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Wang Y, Bi S, Shi X, Dai L. Optical Genome Mapping Identifies a Novel Unbalanced Translocation Between Chromosomes 4q and 6q Leading to Feeding Difficulties and Hypotonia in a Neonate: A Case Report. Appl Clin Genet 2024; 17:63-69. [PMID: 38828444 PMCID: PMC11141715 DOI: 10.2147/tacg.s465244] [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: 02/21/2024] [Accepted: 05/14/2024] [Indexed: 06/05/2024] Open
Abstract
Optical Genome Mapping (OGM) technology has garnered growing interest for the identification of chromosomal structural variations (SVs), particularly complex ones that are implicated in genetic diseases in humans. In this study, we performed genetic diagnostics on a neonatal patient who presented with feeding difficulties, hypotonia, and an atrial septal defect. We utilized a combination of trio-whole exome sequencing and OGM for our analysis. The results revealed an unbalanced translocation between maternal chromosomes 4 and 6 in the proband, ogm[GRch38]t(4:6)(q35.2;q25.3), resulting in a 2.8 Mb deletion at the 4q35 terminal and a 10.2 Mb duplication at the 6q25 terminal. In summary, this study highlights how OGM, in conjunction with other genetic approaches, can unveil the genetic etiology of complex clinical syndromes. Neonatal patients often exhibit low specific phenotypes, underlining the significance of SV detection.
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Affiliation(s)
- Ying Wang
- Division of Neonatology, Anhui Provincial Children’s Hospital, Hefei, Anhui, 230051, People’s Republic of China
| | - Shaohua Bi
- Division of Neonatology, Anhui Provincial Children’s Hospital, Hefei, Anhui, 230051, People’s Republic of China
| | - Xiaoqing Shi
- Division of Neonatology, Anhui Provincial Children’s Hospital, Hefei, Anhui, 230051, People’s Republic of China
| | - Liying Dai
- Division of Neonatology, Anhui Provincial Children’s Hospital, Hefei, Anhui, 230051, People’s Republic of China
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Carrothers E, Appleby M, Lai V, Kozbenko T, Alomar D, Smith BJ, Hamada N, Hinton P, Ainsbury EA, Hocking R, Yauk C, Wilkins RC, Chauhan V. AOP report: Development of an adverse outcome pathway for deposition of energy leading to cataracts. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024. [PMID: 38644659 DOI: 10.1002/em.22594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/23/2024]
Abstract
Cataracts are one of the leading causes of blindness, with an estimated 95 million people affected worldwide. A hallmark of cataract development is lens opacification, typically associated not only with aging but also radiation exposure as encountered by interventional radiologists and astronauts during the long-term space mission. To better understand radiation-induced cataracts, the adverse outcome pathway (AOP) framework was used to structure and evaluate knowledge across biological levels of organization (e.g., macromolecular, cell, tissue, organ, organism and population). AOPs identify a sequence of key events (KEs) causally connected by key event relationships (KERs) beginning with a molecular initiating event to an adverse outcome (AO) of relevance to regulatory decision-making. To construct the cataract AO and retrieve evidence to support it, a scoping review methodology was used to filter, screen, and review studies based on the modified Bradford Hill criteria. Eight KEs were identified that were moderately supported by empirical evidence (e.g., dose-, time-, incidence-concordance) across the adjacent (directly linked) relationships using well-established endpoints. Over half of the evidence to justify the KER linkages was derived from the evidence stream of biological plausibility. Early KEs of oxidative stress and protein modifications had strong linkages to downstream KEs and could be the focus of countermeasure development. Several identified knowledge gaps and inconsistencies related to the quantitative understanding of KERs which could be the basis of future research, most notably directed to experiments in the range of low or moderate doses and dose-rates, relevant to radiation workers and other occupational exposures.
