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Isik S, Gunden G, Gunduz E, Akay OM, Aslan A, Ozen H, Cilingir O, Erzurumluoglu Gokalp E, Kocagil S, Artan S, Gulbas Z, Durak Aras B. An Anomaly with Potential as a New Prognostic Marker in CLL with del(13q): Gain of 16p13.3. Cytogenet Genome Res 2021; 161:479-487. [PMID: 34915466 DOI: 10.1159/000520242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/15/2021] [Indexed: 11/19/2022] Open
Abstract
Deletion 13q [del(13q)] is a favorable prognostic marker if it is detected as a sole abnormality in chronic lymphocytic leukemia (CLL). However the clinical courses of cases with isolated del(13q) are quite heterogeneous. In our study, we investigated copy number variations (CNVs), loss of heterozygosity (LOH), and the size of del(13q) in 30 CLL patients with isolated del(13q). We used CGH+SNP microarrays in order to understand the cause of this clinical heterogeneity. We detected del(13q) in 28/30 CLL cases. The size of the deletion varied from 0.34 to 28.81 Mb, and there was no clinical effect of the deletion size. We found new prognostic markers, especially the gain of 16p13.3. These markers have statistically significant associations with short time to first treatment and advanced disease stage. Detecting both CNVs and LOH at the same time is an advantageous feature of aCGH+SNP. However, it is very challenging for the array analysis to detect mosaic anomalies. Therefore, it is very important to confirm the results by FISH. In our study, we detected approximately 9% mosaic del(13q) by microarray. In addition, the gain of 16p13.3 may affect the disease prognosis in CLL. However, additional studies with more patients are needed to confirm these results.
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Affiliation(s)
- Sevgi Isik
- Department of Medical Genetics, Faculty of Medicine, University of Eskisehir Osmangazi, Eskisehir, Turkey
| | - Gulcin Gunden
- Department of Medical Genetics, Faculty of Medicine, University of Eskisehir Osmangazi, Eskisehir, Turkey
| | - Eren Gunduz
- Department of Hematology, Faculty of Medicine, University of Eskisehir Osmangazi, Eskisehir, Turkey
| | - Olga Meltem Akay
- Department of Hematology, Faculty of Medicine, University of Koc, Istanbul, Turkey
| | - Abdulvahap Aslan
- Department of Hematology, Private Umit Hospital, Eskisehir, Turkey
| | - Hulya Ozen
- Department of Biostatistics, Faculty of Medicine, University of Eskisehir Osmangazi, Eskisehir, Turkey
| | - Oguz Cilingir
- Department of Medical Genetics, Faculty of Medicine, University of Eskisehir Osmangazi, Eskisehir, Turkey
| | - Ebru Erzurumluoglu Gokalp
- Department of Medical Genetics, Faculty of Medicine, University of Eskisehir Osmangazi, Eskisehir, Turkey
| | - Sinem Kocagil
- Department of Medical Genetics, Faculty of Medicine, University of Eskisehir Osmangazi, Eskisehir, Turkey
| | - Sevilhan Artan
- Department of Medical Genetics, Faculty of Medicine, University of Eskisehir Osmangazi, Eskisehir, Turkey
| | - Zafer Gulbas
- Department of Hematology, Anadolu Medical Center, İzmit, Turkey
| | - Beyhan Durak Aras
- Department of Medical Genetics, Faculty of Medicine, University of Eskisehir Osmangazi, Eskisehir, Turkey.,Translational Medicine Research and Clinical Center, University of Eskisehir Osmangazi, Eskisehir, Turkey
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2
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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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3
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Leeksma AC, Baliakas P, Moysiadis T, Puiggros A, Plevova K, van der Kevie-Kersemaekers AM, Posthuma H, Rodriguez-Vicente AE, Tran AN, Barbany G, Mansouri L, Gunnarsson R, Parker H, van der Berg E, Bellido M, Davis Z, Wall M, Scarpelli I, Österborg A, Hansson L, Jarosova M, Ghia P, Poddighe P, Espinet B, Pospisilova S, Tam C, Ysebaert L, Nguyen-Khac F, Oscier D, Haferlach C, Schoumans J, Stevens-Kroef M, Eldering E, Stamatopoulos K, Rosenquist R, Strefford JC, Mellink C, Kater AP. Genomic arrays identify high-risk chronic lymphocytic leukemia with genomic complexity: a multi-center study. Haematologica 2021; 106:87-97. [PMID: 31974198 PMCID: PMC7776256 DOI: 10.3324/haematol.2019.239947] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/22/2020] [Indexed: 01/15/2023] Open
Abstract
Complex karyotype (CK) identified by chromosome-banding analysis (CBA) has shown prognostic value in chronic lymphocytic leukemia (CLL). Genomic arrays offer high-resolution genome-wide detection of copy-number alterations (CNAs) and could therefore be well equipped to detect the presence of a CK. Current knowledge on genomic arrays in CLL is based on outcomes of single center studies, in which different cutoffs for CNA calling were used. To further determine the clinical utility of genomic arrays for CNA assessment in CLL diagnostics, we retrospectively analyzed 2293 arrays from 13 diagnostic laboratories according to established standards. CNAs were found outside regions captured by CLL FISH probes in 34% of patients, and several of them including gains of 8q, deletions of 9p and 18p (p<0.01) were linked to poor outcome after correction for multiple testing. Patients (n=972) could be divided in three distinct prognostic subgroups based on the number of CNAs. Only high genomic complexity (high-GC), defined as ≥5 CNAs emerged as an independent adverse prognosticator on multivariable analysis for time to first treatment (Hazard ratio: 2.15, 95% CI: 1.36-3.41; p=0.001) and overall survival (Hazard ratio: 2.54, 95% CI: 1.54-4.17; p<0.001; n=528). Lowering the size cutoff to 1 Mb in 647 patients did not significantly improve risk assessment. Genomic arrays detected more chromosomal abnormalities and performed at least as well in terms of risk stratification compared to simultaneous chromosome banding analysis as determined in 122 patients. Our findings highlight genomic array as an accurate tool for CLL risk stratification.
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Affiliation(s)
- Alexander C. Leeksma
- Department of Hematology and Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
- Department of Experimental Immunology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
- Cancer Center Amsterdam and Amsterdam Infection and Immunity Institute, Amsterdam, the Netherlands
| | - Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Theodoros Moysiadis
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Anna Puiggros
- Laboratori de Citogenetica Molecular, Servei de Patologia, Hospital del Mar, Barcelona, Spain
- Grup de Recerca Translacional en Neoplasies Hematologiques, Programa de Recerca en Cancer, Institut Hospital del Mar d’Investigacions Mediques (IMIM), Barcelona, Spain
| | - Karla Plevova
- Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | | | - Hidde Posthuma
- Department of Clinical Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Ana E. Rodriguez-Vicente
- Department of Hematology, IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, University Hospital of Salamanca, Salamanca, Spain
| | - Anh Nhi Tran
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Gisela Barbany
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Larry Mansouri
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Rebeqa Gunnarsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Helen Parker
- Cancer Genomics, Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Eva van der Berg
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Mar Bellido
- Department of Hematology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Zadie Davis
- Department of Molecular Pathology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Meaghan Wall
- Cytogenetics Department, St Vincent Hospital, Melbourne, Victoria, Australia
| | - Ilaria Scarpelli
- Oncogenomic Laboratory, Department of Hematology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Anders Österborg
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Lotta Hansson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Marie Jarosova
- Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Paolo Ghia
- Division of Experimental Oncology, IRCCS Ospedale San Raffaele e Universita Vita-Salute San Raffaele, Milan, Italy
| | - Pino Poddighe
- Department of Clinical Genetics, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam, the Netherlands
| | - Blanca Espinet
- Laboratori de Citogenetica Molecular, Servei de Patologia, Hospital del Mar, Barcelona, Spain
- Grup de Recerca Translacional en Neoplasies Hematologiques, Programa de Recerca en Cancer, Institut Hospital del Mar d’Investigacions Mediques (IMIM), Barcelona, Spain
| | - Sarka Pospisilova
- Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Constantine Tam
- Department of Haematology, St Vincent Hospital Melbourne and Peter MacCallum Cancer Center; University of Melbourne, Melbourne, Victoria, Australia
| | - Loïc Ysebaert
- Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Florence Nguyen-Khac
- INSERM U1138; Universite Pierre et Marie Curie-Paris; Service d'Hematologie Biologique, Hopital Pitie-Salpetriere, APHP, Paris, France
| | - David Oscier
- Department of Molecular Pathology, Royal Bournemouth Hospital, Bournemouth, UK
| | | | - Jacqueline Schoumans
- Oncogenomic Laboratory, Department of Hematology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Marian Stevens-Kroef
- Radboud University Medical Center, Department of Human Genetics, Nijmegen, the Netherlands
| | - Eric Eldering
- Department of Experimental Immunology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
- Cancer Center Amsterdam and Amsterdam Infection and Immunity Institute, Amsterdam, the Netherlands
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Jonathan C. Strefford
- Cancer Genomics, Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Clemens Mellink
- Department of Clinical Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Arnon P. Kater
- Department of Hematology and Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
- Cancer Center Amsterdam and Amsterdam Infection and Immunity Institute, Amsterdam, the Netherlands
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4
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Teng X, Aouacheria A, Lionnard L, Metz KA, Soane L, Kamiya A, Hardwick JM. KCTD: A new gene family involved in neurodevelopmental and neuropsychiatric disorders. CNS Neurosci Ther 2019; 25:887-902. [PMID: 31197948 PMCID: PMC6566181 DOI: 10.1111/cns.13156] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/02/2019] [Accepted: 05/13/2019] [Indexed: 12/12/2022] Open
Abstract
The underlying molecular basis for neurodevelopmental or neuropsychiatric disorders is not known. In contrast, mechanistic understanding of other brain disorders including neurodegeneration has advanced considerably. Yet, these do not approach the knowledge accrued for many cancers with precision therapeutics acting on well-characterized targets. Although the identification of genes responsible for neurodevelopmental and neuropsychiatric disorders remains a major obstacle, the few causally associated genes are ripe for discovery by focusing efforts to dissect their mechanisms. Here, we make a case for delving into mechanisms of the poorly characterized human KCTD gene family. Varying levels of evidence support their roles in neurocognitive disorders (KCTD3), neurodevelopmental disease (KCTD7), bipolar disorder (KCTD12), autism and schizophrenia (KCTD13), movement disorders (KCTD17), cancer (KCTD11), and obesity (KCTD15). Collective knowledge about these genes adds enhanced value, and critical insights into potential disease mechanisms have come from unexpected sources. Translation of basic research on the KCTD-related yeast protein Whi2 has revealed roles in nutrient signaling to mTORC1 (KCTD11) and an autophagy-lysosome pathway affecting mitochondria (KCTD7). Recent biochemical and structure-based studies (KCTD12, KCTD13, KCTD16) reveal mechanisms of regulating membrane channel activities through modulation of distinct GTPases. We explore how these seemingly varied functions may be disease related.
