1
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Cheng W, Wang W, Zhu H, Song X, Wu K, Li J. Detection of Antimalarial Resistance-Associated Mutations in Plasmodium falciparum via a Platform of Allele-Specific PCR Combined with a Gold Nanoparticle-Based Lateral Flow Assay. Microbiol Spectr 2022; 10:e0253522. [PMID: 36445076 PMCID: PMC9769821 DOI: 10.1128/spectrum.02535-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022] Open
Abstract
Since single nucleotide polymorphisms (SNPs) have attracted attention, there have been many explorations and improvements in screening and detection methods for SNPs. Traditional methods are complex and time-consuming and rely on expensive instruments. Therefore, there is an urgent need for a low-cost, simple, and accurate method that is convenient for use in resource-poor areas. Thus, a platform based on allele-specific PCR (AS-PCR) and a gold nanoparticle-based lateral flow assay (LFA) was developed, optimized, and used to detect the SNPs of the drug resistance gene pfmdr1. Subsequently, the system was assessed on clinical isolates and compared with nested PCR followed by Sanger sequencing. The sensitivity and specificity of the AS-PCR-LFA platform were up to 99.43% and 100%, respectively, based on the clinical isolates. The limit of detection is approximately 150 fg/μL for plasmid DNA as the template and 50 parasites/μL for dried filter blood spots from clinical isolates. The established and optimized AS-PCR-LFA system is more adaptable and rapidly translated to SNP analysis of other drug resistance genes and genetic diseases. In addition, while actively responding to the point-of-care testing policy, it also contributes to the Global Malaria Eradication Program. IMPORTANCE Rapid detection of single nucleotide polymorphisms (SNPs) is essential for malaria treatment. Based on the techniques of allele-specific PCR (AS-PCR) and lateral flow assay (LFA), an accurate and powerful platform for SNP detection of pfmdr1 was developed and evaluated with plasmid and clinical isolates. It offers a useful tool to identify antimalarial drug resistance and can support the effort to eliminate malaria globally.
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Affiliation(s)
- Weijia Cheng
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Department of Clinical Laboratory, Wuchang Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, China
| | - Wei Wang
- Key Laboratory of National Health Commission on Parasitic Disease Prevention and Control, Jiangsu Provincial Key Laboratory on Parasites and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Huiyin Zhu
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Xiaonan Song
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Kai Wu
- Department of Schistosomiasis and Endemic Diseases, Wuhan City Center for Disease Prevention and Control, Wuhan, China
| | - Jian Li
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
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2
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Lejman M, Chałupnik A, Chilimoniuk Z, Dobosz M. Genetic Biomarkers and Their Clinical Implications in B-Cell Acute Lymphoblastic Leukemia in Children. Int J Mol Sci 2022; 23:ijms23052755. [PMID: 35269896 PMCID: PMC8911213 DOI: 10.3390/ijms23052755] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/27/2022] [Accepted: 02/28/2022] [Indexed: 02/04/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is a heterogeneous group of hematologic malignancies characterized by abnormal proliferation of immature lymphoid cells. It is the most commonly diagnosed childhood cancer with an almost 80% cure rate. Despite favorable survival rates in the pediatric population, a significant number of patients develop resistance to therapy, resulting in poor prognosis. ALL is a heterogeneous disease at the genetic level, but the intensive development of sequencing in the last decade has made it possible to broaden the study of genomic changes. New technologies allow us to detect molecular changes such as point mutations or to characterize epigenetic or proteomic profiles. This process made it possible to identify new subtypes of this disease characterized by constellations of genetic alterations, including chromosome changes, sequence mutations, and DNA copy number alterations. These genetic abnormalities are used as diagnostic, prognostic and predictive biomarkers that play an important role in earlier disease detection, more accurate risk stratification, and treatment. Identification of new ALL biomarkers, and thus a greater understanding of their molecular basis, will lead to better monitoring of the course of the disease. In this article, we provide an overview of the latest information on genomic alterations found in childhood ALL and discuss their impact on patients' clinical outcomes.
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Affiliation(s)
- Monika Lejman
- Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
- Correspondence:
| | - Aleksandra Chałupnik
- Student Scientific Society, Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland; (A.C.); (Z.C.); (M.D.)
| | - Zuzanna Chilimoniuk
- Student Scientific Society, Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland; (A.C.); (Z.C.); (M.D.)
| | - Maciej Dobosz
- Student Scientific Society, Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland; (A.C.); (Z.C.); (M.D.)
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3
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Honda T, Yamaoka M, Terao YM, Hasegawa D, Kumamoto T, Takagi M, Yoshida K, Ogawa S, Goto H, Akiyama M. Successful treatment of hepatosplenic T-cell lymphoma with fludarabine, high-dose cytarabine and subsequent unrelated umbilical cord blood transplantation. Int J Hematol 2022; 115:140-145. [PMID: 34591292 DOI: 10.1007/s12185-021-03229-0] [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: 04/21/2021] [Revised: 09/21/2021] [Accepted: 09/26/2021] [Indexed: 11/30/2022]
Abstract
Hepatosplenic T-cell lymphoma (HSTCL) is a rare subtype of peripheral T-cell lymphoma that occurs most often in adolescents and young adults and is rare in children. Because of the aggressive clinical course, resistance to conventional chemotherapy and poor prognosis of HSTCL, an effective treatment has not been established. We report the case of a 3-year-old girl with HSTCL presenting with trilineage myelodysplasia. Although the HSTCL was refractory to conventional chemotherapy, remission was achieved with salvage chemotherapy that included fludarabine and cytarabine, which were shown to be effective in the drug sensitivity assay. After undergoing umbilical cord blood transplantation with a conditioning regimen consisting of etoposide, cyclophosphamide and total body irradiation, the patient has remained in complete remission for 8 years. Single-nucleotide polymorphism array analysis revealed heterozygous deletions of PAX5 (9p), ETV6 (12p) and homozygous deletions of CDKN2A (9p). Exome analysis showed a heterozygous nonsense c.2961C>G (p.Tyr987Ter) variant of the KMT2C gene. To improve the poor prognosis of HSTCL, the chemotherapeutic regimen can be selected for each patient on the basis of drug sensitivity and molecular genetic characteristics.
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Affiliation(s)
- Takaya Honda
- Department of Pediatrics, The Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Masayoshi Yamaoka
- Department of Pediatrics, The Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Yoko Mikami Terao
- Department of Pediatrics, The Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Daisuke Hasegawa
- Department of Pediatrics, St. Luke's International Hospital, Tokyo, Japan
| | - Tadashi Kumamoto
- Department of Pediatric Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Masatoshi Takagi
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Hiroaki Goto
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Masaharu Akiyama
- Department of Pediatrics, The Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, Tokyo, 105-8461, Japan.
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4
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Ling Y, Xu N, Zhao K, Han L, Zhang Q, Fan Z, Huang F, Chen Z, Xuan L, Liu H, Xu J, Chen X, Yu S, Zhou H, Sun J, Liu Q. Allogeneic hematopoietic cell transplant overcomes the poor prognostic value of CDKN2 deletion in adult B-lineage acute lymphoblastic leukemia. Cancer Lett 2021; 510:59-66. [PMID: 33901594 DOI: 10.1016/j.canlet.2021.04.009] [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: 03/03/2021] [Revised: 04/09/2021] [Accepted: 04/13/2021] [Indexed: 10/21/2022]
Abstract
Emerging evidence suggested that CDKN2 deletion was a poor prognosis predictor in adult B-lineage acute lymphoblastic leukemia (B-ALL). Here, we investigated the effect of allogeneic hematopoietic cell transplant (allo-HCT) on adult B-ALL with CDKN2 deletion. The patients with adult B-ALL underwent more than two courses of chemotherapy were enrolled in the multicenter retrospective study. Relapse and survival were analyzed. A total of 1336 adult B-ALL, including 295 patients with CDKN2 deletion and 1041 wild-type (WT), from five institutes were enrolled. The complete remission (CR) rates were 86.8% and 91.1% (P = 0.229) after two cycles of chemotherapy in patients with CDKN2 deletion and WT, respectively. The 5-year cumulative relapse post-CR were 56% (95% CI, 52-68) and 43% (95% CI, 40-51) (P < 0.001), 5-year disease-free survival (DFS) were 30% (95% CI, 24-36) and 41% (95% CI, 39-46) (P < 0.001), and 5-year overall survival (OS) were 35% (95% CI, 28-39) and 47% (95% CI, 44-49) (P < 0.001) in the two groups, respectively. Subgroup analysis revealed that the 5-year relapse were 89.3% (95% CI, 83.0-96.5) and 68.4% (95% CI, 60.2-72.5) (P < 0.001), 5-year DFS were 4.9% (95% CI, 1.8-10.4) and 22.7% (95% CI, 18.0-27.7) (P < 0.001), and 5-year OS were 6.9% (95% CI, 3.1-12.9) and 23.4% (95% CI, 18.7-28.6) (P < 0.001) in CDKN2 deletion and WT groups undergoing chemotherapy alone, respectively, while there were not different in terms of 5-year relapse (38.1% vs 34.3%, P = 0.211), DFS (48.4% vs 52.2%, P = 0.325) and OS (54.5% vs 56.3%, P = 0.483) between those with CDKN2 deletion and WT undergoing allo-HCT. Multivariate analysis showed that CDKN2 deletion and high-risk stratification both were the risk factors for relapse, DFS and OS, while allo-HCT was a protective factor. CDKN2 deletion might be a poor prognostic predictor of adult B-ALL. Adult B-ALL with CDKN2 deletion might benefit from allo-HCT.
