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Jang MA. Genomic technologies for detecting structural variations in hematologic malignancies. Blood Res 2024; 59:1. [PMID: 38485792 PMCID: PMC10903520 DOI: 10.1007/s44313-024-00001-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 12/18/2023] [Indexed: 03/18/2024] Open
Abstract
Genomic structural variations in myeloid, lymphoid, and plasma cell neoplasms can provide key diagnostic, prognostic, and therapeutic information while elucidating the underlying disease biology. Several molecular diagnostic approaches play a central role in evaluating hematological malignancies. Traditional cytogenetic diagnostic assays, such as chromosome banding and fluorescence in situ hybridization, are essential components of the current diagnostic workup that guide clinical care for most hematologic malignancies. However, each assay has inherent limitations, including limited resolution for detecting small structural variations and low coverage, and can only detect alterations in the target regions. Recently, the rapid expansion and increasing availability of novel and comprehensive genomic technologies have led to their use in clinical laboratories for clinical management and translational research. This review aims to describe the clinical relevance of structural variations in hematologic malignancies and introduce genomic technologies that may facilitate personalized tumor characterization and treatment.
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Affiliation(s)
- Mi-Ae Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul, 06351, Korea.
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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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3
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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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4
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Utility of Fluorescence In Situ Hybridization in Clinical and Research Applications. Clin Lab Med 2022; 42:573-586. [PMID: 36368783 DOI: 10.1016/j.cll.2022.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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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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Invariant phenotype and molecular association of biallelic TET2 mutant myeloid neoplasia. Blood Adv 2020; 3:339-349. [PMID: 30709865 DOI: 10.1182/bloodadvances.2018024216] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 12/12/2018] [Indexed: 12/29/2022] Open
Abstract
Somatic TET2 mutations (TET2 MT) are frequent in myeloid neoplasia (MN), particularly chronic myelomonocytic leukemia (CMML). TET2 MT includes mostly loss-of-function/hypomorphic hits. Impaired TET2 activity skews differentiation of hematopoietic stem cells toward proliferating myeloid precursors. This study was prompted by the observation of frequent biallelic TET2 gene inactivations (biTET2 i ) in CMML. We speculated that biTET2 i might be associated with distinct clinicohematological features. We analyzed TET2 MT in 1045 patients with MN. Of 82 biTET2 i cases, 66 were biTET2 MT, 13 were hemizygous TET2 MT, and 3 were homozygous TET2 MT (uniparental disomy); the remaining patients (denoted biTET2 - hereafter) were either monoallelic TET2 MT (n = 96) or wild-type TET2 (n = 823). Truncation mutations were found in 83% of biTET2 i vs 65% of biTET2 - cases (P = .02). TET2 hits were founder lesions in 72% of biTET2 i vs 38% of biTET2 - cases (P < .0001). In biTET2 i , significantly concurrent hits included SRSF2 MT (33%; P < .0001) and KRAS/NRAS MT (16%; P = .03) as compared with biTET2 - When the first TET2 hit was ancestral in biTET2 i , the most common subsequent hits affected a second TET2 MT, followed by SRSF2 MT, ASXL1 MT, RAS MT, and DNMT3A MT BiTET2 i patients without any monocytosis showed an absence of SRSF2 MT BiTET2 i patients were older and had monocytosis, CMML, normal karyotypes, and lower-risk disease compared with biTET2 - patients. Hence, while a second TET2 hit occurred frequently, biTET2 i did not portend faster progression but rather determined monocytic differentiation, consistent with its prevalence in CMML. Additionally, biTET2 i showed lower odds of cytopenias and marrow blasts (≥5%) and higher odds of myeloid dysplasia and marrow hypercellularity. Thus, biTET2 i might represent an auxiliary assessment tool in MN.
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Veenstra C, Bruce D, Timbs A, Hamblin A. Application of Genomics to Clinical Practice in Haematological Malignancy. CURRENT GENETIC MEDICINE REPORTS 2019. [DOI: 10.1007/s40142-019-00179-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Abstract
Purpose of Review
The usual abundance of fresh cells and high-quality DNA derived from bone marrow aspirate and peripheral blood mean haematological malignancies are at the forefront of the application of genomics to malignancy. This review evaluates where genomics is routinely used in clinical care and where opportunities for further application exist.
