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Alimohamed MZ, Johansson LF, de Boer EN, Splinter E, Klous P, Yilmaz M, Bosga A, van Min M, Mulder AB, Vellenga E, Sinke RJ, Sijmons RH, van den Berg E, Sikkema-Raddatz B. Genetic Screening Test to Detect Translocations in Acute Leukemias by Use of Targeted Locus Amplification. Clin Chem 2018; 64:1096-1103. [DOI: 10.1373/clinchem.2017.286047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/16/2018] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Over 500 translocations have been identified in acute leukemia. To detect them, most diagnostic laboratories use karyotyping, fluorescent in situ hybridization, and reverse transcription PCR. Targeted locus amplification (TLA), a technique using next-generation sequencing, now allows detection of the translocation partner of a specific gene, regardless of its chromosomal origin. We present a TLA multiplex assay as a potential first-tier screening test for detecting translocations in leukemia diagnostics.
METHODS
The panel includes 17 genes involved in many translocations present in acute leukemias. Procedures were optimized by using a training set of cell line dilutions and 17 leukemia patient bone marrow samples and validated by using a test set of cell line dilutions and a further 19 patient bone marrow samples. Per gene, we determined if its region was involved in a translocation and, if so, the translocation partner. To balance sensitivity and specificity, we introduced a gray zone showing indeterminate translocation calls needing confirmation. We benchmarked our method against results from the 3 standard diagnostic tests.
RESULTS
In patient samples passing QC, we achieved a concordance with benchmarking tests of 81% in the training set and 100% in the test set, after confirmation of 4 and nullification of 3 gray zone calls (in total). In cell line dilutions, we detected translocations in 10% aberrant cells at several genetic loci.
CONCLUSIONS
Multiplex TLA shows promising results as an acute leukemia screening test. It can detect cryptic and other translocations in selected genes. Further optimization may make this assay suitable for diagnostic use.
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Affiliation(s)
- Mohamed Z Alimohamed
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Lennart F Johansson
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Eddy N de Boer
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | | | | | | | - Anneke Bosga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | | | - André B Mulder
- University of Groningen, University Medical Center Groningen, Department of Laboratory Medicine, the Netherlands
| | - Edo Vellenga
- University of Groningen, University Medical Center Groningen, Department of Hematology, the Netherlands
| | - Richard J Sinke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Rolf H Sijmons
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Eva van den Berg
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Birgit Sikkema-Raddatz
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
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2
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Sabath DE, Bender MA, Sankaran VG, Vamos E, Kentsis A, Yi HS, Greisman HA. Characterization of Deletions of the HBA and HBB Loci by Array Comparative Genomic Hybridization. J Mol Diagn 2015; 18:92-9. [PMID: 26612711 DOI: 10.1016/j.jmoldx.2015.07.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Revised: 06/22/2015] [Accepted: 07/28/2015] [Indexed: 10/22/2022] Open
Abstract
Thalassemia is among the most common genetic diseases worldwide. α-Thalassemia is usually caused by deletion of one or more of the duplicated HBA genes on chromosome 16. In contrast, most β-thalassemia results from point mutations that decrease or eliminate expression of the HBB gene on chromosome 11. Deletions within the HBB locus result in thalassemia or hereditary persistence of fetal Hb. Although routine diagnostic testing cannot distinguish thalassemia deletions from point mutations, deletional hereditary persistence of fetal Hb is notable for having an elevated HbF level with a normal mean corpuscular volume. A small number of deletions accounts for most α-thalassemias; in contrast, there are no predominant HBB deletions causing β-thalassemia. To facilitate the identification and characterization of deletions of the HBA and HBB globin loci, we performed array-based comparative genomic hybridization using a custom oligonucleotide microarray. We accurately mapped the breakpoints of known and previously uncharacterized HBB deletions defining previously uncharacterized deletion breakpoints by PCR amplification and sequencing. The array also successfully identified the common HBA deletions --(SEA) and --(FIL). In summary, comparative genomic hybridization can be used to characterize deletions of the HBA and HBB loci, allowing high-resolution characterization of novel deletions that are not readily detected by PCR-based methods.
