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Antić Ž, Lentes J, Bergmann AK. Cytogenetics and genomics in pediatric acute lymphoblastic leukaemia. Best Pract Res Clin Haematol 2023; 36:101511. [PMID: 38092485 DOI: 10.1016/j.beha.2023.101511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/24/2023] [Accepted: 08/15/2023] [Indexed: 12/18/2023]
Abstract
The last five decades have witnessed significant improvement in diagnostics, treatment and management of children with acute lymphoblastic leukaemia (ALL). These advancements have become possible through progress in our understanding of the genetic and biological background of ALL, resulting in the introduction of risk-adapted treatment and novel therapeutic targets, e.g., tyrosine kinase inhibitors for BCR::ABL1-positive ALL. Further advances in the taxonomy of ALL and the discovery of new genetic biomarkers and therapeutic targets, as well as the introduction of targeted and immunotherapies into the frontline treatment protocols, may improve management and outcome of children with ALL. In this review we describe the current developments in the (cyto)genetic diagnostics and management of children with ALL, and provide an overview of the most important advances in the genetic classification of ALL. Furthermore, we discuss perspectives resulting from the development of new techniques, including artificial intelligence (AI).
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Affiliation(s)
- Željko Antić
- Department of Human Genetics, Hannover Medical School (MHH), Hannover, Germany
| | - Jana Lentes
- Department of Human Genetics, Hannover Medical School (MHH), Hannover, Germany
| | - Anke K Bergmann
- Department of Human Genetics, Hannover Medical School (MHH), Hannover, Germany.
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2
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Li C, Chen L, Pan G, Zhang W, Li SC. Deciphering complex breakage-fusion-bridge genome rearrangements with Ambigram. Nat Commun 2023; 14:5528. [PMID: 37684230 PMCID: PMC10491683 DOI: 10.1038/s41467-023-41259-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Breakage-fusion-bridge (BFB) is a complex rearrangement that leads to tumor malignancy. Existing models for detecting BFBs rely on the ideal BFB hypothesis, ruling out the possibility of BFBs entangled with other structural variations, that is, complex BFBs. We propose an algorithm Ambigram to identify complex BFB and reconstruct the rearranged structure of the local genome during the cancer subclone evolution process. Ambigram handles data from short, linked, long, and single-cell sequences, and optical mapping technologies. Ambigram successfully deciphers the gold- or silver-standard complex BFBs against the state-of-the-art in multiple cancers. Ambigram dissects the intratumor heterogeneity of complex BFB events with single-cell reads from melanoma and gastric cancer. Furthermore, applying Ambigram to liver and cervical cancer data suggests that the BFB mechanism may mediate oncovirus integrations. BFB also exists in noncancer genomics. Investigating the complete human genome reference with Ambigram suggests that the BFB mechanism may be involved in two genome reorganizations of Homo Sapiens during evolution. Moreover, Ambigram discovers the signals of recurrent foldback inversions and complex BFBs in whole genome data from the 1000 genome project, and congenital heart diseases, respectively.
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Affiliation(s)
- Chaohui Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Lingxi Chen
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Guangze Pan
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Wenqian Zhang
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, China.
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3
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Hormann FM, Hoogkamer AQ, Boeree A, Sonneveld E, Escherich G, den Boer ML, Boer JM. Integrating copy number data of 64 iAMP21 BCP-ALL patients narrows the common region of amplification to 1.57 Mb. Front Oncol 2023; 13:1128560. [PMID: 36910655 PMCID: PMC9996016 DOI: 10.3389/fonc.2023.1128560] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/10/2023] [Indexed: 02/25/2023] Open
Abstract
Background and purpose Intrachromosomal amplification of chromosome 21 (iAMP21) is a rare subtype of B-cell precursor acute lymphoblastic leukaemia (BCP-ALL). It is unknown how iAMP21 contributes to leukaemia. The currently known commonly amplified region is 5.1 Mb. Methods We aimed to narrow down the common region of amplification by using high resolution techniques. Array comparative genomic hybridization (aCGH) was used to determine copy number aberrations, Affymetrix U133 Plus2 expression arrays were used to determine gene expression. Genome-wide expression correlations were evaluated using Globaltest. Results We narrowed down the common region of amplification by combining copy number data from 12 iAMP21 cases with 52 cases from literature. The combined common region of amplification was 1.57 Mb, located from 36.07 to 37.64 Mb (GRCh38). This region is located telomeric from, but not including, RUNX1, which is the locus commonly used to diagnose iAMP21. This narrow region, which falls inside the Down Syndrome critical region, includes 13 genes of which the expression of eight genes was significantly upregulated compared with 143 non-iAMP21 B-other cases. Among these, transcriptional repressor RIPPLY3 (also known as DSCR6) was the highest overexpressed gene (fold change = 4.2, FDR < 0.001) and most strongly correlated (R = 0.58) with iAMP21-related genome-wide expression changes. Discussion The more precise definition of the common region of amplification could be beneficial in the diagnosis of iAMP21 based on copy number analysis from DNA sequencing or arrays as well as stimulate functional research into the role of the included genes in iAMP21 biology.
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Affiliation(s)
- Femke M Hormann
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands.,Oncode Institute, Utrecht, Netherlands.,Erasmus Medical Center (MC) - Sophia Children's Hospital, Department of Pediatric Oncology and Hematology, Rotterdam, Netherlands
| | - Alex Q Hoogkamer
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands.,Oncode Institute, Utrecht, Netherlands
| | - Aurélie Boeree
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands.,Oncode Institute, Utrecht, Netherlands
| | - Edwin Sonneveld
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands.,Dutch Childhood Oncology Group, Utrecht, Netherlands
| | - Gabriele Escherich
- Cooperative study group for childhood acute lymphoblastic leukaemia (COALL) - German Cooperative Study Group for Childhood Acute Lymphoblastic Leukemia, Hamburg, Germany.,Clinic of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Monique L den Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands.,Oncode Institute, Utrecht, Netherlands.,Erasmus Medical Center (MC) - Sophia Children's Hospital, Department of Pediatric Oncology and Hematology, Rotterdam, Netherlands.,Dutch Childhood Oncology Group, Utrecht, Netherlands
| | - Judith M Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands.,Oncode Institute, Utrecht, Netherlands
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4
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Koleilat A, Smadbeck JB, Zepeda‐Mendoza CJ, Williamson CM, Pitel BA, Golden CL, Xu X, Greipp PT, Ketterling RP, Hoppman NL, Peterson JF, Harrison CJ, Akkari YMN, Tsuchiya KD, Shago M, Baughn LB. Characterization of unusual iAMP21 B-lymphoblastic leukemia (iAMP21-ALL) from the Mayo Clinic and Children's Oncology Group. Genes Chromosomes Cancer 2022; 61:710-719. [PMID: 35771717 PMCID: PMC9549522 DOI: 10.1002/gcc.23084] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/06/2022] [Accepted: 06/27/2022] [Indexed: 01/01/2023] Open
Abstract
Acute lymphoblastic leukemia (B-ALL) with intrachromosomal amplification of chromosome 21 (iAMP21-ALL) represents a recurrent high-risk cytogenetic abnormality and accurate identification is critical for appropriate clinical management. Identification of iAMP21-ALL has historically relied on fluorescence in situ hybridization (FISH) using a RUNX1 probe. Current classification requires ≥ five copies of RUNX1 per cell and ≥ three additional copies of RUNX1 on a single abnormal iAMP21-chromosome. We sought to evaluate the performance of the RUNX1 probe in the identification of iAMP21-ALL. This study was a retrospective evaluation of iAMP21-ALL in the Mayo Clinic and Children's Oncology Group cohorts. Of 207 cases of iAMP21-ALL, 188 (91%) were classified as "typical" iAMP21-ALL, while 19 (9%) cases were classified as "unusual" iAMP21-ALL. The "unusual" iAMP21 cases did not meet the current definition of iAMP21 by FISH but were confirmed to have iAMP21 by chromosomal microarray. Half of the "unusual" iAMP21-ALL cases had less than five RUNX1 signals, while the remainder had ≥ five RUNX1 signals with some located apart from the abnormal iAMP21-chromosome. Nine percent of iAMP21-ALL cases fail to meet the FISH definition of iAMP21-ALL demonstrating that laboratories are at risk of misidentification of iAMP21-ALL when relying only on the RUNX1 FISH probe. Incorporation of chromosomal microarray testing circumvents these risks.
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Affiliation(s)
- Alaa Koleilat
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - James B. Smadbeck
- Division of Computational Biology, Department of Quantitative Health SciencesMayo ClinicRochesterMinnesotaUSA
| | | | - Cynthia M. Williamson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Beth A. Pitel
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Crystal L. Golden
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Xinjie Xu
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Patricia T. Greipp
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Rhett P. Ketterling
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Nicole L. Hoppman
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Jess F. Peterson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Christine J. Harrison
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research InstituteNewcastle University Centre for CancerNewcastle‐upon‐TyneUK
| | | | - Karen D. Tsuchiya
- Department of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWAUSA
| | - Mary Shago
- Department of Paediatric Laboratory Medicine, The Hospital for Sick ChildrenUniversity of TorontoTorontoOntarioCanada
| | - Linda B. Baughn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
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5
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Capela de Matos RR, Othman M, Ferreira GM, Monteso K, de Souza MT, Rouxinol M, Melo JB, Carreira IM, Abdelhay E, Liehr T, Ribeiro RC, Silva M. Somatic homozygous loss of SH2B3, and a non-Robertsonian translocation t(15;21)(q25.3;q22.1) with NTRK3 rearrangement, in an adolescent with progenitor B-cell acute lymphoblastic leukemia with the iAMP21. Cancer Genet 2021; 262-263:16-22. [PMID: 34974289 DOI: 10.1016/j.cancergen.2021.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 11/04/2021] [Accepted: 12/20/2021] [Indexed: 11/18/2022]
Abstract
Intrachromosomal amplification of chromosome 21 (iAMP21) occurs in ∼2% of B-cell acute lymphoblastic leukemia (ALL) and is considered to confer a poor prognosis. The relapse risk is associated with therapy intensity, suggesting that other somatic mutations may influence iAMP21-ALL prognosis. This abnormality is characterized by multiple copies of the RUNX1 gene in chromosome 21 and appears to arise through multiple breakage-fusion bridge cycles and chromothripsis. Rob(15;21) or a ring chromosome 21 have been associated with an increased risk for iAMP21-ALL, suggesting that constitutional genetic abnormalities may also drive leukemogenesis. Here we describe homozygous deletion of the SH2B3 gene, chromothripsis of chromosome 21, and a non-Robertsonian somatic t(15;21)(q25.3;q22.1) with NTRK3 gene rearrangement in an adolescent with iAMP21-B-ALL. Molecular cytogenetic studies detected iAMP21 with aCGH analysis revealing further genomic imbalances. The RT-qPCR analysis detected elevated expression levels of RUNX1 (68-fold) and reduced expression of CDK6 (0.057-fold). Studies with constitutive cells collected from mouth swabs showed that SH2B3 biallelic deletion was a somatic alteration occurring during clonal evolution. The identification of novel secondary genetic changes was valuable to discuss sporadic iAMP21 leukemogenic mechanisms. For the first time, we show a t(15;21)(q25.3;q22.1) with NTRK3 rearrangement in an adolescent with iAMP21-ALL.