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Affiliation(s)
- Yiwen Ling
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China; Department of Hematology, The First People's Hospital of Foshan, Foshan, China
| | - Na Xu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ke Zhao
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Lijie Han
- Department of Hematology, Henan Cancer Hospital, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Qing Zhang
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Zhiping Fan
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Fen Huang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhuowen Chen
- Department of Hematology, The First People's Hospital of Foshan, Foshan, China
| | - Li Xuan
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hui Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jun Xu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaoxia Chen
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Sijian Yu
- Department of Hematology, Nanhai Hospital, Southern Medical University, Foshan, China
| | - Hongsheng Zhou
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jing Sun
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qifa Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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5
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Klco JM, Mullighan CG. Advances in germline predisposition to acute leukaemias and myeloid neoplasms. Nat Rev Cancer 2021; 21:122-137. [PMID: 33328584 PMCID: PMC8404376 DOI: 10.1038/s41568-020-00315-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/28/2020] [Indexed: 12/17/2022]
Abstract
Although much work has focused on the elucidation of somatic alterations that drive the development of acute leukaemias and other haematopoietic diseases, it has become increasingly recognized that germline mutations are common in many of these neoplasms. In this Review, we highlight the different genetic pathways impacted by germline mutations that can ultimately lead to the development of familial and sporadic haematological malignancies, including acute lymphoblastic leukaemia, acute myeloid leukaemia (AML) and myelodysplastic syndrome (MDS). Many of the genes disrupted by somatic mutations in these diseases (for example, TP53, RUNX1, IKZF1 and ETV6) are the same as those that harbour germline mutations in children and adolescents who develop these malignancies. Moreover, the presumption that familial leukaemias only present in childhood is no longer true, in large part due to the numerous studies demonstrating germline DDX41 mutations in adults with MDS and AML. Lastly, we highlight how different cooperating events can influence the ultimate phenotype in these different familial leukaemia syndromes.
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Affiliation(s)
- Jeffery M Klco
- Department of Pathology and the Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Charles G Mullighan
- Department of Pathology and the Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, USA.
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6
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Lejman M, Włodarczyk M, Styka B, Pastorczak A, Zawitkowska J, Taha J, Sędek Ł, Skonieczka K, Braun M, Haus O, Szczepański T, Młynarski W, Kowalczyk JR. Advantages and Limitations of SNP Array in the Molecular Characterization of Pediatric T-Cell Acute Lymphoblastic Leukemia. Front Oncol 2020; 10:1184. [PMID: 32766158 PMCID: PMC7379740 DOI: 10.3389/fonc.2020.01184] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/11/2020] [Indexed: 01/03/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a highly heterogeneous disease, and numerous genetic aberrations in the leukemic genome are responsible for the biological and clinical differences among particular ALL subtypes. However, there is limited knowledge regarding the association of whole-genome copy number abnormalities (CNAs) in childhood T-ALL with the course of leukemia and its outcome. The aim of this study was to identify the pattern of whole-genome CNAs in 86 newly diagnosed childhood T-ALL cases using a high-density single-nucleotide polymorphism array. We analyzed the presence of whole-genome CNAs with respect to immunophenotype, clinical features, and treatment outcomes. A total of 769 CNAs, including trisomies, duplications, deletions, and segmental loss of heterozygosity, were detected in 86 analyzed samples. Gain or loss of chromosomal regions exceeding 10 Mb occurred in 46 cases (53%), including six cases (7%) with complex chromosomal alterations. We observed that microdeletions in selected genes (e.g., FIP1L1 and PDGFRB) were related to the clinical features. Interestingly, 13% of samples have a duplication of the two loci (MYB and AIH1—6q23.3), which never occurred alone. Single-nucleotide polymorphism array significantly improved the molecular characterization of pediatric T-ALL. Further studies with larger cohorts of patients may contribute to the selection of prognostic CNAs in this group of patients.
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Affiliation(s)
- Monika Lejman
- Laboratory of Genetic Diagnostics, Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Lublin, Poland
| | - Monika Włodarczyk
- Laboratory of Genetic Diagnostics, University Children's Hospital, Lublin, Poland
| | - Borys Styka
- Laboratory of Genetic Diagnostics, University Children's Hospital, Lublin, Poland
| | - Agata Pastorczak
- Department of Pediatric, Oncology, Hematology and Diabetology, Medical University of Łódz, Łódź, Poland
| | - Joanna Zawitkowska
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Lublin, Poland
| | - Joanna Taha
- Department of Pediatric, Oncology, Hematology and Diabetology, Medical University of Łódz, Łódź, Poland
| | - Łukasz Sędek
- Department of Microbiology and Oncology, Medical University of Silesia in Katowice, Katowice, Poland
| | - Katarzyna Skonieczka
- Department of Clinical Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Marcin Braun
- Department of Pathology, Chair of Oncology, Medical University of Łódz, Łódź, Poland
| | - Olga Haus
- Department of Clinical Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Tomasz Szczepański
- Department of Microbiology and Oncology, Medical University of Silesia in Katowice, Katowice, Poland
| | - Wojciech Młynarski
- Department of Pediatric, Oncology, Hematology and Diabetology, Medical University of Łódz, Łódź, Poland
| | - Jerzy R Kowalczyk
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Lublin, Poland
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7
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Berry NK, Scott RJ, Sutton R, Law T, Trahair TN, Dalla-Pozza L, Ritchie P, Barbaric D, Enjeti AK. Enrichment of atypical hyperdiploidy and IKZF1 deletions detected by SNP-microarray in high-risk Australian AIEOP-BFM B-cell acute lymphoblastic leukaemia cohort. Cancer Genet 2020; 242:8-14. [PMID: 32058318 DOI: 10.1016/j.cancergen.2020.01.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 01/11/2020] [Accepted: 01/28/2020] [Indexed: 02/07/2023]
Abstract
Acute lymphoblastic leukaemia (ALL) is the most common childhood malignancy with the majority of patients being classified as B-cell lineage (B-ALL). The sub-classification of B-ALL is based on genomic architecture. Recent studies have demonstrated the capability of SNP-microarrays to detect genomic changes in B-ALL which cannot be observed by conventional cytogenetic methods. In current clinical trials, B-ALL patients at high risk of relapse are mainly identified by adverse cancer genomics and/or poor response to early therapy. To test the hypothesis that inclusion of SNP-microarrays in frontline diagnostics could more efficiently and accurately identify adverse genomic factors than conventional techniques, we evaluated the Australian high-risk B-ALL cohort enrolled on AIEOP-BFM ALL 2009 study (n = 33). SNP-microarray analysis identified additional aberrations in 97% of patients (32/33) compared to conventional techniques. This changed the genomic risk category of 24% (8/33) of patients. Additionally, 27% (9/33) of patients exhibited a 'hyperdiploid' genome, which is generally associated with a good genomic risk and favourable outcomes. An enrichment of IKZF1 deletions was observed with one third of the cohort affected. Our findings suggest the current classification system could be improved and highlights the need to use more sensitive techniques such as SNP-microarray for cytogenomic risk stratification in B-ALL.
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Affiliation(s)
- Nadine K Berry
- Department of Haematology, Calvary Mater Hospital, Newcastle, New South Wales, Australia; School of Biomedical Sciences and Pharmacy, University of Newcastle, New South Wales, Australia; Department of Molecular Medicine, NSW Health Pathology-Hunter, Newcastle, New South Wales, Australia.
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, New South Wales, Australia; Department of Molecular Medicine, NSW Health Pathology-Hunter, Newcastle, New South Wales, Australia
| | - Rosemary Sutton
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Randwick, Australia; School of Women's and Children's Health, UNSW Medicine, Randwick, Australia
| | - Tamara Law
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Randwick, Australia
| | - Toby N Trahair
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Randwick, Australia; School of Women's and Children's Health, UNSW Medicine, Randwick, Australia; Kids Cancer Centre, Sydney Children's Hospital, Randwick Australia
| | - Luce Dalla-Pozza
- Cancer Centre for Children, The Children's Hospital at Westmead, Australia
| | - Petra Ritchie
- Women's and Children's Hospital, SA Pathology, University of Adelaide, Adelaide, Australia
| | - Draga Barbaric
- School of Women's and Children's Health, UNSW Medicine, Randwick, Australia; Kids Cancer Centre, Sydney Children's Hospital, Randwick Australia
| | - Anoop K Enjeti
- Department of Haematology, Calvary Mater Hospital, Newcastle, New South Wales, Australia; School of Medicine and Public Health, University Newcastle, New South Wales, Australia; Department of Haematology, NSW Health Pathology-Hunter, Newcastle, New South Wales, Australia
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8
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Coccaro N, Anelli L, Zagaria A, Specchia G, Albano F. Next-Generation Sequencing in Acute Lymphoblastic Leukemia. Int J Mol Sci 2019; 20:ijms20122929. [PMID: 31208040 PMCID: PMC6627957 DOI: 10.3390/ijms20122929] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/04/2019] [Accepted: 06/14/2019] [Indexed: 12/25/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer and accounts for about a quarter of adult acute leukemias, and features different outcomes depending on the age of onset. Improvements in ALL genomic analysis achieved thanks to the implementation of next-generation sequencing (NGS) have led to the recent discovery of several novel molecular entities and to a deeper understanding of the existing ones. The purpose of our review is to report the most recent discoveries obtained by NGS studies for ALL diagnosis, risk stratification, and treatment planning. We also report the first efforts at NGS use for minimal residual disease (MRD) assessment, and early studies on the application of third generation sequencing in cancer research. Lastly, we consider the need for the integration of NGS analyses in clinical practice for genomic patients profiling from the personalized medicine perspective.
