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Haas OA, Borkhardt A. Hyperdiploidy: the longest known, most prevalent, and most enigmatic form of acute lymphoblastic leukemia in children. Leukemia 2022; 36:2769-2783. [PMID: 36266323 PMCID: PMC9712104 DOI: 10.1038/s41375-022-01720-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 11/09/2022]
Abstract
Hyperdiploidy is the largest genetic entity B-cell precursor acute lymphoblastic leukemia in children. The diagnostic hallmark of its two variants that will be discussed in detail herein is a chromosome count between 52 and 67, respectively. The classical HD form consists of heterozygous di-, tri-, and tetrasomies, whereas the nonclassical one (usually viewed as "duplicated hyperhaploid") contains only disomies and tetrasomies. Despite their apparently different clinical behavior, we show that these two sub-forms can in principle be produced by the same chromosomal maldistribution mechanism. Moreover, their respective array, gene expression, and mutation patterns also indicate that they are biologically more similar than hitherto appreciated. Even though in-depth analyses of the genomic intricacies of classical HD leukemias are indispensable for the elucidation of the disease process, the ensuing results play at present surprisingly little role in treatment stratification, a fact that can be attributed to the overall good prognoses and low relapse rates of the concerned patients and, consequently, their excellent treatment outcome. Irrespective of this underutilization, however, the detailed genetic characterization of HD leukemias may, especially in planned treatment reduction trials, eventually become important for further treatment stratification, patient management, and the clinical elucidation of outcome data. It should therefore become an integral part of all upcoming treatment studies.
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Affiliation(s)
- Oskar A Haas
- St. Anna Children's Hospital, Pediatric Clinic, Medical University, Vienna, Austria.
- Labdia Labordiagnostik, Vienna, Austria.
| | - Arndt Borkhardt
- Department for Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany.
- German Cancer Consortium (DKTK), partnering site Essen/Düsseldorf, Düsseldorf, Germany.
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RNAseqCNV: analysis of large-scale copy number variations from RNA-seq data. Leukemia 2022; 36:1492-1498. [PMID: 35351983 PMCID: PMC9177690 DOI: 10.1038/s41375-022-01547-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 03/03/2022] [Accepted: 03/11/2022] [Indexed: 11/16/2022]
Abstract
Transcriptome sequencing (RNA-seq) is widely used to detect gene rearrangements and quantitate gene expression in acute lymphoblastic leukemia (ALL), but its utility and accuracy in identifying copy number variations (CNVs) has not been well described. CNV information inferred from RNA-seq can be highly informative to guide disease classification and risk stratification in ALL due to the high incidence of aneuploid subtypes within this disease. Here we describe RNAseqCNV, a method to detect large scale CNVs from RNA-seq data. We used models based on normalized gene expression and minor allele frequency to classify arm level CNVs with high accuracy in ALL (99.1% overall and 98.3% for non-diploid chromosome arms, respectively), and the models were further validated with excellent performance in acute myeloid leukemia (accuracy 99.8% overall and 99.4% for non-diploid chromosome arms). RNAseqCNV outperforms alternative RNA-seq based algorithms in calling CNVs in the ALL dataset, especially in samples with a high proportion of CNVs. The CNV calls were highly concordant with DNA-based CNV results and more reliable than conventional cytogenetic-based karyotypes. RNAseqCNV provides a method to robustly identify copy number alterations in the absence of DNA-based analyses, further enhancing the utility of RNA-seq to classify ALL subtype.
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Chaturvedi A, Shetty D, Ghogale SG, Deshpande N, Badrinath Y, Chatterjee G, Girase K, Sriram H, Khanka T, Mishra C, Dasgupta N, Gujarathi SA, Rajpal S, Patkar N, Amare-Kadam P, Gujral S, Subramanian PG, Tembhare PR. Detecting hypodiploidy with endoreduplication and masked hypodiploidy in B-cell acute lymphoblastic leukemia using multicolor flow cytometry. CYTOMETRY. PART B, CLINICAL CYTOMETRY 2022; 102:199-208. [PMID: 35212133 DOI: 10.1002/cyto.b.22063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 02/06/2022] [Accepted: 02/16/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND Multicolor flow cytometry-based DNA-ploidy (MFC-ploidy) analysis is a simple, sensitive, and popular method for ploidy analysis in B-cell acute lymphoblastic leukemia (B-ALL). However, the utility of MFC-ploidy in the detection of B-ALL with endoreduplication or masked hypodiploidy has not been reported. Herein, we studied the patterns of MFC-ploidy assessment and its utility to detect B-ALL with hypodiploidy and endoreduplication. METHODS MFC-ploidy analysis was performed using FxCycle Violet-dye-based method, and cytogenetic ploidy was evaluated using chromosomal-counting and FISH analysis. A total of 20 B-ALL cases with endoreduplication were studied for the patterns of MFC-ploidy analysis and compared with 250 patients with hyperdiploidy and 11 cases with pure hypodiploidy. RESULTS All B-ALL with endoreduplication revealed two distinct peaks (populations) on MFC-ploidy analysis: the first (hypodiploid) peak (median-DNA-index [DI], 0.82; range, 0.6-0.95) and the second (hyperdiploid) peak with almost twice DI (median-DI, 1.53; range, 1.14-1.75). Cytogenetic findings were available in 19 cases and confirmed hypodiploidy with endoreduplication in 13/19 (68.4%) and only hypodiploidy in 3/19 cases. The remaining three cases showed hyperdiploid blasts in cytogenetic studies. Of these three, two cases had <10% blasts population with hypodiploidy. Thus, masked-hypodiploidy could be diagnosed correctly in 3/19 cases on MFC-ploidy analysis. CONCLUSION MFC-ploidy analysis shows a characteristic pattern of DNA-ploidy in samples with endoreduplication. It allows the distinction between samples with masked hypodiploidy from true hyperdiploidy. An integrated approach involving cytogenetic and MFC-ploidy detection is very helpful in the risk stratification of B-ALL in routine clinical practice.