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Affiliation(s)
- R R Capela de Matos
- Cytogenetics Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil; Post-Graduate Programme in Oncology, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil
| | - Mak Othman
- Jena University Hospital, Institute of Human Genetics, Jena, Germany
| | - G M Ferreira
- Stem Cells Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil
| | - Kca Monteso
- Cytogenetics Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil; Post-Graduate Programme in Oncology, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil
| | - M T de Souza
- Cytogenetics Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil
| | - M Rouxinol
- Lagoa Federal Hospital, Rio de Janeiro, Brazil
| | - J B Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal; Centre of Investigation on Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - I M Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal; Centre of Investigation on Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - E Abdelhay
- Stem Cells Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil; Post-Graduate Programme in Oncology, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil
| | - T Liehr
- Jena University Hospital, Institute of Human Genetics, Jena, Germany
| | - R C Ribeiro
- Departments of Oncology and Global Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mlm Silva
- Cytogenetics Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil; Post-Graduate Programme in Oncology, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil.
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6
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Jain H, Shetty D, Roy Moulik N, Narula G, Subramanian PG, Banavali S. A novel case of intrachromosomal amplification and insertion of RUNX1 on derivative chromosome 2 in pediatric AML. Cancer Genet 2021; 254-255:65-69. [PMID: 33647813 DOI: 10.1016/j.cancergen.2021.02.004] [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: 10/21/2020] [Revised: 01/15/2021] [Accepted: 02/08/2021] [Indexed: 11/18/2022]
Abstract
Intrachromosomal amplification of RUNX1 gene on chromosome 21 (iAMP21) is a rare occurrence in acute myeloid leukemia (AML). Herein, we describe a case of AML with amplification of RUNX1 and its insertion on chromosome 2 detected by conventional karyotyping and confirmed by metaphase FISH. A six-year-old female was diagnosed as acute myeloid leukemia with monocytic differentiation. The patient's bone marrow revealed 74% blasts which were MPO negative. Conventional karyotyping revealed a complex karyotype, with rearrangements in chromosomes 1, 2, 7, 8 and hsr(21). FISH on interphase cells with LSI RUNX1-RUNX1T1 dual colour dual fusion translocation probe showed 6-7 copies of RUNX1 signal. Metaphase FISH with LSI RUNX1-RUNX1T1 probe confirmed amplification of RUNX1 and insertion of amplified RUNX1 sequences on long arm of chromosome 2. Induction chemotherapy was initiated, however, the patient died within one month of diagnosis suggesting poor outcome associated with this novel finding. Insertion of amplified RUNX1 on another chromosome has not yet been reported so far.
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Affiliation(s)
- Hemani Jain
- Cancer Cytogenetics Department, Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Sector-22, Kharghar, Navi Mumbai 410210, India.
| | - Dhanlaxmi Shetty
- Cancer Cytogenetics Department, Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Sector-22, Kharghar, Navi Mumbai 410210, India.
| | - Nirmalya Roy Moulik
- Department of Pediatric Oncology, Tata Memorial Hospital, Dr. E. Borges Road, Parel. Mumbai 400012, India; Cancer Cytogenetics Department, Room No. 6, CCE building, Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Sector-22, Kharghar, Navi Mumbai 410210 India.
| | - Gaurav Narula
- Department of Pediatric Oncology, Tata Memorial Hospital, Dr. E. Borges Road, Parel. Mumbai 400012, India; Cancer Cytogenetics Department, Room No. 6, CCE building, Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Sector-22, Kharghar, Navi Mumbai 410210 India.
| | - P G Subramanian
- Hematopathology Department, CCE building, Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Sector-22, Kharghar, Navi Mumbai 410210, India; Cancer Cytogenetics Department, Room No. 6, CCE building, Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Sector-22, Kharghar, Navi Mumbai 410210 India.
| | - Sripad Banavali
- Department of Pediatric Oncology, Tata Memorial Hospital, Dr. E. Borges Road, Parel. Mumbai 400012, India; Cancer Cytogenetics Department, Room No. 6, CCE building, Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Sector-22, Kharghar, Navi Mumbai 410210 India.
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7
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Agarwal M, Seth R, Chatterjee T. Recent Advances in Molecular Diagnosis and Prognosis of Childhood B Cell Lineage Acute Lymphoblastic Leukemia (B-ALL). Indian J Hematol Blood Transfus 2021; 37:10-20. [PMID: 33707831 PMCID: PMC7900311 DOI: 10.1007/s12288-020-01295-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 05/25/2020] [Indexed: 11/26/2022] Open
Abstract
B cell lineage acute lymphoblastic leukemia is the most common leukemia occurring in children and young adults and is the leading cause of cancer related deaths. The 5 year overall survival outcome in children with B-ALL has improved significantly in the last few decades. In the past, the discovery of various genetic alterations and targeted therapy have played a major role in decreasing disease-related deaths. In addition, numerous advances in the pathogenesis of B-ALL have been found which have provided better understanding of the genes involved in disease biology with respect to diagnostic and prognostic implications. Present review will summarize current understanding of risk stratification, genetic factors including cytogenetics in diagnosis and prognosis of B-ALL.
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Affiliation(s)
- Manisha Agarwal
- Department of Laboratory Sciences and Molecular Medicine, Army Hospital (R&R), New Delhi, India
| | - Rachna Seth
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Tathagata Chatterjee
- Department of Laboratory Sciences and Molecular Medicine, Army Hospital (R&R), New Delhi, India
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8
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MLPA and DNA index improve the molecular diagnosis of childhood B-cell acute lymphoblastic leukemia. Sci Rep 2020; 10:11501. [PMID: 32661308 PMCID: PMC7359332 DOI: 10.1038/s41598-020-68311-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 05/26/2020] [Indexed: 12/17/2022] Open
Abstract
Aneuploidy occurs within a significant proportion of childhood B-cell acute lymphoblastic leukemia (B-ALL). Some copy number variations (CNV), associated with novel subtypes of childhood B-ALL, have prognostic significance. A total of 233 childhood B-ALL patients were enrolled into this study. Focal copy number alterations of ERG, IKZF1, PAX5, ETV6, RB1, BTG1, EBF1, CDKN2A/2B, and the Xp22.33/Yp11.31 region were assessed by Multiplex Ligation-dependent Probe Amplification (MLPA). The MLPA telomere kit was used to identify aneuploidy through detection of whole chromosome loss or gain. We carried out these procedures alongside measurement of DNA index in order to identify, aneuploidy status in our cohort. MLPA telomere data and DNA index correlated well with aneuploidy status at higher sensitivity than cytogenetic analysis. Three masked hypodiploid patients, undetected by cytogenetics, and their associated copy number neutral loss of heterozygosity (CN-LOH) were identified by STR and SNP arrays. Rearrangements of TCF3, located to 19p, were frequently associated with 19p deletions. Other genetic alterations including iAMP21, IKZF1 deletions, ERG deletions, PAX5AMP, which have clinical significance or are associated with novel subtypes of ALL, were identified. In conclusion, appropriate application of MLPA aids the identifications of CNV and aneuploidy in childhood B-ALL.
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9
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Ivanov Öfverholm I, Zachariadis V, Taylan F, Marincevic-Zuniga Y, Tran AN, Saft L, Nilsson D, Syvänen AC, Lönnerholm G, Harila-Saari A, Nordenskjöld M, Heyman M, Nordgren A, Nordlund J, Barbany G. Overexpression of chromatin remodeling and tyrosine kinase genes in iAMP21-positive acute lymphoblastic leukemia. Leuk Lymphoma 2019; 61:604-613. [PMID: 31640433 DOI: 10.1080/10428194.2019.1678153] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Intrachromosomal amplification of chromosome 21 (iAMP21) is a cytogenetic subtype associated with relapse and poor prognosis in pediatric B-cell precursor acute lymphoblastic leukemia (BCP ALL). The biology behind the high relapse risk is unknown and the aim of this study was to further characterize the genomic and transcriptional landscape of iAMP21. Using DNA arrays and sequencing, we could identify rearrangements and aberrations characteristic for iAMP21. RNA sequencing revealed that only half of the genes in the minimal region of amplification (20/45) were differentially expressed in iAMP21. Among them were the top overexpressed genes (p < 0.001) in iAMP21 vs. BCP ALL without iAMP21 and three candidate genes could be identified, the tyrosine kinase gene DYRK1A and chromatin remodeling genes CHAF1B and SON. While overexpression of DYRK1A and CHAF1B is associated with poor prognosis in malignant diseases including myeloid leukemia, this is the first study to show significant correlation with iAMP21-positive ALL.
