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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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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: 20] [Impact Index Per Article: 2.2] [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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Urbankova H, Papajik T, Plachy R, Holzerova M, Balcarkova J, Divoka M, Prochazka V, Pikalova Z, Indrak K, Jarosova M. Array-based karyotyping in chronic lymphocytic leukemia (CLL) detects new unbalanced abnormalities that escape conventional cytogenetics and CLL FISH panel. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2014; 158:56-64. [DOI: 10.5507/bp.2012.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 02/27/2012] [Indexed: 02/07/2023] Open
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Konialis C, Savola S, Karapanou S, Markaki A, Karabela M, Polychronopoulou S, Ampatzidou M, Voulgarelis M, Viniou NA, Variami E, Koumarianou A, Zoi K, Hagnefelt B, Schouten JP, Pangalos C. Routine application of a novel MLPA-based first-line screening test uncovers clinically relevant copy number aberrations in haematological malignancies undetectable by conventional cytogenetics. Hematology 2013; 19:217-24. [DOI: 10.1179/1607845413y.0000000112] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
| | | | | | | | | | - Sophia Polychronopoulou
- Department of Paediatric Haematology-Oncology‘Aghia Sophia’ Children's Hospital, Athens, Greece
| | - Maria Ampatzidou
- Department of Paediatric Haematology-Oncology‘Aghia Sophia’ Children's Hospital, Athens, Greece
| | - Michael Voulgarelis
- Pathophysiology DepartmentSchool of Medicine, University of Athens, Athens, Greece
| | - Nora-Athina Viniou
- 1st Pathology ClinicUniversity of Athens, Laiko Hospital, Athens, Greece
| | - Eleni Variami
- 1st Pathology ClinicUniversity of Athens, Laiko Hospital, Athens, Greece
| | | | - Katerina Zoi
- Haematology Research LaboratoryBiomedical Research Foundation, Academy of Athens, Athens, Greece
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Houldsworth J, Guttapalli A, Thodima V, Yan XJ, Mendiratta G, Zielonka T, Nanjangud G, Chen W, Patil S, Mato A, Brown JR, Rai K, Chiorazzi N, Chaganti RSK. Genomic imbalance defines three prognostic groups for risk stratification of patients with chronic lymphocytic leukemia. Leuk Lymphoma 2013; 55:920-8. [PMID: 24047479 DOI: 10.3109/10428194.2013.845882] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Array comparative genomic hybridization (aCGH) has yet to be fully leveraged in a prognostic setting in chronic lymphocytic leukemia (CLL). Genomic imbalance was assessed in 288 CLL specimens using a targeted array. Based on 20 aberrations in a hierarchical manner, all 228 treatment-naive specimens were classified into a group with poor outcome (20.6%) exhibiting at least one aberration that was univariately associated with adverse outcome (gain: 2p, 3q, 8q, 17q, loss: 7q, 8p, 11q, 17p, 18p), good outcome (32.5%) showing 13q14 loss without any of the other 10 aberrations (gain: 1p, 7p, 12, 18p, 18q, 19, loss: 4p, 5p, 6q, 7p) or intermediate outcome (remainder). The three groups were significantly separated with respect to time to first treatment and overall survival (p < 0.001), and validation of the stratification scheme was performed in two independent datasets. Gain of 3q and 8q, and 17p loss were determined to be independent unfavorable prognostic biomarkers. TP53, NOTCH1 and SF3B1 mutations correlated with the presence of one poor outcome aCGH marker, at a considerably higher frequency than when only considering poor risk aberrations routinely detected by fluorescence in situ hybridization (FISH). These data support genomic imbalance evaluation in CLL by aCGH to assist in risk stratification.