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Affiliation(s)
- Anumeha Chaturvedi
- Hematopathology Laboratory, ACTREC, Tata Memorial Center, Homi Bhabha National Institute (HBNI) University, Navi Mumbai, Maharashtra, India
| | - Dhanalaxmi Shetty
- Cancer Cytogenetics Department, ACTREC, Tata Memorial Center, HBNI University, Navi Mumbai, Maharashtra, India
| | - Sitaram Gundu Ghogale
- Hematopathology Laboratory, ACTREC, Tata Memorial Center, Homi Bhabha National Institute (HBNI) University, Navi Mumbai, Maharashtra, India
| | - Nilesh Deshpande
- Hematopathology Laboratory, ACTREC, Tata Memorial Center, Homi Bhabha National Institute (HBNI) University, Navi Mumbai, Maharashtra, India
| | - Yajamanam Badrinath
- Hematopathology Laboratory, ACTREC, Tata Memorial Center, Homi Bhabha National Institute (HBNI) University, Navi Mumbai, Maharashtra, India
| | - Gaurav Chatterjee
- Hematopathology Laboratory, ACTREC, Tata Memorial Center, Homi Bhabha National Institute (HBNI) University, Navi Mumbai, Maharashtra, India
| | - Karishma Girase
- Hematopathology Laboratory, ACTREC, Tata Memorial Center, Homi Bhabha National Institute (HBNI) University, Navi Mumbai, Maharashtra, India
| | - Harshini Sriram
- Hematopathology Laboratory, ACTREC, Tata Memorial Center, Homi Bhabha National Institute (HBNI) University, Navi Mumbai, Maharashtra, India
| | - Twinkle Khanka
- Hematopathology Laboratory, ACTREC, Tata Memorial Center, Homi Bhabha National Institute (HBNI) University, Navi Mumbai, Maharashtra, India
| | - Chetna Mishra
- Hematopathology Laboratory, ACTREC, Tata Memorial Center, Homi Bhabha National Institute (HBNI) University, Navi Mumbai, Maharashtra, India
| | - Niharika Dasgupta
- Hematopathology Laboratory, ACTREC, Tata Memorial Center, Homi Bhabha National Institute (HBNI) University, Navi Mumbai, Maharashtra, India
| | - Sejal Anil Gujarathi
- Hematopathology Laboratory, ACTREC, Tata Memorial Center, Homi Bhabha National Institute (HBNI) University, Navi Mumbai, Maharashtra, India
| | - Sweta Rajpal
- Hematopathology Laboratory, ACTREC, Tata Memorial Center, Homi Bhabha National Institute (HBNI) University, Navi Mumbai, Maharashtra, India
| | - Nikhil Patkar
- Hematopathology Laboratory, ACTREC, Tata Memorial Center, Homi Bhabha National Institute (HBNI) University, Navi Mumbai, Maharashtra, India
| | - Prathibha Amare-Kadam
- Cancer Cytogenetics Department, ACTREC, Tata Memorial Center, HBNI University, Navi Mumbai, Maharashtra, India
| | - Sumeet Gujral
- Hematopathology Laboratory, ACTREC, Tata Memorial Center, Homi Bhabha National Institute (HBNI) University, Navi Mumbai, Maharashtra, India
| | - Papagudi Ganesan Subramanian
- Hematopathology Laboratory, ACTREC, Tata Memorial Center, Homi Bhabha National Institute (HBNI) University, Navi Mumbai, Maharashtra, India
| | - Prashant Ramesh Tembhare
- Hematopathology Laboratory, ACTREC, Tata Memorial Center, Homi Bhabha National Institute (HBNI) University, Navi Mumbai, Maharashtra, India
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Arpas T, Jelinkova H, Hrabovsky S, Orsulova M, Vrzalova Z, Navrkalova V, Brhelova E, Bryjova L, Bulikova A, Ondrouskova E, Sejnohova M, Folber F, Sedová P, Mayer J, Pospisilova S, Jarosova M, Doubek M. Very rare near‐haploid acute lymphoblastic leukemia resistant to immunotherapy and CAR‐T therapy in 19‐year‐old male patient. Clin Case Rep 2022; 10:e05545. [PMID: 35280086 PMCID: PMC8894580 DOI: 10.1002/ccr3.5545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/17/2022] [Accepted: 02/06/2022] [Indexed: 02/02/2023] Open
Abstract
Near‐haploid acute lymphoblastic leukemia is rare subgroup of the disease, which is very important due to very poor prognosis and resistance to treatment including novel monoclonal antibodies and CAR‐T therapy.
