Poniewierska M. Genomic landscape of copy number variation and copy neutral loss of heterozygosity events in equine sarcoids reveals increased instability of the sarcoid genome. Biochimie 2017; 140:122-132. [PMID: 28743673 DOI: 10.1016/j.biochi.2017.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/20/2017] [Indexed: 12/20/2022]
Abstract
Although they are the most common neoplasms in equids, sarcoids are not fully characterized at the molecular level. Therefore, the objective of this study was to characterize the landscape of structural rearrangements, such as copy number variation (CNV) and copy neutral loss of heterozygosity (cnLOH), in the genomes of sarcoid tumor cells. This information will not only broaden our understanding of the characteristics of this genome but will also improve the general knowledge of this tumor and the mechanisms involved in its generation. To this end, Equine SNP64K Illumina microarrays were applied along with bioinformatics tools dedicated for signal intensity analysis. The analysis revealed increased instability of the genome of sarcoid cells compared with unaltered skin tissue samples, which was manifested by the prevalence of CNV and cnLOH events. Many of the identified CNVs overlapped with the other research results, but the simultaneously observed variability in the number and sizes of detected aberrations indicated a need for further studies and the development of more reliable bioinformatics algorithms. The functional analysis of genes co-localized with the identified aberrations revealed that these genes are engaged in vital cellular processes. In addition, a number of these genes directly contribute to neoplastic transformation. Furthermore, large numbers of cnLOH events identified in the sarcoids suggested that they may play no less significant roles than CNVs in the carcinogenesis of this tumor. Thus, our results indicate the importance of cnLOH and CNV in equine sarcoid oncogenesis and present a direction of future research.
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Affiliation(s)
- Klaudia Pawlina-Tyszko
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Artur Gurgul
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Tomasz Szmatoła
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Katarzyna Ropka-Molik
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Ewelina Semik-Gurgul
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Jolanta Klukowska-Rötzler
- Division of Pedriatric Hematology/Oncology, Department of Clinical Research, University of Bern, Murtenstrasse 35, 3008, Bern, Switzerland; Department of Emergency Medicine, University Hospital Bern, Inselspital, 3010, Bern, Switzerland.
| | - Christoph Koch
- Swiss Institute of Equine Medicine ISME, Faculty of Veterinary Medicine, University of Bern and Agroscope, Länggassstrasse 124c, Postfach 8466, CH-3001, Bern, Switzerland.
| | - Kathrin Mählmann
- Swiss Institute of Equine Medicine ISME, Faculty of Veterinary Medicine, University of Bern and Agroscope, Länggassstrasse 124c, Postfach 8466, CH-3001, Bern, Switzerland; Equine Clinic: Surgery and Radiology, Department of Veterinary Medicine, Free University of Berlin, Oertzenweg 19b, 14163, Berlin, Germany.
| | - Monika Bugno-Poniewierska
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
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Cytogenetic Abnormalities in Myelodysplastic Syndromes: An Overview. Int J Hematol Oncol Stem Cell Res 2017; 11:231-239. [PMID: 28989590 PMCID: PMC5625474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Karyotype is one of the main constituents of the International Prognostic Scoring System (IPSS) and revised-IPSS that are the cornerstones for the prognostication of patients with myelodysplastic syndromes (MDS). Del(5q), -7/del(7q), +8 and -Y are among the most extensively studied cytogenetic abnormalities in MDS. The same applies for normal karyotype. There are hundreds of other rare cytogenetic abnormalities that have been reported in MDS, included but not limited to -X, 3q abnormalities, +13/del(13q), i(17q), +21/-21. However, due to a very low number of patients, their impact on the prognosis of MDS is limited. Knowledge of the molecular consequences of different cytogenetic abnormalities allows us to modify treatment regimens based on drugs most active against the specific karyotype present, allowing for the opportunity to individualize MDS treatment and improve patient care and prognosis.