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Affiliation(s)
- Nicoletta Coccaro
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
| | - Luisa Anelli
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
| | - Antonella Zagaria
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
| | - Giorgina Specchia
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
| | - Francesco Albano
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
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9
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Lejman M, Zawitkowska J, Styka B, Babicz M, Winnicka D, Zaucha-Prażmo A, Pastorczak A, Taha J, Młynarski W, Kowalczyk JR. Microarray testing as an efficient tool to redefine hyperdiploid paediatric B-cell precursor acute lymphoblastic leukaemia patients. Leuk Res 2019; 83:106163. [PMID: 31202078 DOI: 10.1016/j.leukres.2019.05.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/24/2019] [Accepted: 05/25/2019] [Indexed: 11/15/2022]
Abstract
The aim of our study was to characterize genetic alterations in a cohort of paediatric patients with B-cell progenitors (BCP-ALL) and a hyperdiploid karyotype. In our study, we analysed 55 childhood hyperdiploid BCP-ALL patients using single nucleotide polymorphism (SNP) microarray testing. The group consisted mostly of patients with the modal number of chromosomes between 54 and 58 (34 cases). Within this group, Trisomy 4 and Trisomy 10 (30 cases) were the most frequent cases. Additionally, a total of 93 structural abnormalities mainly affecting chromosomes 1, 6, 9, 12, and 17 as well as 68 copy number alterations (CNAs) were identified. The microarray testing revealed a loss of ETV6, IKZF1, CDKN2A/CDKN2B, PAX5, and RB1. Moreover, chromosomal abnormalities resulting in the loss of heterozygosity (LOH) were also observed. Currently, patients with hyperdiploidy constitute a genetically heterogeneous group, and therefore, it is insufficient to rely only on banding cytogenetic analysis for the identification of hyperdiploid karyotype. Microarray testing has been proven an effective and satisfactory tool for the analysis of molecular karyotypes and to redefine the prognostic criteria in hyperdiploid patients.
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Affiliation(s)
- Monika Lejman
- Laboratory of Genetic Diagnostics, Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Poland
| | - Joanna Zawitkowska
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Poland
| | - Borys Styka
- Laboratory of Genetic Diagnostics, University Children's Hospital, Lublin, Poland
| | - Mariusz Babicz
- Laboratory of Genetic Diagnostics, University Children's Hospital, Lublin, Poland
| | - Dorota Winnicka
- Laboratory of Genetic Diagnostics, Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Poland
| | - Agnieszka Zaucha-Prażmo
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Poland
| | - Agata Pastorczak
- Department of Pediatric, Oncology, Hematology and Diabetology, Medical University of Łódź, Poland
| | - Joanna Taha
- Department of Pediatric, Oncology, Hematology and Diabetology, Medical University of Łódź, Poland
| | - Wojciech Młynarski
- Department of Pediatric, Oncology, Hematology and Diabetology, Medical University of Łódź, Poland
| | - Jerzy R Kowalczyk
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Poland
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10
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Sinclair PB, Ryan S, Bashton M, Hollern S, Hanna R, Case M, Schwalbe EC, Schwab CJ, Cranston RE, Young BD, Irving JAE, Vora AJ, Moorman AV, Harrison CJ. SH2B3 inactivation through CN-LOH 12q is uniquely associated with B-cell precursor ALL with iAMP21 or other chromosome 21 gain. Leukemia 2019; 33:1881-1894. [PMID: 30816328 PMCID: PMC6756024 DOI: 10.1038/s41375-019-0412-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 01/24/2019] [Indexed: 12/17/2022]
Abstract
In more than 30% of B-cell precursor acute lymphoblastic leukaemia (B-ALL), chromosome 21 sequence is overrepresented through aneuploidy or structural rearrangements, exemplified by intrachromosomal amplification of chromosome 21 (iAMP21). Although frequent, the mechanisms by which these abnormalities promote B-ALL remain obscure. Intriguingly, we found copy number neutral loss of heterozygosity (CN-LOH) of 12q was recurrent in iAMP21-ALL, but never observed in B-ALL without some form of chromosome 21 gain. As a consequence of CN-LOH 12q, mutations or deletions of the adaptor protein, SH2B3, were converted to homozygosity. In patients without CN-LOH 12q, bi-allelic abnormalities of SH2B3 occurred, but only in iAMP21-ALL, giving an overall incidence of 18% in this sub-type. Review of published data confirmed a tight association between overrepresentation of chromosome 21 and both CN-LOH 12q and SH2B3 abnormalities in B-ALL. Despite relatively small patient numbers, preliminary analysis linked 12q abnormalities to poor outcome in iAMP21-ALL (p = 0.03). Homology modelling of a leukaemia-associated SH2 domain mutation and in vitro analysis of patient-derived xenograft cells implicated the JAK/STAT pathway as one likely target for SH2B3 tumour suppressor activity in iAMP21-ALL.
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Affiliation(s)
- Paul B Sinclair
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK.
| | - Sarra Ryan
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK
| | - Matthew Bashton
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK
| | - Shaun Hollern
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK
| | - Rebecca Hanna
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK
| | - Marian Case
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK
| | - Edward C Schwalbe
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Claire J Schwab
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK
| | - Ruth E Cranston
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK
| | - Brian D Young
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Julie A E Irving
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK
| | - Ajay J Vora
- Great Ormond Street Hospital for Children NHS trust, London, UK
| | - Anthony V Moorman
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK
| | - Christine J Harrison
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK.
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11
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Zhang W, Kuang P, Liu T. Prognostic significance of CDKN2A/B deletions in acute lymphoblastic leukaemia: a meta-analysis. Ann Med 2019; 51:28-40. [PMID: 30592434 PMCID: PMC7857473 DOI: 10.1080/07853890.2018.1564359] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Cyclin-dependent kinase inhibitor 2A/B (CDKN2A/B) genes are frequently altered in acute lymphoblastic leukaemia (ALL) patients. The aim of this meta-analysis was to comprehensively assess the prognostic value of CDKN2A/B deletions in ALL patients. METHODS Systematic literature review was conducted in PubMed, Embase and Cochrane databases up to July 2018. Pooled hazard ratios (HRs) with 95% confidence intervals (CIs) were calculated with fixed-effects or random-effects models. RESULTS A total of thirteen studies including 2857 patients were eligible for this meta-analysis. Combined HRs suggested that CDKN2A/B deletions were poor prognostic factors for both overall survival (OS) (HR = 2.15, 95% CI 1.82-2.54) and event-free survival (EFS)/disease-free survival (DFS)/relapse-free survival (RFS) (HR = 2.16, 95% CI 1.73-2.69). The adverse impact remained significant in both adult and paediatric ALL patients, and also in subgroups by ethnicity, ALL type, detection method of CDKN2A/B deletions, statistical method and endpoint. CONCLUSIONS Our findings suggested that CDKN2A/B deletions were associated with poor prognosis independently in both adult and childhood ALL patients. Inclusion of CDKN2A/B status may further improve the risk stratification of ALL patients. Key Messages Although numerous studies have explored the prognostic significance of cyclin-dependent kinase inhibitor 2A/B (CDKN2A/B) deletions in acute lymphoblastic leukaemia (ALL) patients, the results remain conflicting. In this meta-analysis, we found that CDKN2A/B deletions were independent poor prognostic markers for both adult and paediatric ALL patients. Our findings justify the inclusion of CDKN2A/B status in the risk stratification of ALL patients.
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Affiliation(s)
- Wanhua Zhang
- a Department of Haematology , West China Hospital, Sichuan University , Chengdu , P.R. China
| | - Pu Kuang
- a Department of Haematology , West China Hospital, Sichuan University , Chengdu , P.R. China
| | - Ting Liu
- a Department of Haematology , West China Hospital, Sichuan University , Chengdu , P.R. China
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12
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Abstract
Treatment outcomes for acute lymphoblastic leukemia (ALL), especially pediatric ALL, have greatly improved due to the risk-adapted therapy. Combination of drug development, clinical practice, as well as basic genetic researches has brought the survival rate of ALL from less than 10% to more than 90% today, not only increasing the treatment efficacy but also limiting adverse drug reactions (ADRs). In this review, we summarized the landscape identification of ALL genetic alterations, which provided the opportunity to increase the survival rate and especially minimize the relapse risk of ALL, and highlighted the importance of the development of new technologies of genomic investigation for translational medicine.