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Affiliation(s)
- Tomas Arpas
- Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Hana Jelinkova
- Center of Molecular Biology and Genetics Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Stepan Hrabovsky
- Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Martina Orsulova
- Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Zuzana Vrzalova
- Center of Molecular Biology and Genetics Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
- Central European Institute of Technology (CEITEC) Masaryk University Brno Czechia
| | - Veronika Navrkalova
- Center of Molecular Biology and Genetics Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Eva Brhelova
- Center of Molecular Biology and Genetics Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Lenka Bryjova
- Center of Molecular Biology and Genetics Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Alena Bulikova
- Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
- Department of Clinical Hematology University Hospital Brno Czechia
| | - Eva Ondrouskova
- Center of Molecular Biology and Genetics Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Marketa Sejnohova
- Center of Molecular Biology and Genetics Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Frantisek Folber
- Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Petra Sedová
- Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Jiri Mayer
- Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
| | - Sarka Pospisilova
- Center of Molecular Biology and Genetics Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
- Central European Institute of Technology (CEITEC) Masaryk University Brno Czechia
- Department of Medical Genetics and Genomics University Hospital and Faculty of Medicine Brno Czechia
| | - Marie Jarosova
- Center of Molecular Biology and Genetics Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
- Department of Medical Genetics and Genomics University Hospital and Faculty of Medicine Brno Czechia
| | - Michael Doubek
- Department of Internal Medicine, Hematology and Oncology University Hospital and Faculty of Medicine Brno Czechia
- Central European Institute of Technology (CEITEC) Masaryk University Brno Czechia
- Department of Medical Genetics and Genomics University Hospital and Faculty of Medicine Brno Czechia
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A Systematic Cytogenetic Strategy to Identify Masked Hypodiploidy in Precursor B Acute Lymphoblastic Leukemia in Low Resource Settings. Indian J Hematol Blood Transfus 2021; 37:576-585. [PMID: 34690454 DOI: 10.1007/s12288-021-01409-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/09/2021] [Indexed: 10/22/2022] Open
Abstract
Hypodiploidy with < 40 chromosomes is associated with poor prognosis in B cell precursor acute lymphoblastic leukemia. In some patients, the hypodiploid clone undergoes endoreduplication, resulting in doubling of the number of chromosomes and masquerades as a high hyperdiploid BCP-ALL. Karyotyping reveals metaphases with 50-79 chromosomes masking the hypodiploid clone. Identifying hypodiploidy in such cases requires awareness of non random alterations of chromosomal copy numbers found in hypodiploid BCP-ALL. We used a systematic strategy to identify masked hypodiploidy integrating targeted fluorescence in situ hybridization (FISH) analysis directed towards identifying monosomies of chromosomes 7, 15 and 17 and flow cytometry-based ploidy analysis (FCPA). Of 445 patients diagnosed as BCP ALL, 2.9% (13/445) were classified as hypodiploid including patients with masked hypodiploidy. Karyotype analysis showed hypodiploidy in 3 patients, near triploidy in 4 patients and normal karyotype in 6 patients. Four patients with near triploid clone on karyotype showed either bimodal peak (2 patients) or single low hypodiploid peak (1 patient) or only near triploid peak (1 patient) on FCPA. All 6 patients with normal karyotype revealed either bimodal peak (4 patients) or hypodiploid peak (2 patients) on FCPA. Targeted FISH analysis unmasked hypodiploid clone showing monosomies of chromosomes 7, 15 and 17 in all ten patients. Our algorithm successfully identified masked hypodiploidy in patients, including those with endoreduplication (4 patients) and normal karyotype (6 patients). Integrating FCPA with targeted FISH analysis provides a practical, sensitive and specific approach to identify masked hypodiploidy in low resource settings.
