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Balciuniene J, Ning Y, Lazarus HM, Aikawa V, Sherpa S, Zhang Y, Morrissette JJD. Cancer cytogenetics in a genomics world: Wedding the old with the new. Blood Rev 2024; 66:101209. [PMID: 38852016 DOI: 10.1016/j.blre.2024.101209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 06/10/2024]
Abstract
Since the discovery of the Philadelphia chromosome in 1960, cytogenetic studies have been instrumental in detecting chromosomal abnormalities that can inform cancer diagnosis, treatment, and risk assessment efforts. The initial expansion of cancer cytogenetics was with fluorescence in situ hybridization (FISH) to assess submicroscopic alterations in dividing or non-dividing cells and has grown into the incorporation of chromosomal microarrays (CMA), and next generation sequencing (NGS). These molecular technologies add additional dimensions to the genomic assessment of cancers by uncovering cytogenetically invisible molecular markers. Rapid technological and bioinformatic advances in NGS are so promising that the idea of performing whole genome sequencing as part of routine patient care may soon become economically and logistically feasible. However, for now cytogenetic studies continue to play a major role in the diagnostic testing and subsequent assessments in leukemia with other genomic studies serving as complementary testing options for detection of actionable genomic abnormalities. In this review, we discuss the role of conventional cytogenetics (karyotyping, chromosome analysis) and FISH studies in hematological malignancies, highlighting the continued clinical utility of these techniques, the subtleties and complexities that are relevant to treating physicians and the unique strengths of cytogenetics that cannot yet be paralleled by the current high-throughput molecular technologies. Additionally, we describe how CMA, optical genome mapping (OGM), and NGS detect abnormalities that were beyond the capacity of cytogenetic studies and how an integrated approach (broad molecular testing) can contribute to the detection of actionable targets and variants in malignancies. Finally, we discuss advances in the field of genomic testing that are bridging the advantages of individual (single) cell based cytogenetic testing and broad genomic testing.
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Affiliation(s)
- Jorune Balciuniene
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yi Ning
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Hillard M Lazarus
- Department of Medicine, Case Western Reserve University, Cleveland, OH, United States of America
| | - Vania Aikawa
- Division of Precision and Computational Diagnostics, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarina Sherpa
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yanming Zhang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jennifer J D Morrissette
- Division of Precision and Computational Diagnostics, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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Akkari Y, Baughn LB, Kim A, Karaca E, Raca G, Shao L, Mikhail FM. Section E6.1-6.6 of the American College of Medical Genetics and Genomics (ACMG) Technical Laboratory Standards: Cytogenomic studies of acquired chromosomal abnormalities in neoplastic blood, bone marrow, and lymph nodes. Genet Med 2024; 26:101054. [PMID: 38349293 DOI: 10.1016/j.gim.2023.101054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 04/09/2024] Open
Abstract
Cytogenomic analyses of acquired clonal chromosomal abnormalities in neoplastic blood, bone marrow, and/or lymph nodes are instrumental in the clinical management of patients with hematologic neoplasms. Cytogenetic analyses assist in the diagnosis of such disorders and can provide important prognostic information. Furthermore, cytogenetic studies can provide crucial information regarding specific genetically defined subtypes of these neoplasms that may have targeted therapies. At time of relapse, cytogenetic analysis can confirm recurrence of the original neoplasm, detect clonal disease evolution, or uncover a new unrelated neoplastic process. This section deals specifically with the technical standards applicable to cytogenomic studies of acquired clonal chromosomal abnormalities in neoplastic blood, bone marrow, and/or lymph nodes. This updated Section E6.1-6.6 supersedes the previous Section E6 in Section E: Clinical Cytogenetics of the American College of Medical Genetics and Genomics Technical Standards for Clinical Genetics Laboratories.
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Affiliation(s)
- Yassmine Akkari
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Linda B Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Annette Kim
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Ender Karaca
- Department of Pathology, Baylor University Medical Center, Dallas, TX; Texas A&M School of Medicine, Texas A&M University, Dallas, TX
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA; Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Lina Shao
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
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Yu J. Cell Culture and Slide Preparation for Cytogenetic Studies of Hematological Neoplasms. Methods Mol Biol 2024; 2825:127-135. [PMID: 38913306 DOI: 10.1007/978-1-0716-3946-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Hematological neoplasms are heterogeneous diseases with various subtypes, each with its unique genomic features. Cell culture and slide preparation are essential steps to enrich and collect sufficient neoplastic cells for cytogenetic studies of the neoplasms. This chapter describes methods that are commonly used for culturing hematological neoplastic cells and preparing cytogenetic slides for clinical diagnosis and research of the neoplasms.