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13
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Agarwal M, Bakhshi S, Dwivedi SN, Kabra M, Shukla R, Seth R. Cyclin dependent kinase inhibitor 2A/B gene deletions are markers of poor prognosis in Indian children with acute lymphoblastic leukemia. Pediatr Blood Cancer 2018; 65:e27001. [PMID: 29446543 DOI: 10.1002/pbc.27001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/22/2017] [Accepted: 01/08/2018] [Indexed: 11/09/2022]
Abstract
BACKGROUND Cyclin dependent kinase inhibitor 2A/B (CDKN2A/B) genes are implicated in many malignancies including acute lymphoblastic leukemia (ALL). These tumor suppressor genes, with a key regulatory role in cell cycle are located on chromosome 9p21.3. Previous studies involving CDKN2A/B gene deletions have shown mixed associations with survival outcome in childhood ALL. PROCEDURE Hundred and four newly diagnosed children with ALL (1-14 years) were enrolled in this study. Genomic DNA from pretreatment bone marrow/peripheral blood samples of these children was investigated for copy number alterations in CDKN2A/B genes using multiplex ligation dependent probe amplification assay. Immunophenotype subtyping and cytogenetic and molecular analysis of ALL was performed at start of induction chemotherapy in all children. Children were monitored for response to prednisolone (Day 8), complete morphological remission, and minimal residual disease at the end of induction. The minimum postinduction follow-up period was 6 months. RESULTS CDKN2A/B deletions were seen in 19.8% (18/91) of B lineage acute lymphoblastic leukemia (B-ALL) and 38.5% (5/13) of T lineage acute lymphoblastic leukemia (T-ALL). Monoallelic CDKN2A/B deletions were found in 61.1% of total deletions in B-ALL while all the children with T-ALL harbored biallelic deletions. The prevalence of CDKN2A/B gene deletions was found to be significantly higher in older children (P = 0.002), in those with higher leukocyte count (P = 0.037), and in National Cancer Institute high risk group patients (P = 0.001) in the B-ALL subgroup. Hazard ratio was significantly high for children with CDKN2A/B deletions in total cohort (P = 0.004). Children with CDKN2A/B deletion had significantly lesser event free survival (P = 0.03). CONCLUSIONS CDKN2A/B deletions were significantly more prevalent in T-ALL subgroup and were found to have higher hazard ratio and lesser event free survival in total cohort in our study.
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Affiliation(s)
- Manisha Agarwal
- Division of Oncology, Department of Paediatrics, All India Institute of Medical Science, New Delhi, India
| | - Sameer Bakhshi
- Dr BR Ambedkar Institute of Rotary Club and Hospital, All India Institute of Medical Science, New Delhi, India
| | - Sadanand N Dwivedi
- Department of Biostatistics, All India Institute of Medical Science, New Delhi, India
| | - Madhulika Kabra
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Science, New Delhi, India
| | - Rashmi Shukla
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Science, New Delhi, India
| | - Rachna Seth
- Division of Oncology, Department of Paediatrics, All India Institute of Medical Science, New Delhi, India
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14
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Heng HH, Horne SD, Chaudhry S, Regan SM, Liu G, Abdallah BY, Ye CJ. A Postgenomic Perspective on Molecular Cytogenetics. Curr Genomics 2018; 19:227-239. [PMID: 29606910 PMCID: PMC5850511 DOI: 10.2174/1389202918666170717145716] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/29/2017] [Accepted: 02/03/2017] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The postgenomic era is featured by massive data collection and analyses from various large scale-omics studies. Despite the promising capability of systems biology and bioinformatics to handle large data sets, data interpretation, especially the translation of -omics data into clinical implications, has been challenging. DISCUSSION In this perspective, some important conceptual and technological limitations of current systems biology are discussed in the context of the ultimate importance of the genome beyond the collection of all genes. Following a brief summary of the contributions of molecular cytogenetics/cytogenomics in the pre- and post-genomic eras, new challenges for postgenomic research are discussed. Such discussion leads to a call to search for a new conceptual framework and holistic methodologies. CONCLUSION Throughout this synthesis, the genome theory of somatic cell evolution is highlighted in contrast to gene theory, which ignores the karyotype-mediated higher level of genetic information. Since "system inheritance" is defined by the genome context (gene content and genomic topology) while "parts inheritance" is defined by genes/epigenes, molecular cytogenetics and cytogenomics (which directly study genome structure, function, alteration and evolution) will play important roles in this postgenomic era.
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Affiliation(s)
- Henry H. Heng
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Steven D. Horne
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sophia Chaudhry
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sarah M. Regan
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Guo Liu
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Batoul Y. Abdallah
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Christine J. Ye
- The Division of Hematology/Oncology, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI, USA
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15
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Kato M, Manabe A. Treatment and biology of pediatric acute lymphoblastic leukemia. Pediatr Int 2018; 60:4-12. [PMID: 29143423 DOI: 10.1111/ped.13457] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 10/26/2017] [Accepted: 11/10/2017] [Indexed: 12/12/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy. In the past ALL was intractable but now the survival probability is as high as 80-90%. Improved supportive care, treatment stratification based on relapse risk, biological features of leukemic cells, and optimization of treatment regimens by nationwide and international collaboration have contributed to this dramatic improvement. While including traditional risk factors (e.g. age and leukocyte count at diagnosis), the treatment has been modified based on biological characteristics (aneuploidy and translocation) and treatment response (assessed by minimal residual disease). Treatment for pediatric ALL typically consists of induction therapy with steroids, vincristine, and asparaginase with or without anthracycline, followed by multi-agent consolidation including high-dose methotrexate and re-induction therapy. After consolidation, less intensive maintenance therapy is required for 1-2 years to maintain event-free survival. Recently, using advanced genomic analysis technology, novel sentinel genomic alterations that may provide more precise stratification or therapeutic targets, were identified. Moreover, in the last decade germline variations have been recognized as similarly important contributors to understanding the etiology and sensitivity of ALL to treatment. A more individualized approach based on genomic features (somatic and germline) and treatment response, the introduction of newly developed agents such as molecular targeted drugs or immunotherapy, and social support including long-term follow up are required for further improvement.
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Affiliation(s)
- Motohiro Kato
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan.,Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Atsushi Manabe
- Department of Pediatrics, St Luke's International Hospital, Tokyo, Japan.,Research Center, St Luke's International University, Tokyo, Japan
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16
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Genomic analysis of adult B-ALL identifies potential markers of shorter survival. Leuk Res 2017; 56:44-51. [DOI: 10.1016/j.leukres.2017.01.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/02/2017] [Accepted: 01/29/2017] [Indexed: 11/17/2022]
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17
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Kjeldsen E. Characterization of a novel acquired der(1)del(1)(p13p31)t(1;15)(q42;q15) in a high risk t(12;21)-positive acute lymphoblastic leukemia. Gene 2016; 595:39-48. [PMID: 27664585 DOI: 10.1016/j.gene.2016.09.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/15/2016] [Accepted: 09/20/2016] [Indexed: 11/30/2022]
Abstract
The t(12;21)(p13;q22) with ETV6-RUNX1 fusion occurs in 25% of cases of B-cell precursor acute lymphoblastic leukemia (BCP-ALL); and is generally associated with favorable prognosis. However, 15-20% of the t(12;21)-positive cases are associated with high-risk disease due to for example slow early responses to therapy. It is well-known that development of overt leukemia in t(12;21)-positive ALL requires secondary chromosomal aberrations although the full spectrum of these cytogenetic alterations is yet unsettled, and also, how they may be associated with disease outcome. This report describes the case of an adolescent male with t(12;21)-positive ALL who displayed a G-banded karyotype initially interpreted as del(1)(p22p13) and del(15)(q15). The patient was treated according to NOPHO standard risk protocol at diagnosis, but had minimal residual disease (MRD) at 6,4% on day 29 as determined by flow cytometric immunophenotyping. Because of MRD level>0.1% he was then assigned as a high risk patient and received intensified chemotherapy accordingly. Further molecular cytogenetic studies and oligo-based aCGH (oaCGH) analysis characterized the acquired complex structural rearrangements on chromosomes 1 and 15, which can be described as der(1)del(1)(p13.1p31.1)t(1;15)(q42;q15) with concurrent deletions at 1q31.2-q31.3, 1q42.12-q43, and 15q15.1-q15.3. The unbalanced complex rearrangements have not been described previously. Extended locus-specific FISH analyses showed that the three deletions were on the same chromosome 1 homologue that was involved in the t(1;15), and that the deletion on chromosome 15 also was on the same chromosome 15 homologue as involved in the t(1;15). Together these findings show the great importance of the combined usage of molecular cytogenetic analyses and oaCGH analysis to enhance characterization of apparently simple G-banded karyotypes, and to provide a more complete spectrum of secondary chromosomal aberrations in high risk t(12;21)-positive BCP-ALLs.