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Affiliation(s)
- Daniel E Sabath
- Department of Laboratory Medicine, University of Washington, Seattle, Washington.
| | - Michael A Bender
- Department of Pediatrics, University of Washington, Seattle, Washington; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Esther Vamos
- Departments of Pediatrics and Genetics, Université Libre de Bruxelles, Brussels, Belgium
| | - Alex Kentsis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hye-Son Yi
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Harvey A Greisman
- Department of Laboratory Medicine, University of Washington, Seattle, Washington.
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3
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Durmaz AA, Karaca E, Demkow U, Toruner G, Schoumans J, Cogulu O. Evolution of genetic techniques: past, present, and beyond. BIOMED RESEARCH INTERNATIONAL 2015; 2015:461524. [PMID: 25874212 PMCID: PMC4385642 DOI: 10.1155/2015/461524] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/05/2014] [Indexed: 12/05/2022]
Abstract
Genetics is the study of heredity, which means the study of genes and factors related to all aspects of genes. The scientific history of genetics began with the works of Gregor Mendel in the mid-19th century. Prior to Mendel, genetics was primarily theoretical whilst, after Mendel, the science of genetics was broadened to include experimental genetics. Developments in all fields of genetics and genetic technology in the first half of the 20th century provided a basis for the later developments. In the second half of the 20th century, the molecular background of genetics has become more understandable. Rapid technological advancements, followed by the completion of Human Genome Project, have contributed a great deal to the knowledge of genetic factors and their impact on human life and diseases. Currently, more than 1800 disease genes have been identified, more than 2000 genetic tests have become available, and in conjunction with this at least 350 biotechnology-based products have been released onto the market. Novel technologies, particularly next generation sequencing, have dramatically accelerated the pace of biological research, while at the same time increasing expectations. In this paper, a brief summary of genetic history with short explanations of most popular genetic techniques is given.
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Affiliation(s)
- Asude Alpman Durmaz
- Department of Medical Genetics, Ege University Faculty of Medicine, 35100 Izmir, Turkey
| | - Emin Karaca
- Department of Medical Genetics, Ege University Faculty of Medicine, 35100 Izmir, Turkey
| | - Urszula Demkow
- Department of Laboratory Diagnostics and Clinical Immunology, Warsaw University Faculty of Medicine, 61 02-091 Warsaw, Poland
| | - Gokce Toruner
- Institute of Genomic Medicine, UMDNJ-NJ Medical School, Newark, NJ 07103, USA
| | - Jacqueline Schoumans
- Department of Medical Genetics, Cancer Cytogenetic Unit, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Ozgur Cogulu
- Department of Medical Genetics, Ege University Faculty of Medicine, 35100 Izmir, Turkey
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4
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Abstract
The field of cytogenetics has focused on studying the number, structure, function and origin of chromosomal abnormalities and the evolution of chromosomes. The development of fluorescent molecules that either directly or via an intermediate molecule bind to DNA has led to the development of fluorescent in situ hybridization (FISH), a technology linking cytogenetics to molecular genetics. This technique has a wide range of applications that increased the dimension of chromosome analysis. The field of cytogenetics is particularly important for medical diagnostics and research as well as for gene ordering and mapping. Furthermore, the increased application of molecular biology techniques, such as array-based technologies, has led to improved resolution, extending the recognized range of microdeletion/microduplication syndromes and genomic disorders. In adopting these newly expanded methods, cytogeneticists have used a range of technologies to study the association between visible chromosome rearrangements and defects at the single nucleotide level. Overall, molecular cytogenetic techniques offer a remarkable number of potential applications, ranging from physical mapping to clinical and evolutionary studies, making a powerful and informative complement to other molecular and genomic approaches. This manuscript does not present a detailed history of the development of molecular cytogenetics; however, references to historical reviews and experiments have been provided whenever possible. Herein, the basic principles of molecular cytogenetics, the technologies used to identify chromosomal rearrangements and copy number changes, and the applications for cytogenetics in biomedical diagnosis and research are presented and discussed.