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Affiliation(s)
- Ingegerd Ivanov Öfverholm
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | | | - Fulya Taylan
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Yanara Marincevic-Zuniga
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anh Nhi Tran
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Leonie Saft
- Department of Pathology, Karolinska University Hospital, Stockholm, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, Stockholm, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gudmar Lönnerholm
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Arja Harila-Saari
- Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Mats Heyman
- Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gisela Barbany
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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Nguyen D, Li Y, Safah H, Brown TC. RUNX1 deletion/amplification in therapy-related acute myeloid leukemia: A case report and review of the literature. Cancer Genet 2019; 238:37-43. [DOI: 10.1016/j.cancergen.2019.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/16/2019] [Accepted: 07/12/2019] [Indexed: 12/18/2022]
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11
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Al-Sweedan S, Altahan R. Implications of intrachromosomal amplification of chromosome 21 on outcome in pediatric acute lymphoblastic leukemia: Does it affect our patients too? Hematol Rep 2019; 11:7826. [PMID: 31285807 PMCID: PMC6589538 DOI: 10.4081/hr.2019.7826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 03/25/2019] [Indexed: 01/09/2023] Open
Abstract
Intrachromosomal amplification (iAMP) of chromosome 21 entity is associated with a dismal outcome in B cell Acute Lymphoblastic Leukemia (B-ALL). This cytogenetic abnormality is caused by a novel mechanism; breakage-fusion-bridge cycles followed by chromothripsis along with major gross rearrangements in chromosome 21. Charts of B-ALL diagnosed at King Faisal Specialist Hospital and Research Center between 2005 and 2015 were reviewed. iAMP is a rare entity occurring at around 2.4% of all pediatrics BALL. No statistically significant difference was found among patients with iAMP21, patients with extra copies of 21 and other patients with B-ALL. The reported adverse prognostic effect of iAMP21 could be due to other coexistent adverse factors, including older age at the time of diagnosis. The most common associated abnormality in our population in addition to the hyperdiploidy was ETV6/RUNX1.
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Affiliation(s)
- Suleimman Al-Sweedan
- Department of Pediatrics, Jordan University of Science and Technology, Irbid, Jordan
| | - Rahaf Altahan
- Hematology Unit, Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
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12
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Yi K, Ju YS. Patterns and mechanisms of structural variations in human cancer. Exp Mol Med 2018; 50:1-11. [PMID: 30089796 PMCID: PMC6082854 DOI: 10.1038/s12276-018-0112-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 12/29/2017] [Indexed: 12/16/2022] Open
Abstract
Next-generation sequencing technology has enabled the comprehensive detection of genomic alterations in human somatic cells, including point mutations, chromosomal rearrangements, and structural variations (SVs). Using sophisticated bioinformatics algorithms, unbiased catalogs of SVs are emerging from thousands of human cancer genomes for the first time. Via careful examination of SV breakpoints at single-nucleotide resolution as well as local DNA copy number changes, diverse patterns of genomic rearrangements are being revealed. These "SV signatures" provide deep insight into the mutational processes that have shaped genome changes in human somatic cells. This review summarizes the characteristics of recently identified complex SVs, including chromothripsis, chromoplexy, microhomology-mediated breakage-induced replication (MMBIR), and others, to provide a holistic snapshot of the current knowledge on genomic rearrangements in somatic cells.
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Affiliation(s)
- Kijong Yi
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea.
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13
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Is intrachromosomal amplification of chromosome 21 (iAMP21) always intrachromosomal? Cancer Genet 2017; 218-219:10-14. [DOI: 10.1016/j.cancergen.2017.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 08/20/2017] [Accepted: 08/27/2017] [Indexed: 12/31/2022]
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14
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Arber DA, Borowitz MJ, Cessna M, Etzell J, Foucar K, Hasserjian RP, Rizzo JD, Theil K, Wang SA, Smith AT, Rumble RB, Thomas NE, Vardiman JW. Initial Diagnostic Workup of Acute Leukemia: Guideline From the College of American Pathologists and the American Society of Hematology. Arch Pathol Lab Med 2017; 141:1342-1393. [PMID: 28225303 DOI: 10.5858/arpa.2016-0504-cp] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - A complete diagnosis of acute leukemia requires knowledge of clinical information combined with morphologic evaluation, immunophenotyping and karyotype analysis, and often, molecular genetic testing. Although many aspects of the workup for acute leukemia are well accepted, few guidelines have addressed the different aspects of the diagnostic evaluation of samples from patients suspected to have acute leukemia. OBJECTIVE - To develop a guideline for treating physicians and pathologists involved in the diagnostic and prognostic evaluation of new acute leukemia samples, including acute lymphoblastic leukemia, acute myeloid leukemia, and acute leukemias of ambiguous lineage. DESIGN - The College of American Pathologists and the American Society of Hematology convened a panel of experts in hematology and hematopathology to develop recommendations. A systematic evidence review was conducted to address 6 key questions. Recommendations were derived from strength of evidence, feedback received during the public comment period, and expert panel consensus. RESULTS - Twenty-seven guideline statements were established, which ranged from recommendations on what clinical and laboratory information should be available as part of the diagnostic and prognostic evaluation of acute leukemia samples to what types of testing should be performed routinely, with recommendations on where such testing should be performed and how the results should be reported. CONCLUSIONS - The guideline provides a framework for the multiple steps, including laboratory testing, in the evaluation of acute leukemia samples. Some aspects of the guideline, especially molecular genetic testing in acute leukemia, are rapidly changing with new supportive literature, which will require on-going updates for the guideline to remain relevant.
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Yang M, Yi ES, Kim HJ, Yoo KH, Koo HH, Kim SH. Intrachromosomal amplification of chromosome 21 in Korean pediatric patients with B-cell precursor acute lymphoblastic leukemia in a single institution. Blood Res 2017; 52:100-105. [PMID: 28698845 PMCID: PMC5503886 DOI: 10.5045/br.2017.52.2.100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 02/01/2017] [Accepted: 03/13/2017] [Indexed: 11/17/2022] Open
Abstract
Background Intrachromosomal amplification of chromosome 21 (iAMP21), defined as the presence of three or more RUNX1 signals on one marker chromosome, is a distinct cytogenetic subgroup of childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL) that is known to have a poor prognosis when treated with standard therapy. The aim of this study was to evaluate the clinical characteristics of Korean children with iAMP21. Methods The cytogenetic data from BCP-ALL children were reviewed. The ETV6/RUNX1 ES Dual Color Probe was used for fluorescence in situ hybridization (FISH). Results In total, 295 children were included. Of these, 10 patients (3.4%) had iAMP21. The median age of iAMP21 patients was 9 years, and the median value of white blood cell count was 5.09×109/L. Slow early treatment response was observed more in iAMP21 patients. Patients with iAMP21 had a higher incidence of relapse and worse survival rates. In patients with iAMP21, the estimated 10-year cumulative incidence of relapse was 53.3%. The estimated 10-year event-free survival and overall survival rate were 46.7% and 64.8%, respectively. Most cases of leukemic relapse developed in the late period (median, 43 mo). In multivariate analysis, high risk group was the only factor that had a significant impact on death. Conclusion The existence of iAMP21 was related to delayed treatment response and was likely to affect increased relapse and death in the late period. Further studies are needed to reveal its effect on BCP-ALL treatment outcomes and its role as an independent prognostic factor.
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Affiliation(s)
- Mina Yang
- Department of Laboratory Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Eun Sang Yi
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Jin Kim
- Department of Laboratory Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Keon Hee Yoo
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hong Hoe Koo
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sun-Hee Kim
- Department of Laboratory Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Gu J, Reynolds A, Fang L, DeGraffenreid C, Sterns K, Patel KP, Medeiros LJ, Lin P, Lu X. Coexistence of iAMP21 and ETV6-RUNX1 fusion in an adolescent with B cell acute lymphoblastic leukemia: literature review of six additional cases. Mol Cytogenet 2016; 9:84. [PMID: 27895713 PMCID: PMC5117506 DOI: 10.1186/s13039-016-0294-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 11/11/2016] [Indexed: 12/29/2022] Open
Abstract
Background Intrachromosomal amplification of chromosome 21 (iAMP21) results from breakage-fusion-bridge cycles and chromothripsis is a distinct marker of a subgroup of B cell acute lymphoblastic leukemia (B-ALL) cases associated with a poor prognosis. iAMP21 accounts for 2% of pediatric B-ALL and occurs predominantly in older children or adolescents. ETV6-RUNX1 fusion, resulting from t(12;21)(p13;q22), is associated with an excellent outcome in younger children with B-ALL. Coexistence of iAMP21 with ETV6-RUNX1 fusion is extremely rare with limited clinical information available. Results We report the case of an 18-year old Caucasian man diagnosed with ETV6-RUNX1 fusion positive B-ALL. He was treated with intensive chemotherapy and achieved remission for 6 months before relapse, 15 months after the initial diagnosis. G-band karyotyping and Fluorescence in situ hybridization (FISH) analyses performed on bone marrow revealed complex abnormalities: 41,X,-Y,der(3)t(3;20)(p11.2;q11.2),-4,t(5;22)(q32;q11.2),del(9)(p13),dic(9;17)(p13;p11.2),t(12;21)(p13;q22),der(14)t(14;17)(p11.2;q11.2),der(17;22)(q11.2;q11.2),-20,add(21)(q22),-22[4]/46,XY[15] with an iAMP21 and an ETV6-RUNX1. Additional molecular studies confirmed ETV6-RUNX1 fusion and with a TP53 mutation. High-resolution single nucleotide polymorphism microarray (SNP array) revealed the iAMP21 to be chromothripsis of 21q and subsequent metaphase FISH further delineated complex genomic aberrations. Although the patient received intensive chemotherapy with allogenic stem cell transplant, he died 26 months after initial diagnosis. We searched the literature and identified six cases showing coexisting iAMP21 and ETV6-RUNX1. The median age for these six patients was 10 years (range, 2–18) and males predominated. The median overall survival (OS) was 28 months. Conclusions Patients with B-ALL associated with both iAMP21 and ETV6-RUNX1 tend to be older children or adolescents and have a poor prognosis.