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Affiliation(s)
- Emma Carrothers
- Consumer and Clinical Radiation Protection Bureau, Environmental and Radiation Health Sciences Directorate, Health Canada, Ottawa, Ontario, Canada
| | - Meghan Appleby
- Consumer and Clinical Radiation Protection Bureau, Environmental and Radiation Health Sciences Directorate, Health Canada, Ottawa, Ontario, Canada
| | - Vita Lai
- Consumer and Clinical Radiation Protection Bureau, Environmental and Radiation Health Sciences Directorate, Health Canada, Ottawa, Ontario, Canada
| | - Tatiana Kozbenko
- Consumer and Clinical Radiation Protection Bureau, Environmental and Radiation Health Sciences Directorate, Health Canada, Ottawa, Ontario, Canada
| | - Dalya Alomar
- Consumer and Clinical Radiation Protection Bureau, Environmental and Radiation Health Sciences Directorate, Health Canada, Ottawa, Ontario, Canada
| | - Benjamin J Smith
- Consumer and Clinical Radiation Protection Bureau, Environmental and Radiation Health Sciences Directorate, Health Canada, Ottawa, Ontario, Canada
| | - Nobuyuki Hamada
- Biology and Environmental Chemistry Division, Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry (CRIEPI), Chiba, Japan
| | - Patricia Hinton
- Defense Research & Development Canada, Canadian Forces Environmental Medicine Establishment, Toronto, Ontario, Canada
| | - Elizabeth A Ainsbury
- Radiation, Chemical and Environmental Hazards Division, UK Health Security Agency, Birmingham, UK
- Environmental Research Group within the School of Public Health, Faculty of Medicine at Imperial College of Science, Technology and Medicine, London, UK
| | - Robyn Hocking
- Learning and Knowledge and Library Services, Health Canada, Ottawa, Ontario, Canada
| | - Carole Yauk
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Ruth C Wilkins
- Consumer and Clinical Radiation Protection Bureau, Environmental and Radiation Health Sciences Directorate, Health Canada, Ottawa, Ontario, Canada
| | - Vinita Chauhan
- Consumer and Clinical Radiation Protection Bureau, Environmental and Radiation Health Sciences Directorate, Health Canada, Ottawa, Ontario, Canada
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Yang L, Liu S, He W, Xiong Z, Xia L. Characterisation of tumor microenvironment and prevalence of CD274/PD-L1 genetic alterations difference in colorectal Cancer. BMC Cancer 2023; 23:221. [PMID: 36894899 PMCID: PMC9996909 DOI: 10.1186/s12885-023-10610-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/06/2023] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Large-scale genomic alterations, especially CD274/PD-L1 gene amplification, have great impact on anti-PD-1 efficacy on cancers such as Hodgkin's lymphoma. However, the prevalence of PD-L1 genetic alterations in colorectal cancer (CRC) and its correlation with the tumor immune microenvironment and clinical implications remain unknown. MATERIALS AND METHODS PD-L1 genetic alterations were evaluated in 324 patients with newly diagnosed CRC including 160 mismatch repair-deficient (dMMR) patients and 164 mismatch repair-proficient (pMMR) patients using fluorescence in situ hybridization (FISH) method. The correlation between PD-L1 and the expression of the common immune markers was analyzed. RESULTS Totally 33 (10.2%) patients were identified with aberrant PD-L1 genetic alternations including deletion (2.2%), polysomy (4.9%), and amplification (3.1%); They had more aggressive features such as advanced stage (P = 0.02), shorter overall survival (OS) (P < 0.001) than patients with disomy. The aberrations correlated with positive lymph node (PLN) (p = 0.001), PD-L1 expression by immunohistochemistry (IHC) in tumor cells (TCs) or tumor-infiltrated immunocytes (ICs) (both p < 0.001), and pMMR (p = 0.029). When dMMR and pMMR were analyzed independently, the correlations of aberrant PD-L1 genetic alterations with PD-1 expression (p = 0.016), CD4 + T cells (p = 0.032), CD8 T + cells (p = 0.032) and CD68 + cells (p = 0.04) were only found in dMMR cohort. CONCLUSIONS The prevalence of PD-L1 genetic alterations was relatively low in CRC, but the aberrations usually correlate with aggressive nature. The correlation between PD-L1 genetic alterations and tumor immune features was only observed in dMMR CRC.