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Amarillo I, Bui PH, Kantarci S, Rao N, Shackley BS, García R, Tirado CA. Atypical rearrangement involving 3'-IGH@ and a breakpoint at least 400 Kb upstream of an intact MYC in a CLL patient with an apparently balanced t(8;14)(q24.1;q32) and negative MYC expression. Mol Cytogenet 2013; 6:5. [PMID: 23369149 PMCID: PMC3599416 DOI: 10.1186/1755-8166-6-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 12/13/2012] [Indexed: 12/25/2022] Open
Abstract
The t(8;14)(q24.1;q32), the cytogenetic hallmark of Burkitt's lymphoma, is also found, but rarely, in cases of chronic lymphocytic leukemia (CLL). Such translocation typically results in a MYC-IGH@ fusion subsequently deregulating and overexpressing MYC on der 14q32. In CLL, atypical rearrangements resulting in its gain or loss, within or outside of IGH@ or MYC locus, have been reported, but their clinical significance remains uncertain. Herein, we report a 67 year-old male with complex cytogenetic findings of apparently balanced t(8;14) and unreported complex rearrangements of IGH@ and MYC loci. His clinical, morphological and immunophenotypic features were consistent with the diagnosis of CLL.Interphase FISH studies revealed deletions of 11q22.3 and 13q14.3, and an extra copy of IGH@, indicative of rearrangement. Karyotype analysis showed an apparently balanced t(8;14)(q24.1;q32). Sequential GPG-metaphase FISH studies revealed abnormal signal patterns: rearrangement of IGH break apart probe with the 5'-IGH@ on derivative 8q24.1 and the 3'-IGH@ retained on der 14q; absence of MYC break apart-specific signal on der 8q; and, the presence of unsplit 5'-MYC-3' break apart probe signals on der 14q. The breakpoint on 8q24.1 was found to be at least 400 Kb upstream of 5' of MYC. In addition, FISH studies revealed two abnormal clones; one with 13q14.3 deletion, and the other, with concurrent 11q deletion and atypical rearrangements. Chromosome microarray analysis (CMA) detected a 7.1 Mb deletion on 11q22.3-q23.3 including ATM, a finding consistent with FISH results. While no significant copy number gain or loss observed on chromosomes 8, 12 and 13, a 455 Kb microdeletion of uncertain clinical significance was detected on 14q32.33. Immunohistochemistry showed co-expression of CD19, CD5, and CD23, positive ZAP-70 expression and absence of MYC expression. Overall findings reveal an apparently balanced t(8;14) and atypical complex rearrangements involving 3'-IGH@ and a breakpoint at least 400 Kb upstream of MYC, resulting in the relocation of the intact 5'-MYC-3' from der 8q, and apposition to 3'-IGH@ at der 14q. This case report provides unique and additional cytogenetic data that may be of clinical significance in such a rare finding in CLL. It also highlights the utility of conventional and sequential metaphase FISH in understanding complex chromosome anomalies and their association with other clinical findings in patients with CLL. To the best of our knowledge, this is the first CLL reported case with such an atypical rearrangement in a patient with a negative MYC expression.
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Affiliation(s)
- Ina Amarillo
- Clinical Molecular Cytogenetics Laboratory, Medicine, David Geffen UCLA School of Medicine, Los Angeles, CA, USA.,Department of Pathology & Laboratory, Medicine, David Geffen UCLA School of Medicine, Los Angeles, CA, USA
| | - Peter H Bui
- Clinical Molecular Cytogenetics Laboratory, Medicine, David Geffen UCLA School of Medicine, Los Angeles, CA, USA.,Department of Pathology & Laboratory, Medicine, David Geffen UCLA School of Medicine, Los Angeles, CA, USA
| | - Sibel Kantarci
- Clinical Molecular Cytogenetics Laboratory, Medicine, David Geffen UCLA School of Medicine, Los Angeles, CA, USA.,Department of Pathology & Laboratory, Medicine, David Geffen UCLA School of Medicine, Los Angeles, CA, USA
| | - Nagesh Rao
- Clinical Molecular Cytogenetics Laboratory, Medicine, David Geffen UCLA School of Medicine, Los Angeles, CA, USA.,Department of Pathology & Laboratory, Medicine, David Geffen UCLA School of Medicine, Los Angeles, CA, USA
| | - Brit S Shackley
- Department of Pathology & Laboratory, Medicine, David Geffen UCLA School of Medicine, Los Angeles, CA, USA
| | - Rolando García
- Cytogenetics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Carlos A Tirado
- Clinical Molecular Cytogenetics Laboratory, Medicine, David Geffen UCLA School of Medicine, Los Angeles, CA, USA.,Department of Pathology & Laboratory, Medicine, David Geffen UCLA School of Medicine, Los Angeles, CA, USA
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Harada K, Ikeda K, Matsumoto H, Furukawa M, Takahashi H, Ohkawara H, Noji H, Tasaki K, Abe M, Ogawa K, Takeishi Y. A Japanese case of chronic lymphocytic leukemia with t (1;6). Exp Hematol Oncol 2012; 1:28. [PMID: 23210523 PMCID: PMC3533870 DOI: 10.1186/2162-3619-1-28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 09/06/2012] [Indexed: 11/10/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) rarely exhibits an aggressive clinical course and its patients often have chromosomal deletions or additions. Furthermore, reciprocal translocations are barely observed in CLL. There have only been a few reports of CLL with t(1;6), and here we report the first Asian case of CLL with reciprocal translocation t(1;6). Since our case and previously reported CLL patients with t(1;6) consistently showed aggressive clinical course, t(1;6) may define a distinct type of CLL.
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van der Veken LT, Buijs A. Array CGH in human leukemia: from somatics to genetics. Cytogenet Genome Res 2011; 135:260-70. [PMID: 21893961 DOI: 10.1159/000330629] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
During the past decade, array CGH has been applied to study copy number alterations in the genome in human leukemia in relation to prediction of prognosis or responsiveness to therapy. In the first segment of this review, we will focus on the identification of acquired mutations by array CGH, followed by studies on the pathogenesis of leukemia associated with germline genetic variants, phenotypic presentation and response to treatment. In the last section, we will discuss constitutional genomic aberrations causally related to myeloid leukemogenesis.
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Affiliation(s)
- L T van der Veken
- Section of Genome Diagnostics, Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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