Recent Findings
The 2016 revision of the WHO classification of tumours of haematopoietic and lymphoid tissues increased the number of disease entities defined by, or whose diagnosis was strongly supported by, a specific genetic change. Increasingly combinations of mutations rather than individual lesions are being used to genomically classify heterogeneous disorders to inform prognosis and direct treatment. Furthermore, the role of different genetic aberrations as markers of measurable residual disease is being evaluated in clinical trials to allow intensification/de-intensification of treatment as appropriate and early detection of relapse.
Summary
Implementation of broader sequencing technologies such as whole exome/genome sequencing coupled with continuing developments in genomic technology to improve turn-around-times are likely to further reinforce the centrality of genomics in the management of haematological malignancies.
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Berry NK, Scott RJ, Rowlings P, Enjeti AK. Clinical use of SNP-microarrays for the detection of genome-wide changes in haematological malignancies. Crit Rev Oncol Hematol 2019; 142:58-67. [PMID: 31377433 DOI: 10.1016/j.critrevonc.2019.07.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 12/17/2022] Open
Abstract
Single nucleotide polymorphism (SNP) microarrays are commonly used for the clinical investigation of constitutional genomic disorders; however, their adoption for investigating somatic changes is being recognised. With increasing importance being placed on defining the cancer genome, a shift in technology is imperative at a clinical level. Microarray platforms have the potential to become frontline testing, replacing or complementing standard investigations such as FISH or karyotype. This 'molecular karyotype approach' exemplified by SNP-microarrays has distinct advantages in the investigation of several haematological malignancies. A growing body of literature, including guidelines, has shown support for the use of SNP-microarrays in the clinical laboratory to aid in a more accurate definition of the cancer genome. Understanding the benefits of this technology along with discussing the barriers to its implementation is necessary for the development and incorporation of SNP-microarrays in a clinical laboratory for the investigation of haematological malignancies.
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Affiliation(s)
- Nadine K Berry
- Department of Haematology, Calvary Mater Hospital, Newcastle, New South Wales, Australia; School of Biomedical Sciences and Pharmacy, University of Newcastle, New South Wales, Australia; Department of Molecular Medicine, NSW Health Pathology, Newcastle, New South Wales, Australia.
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, New South Wales, Australia; Department of Molecular Medicine, NSW Health Pathology, Newcastle, New South Wales, Australia
| | - Philip Rowlings
- Department of Haematology, Calvary Mater Hospital, Newcastle, New South Wales, Australia; School of Medicine and Public Health, University Newcastle, New South Wales, Australia
| | - Anoop K Enjeti
- Department of Haematology, Calvary Mater Hospital, Newcastle, New South Wales, Australia; School of Medicine and Public Health, University Newcastle, New South Wales, Australia
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Noronha TRD, Mitne-Neto M, Chauffaille MDL. Additional information offered by single nucleotide polymorphism array advantages in two myelodysplastic syndromes with excess blasts cases and future perspectives. Hematol Transfus Cell Ther 2019; 41:181-184. [PMID: 31084768 PMCID: PMC6738482 DOI: 10.1016/j.htct.2018.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/23/2018] [Accepted: 06/26/2018] [Indexed: 11/28/2022] Open
Affiliation(s)
| | | | - Maria de Lourdes Chauffaille
- Universidade Federal de São Paulo (Unifesp), São Paulo, SP, Brazil; Grupo Fleury, Pesquisa e Desenvolvimento, São Paulo, SP, Brazil
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10
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Egorshina AY, Zamaraev AV, Lavrik IN, Zhivotovsky BD, Kopeina GS. Caspase-2 as an Oncosupressor and Metabolism Regulator: What Life Will Bring over the Long Run? Mol Biol 2018. [DOI: 10.1134/s0026893318050060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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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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12
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The Cytoscan HD Array in the Diagnosis of Neurodevelopmental Disorders. High Throughput 2018; 7:ht7030028. [PMID: 30223503 PMCID: PMC6164295 DOI: 10.3390/ht7030028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/06/2018] [Accepted: 09/06/2018] [Indexed: 12/14/2022] Open
Abstract
Submicroscopic chromosomal copy number variations (CNVs), such as deletions and duplications, account for about 15–20% of patients affected with developmental delay, intellectual disability, multiple congenital anomalies, and autism spectrum disorder. Most of CNVs are de novo or inherited rearrangements with clinical relevance, but there are also rare inherited imbalances with unknown significance that make difficult the clinical management and genetic counselling. Chromosomal microarrays analysis (CMA) are recognized as the first-line test for CNV detection and are now routinely used in the clinical diagnostic laboratory. The recent use of CMA platforms that combine classic copy number analysis with single-nucleotide polymorphism (SNP) genotyping has increased the diagnostic yields. Here we discuss the application of the Cytoscan high-density (HD) SNP-array for the detection of CNVs. We provide an overview of molecular analyses involved in identifying pathogenic CNVs and highlight important guidelines to establish pathogenicity of CNV.