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Affiliation(s)
- Lin Yang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, 1838 Baiyun Avenue North, Guangzhou, 510515, China
| | - Shousheng Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road east, Guangzhou, 510060, China.,Department of General Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road east, Guangzhou, 510060, China
| | - Wenzhuo He
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road east, Guangzhou, 510060, China.,Department of General Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road east, Guangzhou, 510060, China
| | - Zhenchong Xiong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road east, Guangzhou, 510060, China. .,Department of Breast Oncology, Sun Yat-sen University Cancer Center, 651 Dongfeng Road east, Guangzhou, 510060, China.
| | - Liangping Xia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road east, Guangzhou, 510060, China. .,Department of General Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road east, Guangzhou, 510060, China.
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Mindiola Romero AE, Johnston MA, Giffin JT, Khan WA, Lefferts JA, Loo EY. SNP-based chromosomal microarray characterization in a series of pure erythroid leukemia. Leuk Lymphoma 2022; 63:2009-2012. [DOI: 10.1080/10428194.2022.2057489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Andres E. Mindiola Romero
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Michael A. Johnston
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Justin T. Giffin
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Wahab A. Khan
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Joel A. Lefferts
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Eric Y. Loo
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
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The Prognostic Role of Cytogenetics Analysis in Philadelphia Negative Myeloproliferative Neoplasms. ACTA ACUST UNITED AC 2021; 57:medicina57080813. [PMID: 34441019 PMCID: PMC8398709 DOI: 10.3390/medicina57080813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 11/16/2022]
Abstract
Myeloproliferative neoplasms (MPNs) are clonal stem cell disorders characterized collectively by clonal proliferation of myeloid cells with variable morphologic maturity and hematopoietic efficiency. Although the natural history of these neoplasms can be measured sometimes in decades more than years, the cytogenetics analysis can offer useful information regarding the prognosis. Cytogenetics has a well-established prognostic role in acute leukemias and in myelodysplastic syndromes, where it drives the clinical decisions. NGS techniques can find adverse mutations with clear prognostic value and are currently included in the prognostic evaluation of MPNs in scores such as MIPSS, GIPSS, MIPSS-PV, and MIPSS-ET. We suggest that cytogenetics (considering its availability and relative cost) has a role regarding prognostic and therapeutic decisions.
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Papuc SM, Erbescu A, Cisleanu D, Ozunu D, Enache C, Dumitru I, Lupoaia Andrus E, Gaman M, Popov VM, Dobre M, Stanca O, Angelescu S, Berbec N, Colita A, Vladareanu AM, Bumbea H, Arghir A. Delineation of Molecular Lesions in Acute Myeloid Leukemia Patients at Diagnosis: Integrated Next Generation Sequencing and Cytogenomic Studies. Genes (Basel) 2021; 12:genes12060846. [PMID: 34070898 PMCID: PMC8229708 DOI: 10.3390/genes12060846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 12/19/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disorder characterized by a wide range of genetic defects. Cytogenetics, molecular and genomic technologies have proved to be helpful for deciphering the mutational landscape of AML and impacted clinical practice. Forty-eight new AML patients were investigated with an integrated approach, including classical and molecular cytogenetics, array-based comparative genomic hybridization and targeted next generation sequencing (NGS). Various genetic defects were identified in all the patients using our strategy. Targeted NGS revealed known pathogenic mutations as well as rare or unreported variants with deleterious predictions. The mutational screening of the normal karyotype (NK) group identified clinically relevant variants in 86.2% of the patients; in the abnormal cytogenetics group, the mutation detection rate was 87.5%. Overall, the highest mutation prevalence was observed for the NPM1 gene, followed by DNMT3A, FLT3 and NRAS. An unexpected co-occurrence of KMT2A translocation and DNMT3A-R882 was identified; alterations of these genes, which are involved in epigenetic regulation, are considered to be mutually exclusive. A microarray analysis detected CNVs in 25% of the NK AML patients. In patients with complex karyotypes, the microarray analysis made a significant contribution toward the accurate characterization of chromosomal defects. In summary, our results show that the integration of multiple investigative strategies increases the detection yield of genetic defects with potential clinical relevance.