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Affiliation(s)
- Jingwei Yu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
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Tang Z, Kanagal-Shamanna R, Tang G, Patel K, Medeiros LJ, Toruner GA. Analytical and clinical performance of chromosomal microarrays compared with FISH panel and conventional karyotyping in patients with chronic lymphocytic leukemia. Leuk Res 2021; 108:106616. [PMID: 34022744 DOI: 10.1016/j.leukres.2021.106616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/26/2021] [Accepted: 05/10/2021] [Indexed: 11/19/2022]
Abstract
In this single center retrospective analysis on 102 CLL patients, we assessed analytical and clinical performance of CMA against a targeted FISH panel (ATM, TP53, CEP12, D13S319 and LAMP1 loci) and karyotyping. CMA yielded additional information compared to karyotype in 39 cases (38 %). On the other hand, while CMA detected aberrations were also detected by FISH in all 31 cases (30 %), aberrations with low clonal size (<30 %) detected by FISH were missed by CMA. When evaluated with National Cancer Center Network (NCCN) guidelines, the capture rate of prognostic relevant cytogenetic information for FISH only, FISH + Chromosomes and FISH + CMA analyses were 95, 96 and 100 % respectively. With Cancer Cytogenomics Consortium (CGC) Criteria, these figures for FISH only, FISH + Chromosomes and FISH + CMA were 88 %, 92 and 100 % respectively. In conclusion, CMA provides additional analytical information to FISH and karyotyping, but this information has a clinical utility only in a small number of patients. Limit of detection (LOD) issues preclude replacement of FISH by CMA, but CMA may be a viable alternative to karyotyping. Further research is warranted.
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Affiliation(s)
- Zhenya Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Guilin Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Keyur Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Gokce A Toruner
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States.
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Liu HF, Huang HW, Bai SX, Gong YL, Wu CX, Jin ZM, Wang YY, Yang Q, Zhang J, Qiu HY, Chen SN, Pan JL. [Chromosomal aberrations detection in chronic lymphocytic leukemia by conventional cytogenetics using DSP30 and IL-2]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2020; 41:143-148. [PMID: 32135632 PMCID: PMC7357944 DOI: 10.3760/cma.j.issn.0253-2727.2020.02.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Indexed: 12/15/2022]
Abstract
Objective: To study the value of unmethylated cytosine guanine dinucleotide oligodeoxynucleotide (DSP30) and IL-2 in the conventional cytogenetic (CA) detection of the chromosomal aberrations in chronic lymphocytic leukemia (CLL) . Methods: Bone marrow or peripheral blood cells of CLL patients were cultured with DSP30 plus IL-2 for 72 h, following which R-banding analysis was conducted. Fluorescence in situ hybridization (FISH) was performed in 85 patients. CA results were compared with data obtained by FISH. Results: Among 89 CLL patients, the success rate of chromosome analysis was 94.38% (84/89) . Clonal aberrations were detected in 51 patients (51/84, 60.71%) . Of them, 27 (27/51, 52.94%) were complex karyotype. Among 85 CLL patients tested by FISH, chromosomal abnormalities were detected in 74 (74/85, 87.06%) patients, of which 2 (2/74) patients were complex karyotypes, accounting for 2.70%. Of the 85 CLL patients examined by FISH, 50 had abnormal karyotype analysis, 30 had normal karyotype, 5 failed to have chromosome analysis. Among them, 25 cases showed clonal aberrations by FISH assay but normal by CA, and 4 cases were normal by FISH but displayed aberrations in chromosome analysis, and totally 78 (91.76%) cases with abnormality detected by the combination of the two methods. The frequency of 13q- abnormality detected by FISH was significantly higher than that by CA analysis (69.41%vs 16.67%, P<0.001) , while the frequency of 11q-,+12 and 17p- detected by two methods showed no significant difference (P>0.05) . The detection rate of complex abnormalities in conventional karyotype analysis was higher than that in FISH (50.98%vs 2.70%) . In addition, 11 low-risk and 9 intermediate-risk patients according to FISH results showed complex karyotype by cytogenetics, and were classified into high-risk cytogenetic subgroup. Conclusion: DSP30 and IL-2 are effective in improving the detection rate of CA in CLL patients (60.71%) and CA is more effective to detect complex karyotype. However, FISH had a higher overall abnormality detection rate (87.06%) than CA, especially for 13q-. The combination of CA and FISH not only enhanced the detection rate of clonal aberrations to 91.76%, but also provided more precise prognosis stratification for CLL patients, thus to provide more information for clinical implication.