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Affiliation(s)
- Mariluce Riegel
- Serviço de Genética Médica, Hospital de Clínicas, Porto Alegre, RS, Brazil . ; Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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5
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Gibson SE, Luo J, Sathanoori M, Liao J, Surti U, Swerdlow SH. Whole-genome single nucleotide polymorphism array analysis is complementary to classical cytogenetic analysis in the evaluation of lymphoid proliferations. Am J Clin Pathol 2014; 141:247-55. [PMID: 24436273 DOI: 10.1309/ajcprhght28duwla] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVES To explore how much additional information single nucleotide polymorphism (SNP) arrays provide and whether they could partially replace classical cytogenetics. METHODS Twenty-six lymphoid proliferations with available cytogenetic studies were analyzed with the Affymetrix Genome-Wide Human SNP Array 6.0 (Affymetrix, Santa Clara, CA). RESULTS Eleven of 26 cases demonstrated complete concordance between cytogenetics and SNP analysis, and 10 of 26 cases demonstrated partial concordance. Five discordant cases had copy number abnormalities (CNAs) with cytogenetics not identified with SNP arrays. While SNP analysis showed CNAs not apparent by cytogenetics in eight cases and helped clarify the karyotype in six cases, cytogenetics demonstrated CNAs not seen by SNP analysis in 15 cases as well as balanced translocations in 12 cases. CONCLUSIONS The combination of cytogenetics and SNP analysis results in a higher overall yield in identifying numerical chromosomal abnormalities than either technique alone.
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Affiliation(s)
- Sarah E. Gibson
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Jianhua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Malini Sathanoori
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Pittsburgh Cytogenetics Laboratory, Magee-Womens Hospital of UPMC, Pittsburgh, PA
| | - Jun Liao
- Pittsburgh Cytogenetics Laboratory, Magee-Womens Hospital of UPMC, Pittsburgh, PA
| | - Urvashi Surti
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Pittsburgh Cytogenetics Laboratory, Magee-Womens Hospital of UPMC, Pittsburgh, PA
| | - Steven H. Swerdlow
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
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6
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Vandeweyer G, Kooy RF. Detection and interpretation of genomic structural variation in health and disease. Expert Rev Mol Diagn 2014; 13:61-82. [DOI: 10.1586/erm.12.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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7
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Ning Y, Foss A, Kimball AS, Neill N, Matz T, Schultz R. Characterization of a case of follicular lymphoma transformed into B-lymphoblastic leukemia. Mol Cytogenet 2013; 6:34. [PMID: 23985173 PMCID: PMC3846067 DOI: 10.1186/1755-8166-6-34] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 08/01/2013] [Indexed: 02/02/2023] Open
Abstract
Follicular lymphoma (FL) is a common form of non-Hodgkin lymphoma with an ability to transform into a more aggressive disease, albeit infrequently to B-lymphoblastic leukemia/lymphoma. While t(14;18)(q32;q21) has been associated with approximately 90% cases of FL, that alteration alone is insufficient to cause FL and associated mutations are still being elucidated. The transformation of FL to B-lymphoblastic leukemia generally includes the dysregulation of MYC gene expression, typically through IGH rearrangement. Such cases of “double-hit” leukemia/lymphoma with both BCL2 and MYC translocations warrant further study as they are often not identified early, are associated with a poor prognosis, and are incompletely understood in molecular terms. Here we describe a patient with a diagnosis of FL that transformed to B-lymphoblastic leukemia. Detailed cytogenetic characterization of the transformed specimen using karyotype, fluorescence in situ hybridization, microarray and gene rearrangement analyses revealed a complex karyotype comprised principally of whole chromosome or whole arm copy number gains or losses. Smaller, single-gene copy number alterations identified by microarray were limited in number, but included amplification of a truncated EP300 gene and alterations in NEIL1 and GPHN. Analyses defined the presence of an IGH/BCL2 fusion due to a translocation as well as a MYC/IGH fusion due to an insertion, with both rearrangements involving the same IGH allele. The data illustrate the value in characterizing double-hit lymphoma cases with both traditional and novel technologies in the detailed cytogenetic workup.