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Affiliation(s)
- Sorina Mihaela Papuc
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (S.M.P.); (A.E.); (D.O.); (M.D.)
| | - Alina Erbescu
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (S.M.P.); (A.E.); (D.O.); (M.D.)
| | - Diana Cisleanu
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Diana Ozunu
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (S.M.P.); (A.E.); (D.O.); (M.D.)
| | - Cristina Enache
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Ion Dumitru
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Elena Lupoaia Andrus
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Mihaela Gaman
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | | | - Maria Dobre
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (S.M.P.); (A.E.); (D.O.); (M.D.)
| | - Oana Stanca
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Coltea Clinical Hospital, 030167 Bucharest, Romania
| | - Silvana Angelescu
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Coltea Clinical Hospital, 030167 Bucharest, Romania
| | - Nicoleta Berbec
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Coltea Clinical Hospital, 030167 Bucharest, Romania
| | - Andrei Colita
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Coltea Clinical Hospital, 030167 Bucharest, Romania
| | - Ana-Maria Vladareanu
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Horia Bumbea
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (D.C.); (C.E.); (E.L.A.); (M.G.); (O.S.); (S.A.); (N.B.); (A.C.); (A.-M.V.); (H.B.)
- Emergency Universitary Clinical Hospital, 050098 Bucharest, Romania;
| | - Aurora Arghir
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (S.M.P.); (A.E.); (D.O.); (M.D.)
- Correspondence: ; Tel.: +40-2-1319-2732-207; Fax: +40-2-1319-4528
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Jiang L, Pallavajjala A, Huang J, Haley L, Morsberger L, Stinnett V, Hardy M, Park R, Ament C, Finch A, Shane A, Parish R, Nozari A, Long P, Adams E, Smith K, Parimi V, Dougaparsad S, Long L, Gocke CD, Zou YS. Clinical Utility of Targeted Next-Generation Sequencing Assay to Detect Copy Number Variants Associated with Myelodysplastic Syndrome in Myeloid Malignancies. J Mol Diagn 2021; 23:467-483. [PMID: 33577993 DOI: 10.1016/j.jmoldx.2021.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 12/17/2020] [Accepted: 01/05/2021] [Indexed: 12/11/2022] Open
Abstract
Copy number variants (CNVs) and gene mutations are important for diagnosis and treatment of myeloid malignancies. In a routine clinical setting, somatic gene mutations are detected by targeted next-generation sequencing (NGS) assay, but CNVs are commonly detected by conventional chromosome analysis and fluorescence in situ hybridization (FISH). The aim of this proof-of-principle study was to investigate the feasibility of using targeted NGS to simultaneously detect both somatic mutations and CNVs. Herein, we sequenced 406 consecutive patients with myeloid malignancies by targeted NGS and performed a head-to-head comparison with the results from a myelodysplastic syndrome (MDS) FISH and conventional chromosome analysis to detect CNVs. Among 91 patients with abnormal MDS FISH results, the targeted NGS revealed all 120 CNVs detected by MDS FISH (including -5/5q-, -7/7q-, +8, and 20q-) and 193 extra CNVs detected by conventional chromosome analysis. The targeted NGS achieved 100% concordance with the MDS FISH. The lower limit of detection of MDS CNVs by the targeted NGS was generally 5% variant allele fraction for DNA, based on the lowest percentages of abnormal cells detected by MDS FISH in this study. This proof-of-principle study demonstrated that the targeted NGS assay can simultaneously detect both MDS CNVs and somatic mutations, which can provide a more comprehensive genetic profiling for patients with myeloid malignancies using a single assay in a clinical setting.