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Affiliation(s)
- Jun Gu
- School of Health Professions, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0002, Houston, TX 77030 USA
| | - Alexandra Reynolds
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0350, Houston, TX 77030 USA
| | - Lianghua Fang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0149, Houston, TX 77030 USA ; Department of Oncology, Jiangsu Hospital of Traditional Chinese Medicine, Nanjing, Jiangsu China
| | - Corrie DeGraffenreid
- School of Health Professions, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0002, Houston, TX 77030 USA
| | - Kenneth Sterns
- School of Health Professions, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0002, Houston, TX 77030 USA
| | - Keyur P Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0149, Houston, TX 77030 USA
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0072, Houston, TX 77030 USA
| | - Pei Lin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0072, Houston, TX 77030 USA
| | - Xinyan Lu
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0350, Houston, TX 77030 USA ; Department of Pathology, Northwestern University Feinberg School of Medicine, 303 East Chicago Avenue, Tarry 7-723, Chicago, IL 60611 USA
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Kim J, Lyu CJ, Shin S, Lee ST, Choi JR. Frequency and Clinical Characteristics of Intrachromosomal Amplification of Chromosome 21 in Korean Childhood B-lineage Acute Lymphoblastic Leukemia. Ann Lab Med 2016; 36:475-80. [PMID: 27374714 PMCID: PMC4940492 DOI: 10.3343/alm.2016.36.5.475] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/30/2016] [Accepted: 05/11/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Intrachromosomal amplification of chromosome 21 (iAMP21) is known to be associated with poor prognosis in B-cell ALL (B-ALL). To determine the frequency and clinical characteristics of iAMP21 in Korean B-ALL patients, we performed FISH and multiplex ligation-dependent probe amplification (MLPA) analyses. METHODS A total of 102 childhood B-ALL patients were screened with ETV6-RUNX1 FISH probes (Abbott Molecular, USA). The presence of an iAMP21 was confirmed by using MLPA P327 iAMP21-ERG probemix (MRC Holland, The Netherlands). RESULTS iAMP21 was detected in one of the screened B-ALL patients (1/102 patients, 1.0%) who presented the ALL immunophenotype and complex karyotype at initial diagnosis. The patient relapsed twice after bone marrow transplantation. MLPA showed 12.5-Mb and 4.28-Mb regions of amplification and deletion, respectively. CONCLUSIONS The frequency of iAMP21 is considerable in Korean pediatric patients. Our report suggests that iAMP21 in childhood B-ALL has very unfavorable impact on patient's prognosis. Additional methods such as MLPA analysis is essential to rule out patients with equivocal interphase FISH results.
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Affiliation(s)
- Jieun Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Chuhl Joo Lyu
- Department of Pediatrics, Yonsei Cancer Research Center, Yonsei University College of Medicine, Seoul, Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Hallym University College of Medicine, Kangnam Sacred Heart Hospital, Seoul, Korea.
| | - Seung Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea.
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
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Harrison CJ, Schwab C. Constitutional abnormalities of chromosome 21 predispose to iAMP21-acute lymphoblastic leukaemia. Eur J Med Genet 2016; 59:162-5. [PMID: 26836400 DOI: 10.1016/j.ejmg.2016.01.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 01/04/2016] [Accepted: 01/24/2016] [Indexed: 11/30/2022]
Abstract
In addition to Down syndrome, individuals with other constitutional abnormalities of chromosome 21 have an increased risk of developing childhood acute lymphoblastic leukaemia (ALL). Specifically, carriers of the Robertsonian translocation between chromosomes 15 and 21, rob(15;21) (q10; q10)c, have ∼2,700 increased risk of developing ALL with iAMP21 (intrachromosomal amplification of chromosome 21). In these patients, chromosome 15 as well as chromosome 21 is involved in the formation of iAMP21, referred to here as der(21)(15;21). Individuals with constitutional ring chromosomes involving chromosome 21, r(21)c, are also predisposed to iAMP21-ALL, involving the same series of mutational processes as seen in sporadic- and der(21)(15;21)-iAMP21 ALL. Evidence is accumulating that the dicentric nature of the Robertsonian and ring chromosome is the initiating factor in the formation of the complex iAMP21 structure. Unravelling these intriguing predispositions to iAMP21-ALL may provide insight into how other complex rearrangements arise in cancer.
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Affiliation(s)
- Christine J Harrison
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK.
| | - Claire Schwab
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
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Knez VM, Carstens BJ, Swisshelm KL, McGranahan AN, Liang X. Heterogeneity of Abnormal RUNX1 Leading to Clinicopathologic Variations in Childhood B-Lymphoblastic Leukemia. Am J Clin Pathol 2015; 144:305-14. [PMID: 26185316 DOI: 10.1309/ajcpvy5e5ommybfj] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVES Abnormalities of the RUNX1 gene in childhood B-acute lymphoblastic leukemia (B-ALL) are manifested by ETV6-RUNX1 or RUNX1 amplification. A detailed comparison between the two regarding clinicopathologic features with genetic analysis has not been performed previously. This parallel study assessed how different RUNX1 abnormalities affect the clinicopathology of B-ALL. METHODS We compared clinicopathologic factors, including age, sex, WBC count, cerebrospinal fluid (CSF) involvement, immunophenotype, and blast proliferation rate between B-ALL with RUNX1 amplification (10 cases) and B-ALL with ETV6-RUNX1 translocation (67 cases) in childhood B-ALL. RESULTS CD7 was often expressed in RUNX1 amplification but not in ETV6-RUNX1 (44% vs 0%, P = .0001) and appeared to correlate with CSF involvement in the former group (3/4 [75%]). CD13 was often detected in ETV6-RUNX1 with additional RUNX1 gain (38%) with an even higher frequency in double ETV6-RUNX1 translocation (77%), but was not detected in RUNX1 amplification (0%, P < .05). Children with RUNX1 amplification were older and more often CSF positive, while those with ETV6-RUNX1 were younger, more frequently had hyperleukocytosis, and had higher blast proliferation rates. CONCLUSIONS RUNX1 copy numbers seem to be proportional to the age of B-ALL onset and the frequency of CSF involvement, while RUNX1 amplification vs translocation causes aberrant expression of CD7 and CD13, respectively.
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Affiliation(s)
- Virginia M. Knez
- Department of Pathology, University of Colorado School of Medicine, Aurora
| | - Billie J. Carstens
- Department of Pathology, University of Colorado School of Medicine, Aurora
- Colorado Genetics Laboratory, University of Colorado School of Medicine, Aurora
| | - Karen L. Swisshelm
- Department of Pathology, University of Colorado School of Medicine, Aurora
- Colorado Genetics Laboratory, University of Colorado School of Medicine, Aurora
| | | | - Xiayuan Liang
- Department of Pathology, University of Colorado School of Medicine, Aurora
- Department of Pathology, Children’s Hospital Colorado, Aurora
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20
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Johnson RC, Weinberg OK, Cascio MJ, Dahl GV, Mitton BA, Silverman LB, Cherry AM, Arber DA, Ohgami RS. Cytogenetic Variation of B-Lymphoblastic Leukemia With Intrachromosomal Amplification of Chromosome 21 (iAMP21): A Multi-Institutional Series Review. Am J Clin Pathol 2015; 144:103-12. [PMID: 26071468 DOI: 10.1309/ajcpluyf11hqbyrb] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVES B-lymphoblastic leukemia (B-ALL) with intrachromosomal amplification of chromosome 21 (iAMP21) is a relatively uncommon manifestation of acute leukemia and limited predominantly to the pediatric population. Case-specific information regarding flow cytometric, morphologic, and laboratory findings of this subtype of leukemia is currently lacking. METHODS We searched the databases of three large institutions for lymphoblastic leukemia with iAMP21 from 2005 through 2012 and analyzed the clinicopathologic features. RESULTS We identified 17 cases with five or more RUNX1 signals on interphase nuclei, 14 of which were consistent with the Children's Oncology Group (COG) definition for iAMP21—namely, the presence of three or more RUNX1 signals on one marker chromosome. These cases showed a statistically significant lower peripheral WBC count and older age at diagnosis compared with all pediatric cases of B-ALL. We also identified three cases with increased RUNX1 signals scattered on multiple marker chromosomes that did not meet the COG definition of iAMP21 but showed similar 21q instability and older age at presentation. CONCLUSIONS Our findings not only demonstrate that B-ALL with iAMP21 is truly a distinct clinicopathologic entity but also suggest that a subset of cases of B-ALL with iAMP21 can show variable cytogenetic features.