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Affiliation(s)
- H F Liu
- Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
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Assessing copy number aberrations and copy-neutral loss-of-heterozygosity across the genome as best practice: An evidence-based review from the Cancer Genomics Consortium (CGC) working group for chronic lymphocytic leukemia. Cancer Genet 2018; 228-229:236-250. [DOI: 10.1016/j.cancergen.2018.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/29/2018] [Accepted: 07/01/2018] [Indexed: 01/18/2023]
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Wan TSK, Hui EKC, Ng MHL. Significance of Cytogenetics in Leukemia Diagnostics. CURRENT GENETIC MEDICINE REPORTS 2018. [DOI: 10.1007/s40142-018-0147-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Dun KA, Riley LA, Diano G, Adams LB, Chiu E, Sharma A. DSP30 and interleukin-2 as a mitotic stimulant in B-cell disorders including those with a low disease burden. Genes Chromosomes Cancer 2018; 57:260-267. [PMID: 29349871 DOI: 10.1002/gcc.22527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 01/16/2018] [Accepted: 01/16/2018] [Indexed: 11/11/2022] Open
Abstract
Chromosome abnormalities detected during cytogenetic investigations for B-cell malignancy offer prognostic information that can have wide ranging clinical impacts on patients. These impacts may include monitoring frequency, treatment type, and disease staging level. The use of the synthetic oligonucleotide DSP30 combined with interleukin 2 (IL2) has been described as an effective mitotic stimulant in B-cell disorders, not only in chronic lymphocytic leukemia (CLL) but also in a range of other B-cell malignancies. Here, we describe the comparison of two B-cell mitogens, lipopolysaccharide (LPS), and DSP30 combined with IL2 as mitogens in a range of common B-cell disorders excluding CLL. The results showed that DSP30/IL2 was an effective mitogen in mature B-cell disorders, revealing abnormal cytogenetic results in a range of B-cell malignancies. The abnormality rate increased when compared to the use of LPS to 64% (DSP30/IL2) from 14% (LPS). In a number of cases the disease burden was proportionally very low, less than 10% of white cells. In 37% of these cases, the DSP30 culture revealed abnormal results. Importantly, we also obtained abnormal conventional cytogenetics results in 3 bone marrow cases in which immunophenotyping showed an absence of an abnormal B-cell clone. In these cases, the cytogenetics results correlated with the provisional diagnosis and altered their staging level. The use of DSP30 and IL2 is recommended for use in many B-cell malignancies as an effective mitogen and their use has been shown to enable successful culture of the malignant clone, even at very low levels of disease.
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Affiliation(s)
- Karen A Dun
- Cytogenetics Laboratory, Royal Hobart Hospital, Tasmania, Australia
| | - Louise A Riley
- Cytogenetics Laboratory, Royal Hobart Hospital, Tasmania, Australia
| | - Giuseppe Diano
- Cytogenetics Laboratory, Royal Hobart Hospital, Tasmania, Australia
| | - Leanne B Adams
- Cytogenetics Laboratory, Royal Hobart Hospital, Tasmania, Australia
| | - Eleanor Chiu
- Cytogenetics Laboratory, Royal Hobart Hospital, Tasmania, Australia
| | - Archna Sharma
- Department of Haematology, Royal Hobart Hospital, Tasmania, Australia
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Ashok V, Ranganathan R, Chander S, Damodar S, Bhat S, S NK, A SK, Jadav SS, Rajashekaraiah M, T S S. Comparison of Diagnostic Yield of a FISH Panel Against Conventional Cytogenetic Studies for Hematological Malignancies: A South Indian Referral Laboratory Analysis Of 201 Cases. Asian Pac J Cancer Prev 2017; 18:3457-3464. [PMID: 29286619 PMCID: PMC5980910 DOI: 10.22034/apjcp.2017.18.12.3457] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Objectives: Genetic markers are crucial fort diagnostic and prognostic investigation of hematological malignancies (HM). The conventional cytogenetic study (CCS) has been the gold standard for more than five decades. However, FISH (Fluorescence in Situ Hybridization) testing has become a popular modality owing to its targeted approach and the ability to detect abnormalities in non-mitotic cells. We here aimed to compare the diagnostic yields of a FISH panel against CCS in HMs. Methods: Samples of bone marrow and peripheral blood for a total of 201 HMs were tested for specific gene rearrangements using multi-target FISH and the results were compared with those from CCS. Results: Exhibited a greater diagnostic yield with a positive result in 39.8% of the cases, as compared to 17.9% of cases detected by CCS. Cases of chronic lymphocytic leukaemia (CLL) benefited the most by FISH testing, which identified chromosomal aberrations beyond the capacity of CCS. FISH was least beneficial in myelodysplastic syndrome (MDS) where the highest concordance with CCS was exhibited. Acute lymphocytic leukaemia (ALL) demonstrated greater benefit with CCS. In addition, we found the following abnormalities to be most prevalent in HMs by FISH panel testing: RUNX1 (21q22) amplification in ALL, deletion of D13S319/LAMP1 (13q14) in CLL, CKS1B (1q21) amplification in multiple myeloma and deletion of EGR1/RPS14 (5q31/5q32) in MDS, consistent with the literature. Conclusions: In conclusion, FISH was found to be advantageous in only a subset of HMs and cannot completely replace CCS. Utilization of the two modalities in conjunction or independently should depend on the indicated HM for an optimal approach to detecting chromosomal aberrations.
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Affiliation(s)
- Vishal Ashok
- Department of Cytogenetics, Anand Diagnostic Laboratory, Bangalore, India.