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Affiliation(s)
- Liqun Jiang
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Aparna Pallavajjala
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jialing Huang
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Thomas Jefferson University, Philadelphia, Pennsylvania; BioDiscovery Inc., El Segundo, California
| | - Lisa Haley
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Laura Morsberger
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Victoria Stinnett
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Melanie Hardy
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rebecca Park
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Candice Ament
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alexandra Finch
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alison Shane
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rebecca Parish
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Azin Nozari
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Patty Long
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Emily Adams
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kirstin Smith
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Vamsi Parimi
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Lori Long
- MacroGenics Inc., Rockville, Maryland
| | - Christopher D Gocke
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ying S Zou
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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8
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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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Levy MA, Santos S, Kerkhof J, Stuart A, Aref‐Eshghi E, Guo F, Hedley B, Wong H, Rauh M, Feilotter H, Berardi P, Semenuk L, Yang P, Knoll J, Ainsworth P, McLachlin CM, Chin‐Yee I, Kovacs M, Deotare U, Lazo‐Langner A, Hsia C, Keeney M, Xenocostas A, Howlett C, Lin H, Sadikovic B. Implementation of an NGS‐based sequencing and gene fusion panel for clinical screening of patients with suspected hematologic malignancies. Eur J Haematol 2019; 103:178-189. [DOI: 10.1111/ejh.13272] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/27/2019] [Accepted: 06/03/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Michael A. Levy
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Stephanie Santos
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Alan Stuart
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Erfan Aref‐Eshghi
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Fen Guo
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Ben Hedley
- Pathology and Laboratory Medicine London Health Sciences Centre London Ontario Canada
| | - Henry Wong
- Clinical Laboratories Kingston Health Sciences Centre Kingston Ontario Canada
| | - Michael Rauh
- Department of Pathology and Molecular Medicine Queen's University Kingston Ontario Canada
| | - Harriet Feilotter
- Department of Pathology and Molecular Medicine Queen's University Kingston Ontario Canada
- Molecular Diagnostics Kingston Health Sciences Centre Kingston Ontario Canada
| | - Philip Berardi
- University of Ottawa Ottawa Ontario Canada
- Eastern Ontario Regional Laboratory Association (EORLA) The Ottawa Hospital Ottawa Ontario Canada
| | - Laura Semenuk
- DNA Diagnostics & Cytogenetics Laboratory Kingston Health Sciences Centre Kingston Ontario Canada
| | - Ping Yang
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Cytogenetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Joan Knoll
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Peter Ainsworth
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
- Department of Biochemistry Western University London Ontario Canada
| | | | - Ian Chin‐Yee
- Hematology Division London Health Sciences Centre London Ontario Canada
| | - Michael Kovacs
- Hematology Division London Health Sciences Centre London Ontario Canada
| | - Uday Deotare
- Hematology Division London Health Sciences Centre London Ontario Canada
- Schulich School of Medicine and Dentistry Western University London Ontario Canada
- Departments of Medicine and Oncology London Health Sciences Centre London Ontario Canada
| | - Alejandro Lazo‐Langner
- Hematology Division London Health Sciences Centre London Ontario Canada
- Department of Epidemiology and Biostatistics Western University London Ontario Canada
| | - Cyrus Hsia
- Hematology Division London Health Sciences Centre London Ontario Canada
| | - Mike Keeney
- Hematology Division London Health Sciences Centre London Ontario Canada
| | - Anargyros Xenocostas
- Hematology Division London Health Sciences Centre London Ontario Canada
- Schulich School of Medicine and Dentistry Western University London Ontario Canada
| | - Christopher Howlett
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Hanxin Lin
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
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10
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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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11
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Choi SM, Van Norman SB, Bixby DL, Shao L. Cytogenomic array detects a subset of myelodysplastic syndrome with increased risk that is invisible to conventional karyotype. Genes Chromosomes Cancer 2019; 58:756-774. [PMID: 31334569 DOI: 10.1002/gcc.22783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 11/06/2022] Open
Abstract
Conventional karyotyping is essential standard practice in the initial evaluation of myelodysplastic syndrome (MDS) and is the most impactful single component of the Revised International Prognostic Scoring System (IPSS-R). While single nucleotide polymorphism array (SNP-A) has demonstrated the ability to detect chromosomal defects with greater sensitivity than conventional karyotype, widespread adoption is limited by the unknown additional prognostic impact of SNP-A analysis. Here, we investigate the significance of additional SNP-A abnormalities in the setting of MDS and demonstrate differences in survival of patients with additional abnormalities, even those initially characterized as relatively lower risk either by cytogenetic score or IPSS-R. Our findings identify specific abnormalities, particularly KMT2A partial tandem duplication, that are invisible to conventional karyotype and potentially contribute to the poor prognosis of MDS patients. Furthermore, these results demonstrate the added value of SNP-A analysis in identifying patients who may benefit from more aggressive therapy, particularly those who would otherwise be classified into lower risk categories.