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Affiliation(s)
- Xinchen Teng
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical SciencesSoochow UniversitySuzhouChina
- W. Harry Feinstone Department of Molecular Microbiology and ImmunologyJohns Hopkins University Bloomberg School of Public HealthBaltimoreMaryland
| | - Abdel Aouacheria
- ISEM, Institut des Sciences de l'Evolution de Montpellier, CNRS, EPHE, IRDUniversité de MontpellierMontpellierFrance
| | - Loïc Lionnard
- ISEM, Institut des Sciences de l'Evolution de Montpellier, CNRS, EPHE, IRDUniversité de MontpellierMontpellierFrance
| | - Kyle A. Metz
- W. Harry Feinstone Department of Molecular Microbiology and ImmunologyJohns Hopkins University Bloomberg School of Public HealthBaltimoreMaryland
- Present address:
Feinberg School of MedicineNorthwestern UniversityChicagoUSA
| | - Lucian Soane
- W. Harry Feinstone Department of Molecular Microbiology and ImmunologyJohns Hopkins University Bloomberg School of Public HealthBaltimoreMaryland
| | - Atsushi Kamiya
- Department of Psychiatry and Behavioral SciencesJohns Hopkins School of MedicineBaltimoreMaryland
| | - J. Marie Hardwick
- W. Harry Feinstone Department of Molecular Microbiology and ImmunologyJohns Hopkins University Bloomberg School of Public HealthBaltimoreMaryland
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5
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Bioinformatics analysis of prognostic value of TRIM13 gene in breast cancer. Biosci Rep 2019; 39:BSR20190285. [PMID: 30837324 PMCID: PMC6430728 DOI: 10.1042/bsr20190285] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/25/2019] [Accepted: 03/04/2019] [Indexed: 12/15/2022] Open
Abstract
Background: Tripartite motif 13 (TRIM13) plays a significant role in various biological processes including cell growth, apoptosis, transcriptional regulation, and carcinogenesis. However, the prognostic significance of TRIM13 gene in breast cancer treatment remains largely unclear. Methods: We performed a bioinformatics analysis of the clinical parameters and survival data as it relates to TRIM13 in breast cancer patients using several online databases including Oncomine, bcGenExMiner, PrognoScan, and UCSC Xena. Results: We found that TRIM13 was lower-expressed in different subtypes of breast cancer with respect to normal tissues. Estrogen receptor and progesterone receptor status were positively correlated with TRIM13 level; whereas, the Scarff–Bloom–Richardson grade, Nottingham prognostic index, nodal status, basal-like status, and triple-negative status were negatively related to TRIM13 expression in breast cancer patients with respect to normal individuals. Lower TRIM13 expression correlated with worse distant metastasis free survival, relapse free survival, disease specific survival, and metastatic relapse free survival. We also confirmed a positive correlation between TRIM13 and RAB11FIP2 gene expression. Conclusion: Bioinformatics analysis revealed that TRIM13 may be adopted as a promising predictive biomarker for prognosis of breast cancer. More in-depth experiments and clinical trials are needed to validate the value of TRIM13 in breast cancer treatment.
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6
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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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7
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Blanco G, Puiggros A, Baliakas P, Athanasiadou A, García-Malo M, Collado R, Xochelli A, Rodríguez-Rivera M, Ortega M, Calasanz MJ, Luño E, Vargas M, Grau J, Martínez-Laperche C, Valiente A, Cervera J, Anagnostopoulos A, Gimeno E, Abella E, Stalika E, Hernández-Rivas JM, Ortuño FJ, Robles D, Ferrer A, Ivars D, González M, Bosch F, Abrisqueta P, Stamatopoulos K, Espinet B. Karyotypic complexity rather than chromosome 8 abnormalities aggravates the outcome of chronic lymphocytic leukemia patients with TP53 aberrations. Oncotarget 2018; 7:80916-80924. [PMID: 27821812 PMCID: PMC5348364 DOI: 10.18632/oncotarget.13106] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/27/2016] [Indexed: 12/21/2022] Open
Abstract
Patients with chronic lymphocytic leukemia (CLL) harboring TP53 aberrations (TP53abs; chromosome 17p deletion and/or TP53 mutation) exhibit an unfavorable clinical outcome. Chromosome 8 abnormalities, namely losses of 8p (8p−) and gains of 8q (8q+) have been suggested to aggravate the outcome of patients with TP53abs. However, the reported series were small, thus hindering definitive conclusions. To gain insight into this issue, we assessed a series of 101 CLL patients harboring TP53 disruption. The frequency of 8p− and 8q+ was 14.7% and 17.8% respectively. Both were associated with a significantly (P < 0.05) higher incidence of a complex karyotype (CK, ≥3 abnormalities) detected by chromosome banding analysis (CBA) compared to cases with normal 8p (N-8p) and 8q (N-8q), respectively. In univariate analysis for 10-year overall survival (OS), 8p− (P = 0.002), 8q+ (P = 0.012) and CK (P = 0.009) were associated with shorter OS. However, in multivariate analysis only CK (HR = 2.47, P = 0.027) maintained independent significance, being associated with a dismal outcome regardless of chromosome 8 abnormalities. In conclusion, our results highlight the association of chromosome 8 abnormalities with CK amongst CLL patients with TP53abs, while also revealing that CK can further aggravate the prognosis of this aggressive subgroup.