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21
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Fuka G, Farias-Vieira TM, Hummel L, Blunck CB, Santoro JC, Terra-Granado E, Barbosa TC, Emerenciano M, Pombo-de-Oliveira MS. Evaluation of multiplex ligation dependent probe amplification (MLPA) for identification of acute lymphoblastic leukemia with an intrachromosomal amplification of chromosome 21 (iAMP21) in a Brazilian population. Mol Cytogenet 2015; 8:35. [PMID: 26060508 PMCID: PMC4460763 DOI: 10.1186/s13039-015-0147-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 05/20/2015] [Indexed: 12/02/2022] Open
Abstract
Background An intrachromosomal amplification of chromosome 21 (iAMP21) defines a unique subgroup of B-cell precursor acute lymphoblastic leukemia (BCP-ALL). The finding of three or more extra copies of the RUNX1 gene by fluorescence in situ hybridization (FISH) is internationally used to define an iAMP21. Genomic profiling of chromosome 21 has been suggested for assisting diagnostic case identification. Due to limitations of comparative genomic hybridization, in terms of a routine application as first line-screening tests we evaluated the multiplex ligation-dependent probe amplification (MLPA) SALSA P327_A1 and P327_B1 probe sets for detecting chromosome 21 copy number alterations in Brazilian childhood BCP-ALL. Results In 74 out of 368 patients gain of genetic material was detected. For data confirmation RUNX1 directed FISH was performed. Cells with ≥5 RUNX1 signals (n = 9) were considered as “true iAMP21” while <5 RUNX1 signals (n = 41) were counted as evidence for additional copies of intact chromosomes 21. All patients with an iAMP21 had high MLPA peak ratios (≥1.8), while the majority of patients with <5 RUNX1 presented low MLPA peak ratios (<1.8). Observed differences gained statistical strength by comparing probes located within the common region of amplification. Next, a principal component analysis was performed in order to illustrate distribution of cases according to their MLPA peak profile in two dimensions. Cases with an iAMP21 mostly clustered together, however additional cases with <5 RUNX1 signals or no available FISH data located in proximity. Conclusions MLPA qualified as a high throughput technique that could be employed in future studies for a critical comparison with data obtained by FISH, especially in cases where metaphase nuclei are not available. Taking submicroscopic aberrations into account examined by MLPA, cases exhibiting an “iAMP21 like” peak ratio profile but <5 RUNX1 signals should be considered as candidates for this chromosomal abnormality. Electronic supplementary material The online version of this article (doi:10.1186/s13039-015-0147-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gerhard Fuka
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer (INCA), Rua André Cavalcanti, 37, Rio de Janeiro, RJ 20231-050 Brazil
| | - Tállita M Farias-Vieira
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer (INCA), Rua André Cavalcanti, 37, Rio de Janeiro, RJ 20231-050 Brazil
| | - Leticia Hummel
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer (INCA), Rua André Cavalcanti, 37, Rio de Janeiro, RJ 20231-050 Brazil
| | - Caroline B Blunck
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer (INCA), Rua André Cavalcanti, 37, Rio de Janeiro, RJ 20231-050 Brazil
| | - Júlio C Santoro
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer (INCA), Rua André Cavalcanti, 37, Rio de Janeiro, RJ 20231-050 Brazil
| | - Eugênia Terra-Granado
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer (INCA), Rua André Cavalcanti, 37, Rio de Janeiro, RJ 20231-050 Brazil
| | - Thayana Conceição Barbosa
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer (INCA), Rua André Cavalcanti, 37, Rio de Janeiro, RJ 20231-050 Brazil
| | - Mariana Emerenciano
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer (INCA), Rua André Cavalcanti, 37, Rio de Janeiro, RJ 20231-050 Brazil
| | - Maria S Pombo-de-Oliveira
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer (INCA), Rua André Cavalcanti, 37, Rio de Janeiro, RJ 20231-050 Brazil
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Abstract
With the advent of next-generation sequencing technologies, we have witnessed a rapid pace of discovery of new patterns of somatic structural variation in cancer genomes, and an attempt to figure out their underlying mechanisms. Some of these mechanisms are associated with particular cancer types, and in some cases are the main cause of the structural mutations that drive the oncogenic process. This review provides an overview of the patterns of somatic structural variation and chromosomal structures that characterize cancer genomes, their causal mechanisms and their impact in oncogenesis.
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Park Y, Lim J, Ko YH, Kim J, Kwon GC, Koo SH. A case of pentasomy 21 with two isochromosome 21s in acute megakaryoblastic leukemia associated with Down syndrome. Ann Lab Med 2015; 35:373-5. [PMID: 25932450 PMCID: PMC4390710 DOI: 10.3343/alm.2015.35.3.373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/07/2014] [Accepted: 02/07/2015] [Indexed: 01/08/2023] Open
Affiliation(s)
- Yeongchun Park
- Department of Laboratory Medicine, Chungnam National University Hospital, Daejeon, Korea
| | - Jinsook Lim
- Department of Laboratory Medicine, Chungnam National University Hospital, Daejeon, Korea
| | - Yong Hyun Ko
- Department of Laboratory Medicine, Chungnam National University Hospital, Daejeon, Korea
| | - Jimyung Kim
- Department of Laboratory Medicine, Chungnam National University Hospital, Daejeon, Korea
| | - Gye Cheol Kwon
- Department of Laboratory Medicine, Chungnam National University Hospital, Daejeon, Korea
| | - Sun Hoe Koo
- Department of Laboratory Medicine, Chungnam National University Hospital, Daejeon, Korea
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Blood Spotlight on iAMP21 acute lymphoblastic leukemia (ALL), a high-risk pediatric disease. Blood 2015; 125:1383-6. [PMID: 25608562 DOI: 10.1182/blood-2014-08-569228] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intrachromosomal amplification of chromosome 21 (iAMP21) defines a distinct cytogenetic subgroup of childhood B-cell precursor acute lymphoblastic leukemia. Breakage-fusion-bridge cycles followed by chromothripsis and other complex structural rearrangements of chromosome 21 underlie the mechanism giving rise to iAMP21. Patients with iAMP21 are older (median age 9 years), with a low white cell count. They have a high relapse rate when treated as standard risk. Recent studies have shown improved outcome on intensive therapy. Molecular targets for therapy are being sought.
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Baughn LB, Biegel JA, South ST, Smolarek TA, Volkert S, Carroll AJ, Heerema NA, Rabin KR, Zweidler-McKay PA, Loh M, Hirsch B. Integration of cytogenomic data for furthering the characterization of pediatric B-cell acute lymphoblastic leukemia: a multi-institution, multi-platform microarray study. Cancer Genet 2014; 208:1-18. [PMID: 25678190 DOI: 10.1016/j.cancergen.2014.11.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 11/03/2014] [Accepted: 11/10/2014] [Indexed: 11/16/2022]
Abstract
It is well documented that among subgroups of B-cell acute lymphoblastic leukemia (B-ALL), the genetic profile of the leukemic blasts has significant impact on prognosis and stratification for therapy. Recent studies have documented the power of microarrays to screen genome-wide for copy number aberrations (CNAs) and regions of copy number-neutral loss of heterozygosity (CNLOH) that are not detectable by G-banding or fluorescence in situ hybridization (FISH). These studies have involved application of a single array platform for the respective cases. The present investigation demonstrates the feasibility and usefulness of integrating array results from multiple laboratories (ARUP, The Children's Hospital of Philadelphia, Cincinnati Children's Hospital Medical Center, and University of Minnesota Medical Center) that utilize different array platforms (Affymetrix, Agilent, or Illumina) in their respective clinical settings. A total of 65 patients enrolled on the Children's Oncology Group (COG) study AALL08B1 were identified for study, as cytogenetic and FISH studies had also been performed on these patients, with a central review of those results available for comparison. Microarray data were first analyzed by the individual laboratories with their respective software systems; raw data files were then centrally validated using NEXUS software. The results demonstrated the added value of integrating multi-platform data with cytogenetic and FISH data and highlight novel findings identified by array including the co-occurrence of low and high risk abnormalities not previously reported to coexist within a clone, novel regions of chromosomal amplification, clones characterized by numerous whole chromosome LOH that do not meet criteria for doubling of a near-haploid, and characterization of array profiles associated with an IKZF1 deletion. Each of these findings raises questions that are clinically relevant to risk stratification.
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Affiliation(s)
- Linda B Baughn
- Department of Laboratory Medicine and Pathology and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Jaclyn A Biegel
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sarah T South
- ARUP Laboratories, Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Teresa A Smolarek
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Suzanne Volkert
- Department of Laboratory Medicine and Pathology and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Andrew J Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nyla A Heerema
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Karen R Rabin
- Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Mignon Loh
- Department of Pediatrics, Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Betsy Hirsch
- Department of Laboratory Medicine and Pathology and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
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26
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Li Y, Schwab C, Ryan S, Papaemmanuil E, Robinson HM, Jacobs P, Moorman AV, Dyer S, Borrow J, Griffiths M, Heerema NA, Carroll AJ, Talley P, Bown N, Telford N, Ross FM, Gaunt L, McNally RJQ, Young BD, Sinclair P, Rand V, Teixeira MR, Joseph O, Robinson B, Maddison M, Dastugue N, Vandenberghe P, Stephens PJ, Cheng J, Van Loo P, Stratton MR, Campbell PJ, Harrison CJ. Constitutional and somatic rearrangement of chromosome 21 in acute lymphoblastic leukaemia. Nature 2014; 508:98-102. [PMID: 24670643 PMCID: PMC3976272 DOI: 10.1038/nature13115] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 01/30/2014] [Indexed: 12/22/2022]
Abstract
Changes in gene dosage are a major driver of cancer, known to be caused by a finite, but increasingly well annotated, repertoire of mutational mechanisms. This can potentially generate correlated copy-number alterations across hundreds of linked genes, as exemplified by the 2% of childhood acute lymphoblastic leukaemia (ALL) with recurrent amplification of megabase regions of chromosome 21 (iAMP21). We used genomic, cytogenetic and transcriptional analysis, coupled with novel bioinformatic approaches, to reconstruct the evolution of iAMP21 ALL. Here we show that individuals born with the rare constitutional Robertsonian translocation between chromosomes 15 and 21, rob(15;21)(q10;q10)c, have approximately 2,700-fold increased risk of developing iAMP21 ALL compared to the general population. In such cases, amplification is initiated by a chromothripsis event involving both sister chromatids of the Robertsonian chromosome, a novel mechanism for cancer predisposition. In sporadic iAMP21, breakage-fusion-bridge cycles are typically the initiating event, often followed by chromothripsis. In both sporadic and rob(15;21)c-associated iAMP21, the final stages frequently involve duplications of the entire abnormal chromosome. The end-product is a derivative of chromosome 21 or the rob(15;21)c chromosome with gene dosage optimized for leukaemic potential, showing constrained copy-number levels over multiple linked genes. Thus, dicentric chromosomes may be an important precipitant of chromothripsis, as we show rob(15;21)c to be constitutionally dicentric and breakage-fusion-bridge cycles generate dicentric chromosomes somatically. Furthermore, our data illustrate that several cancer-specific mutational processes, applied sequentially, can coordinate to fashion copy-number profiles over large genomic scales, incrementally refining the fitness benefits of aggregated gene dosage changes.