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Affiliation(s)
- Yi Ning
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Aubry Foss
- Signature Genomic Laboratories/Perkin Elmer, 2820 N Astor, Spokane, WA, 99207, USA
| | - Amy S Kimball
- Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nicholas Neill
- Signature Genomic Laboratories/Perkin Elmer, 2820 N Astor, Spokane, WA, 99207, USA
| | - Tricia Matz
- Signature Genomic Laboratories/Perkin Elmer, 2820 N Astor, Spokane, WA, 99207, USA
| | - Roger Schultz
- Signature Genomic Laboratories/Perkin Elmer, 2820 N Astor, Spokane, WA, 99207, USA
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8
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Alayed K, Medeiros LJ, Schultz RA, Cortes J, Lu G, Bueso-Ramos CE, Konoplev S. Value of oligonucleotide-based array comparative genomic hybridization for diagnosis of acute promyelocytic leukemia in a patient negative for t(15;17)(q24.1;q21.2)/promyelocytic leukemia-retinoic acid receptor, alpha by conventional cytogenetics and fluorescence in situ hybridization. CLINICAL LYMPHOMA, MYELOMA & LEUKEMIA 2013; 13:507-510. [PMID: 23770155 PMCID: PMC4259115 DOI: 10.1016/j.clml.2013.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 02/28/2013] [Accepted: 03/27/2013] [Indexed: 06/02/2023]
Affiliation(s)
- Khaled Alayed
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
- Department of Pathology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - L. Jeffrey Medeiros
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | | | - Jorge Cortes
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Gary Lu
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Carlos E. Bueso-Ramos
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Sergej Konoplev
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
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9
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Modified Array-based Comparative Genomic Hybridization Detects Cryptic and Variant PML-RARA Rearrangements in Acute Promyelocytic Leukemia Lacking Classic Translocations. ACTA ACUST UNITED AC 2013; 22:10-21. [DOI: 10.1097/pdm.0b013e31825b8326] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Thieme S, Groth P. Genome Fusion Detection: a novel method to detect fusion genes from SNP-array data. ACTA ACUST UNITED AC 2013; 29:671-7. [PMID: 23341502 PMCID: PMC3597144 DOI: 10.1093/bioinformatics/btt028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Fusion genes result from genomic rearrangements, such as deletions, amplifications and translocations. Such rearrangements can also frequently be observed in cancer and have been postulated as driving event in cancer development. to detect them, one needs to analyze the transition region of two segments with different copy number, the location where fusions are known to occur. Finding fusion genes is essential to understanding cancer development and may lead to new therapeutic approaches. RESULTS Here we present a novel method, the Genomic Fusion Detection algorithm, to predict fusion genes on a genomic level based on SNP-array data. This algorithm detects genes at the transition region of segments with copy number variation. With the application of defined constraints, certain properties of the detected genes are evaluated to predict whether they may be fused. We evaluated our prediction by calculating the observed frequency of known fusions in both primary cancers and cell lines. We tested a set of cell lines positive for the BCR-ABL1 fusion and prostate cancers positive for the TMPRSS2-ERG fusion. We could detect the fusions in all positive cell lines, but not in the negative controls.
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Affiliation(s)
- Sebastian Thieme
- Department of Theoretical Biophysics, Humboldt-University of Berlin, 10115 Berlin, Germany and Therapeutic Research Group Oncology, Bayer Pharma AG, 13353 Berlin, Germany
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11
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Ganesamoorthy D, Bruno DL, McGillivray G, Norris F, White SM, Adroub S, Amor DJ, Yeung A, Oertel R, Pertile MD, Ngo C, Arvaj AR, Walker S, Charan P, Palma-Dias R, Woodrow N, Slater HR. Meeting the challenge of interpreting high-resolution single nucleotide polymorphism array data in prenatal diagnosis: does increased diagnostic power outweigh the dilemma of rare variants? BJOG 2013; 120:594-606. [PMID: 23332022 DOI: 10.1111/1471-0528.12150] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2012] [Indexed: 01/14/2023]
Abstract
OBJECTIVE Several studies have already shown the superiority of chromosomal microarray analysis (CMA) compared with conventional karyotyping for prenatal investigation of fetal ultrasound abnormality. This study used very high-resolution single nucleotide polymorphism (SNP) arrays to determine the impact on detection rates of all clinical categories of copy number variations (CNVs), and address the issue of interpreting and communicating findings of uncertain or unknown clinical significance, which are to be expected at higher frequency when using very high-resolution CMA. DESIGN Prospective validation study. SETTING Tertiary clinical genetics centre. POPULATION Women referred for further investigation of fetal ultrasound anomaly. METHODS We prospectively tested 104 prenatal samples using both conventional karyotyping and high-resolution arrays. MAIN OUTCOME MEASURES The detection rates for each clinical category of CNV. RESULTS Unequivocal pathogenic CNVs were found in six cases, including one with uniparental disomy (paternal UPD 14). A further four cases had a 'likely pathogenic' finding. Overall, CMA improved the detection of 'pathogenic' and 'likely pathogenic' abnormalities from 2.9% (3/104) to 9.6% (10/104). CNVs of 'unknown' clinical significance that presented interpretational difficulties beyond results from parental investigations were detected in 6.7% (7/104) of samples. CONCLUSIONS Increased detection sensitivity appears to be the main benefit of high-resolution CMA. Despite this, in this cohort there was no significant benefit in terms of improving detection of small pathogenic CNVs. A potential disadvantage is the high detection rate of CNVs of 'unknown' clinical significance. These findings emphasise the importance of establishing an evidence-based policy for the interpretation and reporting of CNVs, and the need to provide appropriate pre- and post-test counselling.