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Affiliation(s)
- Gonzalo Blanco
- Laboratori de Citogenètica Molecular, Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, Barcelona, Spain.,Grup de Recerca Translacional en Neoplàsies Hematològiques, Cancer Research Programme, IMIM-Hospital del Mar, Barcelona, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Anna Puiggros
- Laboratori de Citogenètica Molecular, Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, Barcelona, Spain.,Grup de Recerca Translacional en Neoplàsies Hematològiques, Cancer Research Programme, IMIM-Hospital del Mar, Barcelona, Spain
| | - Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | | | - Rosa Collado
- Servicio de Hematología, Consorcio Hospital General Universitario, Valencia, Spain
| | - Aliki Xochelli
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
| | - María Rodríguez-Rivera
- Laboratori de Citogenètica Molecular, Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, Barcelona, Spain.,Grup de Recerca Translacional en Neoplàsies Hematològiques, Cancer Research Programme, IMIM-Hospital del Mar, Barcelona, Spain
| | - Margarita Ortega
- Laboratorio de Citogenética y Servicio de Hematología, Hospital Vall d'Hebron, Barcelona, Spain
| | - Mª José Calasanz
- Servicio de Citogenética, Departamento de Genética, Universidad de Navarra, Pamplona, Spain
| | - Elisa Luño
- Servicio de Hematología, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - MªTeresa Vargas
- UGC de Hematología, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBIS), Sevilla, Spain
| | - Javier Grau
- Servei d'Hematologia, ICO-Hospital Germans Trias i Pujol, Institut de Recerca Contra la Leucèmia Josep Carreras (IJC), Universitat Autònoma de Barcelona, Badalona, Spain
| | - Carolina Martínez-Laperche
- Laboratorio de Genética Hematológica, Servicio de Hematología, Hospital G.U. Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Alberto Valiente
- Servicios de Genética y Hematología, Complejo Hospitalario de Navarra, Pamplona, Spain
| | - José Cervera
- Unidad de Genética, Hospital Universitario La Fe, Valencia, Spain
| | | | - Eva Gimeno
- Servei d'Hematologia, Hospital del Mar, Barcelona, Spain
| | - Eugènia Abella
- Servei d'Hematologia, Hospital del Mar, Barcelona, Spain
| | | | - Jesús Mª Hernández-Rivas
- Servicio de Hematología, Hospital Universitario de Salamanca, IBSAL, IBMCC, Centro de Investigación del Cáncer, Universidad de Salamanca, CSIC, Salamanca, Spain
| | | | - Diego Robles
- Servicio de Hematología, Hospital Txagorritxu, Vitoria, Spain
| | - Ana Ferrer
- Laboratori de Citogenètica Molecular, Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, Barcelona, Spain.,Grup de Recerca Translacional en Neoplàsies Hematològiques, Cancer Research Programme, IMIM-Hospital del Mar, Barcelona, Spain
| | - David Ivars
- Servicio de Hematología, Consorcio Hospital General Universitario, Valencia, Spain
| | - Marcos González
- Servicio de Hematología, Hospital Universitario de Salamanca, IBSAL, IBMCC, Centro de Investigación del Cáncer, Universidad de Salamanca, CSIC, Salamanca, Spain
| | - Francesc Bosch
- Laboratorio de Citogenética y Servicio de Hematología, Hospital Vall d'Hebron, Barcelona, Spain
| | - Pau Abrisqueta
- Laboratorio de Citogenética y Servicio de Hematología, Hospital Vall d'Hebron, Barcelona, Spain
| | - Kostas Stamatopoulos
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece.,Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
| | - Blanca Espinet
- Laboratori de Citogenètica Molecular, Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, Barcelona, Spain.,Grup de Recerca Translacional en Neoplàsies Hematològiques, Cancer Research Programme, IMIM-Hospital del Mar, Barcelona, Spain
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8
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Piao MY, Cao HL, He NN, Xu MQ, Dong WX, Wang WQ, Wang BM, Zhou B. Potential role of TRIM3 as a novel tumour suppressor in colorectal cancer (CRC) development. Scand J Gastroenterol 2016; 51:572-82. [PMID: 26691157 DOI: 10.3109/00365521.2015.1124285] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVE Colorectal cancer (CRC) is the third leading cause of cancer-related mortality in the United States. Recent cancer genome-sequencing efforts and complementary functional studies have led to the identification of a collection of candidate 'driver' genes involved in CRC tumorigenesis. Tripartite motif (TRIM3) is recently identified as a tumour suppressor in glioblastoma but this tumour-suppressive function has not been investigated in CRC. MATERIAL AND METHODS In this study, we investigated the potential role of TRIM3 as a tumour suppressor in CRC development by manipulating the expression of TRIM3 in two authentic CRC cell lines, HCT116 and DLD1, followed by various functional assays, including cell proliferation, colony formation, scratch wound healing, soft agar, and invasion assays. Xenograft experiment was performed to examine in vivo tumour-suppressive properties of TRIM3. RESULTS Small-interfering RNA (siRNA) mediated knockdown of TRIM3 conferred growth advantage in CRC cells. In contrast, overexpression of TRIM3 affected cell survival, cell migration, anchorage independent growth and invasive potential in CRC cells. In addition, TRIM3 was found to be down-regulated in human colon cancer tissues compared with matched normal colon tissues. Overexpression of TRIM3 significantly inhibited tumour growth in vivo using xenograft mouse models. Mechanistic investigation revealed that TRIM3 can regulate p53 protein level through its stabilisation. CONCLUSIONS TRIM3 functions as a tumour suppressor in CRC progression. This tumour-suppressive function is exerted partially through regulation of p53 protein. Therefore, this protein may represent a novel therapeutic target for prevention or intervention of CRC.
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Affiliation(s)
- Mei-Yu Piao
- a Department of Gastroenterology and Hepatology , General Hospital, Tianjin Medical University , Heping District , Tianjin , China
| | - Hai-Long Cao
- a Department of Gastroenterology and Hepatology , General Hospital, Tianjin Medical University , Heping District , Tianjin , China
| | - Na-Na He
- a Department of Gastroenterology and Hepatology , General Hospital, Tianjin Medical University , Heping District , Tianjin , China
| | - Meng-Que Xu
- a Department of Gastroenterology and Hepatology , General Hospital, Tianjin Medical University , Heping District , Tianjin , China
| | - Wen-Xiao Dong
- a Department of Gastroenterology and Hepatology , General Hospital, Tianjin Medical University , Heping District , Tianjin , China
| | - Wei-Qiang Wang
- a Department of Gastroenterology and Hepatology , General Hospital, Tianjin Medical University , Heping District , Tianjin , China
| | - Bang-Mao Wang
- a Department of Gastroenterology and Hepatology , General Hospital, Tianjin Medical University , Heping District , Tianjin , China
| | - Bing Zhou
- b Department of Gastroenterology , Tanggu Traditional Chinese Medicine Hospital of Tianjin Binhai New Area , Tanggu Binhai New Area , Tianjin , China
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9
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Asnaghi L, Alkatan H, Mahale A, Othman M, Alwadani S, Al-Hussain H, Jastaneiah S, Yu W, Maktabi A, Edward DP, Eberhart CG. Identification of multiple DNA copy number alterations including frequent 8p11.22 amplification in conjunctival squamous cell carcinoma. Invest Ophthalmol Vis Sci 2014; 55:8604-13. [PMID: 25491297 DOI: 10.1167/iovs.14-14920] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Little is known about the molecular alterations that drive formation and growth of conjunctival squamous cell carcinoma (cSCC). We therefore sought to identify genetic changes that could be used as diagnostic markers or therapeutic targets. METHODS The DNA extracted from 10 snap-frozen cSCC tumor specimens and 2 in situ carcinomas was analyzed using array-based comparative genomic hybridization (aCGH), and further examined with NanoString and quantitative PCR. RESULTS The number of regions of DNA loss ranged from 1 to 23 per tumor, whereas gains and amplifications ranged from 1 to 15 per tumor. Most large regions of chromosomal gain and loss were confirmed by NanoString karyotype analysis. The commonest alteration was amplification of 8p11.22 in 9 tumors (75%), and quantitative PCR analysis revealed 100-fold or greater overexpression of ADAM3A mRNA from 8p11.22 locus. In addition, recurring losses were observed at 14q13.2 and 22q11.23, both lost in 5 (42%) of the 12 tumors, and at 12p13.31, lost in 4 (33%) of the 12 samples. Of the eight loci associated with the DNA damage repair syndrome xeroderma pigmentosum, three showed loss of at least one allele in our aCGH analysis, including XPA (9q22.33, one tumor), XPE/DDB2 (11p11.2, one tumor) and XPG/ERCC5 (13q33.1, three tumors). CONCLUSIONS Conjunctival SCC contains a range of chromosomal alterations potentially important in tumor formation and growth. Amplification of 8p11.22 and overexpression of ADAM3A suggests a potential role for this protease. Our findings also suggest that defects in DNA repair loci are important in sporadic cSCC.
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Affiliation(s)
- Laura Asnaghi
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States
| | - Hind Alkatan
- King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - Alka Mahale
- King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - Maha Othman
- King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - Saeed Alwadani
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States Department of Ophthalmology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States Department of Ophthalmology, King Saud University, Riyadh, Saudi Arabia
| | | | | | - Wayne Yu
- Microarray Core Facility, Sidney Kimmel Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States
| | - Azza Maktabi
- King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - Deepak P Edward
- King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia Department of Ophthalmology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States
| | - Charles G Eberhart
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States Department of Ophthalmology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States Department of Oncology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States
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10
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Atypical spindle cell lipoma: a clinicopathologic, immunohistochemical, and molecular study emphasizing its relationship to classical spindle cell lipoma. Virchows Arch 2014; 465:97-108. [PMID: 24659226 DOI: 10.1007/s00428-014-1568-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 01/22/2014] [Accepted: 03/06/2014] [Indexed: 12/16/2022]
Abstract
We studied a series of spindle cell lipomas arising in atypical sites and showing unusual morphologic features (which we called atypical spindle cell lipoma) to assess if these lesions have the same chromosomal alterations as classical spindle cell lipoma but different from those found in atypical lipomatous tumor/well-differentiated liposarcoma. We investigated alterations of different genes in the 13q14 region and the amplification status of the MDM2 and CDK4 genes at 12q14-15 by multiplex ligation-dependent probe amplification (MLPA) and fluorescence in situ hybridization (FISH) analysis. In the atypical spindle cell lipomas, MLPA revealed deletions in the two nearest flanking genes of RB1 (ITM2B and RCBTB2) and in multiple important exons of RB1. In contrast, in classical spindle cell lipomas, a less complex loss of RB1 exons was found but no deletion of ITM2B and RCBTB2. Moreover, MLPA identified a deletion of the DLEU1 gene, a finding which has not been reported earlier. We propose an immunohistochemical panel for lipomatous tumors which comprises of MDM2, CDK4, p16, Rb, which we have found useful in discriminating between atypical or classical spindle cell lipomas and other adipocytic neoplasms, especially atypical lipomatous tumor/well-differentiated liposarcoma. Our findings strengthen the link between atypical spindle cell lipoma and classical spindle cell lipoma, and differentiate them from atypical lipomatous tumor/well-differentiated liposarcoma.