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10
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Koczkodaj D, Filip AA. Chromosome Preparation for Chronic Lymphoid Malignancies. Methods Mol Biol 2016; 1541:33-41. [PMID: 27910012 DOI: 10.1007/978-1-4939-6703-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
Conventional cytogenetics is invariably one of the most important methods used in diagnostics of chronic lymphoproliferations. It complements fluorescence in situ hybridization (FISH) and molecular analysis. Presence of particular chromosomal alterations in chronic lymphocytic leukemia enables patients' stratification into appropriate cytogenetic risk groups and influences treatment decisions. In other non-Hodgkin lymphomas cytogenetic analyses are employed also in minimal residual disease assessment.As lymphocytes in chronic lymphoid malignancies are characterized by low proliferation rate in vitro, it is critical to induce their division in the culture properly. Here, we describe methods of lymphocyte isolation from patient's samples, conditions of cell culture, and the most commonly used mitogens for B- and T-lymphocytes in hemato-oncologic analyses.
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Affiliation(s)
- Dorota Koczkodaj
- Department of Cancer Genetics, Medical University of Lublin, Radziwiłłowska 11, Lublin, 20-080, Poland.
| | - Agata A Filip
- Department of Cancer Genetics, Medical University of Lublin, Radziwiłłowska 11, Lublin, 20-080, Poland
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11
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Dubuc AM, Davids MS, Pulluqi M, Pulluqi O, Hoang K, Hernandez-Sánchez JM, Schlich C, Hernández-Rivas JM, Brown JR, Dal Cin P. FISHing in the dark: How the combination of FISH and conventional karyotyping improves the diagnostic yield in CpG-stimulated chronic lymphocytic leukemia. Am J Hematol 2016; 91:978-83. [PMID: 27341486 DOI: 10.1002/ajh.24452] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 05/26/2016] [Accepted: 06/17/2016] [Indexed: 01/01/2023]
Abstract
Despite significant advances in molecular genetic approaches, fluorescence in situ hybridization (FISH) remains the gold standard for the diagnostic evaluation of genomic aberrations in patients with chronic lymphocytic leukemia (CLL). Efforts to improve the diagnostic utility of molecular cytogenetic testing have led to the expansion of the traditional 4-probe CLL FISH panel. Not only do these efforts increase the cost of testing, they remain hindered by the inherent limitations of FISH studies - namely the inability to evaluate genomic changes outside of the targeted loci. While array-based profiling and next generation sequencing (NGS) have critically expanded our understanding of the molecular pathogenesis of CLL, these methodologies are not routinely used by diagnostic laboratories to evaluate copy number changes or the mutational profile of this disease. Mitogenic stimulation of CLL specimens with CpG-oligonucleotide (CpG-ODN) has been identified as a reliable and reproducible means of obtaining a karyotype, facilitating a low-resolution genome-wide analysis. Across a cohort of 1255 CpG-ODN-stimulated CLL specimens, we describe the clinical utility associated with the combinatorial use of FISH and karyotyping. Our testing algorithm achieves a higher diagnostic yield (∼10%) through the detection of complex karyotypes, well-characterized chromosomal aberrations not covered by the traditional CLL FISH panel and through the detection of concurrent secondary malignancies. Moreover, the single cell nature of this approach permits the evaluation of emerging new clinical concepts including clonal dynamics and clonal evolution. This approach can be broadly applied by diagnostic laboratories to improve the utility of traditional and molecular cytogenetic studies of CLL. Am. J. Hematol. 91:978-983, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Adrian M. Dubuc
- Department of Pathology; Brigham and Women's Hospital; Boston Massachusetts
- Harvard Medical School; Boston Massachusetts
| | - Matthew S. Davids
- Harvard Medical School; Boston Massachusetts
- Department of Medical Oncology; Dana-Farber Cancer Institute; Boston Massachusetts
| | - Mirela Pulluqi
- Department of Pathology; Brigham and Women's Hospital; Boston Massachusetts
| | - Olja Pulluqi
- Department of Pathology; Brigham and Women's Hospital; Boston Massachusetts
| | - Kevin Hoang
- Department of Medical Oncology; Dana-Farber Cancer Institute; Boston Massachusetts
| | | | - Cathy Schlich
- Department of Pathology; Brigham and Women's Hospital; Boston Massachusetts
| | - Jesus M. Hernández-Rivas
- IBSAL, IBMCC, Centro de Investigación del Cáncer, Universidad de Salamanca-CSIC; Salamanca 37007 Spain
- Department of Hematology; Hospital Universitario de Salamanca; Salamanca 37007 Spain