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Affiliation(s)
- D Ganesamoorthy
- VCGS Cytogenetics Laboratory, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia
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12
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Swerdlow SH. Lymphoma classification and the tools of our trade: an introduction to the 2012 USCAP Long Course. Mod Pathol 2013; 26 Suppl 1:S1-S14. [PMID: 23281432 DOI: 10.1038/modpathol.2012.177] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The 2012 USCAP Long Course 'Malignant Lymphomas-Building on the Past, Moving to the Future' began with an introduction to lymphoma classification over the last half century and a discussion of our current diagnostic armamentarium, together with a look toward the future. The Rappaport classification, originally published in 1956, was a morphologic classification with few categories. The early 1970s saw a great and tumultuous revolution in the field with the publication of two functional lymphoma classifications that related the malignant lymphomas to the cells of the normal immune system-the Lukes/Collins classification from the United States and the Kiel classification from Professor Lennert and the European Lymphoma Club. With discord abounding, the NCI working formulation, published in 1982, satisfied some but was a step back to a morphologic-based classification. In 1994, the International Lymphoma Study Group published the REAL classification, which reflected state-of-the-art practice for that time, and was shortly followed by preparations for the modern World Health Organization (WHO) classification published in 2001 and revised in 2008. The WHO classification, created by hematopathologists working with the advice and consent of clinical hematologist/oncologists, recognizes numerous distinct entities, defined based on their histopathological, immunophenotypical, molecular/cytogenetic and clinical features. The classification requires use of a multiparameter approach to lymphoma diagnosis although we still rely heavily on histopathology. Immunophenotypical studies, whether using paraffin section immunohistochemistry and/or flow cytometry, are also critical in almost all circumstances. Molecular/cytogenetic techniques that are constantly changing have an increasingly important role, even if not always required. The full impact of next-generation sequencing is yet to be felt but we are beginning to catch a glimpse of what is in our future. Finally, one must not forget the great importance of clinical data in arriving at a diagnosis that best serves the patient, our ultimate goal.
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Affiliation(s)
- Steven H Swerdlow
- Division of Hematopathology, Department of Pathology, UPMC Health System-UPMC Presbyterian, University of Pittsburgh School of Medicine, 200 Lothrop Street, Pittsburgh, PA 15213, USA.
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13
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Schultz RA, Tsuchiya K, Furrow A, Slovak ML, McDaniel LD, Wall M, Crawford E, Ning Y, Saleki R, Fang M, Cawich V, Johnson CE, Minier SL, Neill NJ, Morton SA, Byerly S, Surti U, Brown TC, Ballif BC, Shaffer LG. CGH-based microarray detection of cryptic and novel copy number alterations and balanced translocations in cytogenetically abnormal cases of b-cell all. Health (London) 2013. [DOI: 10.4236/health.2013.55a004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Abstract
SUMMARY Cytogenetic analysis is now considered a mandatory investigation in the diagnostic work-up of hematologic malignancies. Recurring structural aberrations serve as powerful markers not only for diagnosis and prognosis of these conditions, but also guide the selection of targeted drugs for personalized oncology. The FISH approach is established as an indispensable tool to complement conventional cytogenetics, in addition to basic and clinical research applications. FISH is used to identify specific chromosomal aberrations through the detection of target DNA sequences by fluorescently labeled DNA probes. Multicolor FISH analysis allows the accurate identification of recurring translocations in neoplastic cells by means of genomic probes that flank the breakpoints. This review summarizes the panel of FISH probes for selection and the current utilization of these FISH techniques in unraveling chromosomal aberrations. The niche of FISH analysis is also highlighted. Variant signal patterns of the clinically useful FISH probes for hematologic oncology illustrated here provide useful interpretative reference for molecular pathology laboratories. In addition, the recent application of FISH tests in contributing information on drug targets at the genomic level to support personalized oncology will also be discussed.