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Affiliation(s)
- Eigil Kjeldsen
- Hemodiagnostic Laboratory, Cancer Cytogenetics Section, Department of Hematology, Aarhus University Hospital, Tage-Hansens Gade 2, DK-8000 Aarhus C, Denmark.
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18
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BCR-ABL1 gene rearrangement as a subclonal change in ETV6-RUNX1-positive B-cell acute lymphoblastic leukemia. Blood Adv 2016; 1:132-138. [PMID: 29296806 DOI: 10.1182/bloodadvances.2016000463] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/17/2016] [Indexed: 11/20/2022] Open
Abstract
We report here on a case of ETV6-RUNX1-positive B-cell acute lymphoblastic leukemia (B-ALL) that has acquired a BCR-ABL1 gene rearrangement as a subclonal change. The 19-year-old female patient presented with B symptoms, pancytopenia, and circulating blasts. The bone marrow aspirate was hypercellular and was infiltrated by an immature blast population that was confirmed as B-ALL by flow cytometry. Sequential fluorescent in situ hybridization was performed on the patient's leukemic cells, which were shown to contain both ETV6-RUNX1 and BCR-ABL1 gene rearrangements. The majority of nuclei (85%) showed only the ETV6-RUNX1 gene rearrangement; however, an additional 10% also showed a variant BCR-ABL1 gene rearrangement, indicating the ETV6-RUNX1 gene rearrangement was the primary change. A review of the literature has shown that acquisition of a BCR-ABL1 gene rearrangement as a secondary change in B-ALL is a very rare occurrence, and the effect it may have on prognosis is uncertain in the modern therapy age.
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19
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Vojcek Á, Pajor G, Alpár D, Mátics R, Pótó L, Szuhai K, Pajor L. Conserved hierarchical gain of chromosome 4 is an independent prognostic factor in high hyperdiploid pediatric acute lymphoblastic leukemia. Leuk Res 2016; 52:28-33. [PMID: 27870946 DOI: 10.1016/j.leukres.2016.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 11/09/2016] [Accepted: 11/10/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND High hyperdiploid (HeH) pre-B pediatric acute lymphoblastic leukemia (B-pALL) is known to be heterogeneous by prognosis, but the stratification principals according to conventional cytogenetic analysis (CCA) are equivocal. PROCEDURE Untreated bone marrow samples of 214 B-pALL patients were previously classified according to the modal numbers (iMN8) based on the gains of the chromosomes 4, 6, 10, 14, 17, 18, 21, and X as revealed by consecutive and correlated 2×4 color interphase fluorescence in situ hybridization, and at least five years of follow up data were analyzed. RESULTS Data from 48 of the 53 HeH (iMN8>50) B-pALL patients indicated that among the age, gender, WBC, and iMN8 parameters, only the last was significantly associated with overall survival (pOS), which allowed the cases to be classified as iMN8 51-54 (75%) and iMN8 ≥ 55 (95%). Among the specific chromosomal gains of +4, +4/+6, +4/+17 and +4/+18, the first exhibited the most significance in terms of beneficial outcomes. The better prognostic group according to the iMN8 was associated with a significantly reduced complexity of the subclonal landscape. However, iMN8 did not prove to be an independent variable but was instead overridden by isolated trisomy of chromosome 4. CONCLUSIONS These data indicate that the better outcomes in the HeH B-pALL group arose from the gain of a specific chromosome that always ranks at the same position in the sequential acquisition of the affected chromosomes.
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Affiliation(s)
| | | | | | - R Mátics
- Department of Translational Medicine
| | - L Pótó
- Department of Bioanalysis of the University of Pécs Medical Center, Pécs, Hungary
| | - K Szuhai
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
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20
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Ding LW, Sun QY, Tan KT, Chien W, Mayakonda A, Yeoh AEJ, Kawamata N, Nagata Y, Xiao JF, Loh XY, Lin DC, Garg M, Jiang YY, Xu L, Lim SL, Liu LZ, Madan V, Sanada M, Fernández LT, Hema Preethi SS, Lill M, Kantarjian HM, Kornblau SM, Miyano S, Liang DC, Ogawa S, Shih LY, Yang H, Koeffler HP. Mutational Landscape of Pediatric Acute Lymphoblastic Leukemia. Cancer Res 2016; 77:390-400. [PMID: 27872090 DOI: 10.1158/0008-5472.can-16-1303] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 09/30/2016] [Accepted: 10/20/2016] [Indexed: 01/07/2023]
Abstract
Current standard of care for patients with pediatric acute lymphoblastic leukemia (ALL) is mainly effective, with high remission rates after treatment. However, the genetic perturbations that give rise to this disease remain largely undefined, limiting the ability to address resistant tumors or develop less toxic targeted therapies. Here, we report the use of next-generation sequencing to interrogate the genetic and pathogenic mechanisms of 240 pediatric ALL cases with their matched remission samples. Commonly mutated genes fell into several categories, including RAS/receptor tyrosine kinases, epigenetic regulators, transcription factors involved in lineage commitment, and the p53/cell-cycle pathway. Unique recurrent mutational hotspots were observed in epigenetic regulators CREBBP (R1446C/H), WHSC1 (E1099K), and the tyrosine kinase FLT3 (K663R, N676K). The mutant WHSC1 was established as a gain-of-function oncogene, while the epigenetic regulator ARID1A and transcription factor CTCF were functionally identified as potential tumor suppressors. Analysis of 28 diagnosis/relapse trio patients plus 10 relapse cases revealed four evolutionary paths and uncovered the ordering of acquisition of mutations in these patients. This study provides a detailed mutational portrait of pediatric ALL and gives insights into the molecular pathogenesis of this disease. Cancer Res; 77(2); 390-400. ©2016 AACR.
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Affiliation(s)
- Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Qiao-Yang Sun
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Kar-Tong Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Wenwen Chien
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Allen Eng Juh Yeoh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Norihiko Kawamata
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA.,Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, USA
| | - Yasunobu Nagata
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Jin-Fen Xiao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Xin-Yi Loh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - De-Chen Lin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, USA
| | - Manoj Garg
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yan-Yi Jiang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Liang Xu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Su-Lin Lim
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Li-Zhen Liu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Vikas Madan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Masashi Sanada
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Lucia Torres Fernández
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - S S Hema Preethi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Michael Lill
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, USA
| | - Hagop M Kantarjian
- Department of Leukemia, University of Texas, MD Anderson Cancer Center, Houston, USA
| | - Steven M Kornblau
- Department of Leukemia, University of Texas, MD Anderson Cancer Center, Houston, USA
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Laboratory of Sequence Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Der-Cherng Liang
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Lee-Yung Shih
- Division of Hematology-Oncology, Chang Gung Memorial Hospital, Linkou, Chang Gung University, Taipei, Taiwan
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, USA
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21
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Karrman K, Johansson B. Pediatric T-cell acute lymphoblastic leukemia. Genes Chromosomes Cancer 2016; 56:89-116. [PMID: 27636224 DOI: 10.1002/gcc.22416] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/06/2016] [Indexed: 12/29/2022] Open
Abstract
The most common pediatric malignancy is acute lymphoblastic leukemia (ALL), of which T-cell ALL (T-ALL) comprises 10-15% of cases. T-ALL arises in the thymus from an immature thymocyte as a consequence of a stepwise accumulation of genetic and epigenetic aberrations. Crucial biological processes, such as differentiation, self-renewal capacity, proliferation, and apoptosis, are targeted and deranged by several types of neoplasia-associated genetic alteration, for example, translocations, deletions, and mutations of genes that code for proteins involved in signaling transduction, epigenetic regulation, and transcription. Epigenetically, T-ALL is characterized by gene expression changes caused by hypermethylation of tumor suppressor genes, histone modifications, and miRNA and lncRNA abnormalities. Although some genetic and gene expression patterns have been associated with certain clinical features, such as immunophenotypic subtype and outcome, none has of yet generally been implemented in clinical routine for treatment decisions. The recent advent of massive parallel sequencing technologies has dramatically increased our knowledge of the genetic blueprint of T-ALL, revealing numerous fusion genes as well as novel gene mutations. The challenges now are to integrate all genetic and epigenetic data into a coherent understanding of the pathogenesis of T-ALL and to translate the wealth of information gained in the last few years into clinical use in the form of improved risk stratification and targeted therapies. Here, we provide an overview of pediatric T-ALL with an emphasis on the acquired genetic alterations that result in this disease. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Kristina Karrman
- Department of Clinical Genetics, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden.,Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Bertil Johansson
- Department of Clinical Genetics, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden.,Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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An Q, Qi G, Jin M. Current views of pediatric B cell precursor acute leucoyteic leukemia. Minerva Pediatr 2016; 71:376-379. [PMID: 27652901 DOI: 10.23736/s0026-4946.16.04730-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The most common type cancer prevailing in pediatric patients worldwide is acute lymphoblastic leukemia (ALL). The characteristic feature of this cancer is the accumulation of immature lymphoid cell in the bone marrow. Further a subtype of ALL namely B-cell precursor (BCP)-ALL has raised in the recent years and is the most common subtype of ALL prevalent in children worldwide. The present review article will put light on the current aspects of BCP ALL including etiology, causative factors, diagnostic and treatment.