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Affiliation(s)
- Sarah M Choi
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | | | - Dale L Bixby
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Lina Shao
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
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12
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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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13
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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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14
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Merkel D, Soffer S, Novikov I, Avigdor A, Amariglio N, Nagler A, Trakhtenbrot L. Is fluorescence in-situ hybridization sufficient in patients with myelodysplastic syndromes and insufficient cytogenetic testing? Leuk Lymphoma 2018; 60:764-771. [PMID: 30187812 DOI: 10.1080/10428194.2018.1493729] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chromosome banding analysis (CBA) in myelodysplastic syndromes (MDS) remains the 'gold standard' for identification of chromosomal abnormalities, while interphase fluorescence in-situ hybridization (I-FISH) is mainly used to complement CBA. This study, retrospectively, evaluated CBA and I-FISH results in 600 patients with suspected MDS and determined the effect of CBA/FISH reallocation on IPSS-R. Our result demonstrated that in 7/586 (1.2%) patients with satisfactory karyotype, I-FISH provided additional information. In 25/453 (5.5%) of the patients with normal I-FISH, CBA detected chromosomal abnormalities, and in 68/147 (46%) of the patients with abnormal I-FISH, CBA detected additional chromosomal aberrations. When 5q- aberration was alone or accompanied by additional abnormalities by I-FISH, CBA revealed a complex karyotype (16/25;64%, 35/43;81%, respectively). Our results suggest that in cases of karyotype failure, if I-FISH is used alone, patients are at risk of being misclassified into the wrong cytogenetic risk groups and a repeat sample for CBA should be attempted.
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Affiliation(s)
- Drorit Merkel
- a Division of Hematology , Chaim Sheba Medical Center, Tel Hashomer , Ramat Gan , Israel.,b Sackler School of Medicine , Tel Aviv University , Tel Aviv , Israel
| | - Shelly Soffer
- b Sackler School of Medicine , Tel Aviv University , Tel Aviv , Israel
| | - Iliya Novikov
- c Biostatistical Unit , Gertner Institute of Epidemiology and Health Policy Research , Ramat Gan , Israel
| | - Abraham Avigdor
- a Division of Hematology , Chaim Sheba Medical Center, Tel Hashomer , Ramat Gan , Israel.,b Sackler School of Medicine , Tel Aviv University , Tel Aviv , Israel
| | - Ninette Amariglio
- d Hematology Laboratory , Cancer Research Center, Sheba Medical Center , Ramat Gan , Israel
| | - Arnon Nagler
- a Division of Hematology , Chaim Sheba Medical Center, Tel Hashomer , Ramat Gan , Israel.,b Sackler School of Medicine , Tel Aviv University , Tel Aviv , Israel
| | - Luba Trakhtenbrot
- d Hematology Laboratory , Cancer Research Center, Sheba Medical Center , Ramat Gan , Israel
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