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Bommannan K, Arumugam JR, Koshy T, Radhakrishnan V, Sagar TG, Sundersingh S. Blast size-specific flowcytometric ploidy assessment using FxCycle TM Violet dye and its correlation with conventional cytogenetic ploidy in pediatric precursor B-lineage acute lymphoblastic leukemia patients. Int J Lab Hematol 2020; 43:760-770. [PMID: 33345449 DOI: 10.1111/ijlh.13436] [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: 07/28/2020] [Revised: 10/20/2020] [Accepted: 11/28/2020] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Numerical chromosomal abnormalities (aneuploidies), present in approximately 30%-50% of pediatric precursor B-lineage acute lymphoblastic leukemia (B-ALL) patients, are commonly identified through a laborious conventional cytogenetic (CG) technique. Flow cytometry (FCM) can identify both physical and fluorescent properties of cells together, and by using fluorescent nucleic-acid-binding dyes, FCM can identify variations in total nucleic-acid content of cells. FxCycleTM Violet dye (FxCV) is a selective DNA-binding dye which permits simultaneous multiparametric immunophenotyping and cell-cycle/ploidy assessment in a single assay. To date, only two studies have demonstrated the feasibility of FxCV-aided FCM-ploidy analysis in B-ALL patients and only one of these studies have compared their results with CG-ploidy. METHODOLOGY Blast size-specific FCM-ploidy was prospectively analyzed using FxCV-dye in 109 pediatric B-ALL patients, and the results were compared with concurrent CG-ploidy status. RESULTS FCM-ploidy categorization was feasible in 98% of samples tested and the results were 82% concordant with CG-ploidy status. We observed significant correlation between DNA content and blast size (r = .823, P < .001) and could demonstrate size differences between diploid vs low-hyperdiploid (P = .025), diploid vs high-hyperdiploid (P < .001) and low- vs high-hyperdiploid blasts (P = .007). CONCLUSION FCM-ploidy assessment using FxCV dye is a reliable assay and the results closely concur with CG-based ploidy stratification and risk assessment. Using blast size-assisted DNA content analysis, the results of FCM-ploidy analysis can be further fine-tuned.
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Affiliation(s)
- Karthik Bommannan
- Department of Oncopathology, Cancer Institute (W.I.A.), Chennai, India
| | | | - Teena Koshy
- Department of Oncopathology, Cancer Institute (W.I.A.), Chennai, India
| | | | - Tenali Gnana Sagar
- Department of Medical Oncology, Cancer Institute (W.I.A.), Chennai, India
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Wan TSK, Hui EKC, Ng MHL. Significance of Cytogenetics in Leukemia Diagnostics. CURRENT GENETIC MEDICINE REPORTS 2018. [DOI: 10.1007/s40142-018-0147-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Comeaux EQ, Mullighan CG. TP53 Mutations in Hypodiploid Acute Lymphoblastic Leukemia. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026286. [PMID: 28003275 DOI: 10.1101/cshperspect.a026286] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Acute lymphoblastic leukemia (ALL) is an aggressive neoplasm of B- or T-lymphoid progenitors and is the commonest childhood tumor. ALL comprises multiple subtypes characterized by distinct genetic alterations, with stereotyped patterns of aneuploidy present in many cases. Although alterations of TP53 are common in many tumors, they are infrequent in ALL, with the exception of two ALL subtypes associated with poor outcome: relapsed disease and ALL with hypodiploidy. TP53 alterations are present in almost all cases of ALL with low hypodiploidy and are associated with alterations of the lymphoid transcription factor IKZF2 and the tumor-suppressor gene loci CDKN2A and CDKN2B. Remarkably, more than half of TP53 mutations in low-hypodiploid ALL in children are present in nontumor cells, indicating that low-hypodiploid ALL is a manifestation of Li-Fraumeni syndrome. These findings have profound implications for our understanding of the genetic pathogenesis of hypodiploid ALL, suggesting that alteration of TP53 function may promote the distinctive aneuploidy characteristic of hypodiploid ALL. Moreover, the identification of hypodiploidy mandates offering testing for TP53 mutational status to patients and their relatives, with appropriate counseling and disease surveillance.
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Affiliation(s)
- Evan Q Comeaux
- Departments of Pathology and the Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Charles G Mullighan
- Departments of Pathology and the Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
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9
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Near-haploid and low-hypodiploid acute lymphoblastic leukemia: two distinct subtypes with consistently poor prognosis. Blood 2016; 129:420-423. [PMID: 27903530 DOI: 10.1182/blood-2016-10-743765] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/22/2016] [Indexed: 11/20/2022] Open
Abstract
Hypodiploidy <40 chromosomes is an uncommon genetic feature of acute lymphoblastic leukemia (ALL) in both children and adults. It has long been clear by cytogenetic analyses, and recently confirmed by mutational profiling, that these cases may be further subdivided into 2 subtypes: near-haploid ALL with 24 to 30 chromosomes and low-hypodiploid ALL with 31 to 39 chromosomes. Both groups are associated with a very poor prognosis, and these patients are among those who could benefit most from novel treatments.