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Affiliation(s)
- Qi An
- Department of Hematology, Xuzhou Children's Hospital, Xuzhou, China
| | - Gongjian Qi
- Department of Hematology, Xuzhou Children's Hospital, Xuzhou, China
| | - Mingwei Jin
- Department of Hematology, Xuzhou Children's Hospital, Xuzhou, China -
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Oligo-based aCGH analysis reveals cryptic unbalanced der(6)t(X;6) in pediatric t(12;21)-positive acute lymphoblastic leukemia. Exp Mol Pathol 2016; 101:38-43. [PMID: 27215399 DOI: 10.1016/j.yexmp.2016.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/18/2016] [Accepted: 05/18/2016] [Indexed: 11/23/2022]
Abstract
Secondary chromosomal aberrations are necessary for development of overt leukemia in t(12;21)/ETV6-RUNX1-positive acute lymphoblastic leukemia (ALL). Conventional cytogenetic analysis supplemented with locus-specific FISH analyses is gold standard to detect important clonal aberrations in this disease group. However, adequate chromosome banding analysis may often be hampered by poor chromosome morphology and banding patterns in pediatric ALL cases, which may hinder identification of possible clinical important additional chromosomal aberrations. We used oligo-based high-resolution aCGH (oaCGH) analysis as an adjunct tool to enhance conventional cytogenetic analysis in pediatric acute B-cell lymphoblastic leukemia in a prospective single center study during a 4-year period (2012-2015). In a consecutive series of 45 pediatric B-ALLs, we identified eight patients with t(12;21)/ETV6-RUNX1 fusion by FISH analysis. In three of the patients, oaCGH analysis revealed concurrent Xq duplication and 6q deletion, which was cryptic by G-banded analysis. FISH analyses with whole chromosome painting probes confirmed the imbalances and showed an unbalanced translocation der(6)t(X;6) in all three patients. A search in the literature revealed two additional pediatric patients with cryptic der(6)t(X;6) in t(12;21)-positive ALLs. No common break points on Xq or 6q could be determined between the five patients. This study highlights the importance of oaCGH analysis as an adjunct cytogenetic tool to detect cryptic chromosomal aberrations. Further, the study adds to understanding the full spectrum of secondary chromosomal aberrations in the very common t(12;21)-positive pediatric ALL disease group. We suggest that the unbalanced der(6)t(X;6), which is cryptic to conventional cytogenetics, is a non-random secondary event in this disease group. It might be that the specific combination of concurrent Xq duplication and 6q-deletion results in gain of possible oncogenes on Xq and loss of possible tumor suppressor genes on 6q that are important for the leukemic propagation of t(12;21)-positive hematopoietic cells in a subset of ALLs.
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24
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Wang Y, Miller S, Roulston D, Bixby D, Shao L. Genome-Wide Single-Nucleotide Polymorphism Array Analysis Improves Prognostication of Acute Lymphoblastic Leukemia/Lymphoma. J Mol Diagn 2016; 18:595-603. [PMID: 27161658 DOI: 10.1016/j.jmoldx.2016.03.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 03/17/2016] [Accepted: 03/21/2016] [Indexed: 02/08/2023] Open
Abstract
Chromosomal abnormalities are important for the risk stratification of acute lymphoblastic leukemia/lymphoma (ALL). However, approximately 30% of pediatric and 50% of adult patients lack abnormalities with clinical relevance by traditional cytogenetic analysis. We integrated cytogenetic, fluorescence in situ hybridization, and whole-genome single-nucleotide polymorphism array results from 60 consecutive clinical ALL cases. By cytogenetic and/or fluorescence in situ hybridization analyses, recurring abnormalities with clinical relevance were observed in 33 B-cell ALL (B-ALL), including t(9;22), hyperdiploidy, KMT2A translocation, ETV6-RUNX1, intrachromosomal amplification of chromosome 21, near haploidy or low hypodiploidy, and t(8;22). Single-nucleotide polymorphism array analysis found additional aberrations with prognostic or therapeutic implication in 21 B-ALL and two T-cell ALL, including IKZF1 deletion, intrachromosomal amplification of chromosome 21 (one case with a normal karyotype), low hypodiploidy (two cases with a normal karyotype), and one case each with fusion genes ETV6-NTRK3, CRLF2-P2RY8, NUP214-ABL1, and SET-NUP214. IKZF1 deletion was noted in nine B-ALL with t(9;22), one B-ALL with t(4;11), five B-ALL with a normal karyotype, and three B-ALL with nonrecurring karyotypic abnormalities. Combining single-nucleotide polymorphism array with chromosome and fluorescence in situ hybridization assays, the detection rate for clinically significant abnormal results increased from 56% to 75%. Whole-genome single-nucleotide polymorphism array analysis detects cytogenetically undetectable clinically significant aberrations and should be routinely applied at diagnosis of ALL.
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Affiliation(s)
- Yunhong Wang
- Clinical Cytogenetics Laboratory, University of Michigan, Ann Arbor, Michigan; Department of Pathology, Peking University First Hospital, Beijing, China
| | - Sue Miller
- Clinical Cytogenetics Laboratory, University of Michigan, Ann Arbor, Michigan
| | - Diane Roulston
- Clinical Cytogenetics Laboratory, University of Michigan, Ann Arbor, Michigan
| | - Dale Bixby
- Department of Pathology, and the Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Lina Shao
- Clinical Cytogenetics Laboratory, University of Michigan, Ann Arbor, Michigan.
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25
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Ivanov Öfverholm I, Tran AN, Olsson L, Zachariadis V, Heyman M, Rudd E, Syk Lundberg E, Nordenskjöld M, Johansson B, Nordgren A, Barbany G. Detailed gene dose analysis reveals recurrent focal gene deletions in pediatric B-cell precursor acute lymphoblastic leukemia. Leuk Lymphoma 2016; 57:2161-70. [DOI: 10.3109/10428194.2015.1136740] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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26
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Moorman AV. New and emerging prognostic and predictive genetic biomarkers in B-cell precursor acute lymphoblastic leukemia. Haematologica 2016; 101:407-16. [PMID: 27033238 PMCID: PMC5004393 DOI: 10.3324/haematol.2015.141101] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 01/25/2016] [Indexed: 12/19/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is a heterogeneous disease at the genetic level. Chromosomal abnormalities are used as diagnostic, prognostic and predictive biomarkers to provide subtype, outcome and drug response information. t(12;21)/ETV6-RUNX1 and high hyper-diploidy are good-risk prognostic biomarkers whereas KMT2A(MLL) translocations, t(17;19)/TCF3-HLF, haploidy or low hypodiploidy are high-risk biomarkers. t(9;22)/BCR-ABL1 patients require targeted treatment (imatinib/dasatinib), whereas iAMP21 patients achieve better outcomes when treated intensively. High-risk genetic biomarkers are four times more prevalent in adults compared to children. The application of genomic technologies to cases without an established abnormality (B-other) reveals copy number alterations which can be used either individually or in combination as prognostic biomarkers. Transcriptome sequencing studies have identified a network of fusion genes involving kinase genes -ABL1,ABL2,PDGFRB,CSF1R,CRLF2,JAK2 and EPOR in-vitro and in-vivo studies along with emerging clinical observations indicate that patients with a kinase-activating aberration may respond to treatment with small molecular inhibitors like imatinib/dasatinib and ruxolitinib. Further work is required to determine the true frequency of these abnormalities across the age spectrum and the optimal way to incorporate such inhibitors into protocols. In conclusion, genetic biomarkers are playing an increasingly important role in the management of patients with ALL.