| | - Jennifer R. Brown
- Harvard Medical School; Boston Massachusetts
- Department of Medical Oncology; Dana-Farber Cancer Institute; Boston Massachusetts
| | - Paola Dal Cin
- Department of Pathology; Brigham and Women's Hospital; Boston Massachusetts
- Harvard Medical School; Boston Massachusetts
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12
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Holmes PJ, Peiper SC, Uppal GK, Gong JZ, Wang ZX, Bajaj R. Efficacy of DSP30-IL2/TPA for detection of cytogenetic abnormalities in chronic lymphocytic leukaemia/small lymphocytic lymphoma. Int J Lab Hematol 2016; 38:483-9. [PMID: 27565124 DOI: 10.1111/ijlh.12513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 03/14/2016] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Chronic lymphocytic leukaemia (CLL) is the most prevalent leukaemia in the Western Hemisphere. Cytogenetic abnormalities in CLL are used for diagnosis, prognosis and treatment. However, detecting these is difficult because mature B cells do not readily divide in culture. Here, we present data on two mitogen cocktails: CpG-oligonucleotide DSP30/Interleukin-2 (IL-2) and DSP30/IL-2 in combination with 12-O-tetradecanoylphorbol-13-acetate (TPA). METHODS We analysed 165 cases of CLL with FISH and cytogenetics from January 2011 to June 2013. In 2011, three cultures were set-up: unstimulated, DSP30/IL-2-stimulated and TPA-stimulated. In 2012-2013, two cultures were set-up: unstimulated and stimulated with TPA/DSP30/IL-2. RESULTS In 2011, FISH had a detection rate of 91% and cytogenetics using DSP30/IL2 had a detection rate of 91% (n = 22). In 2012-2013, FISH had a detection rate of 79% and cytogenetics using TPA/DSP30/IL-2 had a detection rate of 98% (n = 40). The percentage of cases with normal FISH but abnormal cytogenetics increased from 9% in 2011 to 21% in 2012-2013. The TPA/DSP30/IL-2 cultures in 2012-2013 detected more novel abnormalities (n = 5) as compared to DSP30/IL-2 alone (n = 3). CONCLUSIONS TPA/DSP30/IL2 was as good as or better than DSP30/IL2 alone. TPA/DSP30/IL-2 offers a high detection rate for CLL abnormalities with a single stimulated culture and may increase detection of clinically significant abnormalities.
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Affiliation(s)
- P J Holmes
- The Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University Hospital, Philadelphia, PA, USA
| | - S C Peiper
- The Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University Hospital, Philadelphia, PA, USA
| | - G K Uppal
- The Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University Hospital, Philadelphia, PA, USA
| | - J Z Gong
- The Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University Hospital, Philadelphia, PA, USA
| | - Z-X Wang
- The Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University Hospital, Philadelphia, PA, USA
| | - R Bajaj
- The Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University Hospital, Philadelphia, PA, USA.
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13
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Alhourani E, Aroutiounian R, Harutyunyan T, Glaser A, Schlie C, Pohle B, Liehr T. Interphase Molecular Cytogenetic Detection Rates of Chronic Lymphocytic Leukemia-Specific Aberrations Are Higher in Cultivated Cells Than in Blood or Bone Marrow Smears. J Histochem Cytochem 2016; 64:495-501. [PMID: 27315825 DOI: 10.1369/0022155416655086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 05/25/2016] [Indexed: 11/22/2022] Open
Abstract
Banding cytogenetics is still the gold standard in many fields of leukemia diagnostics. However, in chronic lymphocytic leukemia (CLL), GTG-banding results are hampered by a low mitotic rate of the corresponding malignant lymphatic cells. Thus, interphase fluorescence in situ hybridization (iFISH) for the detection of specific cytogenetic aberrations is done nowadays as a supplement to or even instead of banding cytogenetics in many diagnostic laboratories. These iFISH studies can be performed on native blood or bone marrow smears or in nuclei after cultivation and stimulation by a suitable mitogen. As there are only few comparative studies with partially conflicting results for the detection rates of aberrations in cultivated and native cells, this question was studied in 38 CLL cases with known aberrations in 11q22.2, 11q22.3, 12, 13q14.3, 14q32.33, 17p13.1, or 18q21.32. The obtained results implicate that iFISH directly applied on smears is in general less efficient for the detection of CLL-specific genetic abnormalities than for cultivated cells. This also shows that applied cell culture conditions are well suited for malignant CLL cells. Thus, to detect malignant aberrant cells in CLL, cell cultivation and cytogenetic workup should be performed and the obtained material should be subjected to banding cytogenetics and iFISH.