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Affiliation(s)
- Thomas SK Wan
- Division of Haematology, Department of Pathology, Queen Mary Hospital, The University of Hong Kong, 102, Pokfulam Road, Hong Kong, China
| | - Edmond SK Ma
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
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15
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IgH partner breakpoint sequences provide evidence that AID initiates t(11;14) and t(8;14) chromosomal breaks in mantle cell and Burkitt lymphomas. Blood 2012; 120:2864-7. [PMID: 22915650 DOI: 10.1182/blood-2012-02-412791] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Previous studies have implicated activation-induced cytidine deaminase (AID) in B-cell translocations but have failed to identify any association between their chromosomal breakpoints and known AID target sequences. Analysis of 56 unclustered IgH-CCND1 translocations in mantle cell lymphoma across the ~ 344-kb bcl-1 breakpoint locus demonstrates that half of the CCND1 breaks are near CpG dinucleotides. Most of these CpG breaks are at CGC motifs, and half of the remaining breaks are near WGCW, both known AID targets. These findings provide the strongest evidence to date that AID initiates chromosomal breaks in translocations that occur in human bone marrow B-cell progenitors. We also identify WGCW breaks at the MYC locus in Burkitt lymphoma translocations and murine IgH-MYC translocations, both of which arise in mature germinal center B cells. Finally, we propose a developmental model to explain the transition from CpG breaks in early human B-cell progenitors to WGCW breaks in later stage B cells.
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16
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Simons A, Sikkema-Raddatz B, de Leeuw N, Konrad NC, Hastings RJ, Schoumans J. Genome-wide arrays in routine diagnostics of hematological malignancies. Hum Mutat 2012; 33:941-8. [PMID: 22488943 DOI: 10.1002/humu.22057] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Accepted: 02/03/2012] [Indexed: 11/10/2022]
Abstract
Over the last three decades, cytogenetic analysis of malignancies has become an integral part of disease evaluation and prediction of prognosis or responsiveness to therapy. In most diagnostic laboratories, conventional karyotyping, in conjunction with targeted fluorescence in situ hybridization analysis, is routinely performed to detect recurrent aberrations with prognostic implications. However, the genetic complexity of cancer cells requires a sensitive genome-wide analysis, enabling the detection of small genomic changes in a mixed cell population, as well as of regions of homozygosity. The advent of comprehensive high-resolution genomic tools, such as molecular karyotyping using comparative genomic hybridization or single-nucleotide polymorphism microarrays, has overcome many of the limitations of traditional cytogenetic techniques and has been used to study complex genomic lesions in, for example, leukemia. The clinical impact of the genomic copy-number and copy-neutral alterations identified by microarray technologies is growing rapidly and genome-wide array analysis is evolving into a diagnostic tool, to better identify high-risk patients and predict patients' outcomes from their genomic profiles. Here, we review the added clinical value of an array-based genome-wide screen in leukemia, and discuss the technical challenges and an interpretation workflow in applying arrays in the acquired cytogenetic diagnostic setting.
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Affiliation(s)
- Annet Simons
- Laboratory of Tumor Genetics, Department of Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands
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17
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Shaffer LG, Schultz RA, Ballif BC. The use of new technologies in the detection of balanced translocations in hematologic disorders. Curr Opin Genet Dev 2012; 22:264-71. [PMID: 22336526 DOI: 10.1016/j.gde.2012.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 01/11/2012] [Accepted: 01/12/2012] [Indexed: 01/11/2023]
Abstract
The cytogenetic evaluation of hematologic disease can confirm a diagnosis, determine treatment options, and provide prognostic information to the patient. Among the potential cytogenetic aberrations that can be identified are certain balanced translocations with recurrent breakpoints that provide disease classification and define the sites of disease-causing or disease-promoting genes. In this review, we discuss the importance of balanced translocation identification, the methods traditionally used to identify balanced translocations in the cytogenetics laboratory, and the application of new methodologies such as next generation (NextGen) sequencing and array-based translocation identification through a linear amplification application. These new technologies have the potential to identify all currently known diagnostically and prognostically important rearrangements as well as novel alterations that may provide new therapeutic targets to enhance treatment of hematologic disease.
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Affiliation(s)
- Lisa G Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA, USA.
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