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MESH Headings
- Antineoplastic Agents/therapeutic use
- B-Lymphocytes/drug effects
- B-Lymphocytes/metabolism
- B-Lymphocytes/pathology
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Chromosomes, Human, Pair 12
- Chromosomes, Human, Pair 21
- Chromosomes, Human, Pair 22
- Chromosomes, Human, Pair 9
- Dasatinib/therapeutic use
- Gene Expression
- Humans
- Imatinib Mesylate/therapeutic use
- Nitriles
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/diagnosis
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/drug therapy
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/mortality
- Prognosis
- Pyrazoles/therapeutic use
- Pyrimidines
- Survival Analysis
- Translocation, Genetic
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Affiliation(s)
- Anthony V Moorman
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK
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27
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Auer F, Ingenhag D, Bhatia S, Enczmann J, Cobaleda C, Sanchez-Garcia I, Borkhardt A, Hauer J. GEMMs addressing Pax5 loss-of-function in childhood pB-ALL. Eur J Med Genet 2016; 59:166-72. [DOI: 10.1016/j.ejmg.2015.11.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 11/13/2015] [Accepted: 11/22/2015] [Indexed: 02/08/2023]
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28
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Forero-Castro M, Robledo C, Benito R, Abáigar M, África Martín A, Arefi M, Fuster JL, de las Heras N, Rodríguez JN, Quintero J, Riesco S, Hermosín L, de la Fuente I, Recio I, Ribera J, Labrador J, Alonso JM, Olivier C, Sierra M, Megido M, Corchete-Sánchez LA, Ciudad Pizarro J, García JL, Ribera JM, Hernández-Rivas JM. Genome-Wide DNA Copy Number Analysis of Acute Lymphoblastic Leukemia Identifies New Genetic Markers Associated with Clinical Outcome. PLoS One 2016; 11:e0148972. [PMID: 26872047 PMCID: PMC4752220 DOI: 10.1371/journal.pone.0148972] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/26/2016] [Indexed: 01/13/2023] Open
Abstract
Identifying additional genetic alterations associated with poor prognosis in acute lymphoblastic leukemia (ALL) is still a challenge. Aims: To characterize the presence of additional DNA copy number alterations (CNAs) in children and adults with ALL by whole-genome oligonucleotide array (aCGH) analysis, and to identify their associations with clinical features and outcome. Array-CGH was carried out in 265 newly diagnosed ALLs (142 children and 123 adults). The NimbleGen CGH 12x135K array (Roche) was used to analyze genetic gains and losses. CNAs were analyzed with GISTIC and aCGHweb software. Clinical and biological variables were analyzed. Three of the patients showed chromothripsis (cth6, cth14q and cth15q). CNAs were associated with age, phenotype, genetic subtype and overall survival (OS). In the whole cohort of children, the losses on 14q32.33 (p = 0.019) and 15q13.2 (p = 0.04) were related to shorter OS. In the group of children without good- or poor-risk cytogenetics, the gain on 1p36.11 was a prognostic marker independently associated with shorter OS. In adults, the gains on 19q13.2 (p = 0.001) and Xp21.1 (p = 0.029), and the loss of 17p (p = 0.014) were independent markers of poor prognosis with respect to OS. In summary, CNAs are frequent in ALL and are associated with clinical parameters and survival. Genome-wide DNA copy number analysis allows the identification of genetic markers that predict clinical outcome, suggesting that detection of these genetic lesions will be useful in the management of patients newly diagnosed with ALL.
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Affiliation(s)
- Maribel Forero-Castro
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
- School of Biological Sciences (GEBIMOL), Pedagogical and Technological University of Colombia (UPTC), Tunja, Colombia
| | - Cristina Robledo
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
| | - Rocío Benito
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
| | - María Abáigar
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
| | - Ana África Martín
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
| | - Maryam Arefi
- Department of Hematology, Clinical University Hospital of Valladolid, Valladolid, Spain
| | - José Luis Fuster
- Department of Pediatric Oncohematology, Clinical University Hospital Virgen de la Arrixaca, Murcia, Spain
| | | | - Juan N. Rodríguez
- Department of Hematology, Juan Ramón Jiménez Hospital, Huelva, Spain
| | | | - Susana Riesco
- Department of Pediatric Oncohematology, University Hospital of Salamanca, Salamanca, Spain
| | - Lourdes Hermosín
- Department of Hematology, Jerez Hospital, Jerez de la Frontera, Cádiz, Spain
| | | | - Isabel Recio
- Department of Hematology, Nuestra Señora de Sonsoles Hospital, Avila, Spain
| | - Jordi Ribera
- Department of Hematology, ICO-Hospital Germans Trias i Pujol, Josep Carreras Research Institute, Badalona, Spain
| | - Jorge Labrador
- Department of Hematology, University Hospital of Burgos, Burgos, Spain
| | - José M. Alonso
- Department of Hematology, Rio Carrión Hospital, Palencia, Spain
| | - Carmen Olivier
- Department of Hematology, General Hospital of Segovia, Segovia, Spain
| | - Magdalena Sierra
- Department of Hematology, Virgen de la Concha Hospital, Zamora, Spain
| | - Marta Megido
- Department of Hematology, Bierzo Hospital, León/Ponferrada, Spain
| | | | - Juana Ciudad Pizarro
- Cytometry Service (NUCLEUS Research Support Platform), University of Salamanca (USAL), Salamanca, Spain
| | - Juan Luis García
- Institute of Health Science Studies of Castile and León (IESCYL), Salamanca, Spain
| | - José M. Ribera
- Department of Hematology, ICO-Hospital Germans Trias i Pujol, Josep Carreras Research Institute, Badalona, Spain
| | - Jesús M. Hernández-Rivas
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
- * E-mail:
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29
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Lundin KB, Olsson L, Safavi S, Biloglav A, Paulsson K, Johansson B. Patterns and frequencies of acquired and constitutional uniparental isodisomies in pediatric and adult B-cell precursor acute lymphoblastic leukemia. Genes Chromosomes Cancer 2016; 55:472-9. [PMID: 26773847 DOI: 10.1002/gcc.22349] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/11/2016] [Accepted: 01/11/2016] [Indexed: 12/31/2022] Open
Abstract
Single nucleotide polymorphism (SNP) arrays are increasingly being used in clinical routine for genetic analysis of pediatric B-cell precursor acute lymphoblastic leukemias (BCP ALL). Because constitutional DNA is not readily available as a control at the time of diagnosis, it is important to be able to distinguish between acquired and constitutional aberrations in a diagnostic setting. In the present study we focused on uniparental isodisomies (UPIDs). SNP array analyses of 143 pediatric and 38 adult B-cell precursor acute lymphoblastic leukemias and matched remission samples revealed acquired whole chromosome or segmental UPIDs (wUPIDs, sUPIDs) in 32 cases (18%), without any age- or gender-related frequency differences. Acquired sUPIDs were larger than the constitutional ones (mean 35.3 Mb vs. 10.7 Mb; P < 0.0001) and were more often terminally located in the chromosomes (69% vs. 4.5%; P < 0.0001). Chromosomes 3, 5, and 9 were most often involved in acquired wUPIDs, whilst recurrent acquired sUPIDs targeted 6p, 9p, 9q, and 14q. The majority (56%) of sUPID9p was associated with homozygous CDKN2A deletions. In pediatric ALL, all wUPIDs were found in high hyperdiploid (51-67 chromosomes) cases and an extended analysis, also including unmatched diagnostic samples, revealed a higher frequency of wUPID-positivity in higher modal number (56-67 chromosomes) than in lower modal number (51-55 chromosomes) high hyperdiploid cases (34% vs. 11%; P = 0.04), suggesting different underlying mechanisms of formation of these subtypes of high hyperdiploidy. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Kristina B Lundin
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Linda Olsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
- Department of Clinical Genetics, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden
| | - Setareh Safavi
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Andrea Biloglav
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Kajsa Paulsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Bertil Johansson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
- Department of Clinical Genetics, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden
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30
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Amare PSK, Jain H, Kabre S, Deshpande Y, Pawar P, Banavali S, Menon H, Sengar M, Arora B, Khattry N, Narula G, Sarang D, Kaskar S, Bagal B, Jain H, Dangi U, Subramanian PG, Gujral S. Cytogenetic Profile in 7209 Indian Patients with <i>de novo</i> Acute Leukemia: A Single Centre Study from India. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/jct.2016.77056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Song J, Shao H. SNP Array in Hematopoietic Neoplasms: A Review. MICROARRAYS 2015; 5:microarrays5010001. [PMID: 27600067 PMCID: PMC5003446 DOI: 10.3390/microarrays5010001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/13/2015] [Accepted: 12/14/2015] [Indexed: 12/03/2022]
Abstract
Cytogenetic analysis is essential for the diagnosis and prognosis of hematopoietic neoplasms in current clinical practice. Many hematopoietic malignancies are characterized by structural chromosomal abnormalities such as specific translocations, inversions, deletions and/or numerical abnormalities that can be identified by karyotype analysis or fluorescence in situ hybridization (FISH) studies. Single nucleotide polymorphism (SNP) arrays offer high-resolution identification of copy number variants (CNVs) and acquired copy-neutral loss of heterozygosity (LOH)/uniparental disomy (UPD) that are usually not identifiable by conventional cytogenetic analysis and FISH studies. As a result, SNP arrays have been increasingly applied to hematopoietic neoplasms to search for clinically-significant genetic abnormalities. A large numbers of CNVs and UPDs have been identified in a variety of hematopoietic neoplasms. CNVs detected by SNP array in some hematopoietic neoplasms are of prognostic significance. A few specific genes in the affected regions have been implicated in the pathogenesis and may be the targets for specific therapeutic agents in the future. In this review, we summarize the current findings of application of SNP arrays in a variety of hematopoietic malignancies with an emphasis on the clinically significant genetic variants.
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Affiliation(s)
- Jinming Song
- Department of Hematopathology and Laboratory Medicine, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA.
| | - Haipeng Shao
- Department of Hematopathology and Laboratory Medicine, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA.