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10
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Fang M, Becker PS, Linenberger M, Eaton KD, Appelbaum FR, Dreyer Z, Airewele G, Redell M, Lopez-Terrada D, Patel A, Rabin KR, Lu X. Adult Low-Hypodiploid Acute B-Lymphoblastic Leukemia With IKZF3 Deletion and TP53 Mutation: Comparison With Pediatric Patients. Am J Clin Pathol 2015; 144:263-70. [PMID: 26185311 DOI: 10.1309/ajcpw83oxpykpeen] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
OBJECTIVES Chromosomal ploidy is a major risk stratification tool for acute B-cell lymphoblastic leukemia (B-ALL). Low hypodiploidy and near-haploidy are thought to be confined to pediatric B-ALL and associated with a poor prognosis. Doubling of either a low-hypodiploid or a near-haploid clone results in an apparently high-hyperdiploid karyotype, which is often misclassified for risk. METHODS We studied four patients with B-ALL who had chromosome genomic array testing (CGAT), along with fluorescence in situ hybridization and mutation testing. RESULTS We identified a unique case of adult B-ALL with masked low hypodiploidy (mLH) by genomic duplication, along with a somatic deletion of the IKZF3 gene and a somatic TP53 mutation. Three cases of pediatric B-ALL with mLH, two with TP53 mutations and one untested, were also identified and compared with the adult patient. CONCLUSIONS CGAT was critical in the genotype clarification of these cases through detection of copy-neutral loss of heterozygosity and should be considered performing for B-ALL with apparent hyperdiploidy for accurate prognostic risk stratification and treatment planning.
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Abstract
Most animal genomes are diploid, and mammalian development depends on specific adaptations that have evolved secondary to diploidy. Genomic imprinting and dosage compensation restrict haploid development to early embryos. Recently, haploid mammalian development has been reinvestigated since the establishment of haploid embryonic stem cells (ESCs) from mouse embryos. Haploid cells possess one copy of each gene, facilitating the generation of loss-of-function mutations in a single step. Recessive mutations can then be assessed in forward genetic screens. Applications of haploid mammalian cell systems in screens have been illustrated in several recent publications. Haploid ESCs are characterized by a wide developmental potential and can contribute to chimeric embryos and mice. Different strategies for introducing genetic modifications from haploid ESCs into the mouse germline have been further developed. Haploid ESCs therefore introduce new possibilities in mammalian genetics and could offer an unprecedented tool for genome exploration in the future.
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Affiliation(s)
- Anton Wutz
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zürich, Hönggerberg, 8049 Zürich, Switzerland;
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12
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Near-haploid B lymphoblastic leukemia with an apparent hyperdiploid karyotype: the critical role of SNP analysis in establishing proper diagnosis. J Hematop 2013. [DOI: 10.1007/s12308-013-0189-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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13
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Chen C, Bartenhagen C, Gombert M, Okpanyi V, Binder V, Röttgers S, Bradtke J, Teigler-Schlegel A, Harbott J, Ginzel S, Thiele R, Fischer U, Dugas M, Hu J, Borkhardt A. Next-generation-sequencing-based risk stratification and identification of new genes involved in structural and sequence variations in near haploid lymphoblastic leukemia. Genes Chromosomes Cancer 2013; 52:564-79. [DOI: 10.1002/gcc.22054] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/29/2013] [Indexed: 01/10/2023] Open
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Safavi S, Forestier E, Golovleva I, Barbany G, Nord KH, Moorman AV, Harrison CJ, Johansson B, Paulsson K. Loss of chromosomes is the primary event in near-haploid and low-hypodiploid acute lymphoblastic leukemia. Leukemia 2012; 27:248-50. [PMID: 22889820 DOI: 10.1038/leu.2012.227] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Braoudaki M, Tzortzatou-Stathopoulou F. Clinical Cytogenetics in Pediatric Acute Leukemia: An Update. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2012; 12:230-7. [DOI: 10.1016/j.clml.2012.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 12/25/2011] [Accepted: 04/13/2012] [Indexed: 12/28/2022]
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Sukov WR, Ketterling RP, Wei S, Monaghan K, Blunden P, Mazzara P, Raghavan R, Oliviera AM, Wiktor AE, Keeney GL, Van Dyke DL. Nearly identical near-haploid karyotype in a peritoneal mesothelioma and a retroperitoneal malignant peripheral nerve sheath tumor. ACTA ACUST UNITED AC 2010; 202:123-8. [PMID: 20875874 DOI: 10.1016/j.cancergencyto.2010.07.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Revised: 07/01/2010] [Accepted: 07/02/2010] [Indexed: 01/02/2023]
Abstract
The presence of a near-haploid karyotype is a rare finding in human malignancies, most frequently occurring in acute leukemia. In solid tumors, a near-haploid karyotype has been reported in fewer than 40 cases. We report two nearly identical near-haploid karyotypes from two distinctly different tumor types. The first case is a biphasic malignant mesothelioma from a 53-year-old white woman forming a large retroperitoneal mass. Cytogenetic evaluation revealed a primary hyperdiploid cell population as well as near-haploid and hypertetraploid populations with an overall karyotype of 27,XX,i(5)(p10),+7,add(15)(p11.2),+dic(1;20)(p13;p13)[2]/54,idemx2[90]/101-108,idemx4[19]. The second case is a large pelvic mass from a 48-year-old man. Histologic examination identified a malignant peripheral nerve sheath tumor displaying a karyotype of 26,X,+i(5)(p10),+7,der(15)t(1;15)(q12;p12),+20[5]/52,idemx2[20]. Herein we discuss the potential relationship between these two disparate neoplasms with nearly identical near-haploid karyotypes and present a literature review.