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Jann JC, Nowak D, Nolte F, Fey S, Nowak V, Obländer J, Pressler J, Palme I, Xanthopoulos C, Fabarius A, Platzbecker U, Giagounidis A, Götze K, Letsch A, Haase D, Schlenk R, Bug G, Lübbert M, Ganser A, Germing U, Haferlach C, Hofmann WK, Mossner M. Accurate quantification of chromosomal lesions via short tandem repeat analysis using minimal amounts of DNA. J Med Genet 2017; 54:640-650. [PMID: 28600436 PMCID: PMC5574397 DOI: 10.1136/jmedgenet-2017-104528] [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: 01/10/2017] [Revised: 02/15/2017] [Accepted: 03/22/2017] [Indexed: 11/04/2022]
Abstract
Background Cytogenetic aberrations such as deletion of chromosome 5q (del(5q)) represent key elements in routine clinical diagnostics of haematological malignancies. Currently established methods such as metaphase cytogenetics, FISH or array-based approaches have limitations due to their dependency on viable cells, high costs or semi-quantitative nature. Importantly, they cannot be used on low abundance DNA. We therefore aimed to establish a robust and quantitative technique that overcomes these shortcomings. Methods For precise determination of del(5q) cell fractions, we developed an inexpensive multiplex-PCR assay requiring only nanograms of DNA that simultaneously measures allelic imbalances of 12 independent short tandem repeat markers. Results Application of this method to n=1142 samples from n=260 individuals revealed strong intermarker concordance (R²=0.77–0.97) and reproducibility (mean SD: 1.7%). Notably, the assay showed accurate quantification via standard curve assessment (R²>0.99) and high concordance with paired FISH measurements (R²=0.92) even with subnanogram amounts of DNA. Moreover, cytogenetic response was reliably confirmed in del(5q) patients with myelodysplastic syndromes treated with lenalidomide. While the assay demonstrated good diagnostic accuracy in receiver operating characteristic analysis (area under the curve: 0.97), we further observed robust correlation between bone marrow and peripheral blood samples (R²=0.79), suggesting its potential suitability for less-invasive clonal monitoring. Conclusions In conclusion, we present an adaptable tool for quantification of chromosomal aberrations, particularly in problematic samples, which should be easily applicable to further tumour entities.
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Affiliation(s)
- Johann-Christoph Jann
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
| | - Daniel Nowak
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
| | - Florian Nolte
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
| | - Stephanie Fey
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
| | - Verena Nowak
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
| | - Julia Obländer
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
| | - Jovita Pressler
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
| | - Iris Palme
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
| | - Christina Xanthopoulos
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
| | - Alice Fabarius
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
| | - Uwe Platzbecker
- Medizinische Klinik und Poliklinik I, Universitatsklinikum Carl Gustav Carus, Dresden, Germany
| | | | - Katharina Götze
- III. Medizinischen Klinik des Klinikums rechts der Isar, Technische Universitat Munchen, Munchen, Germany
| | - Anne Letsch
- Medizinische Klinik für Hämatologie, Onkologie, Campus Benjamin Franklin, Charite Universitatsmedizin Berlin, Berlin, Germany
| | - Detlef Haase
- Klinik für Hämatologie und Medizinische Onkologie, Georg-August-Universitat Gottingen Universitatsmedizin, Gottingen, Germany
| | - Richard Schlenk
- NCT Trial Center, Nationales Centrum für Tumorerkrankungen (NCT), Heidelberg, Gemany
| | - Gesine Bug
- Medizinische Klinik II, Abteilung für Hämatologie/Onkologie, Klinikum der Johann Wolfgang Goethe-Universitat Frankfurt, Frankfurt am Main, Germany
| | - Michael Lübbert
- Abteilung für Innere Medizin I, Hämatologie und Onkologie, Universitatsklinikum Freiburg, Freiburg, Germany
| | - Arnold Ganser
- Abteilung für Hämatologie, Hämostaseologie, Onkologie und Stammzelltransplantation, Medizinische Hochschule Hannover, Hannover, Germany
| | - Ulrich Germing
- Abteilung für Hämatologie, Onkologie und klinische Immunologie, Heinrich-Heine-Universitat Dusseldorf Medizinische Fakultat, Dusseldorf, Germany
| | | | - Wolf-Karsten Hofmann
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
| | - Maximilian Mossner
- III Medizinische Klinik, Hämatologie und Onkologie, Universitätsmedizin Mannheim, Mannheim, Germany
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Cull AH, Rauh MJ. Success in bone marrow failure? Novel therapeutic directions based on the immune environment of myelodysplastic syndromes. J Leukoc Biol 2017; 102:209-219. [DOI: 10.1189/jlb.5ri0317-083r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/03/2017] [Accepted: 05/04/2017] [Indexed: 11/24/2022] Open
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Chi K, Li Y, Xu L, Wang X. A novel recurrent copy number loss region on 6q23.3 in MDS-related myeloid malignancy patients with stable survival conditions. Leuk Lymphoma 2017; 58:2470-2479. [PMID: 28394181 DOI: 10.1080/10428194.2017.1292357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Metaphase cytogenetics (MC) karyotyping is a fundamental way to approach cytogenetic pathogenesis of MDS-related myeloid malignancies. However, in some patients, the results are normal while the patients often show discrepancies in survival conditions. To explain this question, we analyzed CytoScan™ HD array results of 20 MC-normal/failure patients who were followed up for three years. Exon sequencing was performed in genes RUNX1, TP53, ASXL1, and TET2. The array enabled the detection of additional aberrations in 16 (80%) patients. Eight patients were detected with cryptic copy number losses and six of them got aggressive disease conditions. RUNX1 mutations were sequenced in P110 and P114. Most importantly, two patients (P114 and P116) with copy number loss aberrations got stable survival conditions during follow-ups, and a novel recurrent copy number loss region harboring the proto-oncogene MYB was detected on chromosome 6q23.3 in both of them, which might benefit the survival of the patients.