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Affiliation(s)
- Eyad Alhourani
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany (EA, AG, CS, BP, TL)
| | - Rouben Aroutiounian
- Department of Genetics and Cytology, Yerevan State University, Yerevan, Armenia (RA, TH)
| | - Tigran Harutyunyan
- Department of Genetics and Cytology, Yerevan State University, Yerevan, Armenia (RA, TH)
| | - Anita Glaser
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany (EA, AG, CS, BP, TL)
| | - Cordula Schlie
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany (EA, AG, CS, BP, TL)
| | - Beate Pohle
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany (EA, AG, CS, BP, TL)
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany (EA, AG, CS, BP, TL)
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14
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Mikhail FM, Heerema NA, Rao KW, Burnside RD, Cherry AM, Cooley LD. Section E6.1-6.4 of the ACMG technical standards and guidelines: chromosome studies of neoplastic blood and bone marrow-acquired chromosomal abnormalities. Genet Med 2016; 18:635-42. [PMID: 27124785 DOI: 10.1038/gim.2016.50] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 03/01/2016] [Indexed: 12/30/2022] Open
Abstract
DISCLAIMER These American College of Medical Genetics and Genomics standards and guidelines are developed primarily as an educational resource for clinical laboratory geneticists to help them provide quality clinical laboratory genetic services. Adherence to these standards and guidelines is voluntary and does not necessarily ensure a successful medical outcome. These standards and guidelines should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, the clinical laboratory geneticist should apply his or her own professional judgment to the specific circumstances presented by the individual patient or specimen. Clinical laboratory geneticists are encouraged to document in the patient's record the rationale for the use of a particular procedure or test, whether or not it is in conformance with these standards and guidelines. They also are advised to take notice of the date any particular guideline was adopted, and to consider other relevant medical and scientific information that becomes available after that date. It also would be prudent to consider whether intellectual property interests may restrict the performance of certain tests and other procedures.Cytogenetic analyses of hematological neoplasms are performed to detect and characterize clonal chromosomal abnormalities that have important diagnostic, prognostic, and therapeutic implications. At the time of diagnosis, cytogenetic abnormalities assist in the diagnosis of such disorders and can provide important prognostic information. At the time of relapse, cytogenetic analysis can be used to confirm recurrence of the original neoplasm, detect clonal disease evolution, or uncover a new unrelated neoplastic process. This section deals specifically with the standards and guidelines applicable to chromosome studies of neoplastic blood and bone marrow-acquired chromosomal abnormalities. This updated Section E6.1-6.4 has been incorporated into and supersedes the previous Section E6 in Section E: Clinical Cytogenetics of the 2009 Edition (Revised 01/2010), American College of Medical Genetics and Genomics Standards and Guidelines for Clinical Genetics Laboratories.Genet Med 18 6, 635-642.
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Affiliation(s)
- Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Nyla A Heerema
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Kathleen W Rao
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Pathology, University of North Carolina, Chapel Hill, North Carolina, USA.,Deceased
| | - Rachel D Burnside
- Laboratory Corporation of America Holdings, Center for Molecular Biology and Pathology, Research Triangle Park, North Carolina, USA
| | - Athena M Cherry
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Linda D Cooley
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, University of Missouri Kansas City Medical School, Kansas City, Missouri, USA
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15
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Salaverria I, Martín‐Garcia D, López C, Clot G, García‐Aragonés M, Navarro A, Delgado J, Baumann T, Pinyol M, Martin‐Guerrero I, Carrió A, Costa D, Queirós AC, Jayne S, Aymerich M, Villamor N, Colomer D, González M, López‐Guillermo A, Campo E, Dyer MJS, Siebert R, Armengol L, Beà S. Detection of chromothripsis-like patterns with a custom array platform for chronic lymphocytic leukemia. Genes Chromosomes Cancer 2015; 54:668-80. [PMID: 26305789 PMCID: PMC4832286 DOI: 10.1002/gcc.22277] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/04/2015] [Accepted: 06/04/2015] [Indexed: 02/04/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a common disease with highly variable clinical course. Several recurrent chromosomal alterations are associated with prognosis and may guide risk-adapted therapy. We have developed a targeted genome-wide array to provide a robust tool for ascertaining abnormalities in CLL and to overcome limitations of the 4-marker fluorescence in situ hybridization (FISH). DNA from 180 CLL patients were hybridized to the qChip®Hemo array with a high density of probes covering commonly altered loci in CLL (11q22-q23, 13q14, and 17p13), nine focal regions (2p15-p16.1, 2p24.3, 2q13, 2q36.3-q37.1, 3p21.31, 8q24.21, 9p21.3, 10q24.32, and 18q21.32-q21.33) and two larger regions (6q14.1-q22.31 and 7q31.33-q33). Overall, 86% of the cases presented copy number alterations (CNA) by array. There was a high concordance of array findings with FISH (84% sensitivity, 100% specificity); all discrepancies corresponded to subclonal alterations detected only by FISH. A chromothripsis-like pattern was detected in eight cases. Three showed concomitant shattered 5p with gain of TERT along with isochromosome 17q. Presence of 11q loss was associated with shorter time to first treatment (P = 0.003), whereas 17p loss, increased genomic complexity, and chromothripsis were associated with shorter overall survival (P < 0.001, P = 0.001, and P = 0.02, respectively). In conclusion, we have validated a targeted array for the diagnosis of CLL that accurately detects, in a single experiment, all relevant CNAs, genomic complexity, chromothripsis, copy number neutral loss of heterozygosity, and CNAs not covered by the FISH panel. This test may be used as a practical tool to stratify CLL patients for routine diagnostics or clinical trials.