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Affiliation(s)
- Yilong Li
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Claire Schwab
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Sarra Ryan
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | | | - Hazel M Robinson
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Patricia Jacobs
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Anthony V Moorman
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Sara Dyer
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
- School of Cancer Sciences, University of Birmingham, Birmingham, UK
| | - Julian Borrow
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
- School of Cancer Sciences, University of Birmingham, Birmingham, UK
| | - Mike Griffiths
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
- School of Cancer Sciences, University of Birmingham, Birmingham, UK
| | - Nyla A Heerema
- Department of Pathology, The Ohio State University, Columbus, OH
| | - Andrew J Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - Polly Talley
- Sheffield Diagnostic Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Nick Bown
- Cytogenetics Laboratory, Northern Genetics Service, Newcastle upon Tyne, UK
| | - Nick Telford
- Oncology Cytogenetics, The Christie NHS Foundation Trust, Manchester, UK
| | - Fiona M Ross
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Lorraine Gaunt
- Regional Cytogenetics Unit, Genetic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Saint Mary's Hospital, Manchester, UK
| | - Richard J Q McNally
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK
| | - Bryan D Young
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Paul Sinclair
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Vikki Rand
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Manuel R Teixeira
- Genetics Department, Portuguese Oncology Institute, and Biomedical Sciences Institute (ICBAS), Porto University, Portugal
| | - Olivia Joseph
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Ben Robinson
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Mark Maddison
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Nicole Dastugue
- Laboratoire d'hématologie, Génétique des Hémopathies, Hôpital Purpan, Toulouse, France
| | - Peter Vandenberghe
- Center for Human Genetics, University Hospital Leuven and KU Leuven, Leuven, Belgium
| | | | - Jiqiu Cheng
- Center for Human Genetics, University Hospital Leuven and KU Leuven, Leuven, Belgium
- Department of Electrical Engineering - ESAT, University of Leuven, Leuven, Belgium
| | - Peter Van Loo
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Center for Human Genetics, University Hospital Leuven and KU Leuven, Leuven, Belgium
| | | | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Christine J Harrison
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
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An international study of intrachromosomal amplification of chromosome 21 (iAMP21): cytogenetic characterization and outcome. Leukemia 2013; 28:1015-21. [PMID: 24166298 DOI: 10.1038/leu.2013.317] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 10/18/2013] [Accepted: 10/22/2013] [Indexed: 11/08/2022]
Abstract
Intrachromosomal amplification of chromosome 21 (iAMP21) defines a distinct cytogenetic subgroup of childhood B-cell precursor acute lymphoblastic leukaemia (BCP-ALL). To date, fluorescence in situ hybridisation (FISH), with probes specific for the RUNX1 gene, provides the only reliable detection method (five or more RUNX1 signals per cell). Patients with iAMP21 are older (median age 9 years) with a low white cell count. Previously, we demonstrated a high relapse risk when these patients were treated as standard risk. Recent studies have shown improved outcome on intensive therapy. In view of these treatment implications, accurate identification is essential. Here we have studied the cytogenetics and outcome of 530 iAMP21 patients that highlighted the association of specific secondary chromosomal and genetic changes with iAMP21 to assist in diagnosis, including the gain of chromosome X, loss or deletion of chromosome 7, ETV6 and RB1 deletions. These iAMP21 patients when treated as high risk showed the same improved outcome as those in trial-based studies regardless of the backbone chemotherapy regimen given. This study reinforces the importance of intensified treatment to reduce the risk of relapse in iAMP21 patients. This now well-defined patient subgroup should be recognised by World Health Organisation (WHO) as a distinct entity of BCP-ALL.
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Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy and a leading case of childhood cancer death. The last decade has witnessed a transformation in our understanding of the genetic basis of ALL due to detailed integrative genomic profiling of large cohorts of childhood ALL. Initially using microarray based approaches, and more recently with next-generation sequencing, these studies have enabled more precise subclassification of ALL, and have shown that each ALL entity is characterized by constellations of structural and sequence mutations that typically perturb key cellular pathways including lymphoid development, cell cycle regulation, tumor suppression, Ras- and tyrosine kinase-driven signaling, and epigenetic regulation. Importantly, several of the newly identified genetic alterations have entered the clinic to improve diagnosis and risk stratification, and are being pursued as new targets for therapeutic intervention. Studies of ALL have also led the way in dissecting the subclonal heterogeneity of cancer, and have shown that individual patients commonly harbor multiple related but genetically distinct subclones, and that this genetically determined clonal heterogeneity is an important determinant of relapse. In addition, genome-wide profiling has identified inherited genetic variants that influence ALL risk. Ongoing studies are deploying detailed integrative genetic transcriptomic and epigenetic sequencing to comprehensively define the genomic landscape of ALL. This review describes the recent advances in our understanding of the genetics of ALL, with an emphasis on those alterations of key pathogenic or therapeutic importance.
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Affiliation(s)
- Charles G Mullighan
- Department of Pathology and the Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN.
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29
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Heerema NA, Carroll AJ, Devidas M, Loh ML, Borowitz MJ, Gastier-Foster JM, Larsen EC, Mattano LA, Maloney KW, Willman CL, Wood BL, Winick NJ, Carroll WL, Hunger SP, Raetz EA. Intrachromosomal amplification of chromosome 21 is associated with inferior outcomes in children with acute lymphoblastic leukemia treated in contemporary standard-risk children's oncology group studies: a report from the children's oncology group. J Clin Oncol 2013; 31:3397-402. [PMID: 23940221 DOI: 10.1200/jco.2013.49.1308] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Five-year overall survival (OS) for children with B-cell precursor acute lymphoblastic leukemia (B-ALL) exceeds 90% with risk-adapted therapy. Age, initial WBC count, genetic aberrations, and minimal residual disease (MRD) are used for risk stratification. Intrachromosomal amplification of a region of chromosome 21 (iAMP21; three or more extra copies of RUNX1 on an abnormal chromosome 21) is a recently identified recurrent genomic lesion associated with inferior outcome in some studies. We investigated the impact of iAMP21 in a large cohort treated in contemporary Children's Oncology Group (COG) ALL trials. PATIENTS AND METHODS Fluorescent in situ hybridization for specific genetic aberrations was required at diagnosis. MRD was measured by flow cytometry at end induction. Outcome was measured as event-free survival (EFS) and OS. RESULTS iAMP21 was found in 158 (2%) of 7,793 patients with B-ALL age ≥ 1 year; 74 (1.5%) of 5,057 standard-risk (SR) patients, and 84 (3.1%) of 2,736 high-risk (HR) patients. iAMP21 was associated with age ≥ 10 years, WBC less than 50,000/μL, female sex, and detectable MRD at day 29. Four-year EFS and OS were significantly worse for patients with iAMP21 and SR B-ALL, but iAMP21 was not a statistically significant prognostic factor in HR patients. There was no interaction between MRD and iAMP21. Among SR patients, day 29 MRD ≥ 0.01% and iAMP21 were associated with the poorest EFS and OS; absence of both was associated with the best outcome. CONCLUSION iAMP21 is associated with inferior outcome in pediatric B-ALL, particularly SR patients who require more intensive therapy and are now treated on HR COG ALL protocols.
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Affiliation(s)
- Nyla A Heerema
- Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University Wexner Medical Center; Julie M. Gastier-Foster, The Ohio State University College of Medicine and Nationwide Children's Hospital, Columbus, OH; Andrew J. Carroll, University of Alabama at Birmingham, Birmingham, AL; Meenakshi Devidas, University of Florida, Gainesville, FL; Mignon L. Loh, University of California at San Francisco, San Francisco, CA; Michael J. Borowitz, Johns Hopkins Medical Institutions, Baltimore, MD; Eric C. Larsen, Maine Children's Cancer Program, Scarborough, ME; Leonard A. Mattano Jr, Michigan State University College of Human Medicine, Kalamazoo, MI; Kelly W. Maloney and Stephen P. Hunger, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO; Cheryl L. Willman, University of New Mexico, Albuquerque, NM; Brent L. Wood, University of Washington, Seattle, WA; Naomi J. Winick, University of Texas Southwestern Medical Center, Dallas, TX; and William L. Carroll and Elizabeth A. Raetz, The New York University Cancer Institute, New York University Langone Medical Center, New York, NY
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Moorman AV, Robinson H, Schwab C, Richards SM, Hancock J, Mitchell CD, Goulden N, Vora A, Harrison CJ. Risk-directed treatment intensification significantly reduces the risk of relapse among children and adolescents with acute lymphoblastic leukemia and intrachromosomal amplification of chromosome 21: a comparison of the MRC ALL97/99 and UKALL2003 trials. J Clin Oncol 2013; 31:3389-96. [PMID: 23940220 DOI: 10.1200/jco.2013.48.9377] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
PURPOSE To evaluate the effect on outcome of intensifying therapy for patients with acute lymphoblastic leukemia (ALL) and an intrachromosomal amplification of chromosome 21 (iAMP21). PATIENTS AND METHODS We report two cohorts of patients treated on Medical Research Council ALL97 or United Kingdom (UK) ALL2003. iAMP21 was identified retrospectively in ALL97 and was not used to guide therapy. However, in UKALL2003, iAMP21 was determined prospectively, and patients were allocated to the most intensive treatment arm (regimen C), which included augmented Berlin-Frankfurt-Munster consolidation, escalating Capizzi maintenance, double delayed intensification, and an option for first remission transplantation. The presence of iAMP21 was determined by fluorescence in situ hybridization using probes specific for the RUNX1 gene. RESULTS iAMP21 was identified in 2% of patients with B-cell precursor ALL treated on UKALL2003 and ALL97. The event-free survival, relapse, and overall survival rates at 5 years for iAMP21 patients treated on ALL97 and UKALL2003 were 29% and 78%, 70% and 16%, and 67% and 89%, respectively (all P < .01). Patients treated on ALL97 had an increased risk of relapse compared with patients treated on UKALL2003 (hazard ratio, 7.2; 95% CI, 2.91 to 17.87; P < .001). CONCLUSION iAMP21 patients with ALL benefitted from receiving more intensive therapy in UKALL2003. In UKALL2011, they will continue to be treated as cytogenetic high risk, receive intensive chemotherapy (regimen C), and will only be recommended for transplantation if they do not achieve a complete remission by the end of induction therapy. This study illustrates how the discovery and characterization of disease-specific genetic aberrations can be used to tailor therapy more precisely.