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Shallis RM, Ahmad R, Zeidan AM. The genetic and molecular pathogenesis of myelodysplastic syndromes. Eur J Haematol 2018; 101:260-271. [PMID: 29742289 DOI: 10.1111/ejh.13092] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2018] [Indexed: 12/14/2022]
Abstract
Myelodysplastic syndromes (MDS) comprise a diverse group of clonal and malignant myeloid disorders characterized by ineffective hematopoiesis, resultant peripheral cytopenias, and a meaningful increased risk of progression to acute myeloid leukemia. A wide array of recurring genetic mutations involved in RNA splicing, histone manipulation, DNA methylation, transcription factors, kinase signaling, DNA repair, cohesin proteins, and other signal transduction elements has been identified as important substrates for the development of MDS. Cytogenetic abnormalities, namely those characterized by loss of genetic material (including 5q- and 7q-), have also been strongly implicated and may influence the clonal architecture which predicts such mutations and may provoke an inflammatory bone marrow microenvironment as the substrate for clonal expansion. Other aspects of the molecular pathogenesis of MDS continue to be further elucidated, predicated upon advances in gene expression profiling and the development of new, and improved high-throughput techniques. More accurate understanding of the genetic and molecular basis for the development of MDS directly provides additional opportunity for treatment, which to date remains limited. In this comprehensive review, we examine the current understanding of the molecular pathogenesis and pathophysiology of MDS, as well as review future prospects which may enhance this understanding, treatment strategies, and hopefully outcomes.
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Affiliation(s)
- Rory M Shallis
- Division of Hematology/Medical Oncology, Department of Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Rami Ahmad
- Division of Hematology/Medical Oncology, Department of Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Amer M Zeidan
- Division of Hematology/Medical Oncology, Department of Medicine, Yale University School of Medicine, New Haven, CT, USA.,Cancer Outcomes, Public Policy, and Effectiveness Research (COPPER) Center, Yale University, New Haven, CT, USA
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14
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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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Song Q, Peng M, Chu Y, Huang S. Techniques for detecting chromosomal aberrations in myelodysplastic syndromes. Oncotarget 2017; 8:62716-62729. [PMID: 28977983 PMCID: PMC5617543 DOI: 10.18632/oncotarget.17698] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/19/2017] [Indexed: 11/25/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are a group of heterogeneous hematologic diseases. Chromosomal aberrations are important for the initiation, development, and progression of MDS. Detection of chromosomal abnormalities in MDS is important for categorization, risk stratification, therapeutic selection, and prognosis evaluation of the disease. Recent progress of multiple techniques has brought powerful molecular cytogenetic information to reveal copy number variation, uniparental disomy, and complex chromosomal aberrations in MDS. In this review, we will introduce some common chromosomal aberrations in MDS and their clinical significance. Then we will explain the application, advantages, and limitations of different techniques for detecting chromosomal abnormalities in MDS. The information in this review may be helpful for clinicians to select appropriate methods in patient-related decision making.
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Affiliation(s)
- Qibin Song
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Min Peng
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yuxin Chu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Shiang Huang
- Molecular department, Kindstar Global, Wuhan, China
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