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Affiliation(s)
- William R Sukov
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
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Paulsson K, Johansson B. High hyperdiploid childhood acute lymphoblastic leukemia. Genes Chromosomes Cancer 2009; 48:637-60. [PMID: 19415723 DOI: 10.1002/gcc.20671] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
High hyperdiploidy (51-67 chromosomes) is the most common cytogenetic abnormality pattern in childhood B-cell precursor acute lymphoblastic leukemia (ALL), occurring in 25-30% of such cases. High hyperdiploid ALL is characterized cytogenetically by a nonrandom gain of chromosomes X, 4, 6, 10, 14, 17, 18, and 21 and clinically by a favorable prognosis. Despite the high frequency of this karyotypic subgroup, many questions remain regarding the epidemiology, etiology, presence of other genetic changes, the time and cell of origin, and the formation and pathogenetic consequences of high hyperdiploidy. However, during the last few years, several studies have addressed some of these important issues, and these, as well as previous reports on high hyperdiploid childhood ALL, are reviewed herein.
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Affiliation(s)
- Kajsa Paulsson
- Department of Clinical Genetics, Lund University Hospital, Lund, Sweden.
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Sunil SK, Prakash PN, Hariharan S, Vinod G, Preethi RT, Geetha N, Ankathil R. Adult acute lymphoblastic leukemia with near haploidy, hyperdiploidy and Ph positive lines: a rare entity with poor prognosis. Leuk Lymphoma 2006; 47:561-3. [PMID: 16396782 DOI: 10.1080/10428190500361094] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Chromosomal ploidies provide a wealth of information with respect to the prognosis of patients with acute lymphoblastic leukemia (ALL). The prognosis is favourable in hyperdiploidy (>50 ALL), whereas pseudodiploidy and hypodiploidy have an overall poor clinical outcome. Near haploid ALL with less than 30 chromosomes in the leukemic blasts has been reported. This is an extremely rare malignancy with an adverse clinical course compared to other lymphoblastic leukemias. We present a case of near haploid ALL in an adult male with a diagnosis of pre-B-cell ALL. The presenting features and relevance to the progression of disease are discussed with respect to the near haploid lines. Occurrence in an adult male and the presence of additional clones with structural abnormalities are both unique to the present study. Caution must be exercised when the hyperdiploid metaphases consists exclusively of tetrasomic chromosomes and morphological examination reveals definite dual populations of large and small lymphoblasts. Despite current developments in ALL therapy, near haploid ALL continues to be a disease with an adverse clinical outcome and newer therapeutic strategies are warranted for better management of the disease.
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Affiliation(s)
- Sidharthan K Sunil
- Divisions of Cancer Research, Regional Cancer Centre, Medical College Campus, Trivandrum, Kerala, India
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Harrison CJ, Moorman AV, Broadfield ZJ, Cheung KL, Harris RL, Reza Jalali G, Robinson HM, Barber KE, Richards SM, Mitchell CD, Eden TOB, Hann IM, Hill FGH, Kinsey SE, Gibson BES, Lilleyman J, Vora A, Goldstone AH, Franklin IM, Durrant J, Martineau M. Three distinct subgroups of hypodiploidy in acute lymphoblastic leukaemia. Br J Haematol 2004; 125:552-9. [PMID: 15147369 DOI: 10.1111/j.1365-2141.2004.04948.x] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This study of children and adults with acute lymphoblastic leukaemia (ALL) is the largest series of patients with hypodiploidy (<46 chromosomes) yet reported. The incidence of 5% was independent of age. Patients were subdivided by the number of chromosomes; near-haploidy (23-29 chromosomes), low hypodiploidy (33-39 chromosomes) and high hypodiploidy (42-45 chromosomes). The near-haploid and low hypodiploid groups were characterized by their chromosomal gains and a doubled hyperdiploid population. Structural abnormalities were more frequent in the low hypodiploid group. Near-haploidy was restricted to children of median age 7 years (range 2-15) whereas low hypodiploidy occurred in an older group of median age 15 years (range 9-54). Patients with 42-45 chromosomes were characterized by complex karyotypes involving chromosomes 7, 9 and 12. The features shared by the few patients with 42-44 chromosomes and the large number with 45 justified their inclusion in the same group. Survival analysis showed a poor outcome for the near-haploid and low hypodiploid groups compared to those with 42-45 chromosomes. Thus cytogenetics, or at least a clear definition of the modal chromosome number, is essential at diagnosis in order to stratify patients with hypodiploidy into the appropriate risk group for treatment.
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Affiliation(s)
- Christine J Harrison
- Leukaemia Research Fund Cytogenetics Group, Cancer Sciences Division, University of Southampton, Southampton, UK.