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11
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Genome-wide screening of cytogenetic abnormalities in multiple myeloma patients using array-CGH technique: a Czech multicenter experience. BIOMED RESEARCH INTERNATIONAL 2014; 2014:209670. [PMID: 24987674 PMCID: PMC4060785 DOI: 10.1155/2014/209670] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 05/02/2014] [Indexed: 11/23/2022]
Abstract
Characteristic recurrent copy number aberrations (CNAs) play a key role in multiple myeloma (MM) pathogenesis and have important prognostic significance for MM patients. Array-based comparative genomic hybridization (aCGH) provides a powerful tool for genome-wide classification of CNAs and thus should be implemented into MM routine diagnostics. We demonstrate the possibility of effective utilization of oligonucleotide-based aCGH in 91 MM patients. Chromosomal aberrations associated with effect on the prognosis of MM were initially evaluated by I-FISH and were found in 93.4% (85/91). Incidence of hyperdiploidy was 49.5% (45/91); del(13)(q14) was detected in 57.1% (52/91); gain(1)(q21) occurred in 58.2% (53/91); del(17)(p13) was observed in 15.4% (14/91); and t(4;14)(p16;q32) was found in 18.6% (16/86). Genome-wide screening using Agilent 44K aCGH microarrays revealed copy number alterations in 100% (91/91). Most common deletions were found at 13q (58.9%), 1p (39.6%), and 8p (31.1%), whereas gain of whole 1q was the most often duplicated region (50.6%). Furthermore, frequent homozygous deletions of genes playing important role in myeloma biology such as TRAF3, BIRC1/BIRC2, RB1, or CDKN2C were observed. Taken together, we demonstrated the utilization of aCGH technique in clinical diagnostics as powerful tool for identification of unbalanced genomic abnormalities with prognostic significance for MM patients.
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12
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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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13
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Affiliation(s)
- Joanne Mason
- West Midlands Regional Genetics Laboratory, Birmingham Women’s NHS Foundation Trust, Edgbaston, Birmingham, B15 2TG, UK
| | - Michael Griffiths
- West Midlands Regional Genetics Laboratory, Birmingham Women’s NHS Foundation Trust, Edgbaston, Birmingham, B15 2TG, UK
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14
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Jimenez-Zepeda VH, Chng WJ, Schop RF, Braggio E, Leis JF, Kay N, Fonseca R. Recurrent Chromosome Abnormalities Define Nonoverlapping Unique Subgroups of Tumors in Patients With Chronic Lymphocytic Leukemia and Known Karyotypic Abnormalities. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2013; 13:467-76. [DOI: 10.1016/j.clml.2013.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 05/02/2013] [Accepted: 05/02/2013] [Indexed: 11/16/2022]
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15
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Mraz M, Stano Kozubik K, Plevova K, Musilova K, Tichy B, Borsky M, Kuglik P, Doubek M, Brychtova Y, Mayer J, Pospisilova S. The origin of deletion 22q11 in chronic lymphocytic leukemia is related to the rearrangement of immunoglobulin lambda light chain locus. Leuk Res 2013; 37:802-8. [PMID: 23608880 DOI: 10.1016/j.leukres.2013.03.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 03/19/2013] [Accepted: 03/21/2013] [Indexed: 10/26/2022]
Abstract
The technology of array comparative genomic hybridization (array-CGH/aCGH) enabled the identification of novel genomic aberrations in chronic lymphocytic leukemia (CLL) including the monoallelic and biallelic deletions affecting 22q11 locus. In contrast to previous publications, we hypothesized that the described 22q11 deletions are a consequence of the rearrangement of immunoglobulin lambda light chain locus (IGL) segments surrounding several protein-coding genes located in this region. Indeed, using array-CGH and PCR analysis we show that all deletions (n=7) affecting the 22q11 locus in our cohort (n=40) are based on the physiological mechanism of IGL rearrangement. This demonstrates that this loss of genetic material is likely not pathogenic and in fact is merely a marker of IGL rearrangement.
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Affiliation(s)
- Marek Mraz
- CEITEC, Center of Molecular Medicine, Masaryk University, Brno, Czech Republic.
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16
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Rodríguez-Vicente AE, Díaz MG, Hernández-Rivas JM. Chronic lymphocytic leukemia: a clinical and molecular heterogenous disease. Cancer Genet 2013; 206:49-62. [DOI: 10.1016/j.cancergen.2013.01.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 01/21/2013] [Accepted: 01/24/2013] [Indexed: 12/11/2022]
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17
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Fabris S, Mosca L, Cutrona G, Lionetti M, Agnelli L, Ciceri G, Barbieri M, Maura F, Matis S, Colombo M, Gentile M, Recchia AG, Anna Pesce E, Di Raimondo F, Musolino C, Gobbi M, Di Renzo N, Mauro FR, Brugiatelli M, Ilariucci F, Lipari MG, Angrilli F, Consoli U, Fragasso A, Molica S, Festini G, Vincelli I, Cortelezzi A, Federico M, Morabito F, Ferrarini M, Neri A. Chromosome 2p gain in monoclonal B-cell lymphocytosis and in early stage chronic lymphocytic leukemia. Am J Hematol 2013; 88:24-31. [PMID: 23044996 DOI: 10.1002/ajh.23340] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 08/03/2012] [Accepted: 09/05/2012] [Indexed: 12/17/2022]
Abstract
Recent studies have described chromosome 2p gain as a recurrent lesion in chronic lymphocytic leukemia (CLL). We investigated the 2p gain and its relationship with common prognostic biomarkers in a prospective series of 69 clinical monoclonal B-cell lymphocytosis (cMBL) and 218 early stage (Binet A) CLL patients. The 2p gain was detected by FISH in 17 patients (6%, 16 CLL, and 1 cMBL) and further characterized by single nucleotide polymorphism-array. Overall, unfavorable cytogenetic deletions, i.e., del(11)(q23) and del(17)(p13) (P = 0.002), were significantly more frequent in 2p gain cases, as well as unmutated status of IGHV (P < 1 × 10(-4) ) and CD38 (P < 1 × 10(-4) ) and ZAP-70 positive expression (P = 0.003). Furthermore, 2p gain patients had significantly higher utilization of stereotyped B-cell receptors compared with 2p negative patients (P = 0.009), and the incidence of stereotyped subset #1 in 2p gain patients was significantly higher than that found in the remaining CLLs (P = 0.031). Transcriptional profiling analysis identified several genes significantly upregulated in 2p gain CLLs, most of which mapped to 2p. Among these, NCOA1 and ROCK2 are known for their involvement in tumor progression in several human cancers, whereas among those located in different chromosomes, CAV1 at 7q31.1 has been recently identified to play a critical role in CLL progression. Thus, 2p gain can be present since the early stages of the disease, particularly in those cases characterized by other poor prognosis markers. The finding of genes upregulated in the cells with 2p gain provides new insights to define the pathogenic role of this lesion.
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MESH Headings
- Adult
- Aged
- Biomarkers, Tumor/biosynthesis
- Biomarkers, Tumor/genetics
- Chromosomes, Human, Pair 2/genetics
- Chromosomes, Human, Pair 2/metabolism
- Chromosomes, Human, Pair 7/genetics
- Chromosomes, Human, Pair 7/metabolism
- Female
- Gene Expression Regulation, Leukemic
- Humans
- In Situ Hybridization, Fluorescence
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Lymphocytosis/diagnosis
- Lymphocytosis/genetics
- Lymphocytosis/metabolism
- Male
- Middle Aged
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/genetics
- Neoplasm Staging
- Prognosis
- Prospective Studies
- Up-Regulation/genetics
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Affiliation(s)
- Sonia Fabris
- Dipartimento di Scienze Cliniche e di Comunità, Università degli Studi di Milano e Ematologia 1 CTMO, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Italy
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18
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Puiggros A, Puigdecanet E, Salido M, Ferrer A, Abella E, Gimeno E, Nonell L, Herranz MJ, Galván AB, Rodríguez-Rivera M, Melero C, Pairet S, Bellosillo B, Serrano S, Florensa L, Solé F, Espinet B. Genomic arrays in chronic lymphocytic leukemia routine clinical practice: are we ready to substitute conventional cytogenetics and fluorescence in situ hybridization techniques? Leuk Lymphoma 2012; 54:986-95. [PMID: 22994157 DOI: 10.3109/10428194.2012.731598] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is characterized by a highly variable clinical course. Del(11q) and del(17p), routinely studied by conventional G-banding cytogenetics (CGC) and fluorescence in situ hybridization (FISH), have been related to progression and shorter overall survival. Recently, array-based karyotyping has gained acceptance as a high-resolution new tool for detecting genomic imbalances. The aim of the present study was to compare genomic arrays with CGC and FISH to ascertain whether the current techniques could be substituted in routine procedures. We analyzed 70 patients with CLL using the Cytogenetics Whole-Genome 2.7M Array and CytoScan HD Array (Affymetrix), CGC and FISH with the classical CLL panel. Whereas 31.4% and 68.6% of patients presented abnormalities when studied by CGC and FISH, respectively, these rates increased when arrays were also analyzed (78.6% and 80%). Although abnormality detection is higher when arrays are applied, one case with del(11q) and three with del(17p) were missed by genomic arrays due to their limited sensitivity. We consider that the complete substitution of CGC and FISH by genomic arrays in routine laboratories could negatively affect the management of some patients harboring 11q or 17p deletions. In conclusion, genomic arrays are valid to detect known and novel genomic imbalances in CLL, but should be maintained as a complementary tool to the current techniques.