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Affiliation(s)
- Anthony V Moorman
- Anthony V. Moorman, Hazel Robinson, Claire Schwab, and Christine J. Harrison, Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle University, Newcastle; Sue M. Richards, University of Oxford; Christopher D. Mitchell, John Radcliffe Hospital, Oxford; Jeremy Hancock, Bristol Genetics Laboratory, North Bristol National Health Service Trust, Bristol; Nicholas Goulden, Great Ormond Street Hospital, London; and Ajay Vora, Sheffield Children's Hospital, Sheffield, United Kingdom
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31
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Abstract
Acute lymphoblastic leukaemia occurs in both children and adults but its incidence peaks between 2 and 5 years of age. Causation is multifactorial and exogenous or endogenous exposures, genetic susceptibility, and chance have roles. Survival in paediatric acute lymphoblastic leukaemia has improved to roughly 90% in trials with risk stratification by biological features of leukaemic cells and response to treatment, treatment modification based on patients' pharmacodynamics and pharmacogenomics, and improved supportive care. However, innovative approaches are needed to further improve survival while reducing adverse effects. Prognosis remains poor in infants and adults. Genome-wide profiling of germline and leukaemic cell DNA has identified novel submicroscopic structural genetic changes and sequence mutations that contribute to leukaemogenesis, define new disease subtypes, affect responsiveness to treatment, and might provide novel prognostic markers and therapeutic targets for personalised medicine.
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Affiliation(s)
- Hiroto Inaba
- Department of Oncology, St Jude Children's Research Hospital and University of Tennessee Health Science Center, Memphis, TN 38105, USA.
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32
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Schwab CJ, Chilton L, Morrison H, Jones L, Al-Shehhi H, Erhorn A, Russell LJ, Moorman AV, Harrison CJ. Genes commonly deleted in childhood B-cell precursor acute lymphoblastic leukemia: association with cytogenetics and clinical features. Haematologica 2013; 98:1081-8. [PMID: 23508010 DOI: 10.3324/haematol.2013.085175] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In childhood B-cell precursor acute lymphoblastic leukemia, cytogenetics is important in diagnosis and as an indicator of response to therapy, thus playing a key role in risk stratification of patients for treatment. Little is known of the relationship between different cytogenetic subtypes in B-cell precursor acute lymphoblastic leukemia and the recently reported copy number abnormalities affecting significant leukemia associated genes. In a consecutive series of 1427 childhood B-cell precursor acute lymphoblastic leukemia patients, we have determined the incidence and type of copy number abnormalities using multiplex ligation-dependent probe amplification. We have shown strong links between certain deletions and cytogenetic subtypes, including the novel association between RB1 deletions and intrachromosomal amplification of chromosome 21. In this study, we characterized the different copy number abnormalities and show heterogeneity of PAX5 and IKZF1 deletions and the recurrent nature of RB1 deletions. Whole gene losses are often indicative of larger deletions, visible by conventional cytogenetics. An increased number of copy number abnormalities is associated with NCI high risk, specifically deletions of IKZF1 and CDKN2A/B, which occur more frequently among these patients. IKZF1 deletions and rearrangements of CRLF2 among patients with undefined karyotypes may point to the poor risk BCR-ABL1-like group. In conclusion, this study has demonstrated in a large representative cohort of children with B-cell precursor acute lymphoblastic leukemia that the pattern of copy number abnormalities is highly variable according to the primary genetic abnormality.
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Affiliation(s)
- Claire J Schwab
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK
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33
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Mullighan CG. Molecular genetics of B-precursor acute lymphoblastic leukemia. J Clin Invest 2012; 122:3407-15. [PMID: 23023711 DOI: 10.1172/jci61203] [Citation(s) in RCA: 181] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
B-precursor acute lymphoblastic leukemia (B-ALL) is the most common childhood tumor and the leading cause of cancer-related death in children and young adults. The majority of B-ALL cases are aneuploid or harbor recurring structural chromosomal rearrangements that are important initiating events in leukemogenesis but are insufficient to explain the biology and heterogeneity of disease. Recent studies have used microarrays and sequencing to comprehensively identify all somatic genetic alterations in acute lymphoblastic leukemia (ALL). These studies have identified cryptic or submicroscopic genetic alterations that define new ALL subtypes, cooperate with known chromosomal rearrangements, and influence prognosis. This article reviews these advances, discusses results from ongoing second-generation sequencing studies of ALL, and highlights challenges and opportunities for future genetic profiling approaches.
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Affiliation(s)
- Charles G Mullighan
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA.
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34
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Moorman AV. The clinical relevance of chromosomal and genomic abnormalities in B-cell precursor acute lymphoblastic leukaemia. Blood Rev 2012; 26:123-35. [DOI: 10.1016/j.blre.2012.01.001] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Reichard KK, Kang H, Robinett S. Pediatric B-lymphoblastic leukemia with RUNX1 amplification: clinicopathologic study of eight cases. Mod Pathol 2011; 24:1606-11. [PMID: 21822204 DOI: 10.1038/modpathol.2011.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
B-lymphoblastic leukemia (a.k.a. precursor B-cell acute lymphoblastic leukemia) is a heterogeneous disease at the clinical, morphologic, immunophenotypic and genetic levels. Recurrent genetic abnormalities in B-lymphoblastic leukemia with prognostic significance are well known and specifically delineated in the WHO 2008 classification (eg hyperdiploidy, t(9;22)(q34;q11.2); BCR-ABL1, t(12;21)(p13;q22); ETV6-RUNX1). In recent years, a subgroup of B-lymphoblastic leukemia with the recurring genetic alteration of RUNX1 amplification has emerged. This subgroup has a low incidence (2%) and an increased risk of relapse and overall worse outcome. Given these apparently distinctive clinicopathologic features, we evaluated eight cases of pediatric B-lymphoblastic leukemia with RUNX1 amplification treated on Children's Oncology Group protocols from 2000-2009. Compared with 25 consecutive B-lymphoblastic leukemia cases without RUNX1 amplification, we identified a trend toward male predominance (P-value=0.082) and low white blood cell count at presentation (P-value=0.081) in B-lymphoblastic leukemia with RUNX1 amplification. Older age at presentation was significant (median age 9.5 years, P-value=0.006). There was no significant difference in the presence of central nervous system disease, CD20 or myeloid antigen positivity on the blasts or percent circulating blasts in B-lymphoblastic leukemia with RUNX1 amplification versus other B-lymphoblastic leukemia types. Seven of eight patients (88%) are alive and free of disease at the time of last checkup (mean 50 months, range 14-116 months). Although we see a relatively good outcome in our small cohort of patients, recent findings from the Children's Oncology Group on a large set of patients suggests otherwise that these patients may have an inferior outcome compared with patients with B-lymphoblastic leukemia without RUNX1 amplification. Long-term follow-up in larger cohorts including minimal residual disease correlation is required.
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Affiliation(s)
- Kaaren K Reichard
- Department of Pathology, University of New Mexico, Health Sciences Center, Albuquerque, NM, USA.
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36
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37
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Mullighan CG. Genomic profiling of B-progenitor acute lymphoblastic leukemia. Best Pract Res Clin Haematol 2011; 24:489-503. [PMID: 22127311 DOI: 10.1016/j.beha.2011.09.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Childhood acute lymphoblastic leukemia (ALL) is comprised of multiple subtypes defined by recurring chromosomal alterations that are important events in leukemogenesis and are widely used in diagnosis and risk stratification, yet fail to fully explain the biology of this disease. In the last 5 years, genome-wide profiling of gene expression, structural DNA alterations and sequence variations has yielded important insights into the nature of submicroscopic genetic alterations that define novel subgroups of acute lymphoblastic leukemia and cooperate with known cytogenetic alterations in leukemogenesis. Importantly, several of these alterations are important determinants of risk of relapse and are potential targets for therapeutic intervention. Here, these advances and future directions in the genomic analysis of ALL are discussed.
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Affiliation(s)
- Charles G Mullighan
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN 38105, USA.
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38
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Genomic characterization implicates iAMP21 as a likely primary genetic event in childhood B-cell precursor acute lymphoblastic leukemia. Blood 2011; 117:6848-55. [DOI: 10.1182/blood-2011-01-329961] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Intrachromosomal amplification of chromosome 21 (iAMP21) defines a distinct subgroup of childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL) that has a dismal outcome when treated with standard therapy. For improved diagnosis and risk stratification, the initiating genetic events need to be elucidated. To investigate the genetic basis of BCP-ALL, genomes of 94 iAMP21 patients were interrogated by arrays, FISH, and multiplex ligation-dependent probe amplification. Most copy number alterations targeted chromosome 21, reinforcing the complexity of this chromosome. The common region of amplification on chromosome 21 was refined to a 5.1-mb region that included RUNX1, miR-802, and genes mapping to the Down syndrome critical region. Recurrent abnormalities affecting genes in key pathways were identified: IKZF1 (22%), CDKN2A/B (17%), PAX5 (8%), ETV6 (19%), and RB1 (37%). Investigation of clonal architecture provided evidence that these abnormalities, and P2RY8-CRLF2, were secondary to chromosome 21 rearrangements. Patient outcome was uniformly poor with standard therapy irrespective of the presence or absence of these changes. This study has provided evidence that chromosome 21 instability is the only anomaly among those so far investigated that is common to all iAMP21 patients, and therefore the initiating event is likely to be found among the complex structural rearrangements of this abnormal chromosome.