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Affiliation(s)
- Kun Chi
- a Department of Laboratory Medicine , Qingdao Women & Children's Hospital , Qingdao , China.,b State Key Laboratory of Medical Genomics , Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine , Shanghai , China
| | - Yang Li
- b State Key Laboratory of Medical Genomics , Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine , Shanghai , China
| | - Lan Xu
- c Department of Hematology , Ruijin Hospital, Shanghai Jiaotong University School of Medicine , Shanghai , China
| | - Xuefeng Wang
- d Department of Laboratory Medicine , Ruijin Hospital, Shanghai Jiaotong University School of Medicine , Shanghai , China
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Stevens-Kroef MJ, Olde Weghuis D, ElIdrissi-Zaynoun N, van der Reijden B, Cremers EMP, Alhan C, Westers TM, Visser-Wisselaar HA, Chitu DA, Cunha SM, Vellenga E, Klein SK, Wijermans P, de Greef GE, Schaafsma MR, Muus P, Ossenkoppele GJ, van de Loosdrecht AA, Jansen JH. Genomic array as compared to karyotyping in myelodysplastic syndromes in a prospective clinical trial. Genes Chromosomes Cancer 2017; 56:524-534. [DOI: 10.1002/gcc.22455] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/16/2017] [Accepted: 02/16/2017] [Indexed: 02/06/2023] Open
Affiliation(s)
| | - Daniel Olde Weghuis
- Department of Human Genetics; Radboud University Medical Center; Nijmegen The Netherlands
| | | | - Bert van der Reijden
- Department of Laboratory Medicine; Radboud University Medical Center; Nijmegen The Netherlands
| | - Eline M. P. Cremers
- Department of Hematology; VU University Medical Center, Cancer Center Amsterdam; Amsterdam The Netherlands
| | - Canan Alhan
- Department of Hematology; VU University Medical Center, Cancer Center Amsterdam; Amsterdam The Netherlands
| | - Theresia M. Westers
- Department of Hematology; VU University Medical Center, Cancer Center Amsterdam; Amsterdam The Netherlands
| | - Heleen A. Visser-Wisselaar
- Department of Hematology; Erasmus MC Cancer Institute, HOVON Data Center, Erasmus University Medical Center-Daniel den Hoed; Rotterdam The Netherlands
| | - Dana A. Chitu
- Department of Hematology; Erasmus MC Cancer Institute, HOVON Data Center, Erasmus University Medical Center-Daniel den Hoed; Rotterdam The Netherlands
| | - Sonia M. Cunha
- Department of Hematology; Erasmus MC Cancer Institute, HOVON Data Center, Erasmus University Medical Center-Daniel den Hoed; Rotterdam The Netherlands
| | - Edo Vellenga
- Department of Experimental Hematology; University Medical Center Groningen; Groningen The Netherlands
| | - Saskia K. Klein
- Department of Internal Medicine; Meander Medisch Centrum; Amersfoort The Netherlands
| | - Pierre Wijermans
- Department of Internal Medicine; Haga Ziekenhuis; The Hague The Netherlands
| | - Georgine E. de Greef
- Department of Hematology; Erasmus University Medical Center-Daniel den Hoed; Rotterdam The Netherlands
| | - M. Ron Schaafsma
- Department of Internal Medicine; Medisch Centrum Twente; Enschede The Netherlands
| | - Petra Muus
- Department of Hematology; Radboud University Medical Center; Nijmegen The Netherlands
| | - Gert J. Ossenkoppele
- Department of Hematology; VU University Medical Center, Cancer Center Amsterdam; Amsterdam The Netherlands
| | - Arjan A. van de Loosdrecht
- Department of Hematology; VU University Medical Center, Cancer Center Amsterdam; Amsterdam The Netherlands
| | - Joop H. Jansen
- Department of Laboratory Medicine; Radboud University Medical Center; Nijmegen The Netherlands
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Abstract
Cytogenetic analysis has an essential role in diagnosis, classification, and prognosis of myelodysplastic syndromes (MDS). Some cytogenetic abnormalities are sufficiently characteristic of MDS to be considered MDS defining in the appropriate clinical context. MDS with isolated del(5q) is the only molecularly defined MDS subtype. The genes responsible for many aspects of 5q- syndrome, the distinct clinical phenotype associated with this condition, have now been identified. Cytogenetics forms the cornerstone of the most widely adopted prognostic scoring systems in MDS, the international prognostic scoring system (IPSS) and the revised international prognostic scoring system (IPPS-R). Cytogenetic parameters also have utility in chronic myelomonocytic leukemia (CMML) and have been incorporated into specific prognostic scoring systems for this condition. More recently, it has been appreciated that submicroscopic copy number changes and gene mutations play a significant part in MDS pathogenesis. Integration of molecular genetics and cytogenetics holds much promise for improving clinical care and outcomes for patients with MDS.