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Affiliation(s)
- Anna Puiggros
- Programa de Recerca en Càncer, Grup de Recerca Translacional en Neoplàsies Hematològiques (GRETNHE), IMIM-Hospital del Mar, Barcelona, Spain
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19
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Clinical Application of Array-Based Comparative Genomic Hybridization for the Identification of Prognostically Important Genetic Alterations in Chronic Lymphocytic Leukemia. Mol Diagn Ther 2012; 12:271-80. [DOI: 10.1007/bf03256292] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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20
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Rodríguez AE, Robledo C, García JL, González M, Gutiérrez NC, Hernández JA, Sandoval V, García de Coca A, Recio I, Risueño A, Martín-Núñez G, García E, Fisac R, Conde J, de Las Rivas J, Hernández JM. Identification of a novel recurrent gain on 20q13 in chronic lymphocytic leukemia by array CGH and gene expression profiling. Ann Oncol 2012; 23:2138-2146. [PMID: 22228453 DOI: 10.1093/annonc/mdr579] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND The presence of genetic changes is a hallmark of chronic lymphocytic leukemia (CLL). The most common cytogenetic abnormalities with independent prognostic significance in CLL are 13q14, ATM and TP53 deletions and trisomy 12. However, CLL displays a great genetic and biological heterogeneity. The aim of this study was to analyze the genomic imbalances in CLL cytogenetic subsets from both genomic and gene expression perspectives to identify new recurrent alterations. PATIENTS AND METHODS The genomic imbalances and expression levels of 67 patients were analyzed. The novel recurrent abnormalities detected with bacterial artificial chromosome array were confirmed by FISH and oligonucleotide microarrays. In all cases, gene expression profiling was assessed. RESULTS Copy number alterations were identified in 75% of cases. Overall, the results confirmed FISH studies for the regions frequently involved in CLL and also defined a new recurrent gain on chromosome 20q13.12, in 19% (13/67) of the CLL patients. Oligonucleotide expression correlated with the regions of loss or gain of genomic material, suggesting that the changes in gene expression are related to alterations in copy number. CONCLUSION Our study demonstrates the presence of a recurrent gain in 20q13.12 associated with overexpression of the genes located in this region, in CLL cytogenetic subgroups.
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Affiliation(s)
- A E Rodríguez
- IBMCC, Centro de Investigación del Cáncer, Universidad de Salamanca-CSIC, Salamanca
| | - C Robledo
- IBMCC, Centro de Investigación del Cáncer, Universidad de Salamanca-CSIC, Salamanca
| | - J L García
- Instituto de Estudios de Ciencias de la Salud de Castilla y León (IECSCYL)-HUSAL, Castill y León
| | - M González
- Department of Hematology, Hospital Clínico Universitario de Salamanca, Salamanca
| | - N C Gutiérrez
- Department of Hematology, Hospital Clínico Universitario de Salamanca, Salamanca
| | - J A Hernández
- Department of Hematology, Hospital Infanta Leonor, Madrid
| | - V Sandoval
- Department of Hematology, Hospital Virgen Blanca, León
| | - A García de Coca
- Department of Hematology, Hospital Clínico Universitario, Valladolid
| | - I Recio
- Department of Hematology, Hospital Nuestra Señora de Sonsoles, Ávila
| | - A Risueño
- Bioinformatics and Functional Genomics, Centro de Investigación del Cáncer, Universidad de Salamanca-CSIC, Salamanca
| | - G Martín-Núñez
- Department of Hematology, Hospital Virgen del Puerto, Plasencia
| | - E García
- Genomics and Proteomics Unit, Centro de Investigación del Cáncer, Universidad de Salamanca-CSIC, Salamanca
| | - R Fisac
- Department of Hematology, Hospital General de Segovia, Segovia
| | - J Conde
- Department of Hematology, Hospital del Río Hortega, Valladolid, Spain
| | - J de Las Rivas
- Bioinformatics and Functional Genomics, Centro de Investigación del Cáncer, Universidad de Salamanca-CSIC, Salamanca
| | - J M Hernández
- IBMCC, Centro de Investigación del Cáncer, Universidad de Salamanca-CSIC, Salamanca; Department of Hematology, Hospital Clínico Universitario de Salamanca, Salamanca.
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21
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Abstract
Whole-genome genetic diagnostics has changed the clinical landscape of pediatric and adolescent medicine. In this article, we review the history of clinical cytogenetics as the field has progressed from studying chromosomes prepared from cells squashed between 2 slides to the high-resolution, whole-genome technology in use today, which has allowed for the identification of numerous previously unrecognized microdeletion and microduplication syndromes. Types of arrays and the data they collect are addressed, as are the types of results that array comparative genomic hybridization studies may generate. Throughout the review, we present case stories to illustrate the familiar (Down syndrome) and the new (a never-before reported microdeletion on the long arm of chromosome 12).
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22
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Abstract
Emerging clinical evidence shows that the deregulation of ubiquitin-mediated degradation of oncogene products or tumour suppressors is likely to be involved in the aetiology of carcinomas and leukaemias. Recent studies have indicated that some members of the tripartite motif (TRIM) proteins (one of the subfamilies of the RING type E3 ubiquitin ligases) function as important regulators for carcinogenesis. This Review focuses on TRIM proteins that are involved in tumour development and progression.
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Affiliation(s)
- Shigetsugu Hatakeyama
- Department of Biochemistry, Institute for Animal Experimentation, and Central Institute of Isotope Science, Hokkaido University Graduate School of Medicine, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido 060-8638, Japan.
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23
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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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24
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Array comparative genomic hybridization analysis identifies recurrent gain of chromosome 2p25.3 involving the ACP1 and MYCN genes in chronic lymphocytic leukemia. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2011; 11 Suppl 1:S17-24. [PMID: 22035742 DOI: 10.1016/j.clml.2011.03.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 03/12/2011] [Accepted: 03/15/2011] [Indexed: 11/20/2022]
Abstract
Chromosomal aberrations are independent prognostic markers in chronic lymphocytic leukemia (CLL). Recent studies using genomic arrays have shown recurrent gains of the short arm of chromosome 2 (2p) in a subset of CLL. We evaluated 178 CLL cases for 2p gains using custom-designed oligonucleotide array-based comparative genomic hybridization (aCGH). A high frequency of 2p gains was observed in 53 of 178 (30%) cases, which ranged from a small 29-kb region to large segments involving the entire short arm. Besides several common chromosomal aberrations associated with 2p gain, we demonstrated a novel observation that gain of the telomeric region 2p25.3 harboring the ACP1 gene is common in CLL (25%, 44 of 178 cases). The ACP1 gene has been previously shown to regulate T-cell receptor signaling through ZAP-70, and both genes are unfavorable clinical markers for CLL. Quantitative polymerase chain reaction (qPCR) confirmed the presence of 3-6 copies of ACP1 in 35 of 40 (88%) of these cases. Interestingly, none of the aCGH diploid CLL cases showed gain of ACP1. Assessment of 73 healthy individuals by qPCR revealed ACP1 copy number gain in only two cases (2.7%). Gain of 2p25.3 was associated with ZAP-70 expression (P < .002) and unmutated immunoglobulin heavy chain variable (IGHV) gene mutation (P < .0001). A high frequency of MYCN co-amplication with ACP1 was observed (14 of 40 cases, 35%). The frequent 2p25.3 gain involving the ACP1 and MYCN genes may help define the critical region of 2p that contributes to pathogenesis of CLL together with other chromosomal abnormalities.
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25
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Abstract
Inherited susceptibility to chronic lymphocytic leukemia (CLL) has been recognized for decades. Approximately 10% of individuals with CLL report a family history of CLL or a related lymphoproliferative disorder, and genetic predisposition is the best understood risk factor for CLL. Studies of familial CLL have suggested that the disease features are largely similar to sporadic CLL, although recent data suggest that familial CLL may more commonly show somatic hypermutation of the immunoglobulin heavy-chain variable region, suggesting a more indolent disease course. Monoclonal B-cell lymphocytosis (MBL) has been identified recently as a likely precursor to CLL; it is found in the general population with increasing age and enriched in unaffected relatives of individuals with familial CLL. Studies of MBL as well as mouse models of CLL may lead to better understanding of early CLL pathogenesis that is relevant to familial predisposition. To date, the identification of genes that predispose to familial CLL has been slow, primarily due to the relatively few families available for study, the small size of those families and disease causation most likely by multiple genes that each confer smaller risks. In the coming years, the application of systematic genomics approaches to familial CLL should, hopefully, lead to the identification of novel loci involved in the disease.