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Sinclair PB, Parker H, An Q, Rand V, Ensor H, Harrison CJ, Strefford JC. Analysis of a breakpoint cluster reveals insight into the mechanism of intrachromosomal amplification in a lymphoid malignancy. Hum Mol Genet 2011; 20:2591-602. [PMID: 21487021 DOI: 10.1093/hmg/ddr159] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A distinct sub-group of B-cell precursor acute lymphoblastic leukemia, defined by intrachromosomal amplification of chromosome 21 (iAMP21), is restricted to older children and has been associated with a poor outcome. Accurate diagnosis is important for appropriate risk stratification for treatment. It could be improved by understanding the initiating mechanism. iAMP21 is characterized by amplification of a 5.1-24 Mb region of chromosome 21, which includes the RUNX1 gene. It is thought to arise through a breakage-fusion-bridge (BFB) mechanism. Breakpoints initiating BFB cycles were determined from recent array data from 18 patients. Three occurred within the PDE9A gene. Other patients with breakpoints in PDE9A were identified by fluorescence in situ hybridization and molecular copy number counting. Sequencing defined a 1.7 Kb breakpoint cluster region, positioned 400 bp distal to an extensive region enriched for CA repeats with the potential to form Z-DNA. None of the rearranged sequences showed the inverted repeat structure characteristic of BFB; instead PDE9A was fused to intergenic regions of chromosome 21 or to genes on other chromosomes. These observations indicated that previously unrecognized complex events, involving microhomology-mediated end joining, preceded or accompanied initiation of the BFB cycle. A chi-like heptomer, CCTCAGC, contained four of the breakpoints, two within PDE9A and two within partner Alu-repeat sequences. This heptomer was closely homologous to a breakpoint hotspot within the TCF3 gene, suggesting involvement of a common novel recombinogenic mechanism that might also contribute to the recombinogenic potential of Alu repeats. These findings provide insight into potential mechanisms involved in the formation of iAMP21.
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Affiliation(s)
- Paul B Sinclair
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle University, Sir James Spence Institute, Royal Victoria Infirmary, Newcastle-upon-Tyne, UK
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Yamamoto K, Shimoyama M, Katayama Y, Matsui T. Unbalanced whole-arm translocation der(18;21)(q10;q10) is a recurrent cytogenetic aberration appearing during progression in myeloid leukemias. Leuk Res 2010; 34:e339-41. [PMID: 20863563 DOI: 10.1016/j.leukres.2010.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 07/31/2010] [Accepted: 08/22/2010] [Indexed: 11/29/2022]
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41
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Harrison CJ, Haas O, Harbott J, Biondi A, Stanulla M, Trka J, Izraeli S. Detection of prognostically relevant genetic abnormalities in childhood B-cell precursor acute lymphoblastic leukaemia: recommendations from the Biology and Diagnosis Committee of the International Berlin-Frankfürt-Münster study group. Br J Haematol 2010; 151:132-42. [DOI: 10.1111/j.1365-2141.2010.08314.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Fonatsch C. The role of chromosome 21 in hematology and oncology. Genes Chromosomes Cancer 2010; 49:497-508. [DOI: 10.1002/gcc.20764] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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De Braekeleer E, Douet-Guilbert N, Morel F, Le Bris MJ, Berthou C, Férec C, De Braekeleer M. RUNX1amplification in B-cell acute lymphoblastic leukemia. Leuk Lymphoma 2009; 51:329-32. [DOI: 10.3109/10428190903456967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Duplication of isodicentric chromosome 21, idic(21)(p11.2), leading to pentasomy 21q in acute myeloid leukemia with multilineage dysplasia. ACTA ACUST UNITED AC 2009; 194:38-43. [DOI: 10.1016/j.cancergencyto.2009.04.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2009] [Revised: 03/30/2009] [Accepted: 04/06/2009] [Indexed: 11/23/2022]
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Moosavi SA, Sanchez J, Adeyinka A. Marker chromosomes are a significant mechanism of high-level RUNX1 gene amplification in hematologic malignancies. ACTA ACUST UNITED AC 2009; 189:24-8. [DOI: 10.1016/j.cancergencyto.2008.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Accepted: 10/08/2008] [Indexed: 10/21/2022]
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Abstract
Cytogenetics has determined the incidence and prognostic significance of chromosomal abnormalities in acute lymphoblastic leukaemia (ALL). The development of fluorescence in situ hybridization (FISH) and array technologies has led to the discovery of novel aberrations. Five 'hot topics' are presented in which cytogenetics and related techniques have been instrumental in understanding the role of genetics in leukaemogenesis: (i) genetic changes are integral to the biology of T-cell ALL; (ii) intrachromosomal amplification of chromosome 21 is a new recurrent abnormality in precursor-B ALL (BCP-ALL); (iii) the immunoglobulin heavy chain gene (IGH@) is significant in BCP-ALL; (iv) alterations in genes involved in B-cell development and cell cycle control contribute to the pathogenesis of BCP-ALL; (v) age-related cytogenetic profiles define ALL in children and adolescents as distinct biological entities. In this molecular era, cytogenetics continues to be integral to our understanding of the genetics of this disease.
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Affiliation(s)
- Christine J Harrison
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK.
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Haltrich I, Csóka M, Kovács G, Fekete G. [Cytogenetic and FISH findings are complementary in childhood ALL]. Magy Onkol 2008; 52:283-91. [PMID: 18845499 DOI: 10.1556/monkol.52.2008.3.6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Primary genetic abnormalities of leukemia cells have important prognostic significance in childhood acute leukemia. In the last two years 30 newly diagnosed or recurrent childhood ALL bone marrow samples were analyzed for chromosomal abnormalities with conventional G-banding and interphase-fluorescence in situ hybridization (I-FISH) using probes to detect BCR/ABL fusions, cryptic TEL/AML1 and MLL rearrangements and p16(9p21) tumor suppressor gene deletions. G-banded karyotype analysis found clonal chromosomal aberrations in 50% of cases. With the use of complementary I-FISH techniques, ALL-specific structural and numerical changes could be identified in 70% of the patients. Nine cases (30%) had subtle chromosomal aberrations with prognostic importance that had not been detected in G-banded analysis. Conventional G-banding yielded additional information (rare and complex structural aberrations) in 19% of patients. The most common aberration (30%) was AML1 copy number increase present in G-banded hyperdiploid karyotype as a chromosome 21 tetrasomy in the majority of cases; one case displayed 5-6 copies and in another case amplification of AML1 gene on der(21) was combined with TEL/AML1 fusion of the homologue AML1 gene and deletion of the remaining TEL allele. High hiperdiploidy was detected in 6 cases, in one patient with normal G-banding karyotype. TEL/AML1 fusion signals were identified in four patients. Deletion of p16 locus was found in eight cases (23%), of which only two had cytogenetically visible rearrangements. G-banding in combination with I-FISH has produced major improvements in the sensitivity and accuracy of cytogenetic analysis of ALL patients and this method helps to achieve a more precise identification of different risk categories in order to choose the optimal treatment.
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Affiliation(s)
- Irén Haltrich
- Semmelweis Egyetem II. sz. Gyermekgyógyászati Klinika 1094 Budapest Tuzoltó utca 7-9.
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Kitada K, Yamasaki T. The complicated copy number alterations in chromosome 7 of a lung cancer cell line is explained by a model based on repeated breakage-fusion-bridge cycles. ACTA ACUST UNITED AC 2008; 185:11-9. [PMID: 18656688 DOI: 10.1016/j.cancergencyto.2008.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 03/31/2008] [Accepted: 04/07/2008] [Indexed: 10/21/2022]
Abstract
The drug-resistant lung cancer cell line PTX250, which has been previously established by exposure to an anti-cancer drug paclitaxel, has an increased copy number in the MDR1/ABCB1 locus region. In addition, the flanking regions also exhibit aberrant copy numbers, making the copy number profile of chromosome 7 complicated. In this study, we tested whether the breakage-fusion-bridge (BFB) cycle model can explain such copy number alterations. An analysis using fluorescence in situ hybridization (FISH) with a painting probe demonstrated that the aberrant chromosome, designated chromosome 7(amp), was derived from an intact chromosome 7. Using high-density comparative genomic hybridization arrays, we examined the copy number profile in detail and divided chromosome 7(amp) into seven segments. Based on copy numbers of each segment, which were determined using interphase- and metaphase-FISH analysis, we constructed a formation model for the complicated copy number alteration. Six-time BFB cycles and the cycle-termination by healing of broken ends were presupposed in the model. Locations and orientations of the segments observed in chromosome 7(amp) agreed well with those predicted from the model. Telomere addition was also cytogenetically confirmed. In all, it could be concluded that the complicated copy number alteration found in chromosome 7(amp) is generated from the intact chromosome 7 by the repeated BFB cycles.
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Affiliation(s)
- Kunio Kitada
- Kamakura Research Laboratories, Chugai Pharmaceutical Co. Ltd., 200-Kajiwara, Kamakura, Kanagawa 247-8530, Japan.
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Haltrich I, Csóka M, Kovács G, Fekete G. [Intrachromosomal amplification of AML1 gene in childhood acute lymphoblastic leukemia]. Orv Hetil 2008; 149:1143-6. [PMID: 18539581 DOI: 10.1556/oh.2008.28388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The introduction of routine molecular cytogenetic assays enabled us to reveal hitherto unknown genetic disorders of childhood acute leukemias. Of special interest is the recognition of those rare cytogenetic mutations of negative prognostic value, which are associated with well-known markers of good prognosis. In our present study we review a novel cytogenetic mutation typical for childhood B-cell ALL, the intrachromosomal amplification of chromosome 21, which requires high-risk therapy irrespective of other risk factors, and which is associated with a cryptic 12;21 translocation of good prognostic value.
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Affiliation(s)
- Irén Haltrich
- Semmelweis Egyetem, Altalános Orvostudományi Kar, II. Gyermekgyógyászati Klinika, Budapest.
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