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Shiras A, Bhosale A, Shepal V, Shukla R, Baburao VS, Prabhakara K, Shastry P. A unique model system for tumor progression in GBM comprising two developed human neuro-epithelial cell lines with differential transforming potential and coexpressing neuronal and glial markers. Neoplasia 2004; 5:520-32. [PMID: 14965445 PMCID: PMC1502577 DOI: 10.1016/s1476-5586(03)80036-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The molecular mechanisms involved in tumor progression from a low-grade astrocytoma to the most malignant glioblastoma multiforme (GBM) have been hampered due to lack of suitable experimental models. We have established a model of tumor progression comprising of two cell lines derived from the same astrocytoma tumor with a set of features corresponding to low-grade glioma (as in HNGC-1) and high-grade GBM (as in HNGC-2). The HNGC-1 cell line is slow-growing, contact-inhibited, nontumorigenic, and noninvasive, whereas HNGC-2 is a rapidly proliferating, anchorage-independent, highly tumorigenic, and invasive cell line. The proliferation of cell lines is independent of the addition of exogenous growth factors. Interestingly, the HNGC-2 cell line displays a near-haploid karyotype except for a disomy of chromosome 2. The two cell lines express the neuronal precursor and progenitor markers vimentin, nestin, MAP-2, and NFP160, as well as glial differentiation protein S100beta. The HNGC-1 cell line also expresses markers of mature neurons like Tuj1 and GFAP, an astrocytic differentiation marker, hence contributing toward a more morphologically differentiated phenotype with a propensity for neural differentiation in vitro. Additionally, overexpression of epidermal growth factor receptor and c-erbB2, and loss of fibronectin were observed only in the HNGC-2 cell line, implicating the significance of these pathways in tumor progression. This in vitro model system assumes importance in unraveling the cellular and molecular mechanisms in differentiation, transformation, and gliomagenesis.
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Affiliation(s)
- Anjali Shiras
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, Pune, India.
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Raimondi SC, Zhou Y, Mathew S, Shurtleff SA, Sandlund JT, Rivera GK, Behm FG, Pui CH. Reassessment of the prognostic significance of hypodiploidy in pediatric patients with acute lymphoblastic leukemia. Cancer 2004; 98:2715-22. [PMID: 14669294 DOI: 10.1002/cncr.11841] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND The purpose of the current study was to evaluate the cytogenetic features of the hypodiploid leukemic cells of pediatric patients with this rare subgroup of acute lymphoblastic leukemia (ALL). In addition, the authors determined whether subdivision of the hypodiploid category served a prognostic purpose for these patients. METHODS The authors evaluated the cytogenetic records of 979 patients with ALL admitted to St. Jude Children's Research Hospital (Memphis, TN) between 1984 and 1999. RESULTS Of 67 patients (6.8%) whose leukemic cells contained a modal number (MN) of chromosomes less than or equal to 45 (i.e., hypodiploid leukemic cells), 57 had an MN of 45 and 10 had an MN of less than 45. In 19 patients, cells with an MN of 45 had a whole chromosome missing (42%), which was a sex chromosome in 12 patients (63%). Leukemic cells with an MN of 45 contained dicentric chromosomes (n = 33) formed from chromosome 9p (55%), 12p (18%), or both (21%). The ETV6-CBFA2 fusion was present in 39% of 28 evaluable B-lineage cases with an MN of 45. The event-free survival rate (EFS) for patients with hypodiploid leukemic cells of MN less than 45 (5-year EFS = 20.0% +/- 10.3%) was significantly (P < 0.001) lower than that for patients with leukemic cells of MN greater than or equal to 45 (5-year EFS = 74.9% +/- 1.6%). CONCLUSIONS Low hypodiploidy (MN < 45) should be recognized as a high-risk feature in pediatric ALL. Only two hypodiploid groups (MN < 45 and MN = 45) may be necessary in prognostic assessments.
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Affiliation(s)
- Susana C Raimondi
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105-2794, USA.