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Affiliation(s)
- Itziar Salaverria
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - David Martín‐Garcia
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Cristina López
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
- Institute of Human Genetics, University Hospital Schleswig‐Holstein, Campus Kiel/Christian‐Albrechts UniversityKielGermany
| | - Guillem Clot
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Manel García‐Aragonés
- R&D, Department, Quantitative Genomic Medicine Laboratories (qGenomics)BarcelonaSpain
| | - Alba Navarro
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Julio Delgado
- Department of HematologyHospital Clínic, IDIBAPSBarcelonaSpain
| | - Tycho Baumann
- Department of HematologyHospital Clínic, IDIBAPSBarcelonaSpain
| | - Magda Pinyol
- Genomics UnitInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Idoia Martin‐Guerrero
- Institute of Human Genetics, University Hospital Schleswig‐Holstein, Campus Kiel/Christian‐Albrechts UniversityKielGermany
- Department of Genetics, Physical Anthropology and Animal PhysiologyUniversity of the Basque CountryLeioaSpain
| | - Ana Carrió
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Dolors Costa
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Ana C. Queirós
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Sandrine Jayne
- Ernest and Helen Scott Haematological Research Institute, Department of Biochemistry, University of LeicesterLeicesterUK
| | - Marta Aymerich
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Neus Villamor
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Dolors Colomer
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Marcos González
- Department of HematologyHospital Clínico‐IBSAL, Cancer Institute of Salamanca‐IBMCC (USAL‐CSIC)SalamancaSpain
| | | | - Elías Campo
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Martin J. S. Dyer
- Ernest and Helen Scott Haematological Research Institute, Department of Biochemistry, University of LeicesterLeicesterUK
| | - Reiner Siebert
- Institute of Human Genetics, University Hospital Schleswig‐Holstein, Campus Kiel/Christian‐Albrechts UniversityKielGermany
| | - Lluís Armengol
- R&D, Department, Quantitative Genomic Medicine Laboratories (qGenomics)BarcelonaSpain
| | - Sílvia Beà
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
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Jenderny J, Goldmann C, Thede R, Ebrecht M, Korioth F. Detection of clonal aberrations by cytogenetic analysis after different culture methods and by FISH in 129 patients with Chronic Lymphocytic Leukemia. Cytogenet Genome Res 2014; 144:163-8. [PMID: 25502547 DOI: 10.1159/000369543] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2014] [Indexed: 11/19/2022] Open
Abstract
There are only a few cytogenetic analysis (CA) studies that directly compare the novel cultivation technique using immunostimulatory CpG-oligonucleotide DSP30/interleukin-2 (DSP30/IL2) with other culture methods. Therefore, parallel cultures of peripheral blood of 129 chronic lymphocytic leukemia (CLL) patients were set up in unstimulated cultures, in the presence of pokeweed medium (PWM), and with DSP30/IL2. Furthermore, CA results were compared with data obtained by FISH. Clonal aberrations were observed by CA in 6% of the cases in unstimulated cultures, in 27% of the cases with PWM, and in 40% of the cases with DSP30/IL2. Some clonal aberrations were detected by CA only with one culture method. Using 3 different culture methods, clonal aberrations were detected in 41% of the cases by CA and in 71% of the cases by FISH. Altogether, 78% of the cases exhibited clonal aberrations discovered by CA and FISH. Also, CA detected clonal aberrations not targeted by FISH in 7% of the cases, and FISH identified clonal aberrations not detected by CA in 36% of the cases. Our study demonstrates that the combined use of CA with different culture methods together with FISH increases our knowledge of the genetic complexity and heterogeneity in CLL pathogenesis.
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Liaw FPS, Lau LC, Lim AST, Lim TH, Lee GY, Tien SL. CpG Oligonucleotide and Interleukin 2 stimulation enables higher cytogenetic abnormality detection rates than 12-o-tetradecanolyphorbol-13-acetate in Asian patients with B-cell chronic lymphocytic leukemia (B-CLL). Int J Hematol 2014; 100:545-53. [PMID: 25301672 DOI: 10.1007/s12185-014-1681-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 09/19/2014] [Accepted: 09/21/2014] [Indexed: 10/24/2022]
Abstract
The present study was designed to compare abnormality detection rates using DSP30 + IL2 and 12-O-Tetradecanoylphorbol-13-acetate (TPA) in Asian patients with B-CLL. Hematological specimens from 47 patients (29 newly diagnosed, 18 relapsed) were established as 72 h-DSP30 + IL2 and TPA cultures. Standard methods were employed to identify clonal aberrations by conventional cytogenetics (CC). The B-CLL fluorescence in situ hybridization (FISH) panel comprised ATM, CEP12, D13S25, and TP53 probes. DSP30 + IL2 cultures had a higher chromosomal abnormality detection rate (67 %) compared to TPA (44 %, p < 0.001). The mean number of analyzable metaphases and abnormal metaphases per slide was also higher (p < 0.005, p < 0.001, respectively). Culture success rate, percentage of complex karyotype, and percentage of non-clonal abnormal cell were not significantly different (p > 0.05). Thirteen cases with abnormalities were found exclusively in DSP30 + IL2 cultures compared to one found solely in TPA cultures. DSP30 + IL2 cultures were comparable to the FISH panel in detecting 11q-, +12 and 17p- but not 13q-. It also has a predilection for 11q- bearing leukemic cells compared to TPA. FISH had a higher abnormality detection rate (84.1 %) compared to CC (66.0 %) with borderline significance (p = 0.051), albeit limited by its coverage. In conclusion, DSP30 + IL2 showed a higher abnormality detection rate. However, FISH is indispensable to circumvent low mitotic indices and detect subtle abnormalities.