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Affiliation(s)
- Meaghan Wall
- Victorian Cancer Cytogenetics Service, St. Vincent's Hospital, 41 Victoria Parade, Fitzroy, Melbourne, VIC, 3065, Australia.
- Department of Medicine, St Vincent's Hospital, The University of Melbourne, Melbourne, Australia.
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da Silva FB, Machado-Neto JA, Bertini VHLL, Velloso EDRP, Ratis CA, Calado RT, Simões BP, Rego EM, Traina F. Single-nucleotide polymorphism array (SNP-A) improves the identification of chromosomal abnormalities by metaphase cytogenetics in myelodysplastic syndrome. J Clin Pathol 2016; 70:435-442. [DOI: 10.1136/jclinpath-2016-204023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/22/2016] [Accepted: 09/27/2016] [Indexed: 12/31/2022]
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46
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Evans AG, Ahmad A, Burack WR, Iqbal MA. Combined comparative genomic hybridization and single-nucleotide polymorphism array detects cryptic chromosomal lesions in both myelodysplastic syndromes and cytopenias of undetermined significance. Mod Pathol 2016; 29:1183-99. [PMID: 27389314 DOI: 10.1038/modpathol.2016.104] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 12/28/2022]
Abstract
The diagnosis of myelodysplastic syndrome (MDS) can be challenging, and may be facilitated by correlation with cytogenetic testing. Microarray analysis using comparative genomic hybridization and/or single-nucleotide polymorphism array can detect chromosomal abnormalities not seen by standard metaphase cytogenetics. We examined the ability of combined comparative genomic hybridization and single-nucleotide polymorphism analysis (hereafter referred to as 'combined array') to detect changes among 83 patients with unexplained cytopenias undergoing pathologic evaluation for MDS and compared results with 18 normal bone marrow controls. Thirty-seven patients (45%) were diagnosed with MDS, 12 patients (14%) were demonstrated to have 'indeterminate dyspoiesis' (insufficient for classification of MDS), 27 (33%) were essentially normal, and 7 patients (8%) had alternative pathologic diagnoses. Twenty-one MDS patients (57% of diagnoses) had effectively normal metaphase cytogenetics, but combined array showed that 5 of these (13% of MDS patients) harbored major cryptic chromosomal aberrations. Furthermore, nearly half of patients with 'indeterminate dyspoiesis' and 1 with normal morphology had clonal cytopenia(s) of undetermined significance by combined array analysis. Cryptic array findings among MDS patients and those with clonal cytopenias(s) included large-scale copy-neutral loss of heterozygosity (up to 118 Mb) and genomic deletion of loci implicated in MDS pathogenesis (eg, TET2 (4q22) and NUP98 (11p15)). By comparison, in MDS patients with abnormal metaphase cytogenetics, microarray mostly recapitulated findings seen by routine karyotype. Combined array analysis has considerable diagnostic yield in detecting cryptic chromosomal aberrations in MDS and in demonstrating aberrant clonal hematopoiesis in cytopenic patients with indeterminate morphologic dysplasia.
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Affiliation(s)
- Andrew G Evans
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Ausaf Ahmad
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - W Richard Burack
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - M Anwar Iqbal
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
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47
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Abstract
Application of next-generation sequencing (NGS) on myeloid neoplasms has expanded our knowledge of genomic alterations in this group of diseases. Genomic alterations in myeloid neoplasms are complex, heterogeneous, and not specific to a disease entity. NGS-based panel testing of myeloid neoplasms can complement existing diagnostic modalities and is gaining acceptance in the clinics and diagnostic laboratories. Prospective, randomized trials to evaluate the prognostic significance of genomic markers in myeloid neoplasms are under way in academic medical centers.
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Affiliation(s)
- Frank C Kuo
- Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA.
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48
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Mutations of myelodysplastic syndromes (MDS): An update. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2016; 769:47-62. [DOI: 10.1016/j.mrrev.2016.04.009] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/11/2016] [Indexed: 01/08/2023]
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49
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Aberrations identified by genomic arrays in normal karyotype CMML can be detected in 40% of patients, but do not add prognostic information to molecular mutations. Leukemia 2016; 30:2235-2238. [PMID: 27220668 DOI: 10.1038/leu.2016.158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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50
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The prevalence of chromosomal aberrations associated with myelodysplastic syndromes in China. Ann Hematol 2016; 95:1241-8. [DOI: 10.1007/s00277-016-2698-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 05/16/2016] [Indexed: 02/05/2023]
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