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Mukherjee S, Das Gupta A, Khodaiji S, Agarwal MB. Near-haploidy in myeloid antigen positive childhood acute lymphoblastic leukemia. Am J Hematol 2001; 67:276-7. [PMID: 11443648 DOI: 10.1002/ajh.1135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Stark B, Jeison M, Gobuzov R, Krug H, Glaser-Gabay L, Luria D, El-Hasid R, Harush MB, Avrahami G, Fisher S, Stein J, Zaizov R, Yaniv I. Near haploid childhood acute lymphoblastic leukemia masked by hyperdiploid line: detection by fluorescence in situ hybridization. CANCER GENETICS AND CYTOGENETICS 2001; 128:108-13. [PMID: 11463448 DOI: 10.1016/s0165-4608(01)00411-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Near-haploid (<30 chromosomes) acute lymphoblastic leukemia (ALL) is a rare and unique subgroup of childhood common ALL associated with a very poor outcome. It may be underdiagnosed when masked by a co-existing hyperdiploid line, which has to be distinguished from the common good-prognostic hyperdiploid (>50 chromosomes) ALL. We present three children in whom, by conventional cytogenetics, near-haploid ALL was detected on relapse. Using interphase FISH probes of chromosomes X, Y, 4, 12, and 21, we were able, in two cases, to trace the hidden near-haploid lines of approximately 5% and 20% of the cells, masked by hyperdiploid cells of approximately 80% and 70%, respectively; at relapse, the proportion was reversed, with predominant near-haploid lines of over 80% and residual hyperdiploidy of less than 10%. The near-haploid lines consisted of 24 and 27 chromosomes, and always retained the second copy of chromosome 21 or its derivative, as detected in one of our patients by SKY. The hyperdiploid clones were the exact duplicates of the near-haploid ones and contained four and two copies of the chromosomes represented in two and one copies in the near-haploid stem line, respectively. Unlike the common hyperdiploid ALL, no trisomies were observed. The patients were all aged >10 years, with WBC 0.7-30 x 10(9)/L, and a common ALL phenotype. They were treated with the ALL-BFM-95 protocol, medium risk group, and responded well to 8 days of steroid therapy, but relapsed early, within 11 months, and died a few months later. Interphase FISH technique is recommended for the detection of cryptic near-haploid clones in the diagnostic survey of ALL. To assess the prognostic value of near-haploidy in the context of the ALL-BFM protocols, a larger cohort of patients is required.
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Affiliation(s)
- B Stark
- Cancer Cytogenetic Laboratory, Schneider Children's Medical Center of Israel, Petah Tiqva, Israel.
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Pérez-Vera P, Mújica-Sánchez M, Carnevale A, Rivera-Luna R, Paredes R, Martínez A, Frías S. Cytogenetics in acute lymphoblastic leukemia in Mexican children: an institutional experience. Arch Med Res 2001; 32:202-7. [PMID: 11395185 DOI: 10.1016/s0188-4409(01)00260-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Cytogenetic studies in acute lymphoblastic leukemia (ALL) have identified numerical and structural chromosomal abnormalities related to the disease's pathophysiologic characteristics. These findings correlate with prognosis and response to treatment in ALL patients. The purpose of this study was to define the frequency of chromosomal abnormalities in a group of Mexican children with ALL and to compare these data with those reported in the literature. METHODS Bone marrow chromosome studies with GTG bands were performed in 150 pediatric patients with ALL who were naive to antileukemic treatment and aged from 5 months to 16 years; the majority was diagnosed as L1. RESULTS Among 131 patients, 30 (22.9%) karyotypes were normal and the remaining 101 (77.1%) had abnormal karyotypes with numerical and/or structural abnormalities. Among patients with numerical abnormalities, the most frequent karyotypes were hyperdiploidy with 51-65 chromosomes (30 patients) and hyperdiploidy with 47-50 chromosomes (18 patients). Among recurrent, non-random, and primary structural abnormalities, the most frequent was t(9;22), followed by t(1;19). Aberrations involving band 11q23 were not detected, and only one of two patients with L3 had the t(8;14). Of the secondary non-random abnormalities, dup(1q), del(6q), and i(7)(q10) were found. CONCLUSIONS The frequency and type of chromosomal abnormalities found was comparable to those reported in the literature with similar methodology and pediatric populations; however, the number of cases analyzed should be increased to create a database of Mexican children with ALL, and several patients require molecular analysis to identify chromosomal abnormalities not detected through conventional cytogenetic studies.
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Affiliation(s)
- P Pérez-Vera
- Departamento de Investigación en Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico
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Abstract
Childhood leukemia is the commonest form of childhood cancer and represents clonal proliferation of transformed hemopoietic cells as a result of genetic changes. Molecular characterization of these changes, in particular chromosomal translocations, has yielded a wealth of information on the mechanisms of leukemogenesis. These findings have also allowed the development of sensitive assays for the identification of underlying molecular defects, which is applicable to disease diagnosis and to monitor response to treatment. Genetic alterations in childhood leukemia are powerful prognostic indicators. TEL-AML1 fusion and hyperdiploidy >50 chromosomes are associated with a good prognosis in childhood acute lymphoblastic leukemia, whereas BCR-ABL fusion and MLL rearrangements are associated with a poor prognosis. Hence cytogenetic and molecular genetic classification of childhood leukemia will significantly improve the ability of clinicians to predict therapeutic response and prognosis, which paves the way for risk stratification based on clinical and genetic features. Finally, deciphering of genetic lesions in leukemia has allowed elucidation of the molecular basis of current treatment, as typified by the success of all-trans retinoic treatment in acute promyelocytic leukemia, and has identified targets for novel therapeutic approaches. It is envisaged that efforts in characterization of molecular defects in childhood leukemia will ultimately be translated into better clinical outcome for patients.
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Affiliation(s)
- S K Ma
- Hematology Section, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Hong Kong
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