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Affiliation(s)
- Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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Gene dosage effects in chronic lymphocytic leukemia. ACTA ACUST UNITED AC 2011; 203:149-60. [PMID: 21156227 DOI: 10.1016/j.cancergencyto.2010.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 08/25/2010] [Accepted: 09/01/2010] [Indexed: 11/21/2022]
Abstract
To understand the influence of chromosomal alterations on gene expression in a genome-wide view, chromosomal imbalances detected by single nucleotide polymorphism (SNP) chips were compared with global gene expression in 16 cases of chronic lymphocytic leukemia (CLL). A strong concordance between chromosomal gain or loss and increased or reduced expression of genes in the affected regions was found, respectively. Regions of uniparental disomy (UPD) were rare and had usually no consistent influence on gene expression, but in one instance, a large UPD was associated with a downregulation of most genes in the affected chromosome. The frequently deleted miRNAs, MIRN15A and MIRN16-1, did not show a reduced expression in cases with monoallelic deletions. The BCL2 protein, considered to be downregulated by these miRNAs, was upregulated not only in CLL with biallelic deletion of MIRN15A and MIRN16-1, but also in cases with monoallelic deletion. This suggests a complex regulation of BCL2 levels in CLL cells. Taken together, in CLL, a global gene dosage effect exists for chromosomal gains and deletions and in some instances for UPDs. We did not confirm a consistent correlation between MIRN15A and MIRN16-1 expression levels and BCL2 protein levels, indicating a complex regulation of BCL2 expression.
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O’MALLEY DP, GIUDICE C, CHANG AS, CHANG D, BARRY TS, HIBBARD MK, CHEN R, CHEN ST. Comparison of array comparative genomic hybridization (aCGH) to FISH and cytogenetics in prognostic evaluation of chronic lymphocytic leukemia. Int J Lab Hematol 2010; 33:238-44. [DOI: 10.1111/j.1751-553x.2010.01284.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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28
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Praulich I, Tauscher M, Göhring G, Glaser S, Hofmann W, Feurstein S, Flotho C, Lichter P, Niemeyer CM, Schlegelberger B, Steinemann D. Clonal heterogeneity in childhood myelodysplastic syndromes--challenge for the detection of chromosomal imbalances by array-CGH. Genes Chromosomes Cancer 2010; 49:885-900. [PMID: 20589934 DOI: 10.1002/gcc.20797] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
To evaluate whether copy number alterations (CNAs) are present that may contribute to disease development and/or progression of childhood myelodysplastic syndromes (MDS), 36 pediatric MDS patients were analyzed using array-based comparative genome hybridization (aCGH). In addition to monosomy 7, the most frequent chromosome aberration in childhood MDS, novel recurrent CNAs were detected. They included a loss of 3p14.3-p12.3, which contains the putative tumor suppressor gene FHIT, a loss of 7p21.3-p15.3, a loss of 9q33.3-q34.3 (D184) and microdeletions in 17p11.2, 6q23 containing MYB, and 17p13 containing TP53. In this small patient cohort, patients without CNA, patients with monosomy 7 only and patients with one CNA in addition to monosomy 7 did not differ in their survival. As expected, all patients with complex karyotypes, including two patients with deletions of TP53, died. A challenge inherent to aCGH analysis of MDS is the low percentage of tumor cells. We evaluated several approaches to overcome this limitation. Genomic profiles from isolated granulocytes were of higher quality than those from bone marrow mononuclear cells. Decreased breakpoint calling stringency increased recognition of CNAs present in small clonal populations. However, further analysis using a custom-designed array showed that these CNAs often did not confirm the findings from 244k arrays. In contrast, constitutional CNVs were reliably detected on both arrays. Moreover, aCGH on amplified DNA from distinct myeloid clusters is a new approach to determine CNAs in small subpopulations. Our results clearly emphasize the need to verify array-CGH results by independent methods like FISH or quantitative PCR.
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Affiliation(s)
- Inka Praulich
- Institute of Cell and Molecular Pathology, Hannover Medical School, Hannover, Germany
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29
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Setlur SR, Ihm C, Tchinda J, Shams S, Werner L, Cho EK, Thompson C, Phillips K, Rassenti LZ, Kipps TJ, Neuberg D, Freedman AS, Lee C, Brown JR. Comparison of familial and sporadic chronic lymphocytic leukaemia using high resolution array comparative genomic hybridization. Br J Haematol 2010; 151:336-45. [PMID: 20812997 DOI: 10.1111/j.1365-2141.2010.08341.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Approximately 10% of patients with chronic lymphocytic leukaemia (CLL) have a family history of the disease or a related lymphoproliferative disorder, yet the relationship of familial CLL to genomic abnormalities has not been characterized in detail. We therefore studied 75 CLL patients, half familial and half sporadic, using high-resolution array comparative genomic hybridization (CGH), in order to better define the relationship of genomic abnormalities to familial disease and other biological prognostic factors. Our results showed that the most common high-risk deletion in CLL, deletion 11q, was significantly associated with sporadic disease. Comparison of familial to sporadic disease additionally identified a copy number variant region near the centromere on 14q, proximal to IGH@, in which gains were associated both with familial CLL, and with mutated IGHV and homozygous deletion of 13q. Homozygous deletion of 13q was also found to be associated with mutated IGHV and low expression of ZAP-70, and a significantly longer time to first treatment compared to heterozygous deletion or lack of alteration. This study is the first high resolution effort to investigate and report somatic genetic differences between familial and sporadic CLL.
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Affiliation(s)
- Sunita R Setlur
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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Usvasalo A, Ninomiya S, Räty R, Hollmén J, Saarinen-Pihkala UM, Elonen E, Knuutila S. Focal 9p instability in hematologic neoplasias revealed by comparative genomic hybridization and single-nucleotide polymorphism microarray analyses. Genes Chromosomes Cancer 2010; 49:309-18. [PMID: 20013897 DOI: 10.1002/gcc.20741] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Copy number losses in chromosome arm 9p are well-known aberrations in malignancies, including leukemias. The CDKN2A gene is suggested to play a key role in these aberrations. In this study overviewing 9p losses in hematologic neoplasias, we introduce the term focal 9p instability to indicate multiple areas of copy number loss or homozygous loss within a larger heterozygous one in 9p. We have used microarray comparative genomic hybridization to study patients with acute lymphoblastic leukemia (ALL, n = 140), acute myeloid leukemia (n = 50), chronic lymphocytic leukemia (n = 20), and myelodysplastic syndromes (n = 37). Our results show that 9p instability is restricted to ALL. In total, 58/140 (41%) patients with ALL had a loss in 9p. The 9p instability was detected in 19% of the patients with ALL and always included homozygous loss of CDKN2A along with loss of CDKN2B. Other possibly important genes included MTAP, IFN, MLLT3, JAK2, PTPLAD2, and PAX5. 13/27 (48%) patients with the instability had the BCR/ABL1 fusion gene or other oncogene-activating translocation or structural aberrations. Two patients had homozygous loss of hsa-mir -31, a microRNA known to regulate IKZF1. IKZF1 deletion at 7p12.1 was seen in 10 (37%) patients with the 9p instability. These findings suggest that, in ALL leukemogenesis, loss of CDKN2A and other target genes in the instability region is frequently associated with BCR/ABL1 and IKZF1 dysfunction. The multiple mechanisms leading to 9p instability including physical or epigenetic loss of the target genes, loss of the microRNA cluster, and the role of FRA9G fragile site are discussed.
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Affiliation(s)
- Anu Usvasalo
- Hospital for Children and Adolescents, University of Helsinki, Helsinki, Finland
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Gulten T, Yakut T, Karkucak M, Baytan B, Guneş AM. AML1 amplification and 17q25 deletion in a case of childhood acute lymphoblastic leukemia. J Clin Lab Anal 2010; 23:368-71. [PMID: 19927343 DOI: 10.1002/jcla.20343] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We report a case of childhood acute lymphoblastic leukemia (ALL) with both acute myeloid leukemia 1 (AML1) amplification and 17q25 deletion. AML1 gene is located on 21q22 and encodes a transcription factor. AML1 amplification is a common finding in childhood ALL, and itis observed as an increase in gene copy number by the FISH analysis. The mechanism of AML1 amplification is not associated with AML1 gene mutations. The 17q25 is a gene-rich chromosomal location and distinct abnormalities of this region have been observed in previous cases of different kinds of leukemia. Deletion of the 17q25 region has been reported in two leukemia patients. Septin 9 (SEPT9) and survivin genes are located on 17q25. High expression of these genes and AML1 amplification are regarded as markers in tumorigenesis and disease progression; however, more data are needed for accurate prognostic evaluation.
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Affiliation(s)
- Tuna Gulten
- Medical Genetics Department, Medical Faculty, Uludag University, Bursa, Turkey.