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Affiliation(s)
- Fiona Pui San Liaw
- Cytogenetics Laboratory, Department of Pathology, Singapore General Hospital, Academia, Level 9, Diagnostics Tower, 20 College Road, Singapore, 169856, Singapore,
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18
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Douet-Guilbert N, Tous C, Le Flahec G, Bovo C, Le Bris MJ, Basinko A, Morel F, De Braekeleer M. Translocation t(2;7)(p11;q21) associated with the CDK6/IGK rearrangement is a rare but recurrent abnormality in B-cell lymphoproliferative malignancies. Cancer Genet 2014; 207:83-6. [PMID: 24726269 DOI: 10.1016/j.cancergen.2014.02.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 02/21/2014] [Accepted: 02/24/2014] [Indexed: 01/22/2023]
Abstract
Structural abnormalities of chromosome 7q have been regularly reported in chronic B-cell lymphoproliferative disorders. They include chromosomal translocations involving 7q21, leading to overexpression of the CDK6 gene. Three different translocations, t(7;14)(q21;q32), t(7;22)(q21;q11), and t(2;7)(p11;q21), leading to the juxtaposition of the CDK6 gene with a immunoglobulin gene enhancer during B-cell differentiation, have been described. In the past 2 years, we identified three patients with lymphoproliferative malignancy associated with a t(2;7)(p11;q21). Fluorescent in situ hybridization using an IGK probe and a library of bacterial artificial chromosome (BAC) clones located in bands 7q21.2 and 7q21.3, containing CDK6, revealed that the telomeric part of the IGK probe was translocated on the der(7) within a 51-kb region upstream of the transcriptional start site of CDK6. A total of 23 patients with indolent B-cell lymphoproliferative disorders and juxtaposition of the IG and CDK6 genes, including 20 with IGK and CDK6 juxtaposition, have been reported thus far. This rearrangement leads to the overexpression of CDK6, which encodes a cyclin-dependent protein kinase involved in cell cycle G1 phase progression and G1/S transition.
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Affiliation(s)
- Nathalie Douet-Guilbert
- Laboratory of Histology, Embryology and Cytogenetics, Faculty of Medicine and Health Sciences, Université de Bretagne Occidentale, Brest, France; National Institute of Health and Medical Research (INSERM), Brest, France; Department of Cytogenetics and Reproductive Biology, Morvan Hospital, Brest University and Regional Hospital, Brest, France
| | - Corinne Tous
- Department of Cytogenetics and Reproductive Biology, Morvan Hospital, Brest University and Regional Hospital, Brest, France
| | - Glen Le Flahec
- Department of Cytogenetics and Reproductive Biology, Morvan Hospital, Brest University and Regional Hospital, Brest, France
| | - Clément Bovo
- Laboratory of Histology, Embryology and Cytogenetics, Faculty of Medicine and Health Sciences, Université de Bretagne Occidentale, Brest, France; National Institute of Health and Medical Research (INSERM), Brest, France
| | - Marie-Josée Le Bris
- Department of Cytogenetics and Reproductive Biology, Morvan Hospital, Brest University and Regional Hospital, Brest, France
| | - Audrey Basinko
- Department of Cytogenetics and Reproductive Biology, Morvan Hospital, Brest University and Regional Hospital, Brest, France
| | - Frédéric Morel
- Laboratory of Histology, Embryology and Cytogenetics, Faculty of Medicine and Health Sciences, Université de Bretagne Occidentale, Brest, France; National Institute of Health and Medical Research (INSERM), Brest, France; Department of Cytogenetics and Reproductive Biology, Morvan Hospital, Brest University and Regional Hospital, Brest, France
| | - Marc De Braekeleer
- Laboratory of Histology, Embryology and Cytogenetics, Faculty of Medicine and Health Sciences, Université de Bretagne Occidentale, Brest, France; National Institute of Health and Medical Research (INSERM), Brest, France; Department of Cytogenetics and Reproductive Biology, Morvan Hospital, Brest University and Regional Hospital, Brest, France.
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