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32
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Jarosova M, Urbankova H, Plachy R, Papajik T, Holzerova M, Balcarkova J, Pikalova Z, Divoky V, Indrak K. Gain of chromosome 2p in chronic lymphocytic leukemia: significant heterogeneity and a new recurrent dicentric rearrangement. Leuk Lymphoma 2010; 51:304-13. [DOI: 10.3109/10428190903518311] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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33
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Birerdinc A, Nohelty E, Marakhonov A, Manyam G, Panov I, Coon S, Nikitin E, Skoblov M, Chandhoke V, Baranova A. Pro-apoptotic and antiproliferative activity of human KCNRG, a putative tumor suppressor in 13q14 region. Tumour Biol 2009; 31:33-45. [PMID: 20237900 PMCID: PMC2803748 DOI: 10.1007/s13277-009-0005-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Accepted: 11/04/2009] [Indexed: 12/04/2022] Open
Abstract
Deletion of 13q14.3 and a candidate gene KCNRG (potassium channel regulating gene) is the most frequent chromosomal abnormality in B-cell chronic lymphocytic leukemia and is a common finding in multiple myeloma (MM). KCNRG protein may interfere with the normal assembly of the K+ channel proteins causing the suppression of Kv currents. We aimed to examine possible role of KCNRG haploinsufficiency in chronic lymphocytic leukemia (CLL) and MM cells. We performed detailed genomic analysis of the KCNRG locus; studied effects of the stable overexpression of KCNRG isoforms in RPMI-8226, HL-60, and LnCaP cells; and evaluated relative expression of its transcripts in various human lymphomas. Three MM cell lines and 35 CLL PBL samples were screened for KCNRG mutations. KCNRG exerts growth suppressive and pro-apoptotic effects in HL-60, LnCaP, and RPMI-8226 cells. Direct sequencing of KCNRG exons revealed point mutation delT in RPMI-8226 cell line. Levels of major isoform of KCNRG mRNA are lower in DLBL lymphomas compared to normal PBL samples, while levels of its minor mRNA are decreased across the broad range of the lymphoma types. The haploinsufficiency of KCNRG might be relevant to the progression of CLL and MM at least in a subset of patients.
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Affiliation(s)
- Aybike Birerdinc
- Molecular Biology and Microbiology Department, College of Science, George Mason University, David King Hall, MSN 3E1, Fairfax, VA 22030 USA
| | - Elizabeth Nohelty
- Molecular Biology and Microbiology Department, College of Science, George Mason University, David King Hall, MSN 3E1, Fairfax, VA 22030 USA
| | - Andrey Marakhonov
- Research Center for Medical Genetics, RAMS, Moskvorechie Str., 1, Moscow, Russian Federation
| | - Ganiraju Manyam
- Molecular Biology and Microbiology Department, College of Science, George Mason University, David King Hall, MSN 3E1, Fairfax, VA 22030 USA
| | - Ivan Panov
- Molecular Biology and Microbiology Department, College of Science, George Mason University, David King Hall, MSN 3E1, Fairfax, VA 22030 USA
| | - Stephanie Coon
- Molecular Biology and Microbiology Department, College of Science, George Mason University, David King Hall, MSN 3E1, Fairfax, VA 22030 USA
| | - Eugene Nikitin
- Hematology Research Center of Russia, Moscow, Russian Federation
| | - Mikhail Skoblov
- Research Center for Medical Genetics, RAMS, Moskvorechie Str., 1, Moscow, Russian Federation
| | - Vikas Chandhoke
- Molecular Biology and Microbiology Department, College of Science, George Mason University, David King Hall, MSN 3E1, Fairfax, VA 22030 USA
| | - Ancha Baranova
- Molecular Biology and Microbiology Department, College of Science, George Mason University, David King Hall, MSN 3E1, Fairfax, VA 22030 USA
- Research Center for Medical Genetics, RAMS, Moskvorechie Str., 1, Moscow, Russian Federation
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Stevens-Kroef M, Simons A, Gorissen H, Feuth T, Weghuis DO, Buijs A, Raymakers R, Geurts van Kessel A. Identification of chromosomal abnormalities relevant to prognosis in chronic lymphocytic leukemia using multiplex ligation-dependent probe amplification. ACTA ACUST UNITED AC 2009; 195:97-104. [PMID: 19963108 DOI: 10.1016/j.cancergencyto.2009.06.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 06/17/2009] [Accepted: 06/20/2009] [Indexed: 01/10/2023]
Abstract
B-cell chronic lymphocytic leukemia (CLL) is characterized by a highly variable clinical course. Characteristic genomic abnormalities provide clinically important prognostic information. Because karyotyping and fluorescence in situ hybridization (FISH) are laborious techniques, we investigated the diagnostic efficacy of the more recently developed multiplex ligation-dependent probe amplification (MLPA) technique. MLPA and interphase FISH data of 88 CLL patients were compared for loci encompassing the 13q14 region, chromosome 12, and the ATM (11q22) and TP53 (17p13) genes. We found a perfect correlation, provided that the abnormal clone was present in at least 10-20% of the cells. Because multiple loci and multiple probes per locus were included in the MLPA assay, additional abnormalities not covered by the FISH probes were detected. Furthermore, in 13 cases deletions partly covering the 13q14.3 locus were observed, including three deletions that remained undetected by FISH. All the deletions included the noncoding RNA locus DLEU1 (previously BCMS), which is considered to be the most likely CLL-associated candidate tumor suppressor gene within the 13q14 region. We conclude that MLPA serves as a comprehensive and reliable technique for the simultaneous identification of different clinically relevant and region-specific genomic aberrations in CLL.
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Affiliation(s)
- Marian Stevens-Kroef
- Department of Human Genetics, Radboud University Nijmegen Medical Center, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
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35
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36
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Gunn SR, Bolla AR, Barron LL, Gorre ME, Mohammed MS, Bahler DW, Mellink CHM, van Oers MHJ, Keating MJ, Ferrajoli A, Coombes KR, Abruzzo LV, Robetorye RS. Array CGH analysis of chronic lymphocytic leukemia reveals frequent cryptic monoallelic and biallelic deletions of chromosome 22q11 that include the PRAME gene. Leuk Res 2009; 33:1276-81. [PMID: 19027161 DOI: 10.1016/j.leukres.2008.10.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2008] [Revised: 10/09/2008] [Accepted: 10/10/2008] [Indexed: 02/03/2023]
Abstract
We used BAC array-based CGH to detect genomic imbalances in 187 CLL cases. Submicroscopic deletions of chromosome 22q11 were observed in 28 cases (15%), and the frequency of these deletions was second only to loss of the 13q14 region, the most common genomic aberration in CLL. Oligonucleotide-based array CGH analysis showed that the 22q11 deletions ranged in size from 0.34 Mb up to approximately 1 Mb. The minimally deleted region included the ZNF280A, ZNF280B, GGTLC2, and PRAME genes. Quantitative real-time PCR revealed that ZNF280A, ZNF280B, and PRAME mRNA expression was significantly lower in the 22q11 deletion cases compared to non-deleted cases.
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Affiliation(s)
- Shelly R Gunn
- Department of Pathology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
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37
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Maciejewski JP, Tiu RV, O'Keefe C. Application of array-based whole genome scanning technologies as a cytogenetic tool in haematological malignancies. Br J Haematol 2009; 146:479-88. [PMID: 19563474 DOI: 10.1111/j.1365-2141.2009.07757.x] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Karyotypic analysis provides useful diagnostic information in many haematological malignancies. However, standard metaphase cytogenetics has technical limitations that result in the underestimation of the degree of chromosomal changes. Array-based technologies can be used for karyotyping and can supplant some of the shortcomings of metaphase cytogenetics, and include single nucleotide polymorphism arrays (SNP-A) and comparative genomic hybridization arrays (CGH-A). Array-based cytogenetic tools do not rely on cell division, have superb resolution for unbalanced lesions and allow for the detection of copy number-neutral loss of heterozygosity, a type of lesion not seen with metaphase cytogenetics. Moreover, genomic array analysis is automated and results can be objectively and systematically analysed using biostatistical algorithms. As a potential advantage over genomic approaches, metaphase cytogenetics can detect balanced chromosomal defects and resolves clonal mosaicism. Initial studies performed in various haematological malignancies indicate the potential of SNP-A-based karyotyping as a useful clinical cytogenetic detection tool. The current effort is aimed at developing rational diagnostic algorithms for the detection of somatic defects and the establishment of clinical correlations for novel SNP-A-detected chromosomal defects, including acquired somatic uniparental disomy. SNP-A can complement metaphase karyotyping and will probably play an important role in clinical cytogenetic diagnostics.
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Affiliation(s)
- Jaroslaw P Maciejewski
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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38
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Sargent R, Jones D, Abruzzo LV, Yao H, Bonderover J, Cisneros M, Wierda WG, Keating MJ, Luthra R. Customized oligonucleotide array-based comparative genomic hybridization as a clinical assay for genomic profiling of chronic lymphocytic leukemia. J Mol Diagn 2009; 11:25-34. [PMID: 19074592 PMCID: PMC2607562 DOI: 10.2353/jmoldx.2009.080037] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2008] [Indexed: 11/20/2022] Open
Abstract
Chromosome gains and losses used for risk stratification in chronic lymphocytic leukemia (CLL) are commonly assessed by multiprobe fluorescence in situ hybridization (FISH) studies. We designed and validated a customized array-comparative genomic hybridization (aCGH) platform as a clinical assay for CLL genomic profiling. A 60-mer, 44,000-probe oligonucleotide array with a 50-kb average spatial resolution was augmented with high-density probe tiling at loci that are frequently aberrant in CLL. Aberrations identified by aCGH were compared with those identified by a FISH panel, including locus-specific probes to ATM (11q22.3), the centromeric region of chromosome 12 (12p11.1-q11), D13S319 (13q14.3), LAMP1 (13q34), and TP53 (17p13.1). In 100 CLL samples, aCGH/FISH concordance was seen for 89% of FISH-called aberrations at the ATM (n=18), D13S319 (n=42), LAMP (n=12), and TP53 (n=22) loci and for chromosome 12 (n=14). Eighty-four percentage of FISH/aCGH discordant calls were in samples either at or below the limit of aCGH sensitivity (10% to 25% FISH aberration-containing cells). Therefore, aCGH profiling is a feasible routine clinical test with comparable results to multiprobe FISH studies; however, it may be less sensitive than FISH in cases with low-level aberrations. Further, a customized array design can provide comprehensive genomic profiling with additional accuracy in both identifying and defining the extent of small aberrations at target loci.
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Affiliation(s)
- Rachel Sargent
- Department of Hematopathology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - Dan Jones
- Department of Hematopathology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - Lynne V Abruzzo
- Department of Hematopathology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - Hui Yao
- Division of Quantitative Sciences, The University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - Jaime Bonderover
- Department of Hematopathology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - Marissa Cisneros
- Department of Hematopathology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - William G Wierda
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - Michael J Keating
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas.
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Abstract
A 15-month-old girl with Miller-Dieker syndrome, a contiguous gene deletion syndrome involving chromosome 17p13.3 and resulting in lissencephaly, was diagnosed with precursor B-cell acute lymphoblastic leukemia. Cytogenetic analysis identified both the previously detected 17p13.3 deletion and additional complex numerical and structural abnormalities, including loss of chromosome 9, isochromosome 9q and interstitial deletion of 20q. This is, to our knowledge, the first report of acute leukemia in the setting of Miller-Dieker syndrome. Herein we review the literature regarding Miller-Dieker syndrome, with particular attention to the presence of several candidate tumor suppressor genes within the deleted material.
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Novel genomic alterations and clonal evolution in chronic lymphocytic leukemia revealed by representational oligonucleotide microarray analysis (ROMA). Blood 2008; 113:1294-303. [PMID: 18922857 DOI: 10.1182/blood-2008-05-158865] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We examined copy number changes in the genomes of B cells from 58 patients with chronic lymphocytic leukemia (CLL) by using representational oligonucleotide microarray analysis (ROMA), a form of comparative genomic hybridization (CGH), at a resolution exceeding previously published studies. We observed at least 1 genomic lesion in each CLL sample and considerable variation in the number of abnormalities from case to case. Virtually all abnormalities previously reported also were observed here, most of which were indeed highly recurrent. We observed the boundaries of known events with greater clarity and identified previously undescribed lesions, some of which were recurrent. We profiled the genomes of CLL cells separated by the surface marker CD38 and found evidence of distinct subclones of CLL within the same patient. We discuss the potential applications of high-resolution CGH analysis in a clinical setting.
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Puces à ADN (CGH-array) : application pour le diagnostic de déséquilibres cytogénétiques cryptiques. ACTA ACUST UNITED AC 2008; 56:368-74. [DOI: 10.1016/j.patbio.2008.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Accepted: 04/16/2008] [Indexed: 01/05/2023]
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Gunn SR, Mohammed MS, Gorre ME, Cotter PD, Kim J, Bahler DW, Preobrazhensky SN, Higgins RA, Bolla AR, Ismail SH, de Jong D, Eldering E, van Oers MHJ, Mellink CHM, Keating MJ, Schlette EJ, Abruzzo LV, Robetorye RS. Whole-genome scanning by array comparative genomic hybridization as a clinical tool for risk assessment in chronic lymphocytic leukemia. J Mol Diagn 2008; 10:442-51. [PMID: 18687794 DOI: 10.2353/jmoldx.2008.080033] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Array-based comparative genomic hybridization (array CGH) provides a powerful method for simultaneous genome-wide scanning and prognostic marker assessment in chronic lymphocytic leukemia (CLL). In the current study, commercially available bacterial artificial chromosome and oligonucleotide array CGH platforms were used to identify chromosomal alterations of prognostic significance in 174 CLL cases. Tumor genomes were initially analyzed by bacterial artificial chromosome array CGH followed by confirmation and breakpoint mapping using oligonucleotide arrays. Genomic changes involving loci currently interrogated by fluorescence in situ hybridization (FISH) panels were detected in 155 cases (89%) at expected frequencies: 13q14 loss (47%), trisomy 12 (13%), 11q loss (11%), 6q loss (7.5%), and 17p loss (4.6%). Genomic instability was the second most commonly identified alteration of prognostic significance with three or more alterations involving loci not interrogated by FISH panels identified in 37 CLL cases (21%). A subset of 48 CLL cases analyzed by six-probe FISH panels (288 total hybridizations) was concordant with array CGH results for 275 hybridizations (95.5%); 13 hybridizations (4.5%) were discordant because of clonal populations that comprised less than 30% of the sample. Array CGH is a powerful, cost-effective tool for genome-wide risk assessment in the clinical evaluation of CLL.
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Affiliation(s)
- Shelly R Gunn
- The University of Texas Health Science Center at San Antonio, Department of Pathology, Mail Code 7750, 7703 Floyd Curl Dr., San Antonio, TX, USA.
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43
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Gunnarsson R, Staaf J, Jansson M, Ottesen AM, Göransson H, Liljedahl U, Ralfkiaer U, Mansouri M, Buhl AM, Smedby KE, Hjalgrim H, Syvänen AC, Borg A, Isaksson A, Jurlander J, Juliusson G, Rosenquist R. Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia--a comparative study of four differently designed, high resolution microarray platforms. Genes Chromosomes Cancer 2008; 47:697-711. [PMID: 18484635 DOI: 10.1002/gcc.20575] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Screening for gene copy-number alterations (CNAs) has improved by applying genome-wide microarrays, where SNP arrays also allow analysis of loss of heterozygozity (LOH). We here analyzed 10 chronic lymphocytic leukemia (CLL) samples using four different high-resolution platforms: BAC arrays (32K), oligonucleotide arrays (185K, Agilent), and two SNP arrays (250K, Affymetrix and 317K, Illumina). Cross-platform comparison revealed 29 concordantly detected CNAs, including known recurrent alterations, which confirmed that all platforms are powerful tools when screening for large aberrations. However, detection of 32 additional regions present in 2-3 platforms illustrated a discrepancy in detection of small CNAs, which often involved reported copy-number variations. LOH analysis using dChip revealed concordance of mainly large regions, but showed numerous, small nonoverlapping regions and LOH escaping detection. Evaluation of baseline variation and copy-number ratio response showed the best performance for the Agilent platform and confirmed the robustness of BAC arrays. Accordingly, these platforms demonstrated a higher degree of platform-specific CNAs. The SNP arrays displayed higher technical variation, although this was compensated by high density of elements. Affymetrix detected a higher degree of CNAs compared to Illumina, while the latter showed a lower noise level and higher detection rate in the LOH analysis. Large-scale studies of genomic aberrations are now feasible, but new tools for LOH analysis are requested.
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Affiliation(s)
- Rebeqa Gunnarsson
- Lund Strategic Research Center for Stem Cell Biology and Cell Therapy, Hematology and Transplantation, Lund University, Lund, Sweden
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Gunn SR, Mohammed MS, Mellink CHM, Abruzzo LV, Robetorye RS. The HemeScan test for genomic prognostic marker assessment in chronic lymphocytic leukemia. ACTA ACUST UNITED AC 2008; 2:731-40. [DOI: 10.1517/17530059.2.6.731] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Abstract
Over the years, methods of cytogenetic analysis evolved and became part of routine laboratory testing, providing valuable diagnostic and prognostic information in hematologic disorders. Karyotypic aberrations contribute to the understanding of the molecular pathogenesis of disease and thereby to rational application of therapeutic modalities. Most of the progress in this field stems from the application of metaphase cytogenetics (MC), but recently, novel molecular technologies have been introduced that complement MC and overcome many of the limitations of traditional cytogenetics, including a need for cell culture. Whole genome scanning using comparative genomic hybridization and single nucleotide polymorphism arrays (CGH-A; SNP-A) can be used for analysis of somatic or clonal unbalanced chromosomal defects. In SNP-A, the combination of copy number detection and genotyping enables diagnosis of copy-neutral loss of heterozygosity, a lesion that cannot be detected using MC but may have important pathogenetic implications. Overall, whole genome scanning arrays, despite the drawback of an inability to detect balanced translocations, allow for discovery of chromosomal defects in a higher proportion of patients with hematologic malignancies. Newly detected chromosomal aberrations, including somatic uniparental disomy, may lead to more precise prognostic schemes in many diseases.
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