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32
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Molecular genetic and cytogenetic analysis of a primary cutaneous CD8-positive aggressive epidermotropic cytotoxic T-cell lymphoma. Int J Hematol 2015; 103:196-201. [PMID: 26676804 DOI: 10.1007/s12185-015-1895-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 10/30/2015] [Accepted: 11/04/2015] [Indexed: 10/22/2022]
Abstract
We performed cytogenetic and molecular cytogenetic analyses of a primary cutaneous CD8-positive aggressive epidermotropic cytotoxic T-cell lymphoma, a rare type of primary cutaneous T-cell lymphoma. G-banded analysis at initial diagnosis and recurrence revealed complex karyotype and clonal evolution reflecting genomic instability that parallels the aggressive clinical course observed. Spectral karyotyping revealed numerous structural abnormalities. SNP array-based analysis of an initial diagnostic sample revealed numerous gains and losses of chromosomal material, including loss of short arm of the chromosome 17, to which TP53 is mapped. The molecular cytogenetics and array data of this case suggest genomic instability, particularly chromosomal instability and haploinsufficiency for TP53, the latter possibly giving rise to alteration of p14ARF-Mdm2-p53 tumor suppressor protein pathway, likely to be associated with unfavorable clinical course.
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33
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Xu N, Li YL, Zhou X, Cao R, Li H, Lu QS, Li L, Lu ZY, Huang JX, Sun J, Liu QF, Du QF, Liu XL. CDKN2 Gene Deletion as Poor Prognosis Predictor Involved in the Progression of Adult B-Lineage Acute Lymphoblastic Leukemia Patients. J Cancer 2015; 6:1114-20. [PMID: 26516359 PMCID: PMC4615347 DOI: 10.7150/jca.11959] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 07/20/2015] [Indexed: 12/02/2022] Open
Abstract
Deletion of cyclin-dependent kinase inhibitor 2A/B (CDKN2A/B) is well known in many hematologic malignancies, but only few reports have investigated this deletion effect on clinical prognosis. This study performed analysis of the CDKN2 deletion in 215 adult B- lineage acute lymphoblastic leukemia (B-ALL) patients, and related cytogenetic prognostic factors (BCR/ABL; E2A/PBXl; TEL/AML1; Mixed Lineage Leukemia (MLL) rearrangement; MYC, Immunoglobulin heavy locus (IGH) translocation). The prevalence of CDKN2 deletions in all study populations was 28.4%. There is no difference between patients with CDKN2 deletion and wild-type patients in sex, age, white blood cells (WBC) count, BM blast percentage, extra infiltration and induction complete remission (CR) rate. Analysis in relapse patients revealed that the distribution of CDKN2 deletion is higher in relapse patients (44.6%) than all patients (28.4%, P=0.006). Deletion of CDKN2 was significantly associated with poor outcomes including decreased overall survival (OS) (P<0.001), lower disease free-survival (DFS) (P<0.001), and increased cumulative incidence of relapse (P=0.002); Also, CDKN2 deletion was strongly associated with IGH translocation (P=0.021); and had an adverse effect on patients with BCR-ABL fusion gene or with MLL rearrangement. Patients with CDKN2 gene deletion benefited from allogenic hematopoietic stem cell transplantation (Allo-HSCT). Deletion of CDKN2 gene was commonly observed through leukemia progression and was poor prognostic marker in long-term outcomes.
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Affiliation(s)
- Na Xu
- 1. Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou Dadao North Street, 1838, Guangzhou 510515, China
| | - Yu-Ling Li
- 1. Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou Dadao North Street, 1838, Guangzhou 510515, China
| | - Xuan Zhou
- 1. Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou Dadao North Street, 1838, Guangzhou 510515, China
| | - Rui Cao
- 1. Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou Dadao North Street, 1838, Guangzhou 510515, China
| | - Huan Li
- 1. Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou Dadao North Street, 1838, Guangzhou 510515, China
| | - Qi-Si Lu
- 1. Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou Dadao North Street, 1838, Guangzhou 510515, China
| | - Lin Li
- 1. Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou Dadao North Street, 1838, Guangzhou 510515, China
| | - Zi-Yuan Lu
- 1. Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou Dadao North Street, 1838, Guangzhou 510515, China
| | - Ji-Xian Huang
- 1. Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou Dadao North Street, 1838, Guangzhou 510515, China
| | - Jing Sun
- 1. Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou Dadao North Street, 1838, Guangzhou 510515, China
| | - Qi-Fa Liu
- 1. Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou Dadao North Street, 1838, Guangzhou 510515, China
| | - Qing-Feng Du
- 1. Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou Dadao North Street, 1838, Guangzhou 510515, China ; 2. Department of Management and Development, Nanfang Hospital, Southern Medical University, Guangzhou Dadao North Street, 1838, Guangzhou 510515, China
| | - Xiao-Li Liu
- 1. Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou Dadao North Street, 1838, Guangzhou 510515, China
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34
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Chen C, Bartenhagen C, Gombert M, Okpanyi V, Binder V, Röttgers S, Bradtke J, Teigler-Schlegel A, Harbott J, Ginzel S, Thiele R, Husemann P, Krell PF, Borkhardt A, Dugas M, Hu J, Fischer U. Next-generation-sequencing of recurrent childhood high hyperdiploid acute lymphoblastic leukemia reveals mutations typically associated with high risk patients. Leuk Res 2015; 39:990-1001. [DOI: 10.1016/j.leukres.2015.06.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 06/08/2015] [Accepted: 06/10/2015] [Indexed: 01/07/2023]
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35
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Sunaoshi M, Amasaki Y, Hirano-Sakairi S, Blyth BJ, Morioka T, Kaminishi M, Shang Y, Nishimura M, Shimada Y, Tachibana A, Kakinuma S. The effect of age at exposure on the inactivating mechanisms and relative contributions of key tumor suppressor genes in radiation-induced mouse T-cell lymphomas. Mutat Res 2015; 779:58-67. [PMID: 26141385 DOI: 10.1016/j.mrfmmm.2015.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 05/15/2015] [Accepted: 06/07/2015] [Indexed: 06/04/2023]
Abstract
Children are considered more sensitive to radiation-induced cancer than adults, yet any differences in genomic alterations associated with age-at-exposure and their underlying mechanisms remain unclear. We assessed genome-wide DNA copy number and mutation of key tumor suppressor genes in T-cell lymphomas arising after weekly irradiation of female B6C3F1 mice with 1.2Gy X-rays for 4 consecutive weeks starting during infancy (1 week old), adolescence (4 weeks old) or as young adults (8 weeks old). Although T-cell lymphoma incidence was similar, loss of heterozygosity at Cdkn2a on chromosome 4 and at Ikaros on chromosome 11 was more frequent in the two older groups, while loss at the Pten locus on chromosome 19 was more frequent in the infant-irradiated group. Cdkn2a and Ikaros mutation/loss was a common feature of the young adult-irradiation group, with Ikaros frequently (50%) incurring multiple independent hits (including deletions and mutations) or suffering a single hit predicted to result in a dominant negative protein (such as those lacking exon 4, an isoform we have designated Ik12, which lacks two DNA binding zinc-finger domains). Conversely, Pten mutations were more frequent after early irradiation (60%) than after young adult-irradiation (30%). Homozygous Pten mutations occurred without DNA copy number change after irradiation starting in infancy, suggesting duplication of the mutated allele by chromosome mis-segregation or mitotic recombination. Our findings demonstrate that while deletions on chromosomes 4 and 11 affecting Cdkn2a and Ikaros are a prominent feature of young adult irradiation-induced T-cell lymphoma, tumors arising after irradiation from infancy suffer a second hit in Pten by mis-segregation or recombination. This is the first report showing an influence of age-at-exposure on genomic alterations of tumor suppressor genes and their relative involvement in radiation-induced T-cell lymphoma. These data are important for considering the risks associated with childhood exposure to radiation.
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Affiliation(s)
- Masaaki Sunaoshi
- Radiobiology for Children's Health Program, Research Center for Radiation Protection, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan; Department of Biological Sciences, College of Science, Ibaraki University, Bunkyo 2-1-1, Mito, Ibaraki 310-8512, Japan
| | - Yoshiko Amasaki
- Radiobiology for Children's Health Program, Research Center for Radiation Protection, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
| | - Shinobu Hirano-Sakairi
- Radiobiology for Children's Health Program, Research Center for Radiation Protection, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
| | - Benjamin J Blyth
- Radiobiology for Children's Health Program, Research Center for Radiation Protection, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
| | - Takamitsu Morioka
- Radiobiology for Children's Health Program, Research Center for Radiation Protection, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan; Radiation Effect Accumulation and Prevention Project, Fukushima Project Headquarters, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
| | - Mutsumi Kaminishi
- Radiobiology for Children's Health Program, Research Center for Radiation Protection, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
| | - Yi Shang
- Radiation Effect Accumulation and Prevention Project, Fukushima Project Headquarters, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
| | - Mayumi Nishimura
- Radiobiology for Children's Health Program, Research Center for Radiation Protection, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan; Radiation Effect Accumulation and Prevention Project, Fukushima Project Headquarters, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
| | - Yoshiya Shimada
- Radiobiology for Children's Health Program, Research Center for Radiation Protection, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan; Radiation Effect Accumulation and Prevention Project, Fukushima Project Headquarters, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
| | - Akira Tachibana
- Department of Biological Sciences, College of Science, Ibaraki University, Bunkyo 2-1-1, Mito, Ibaraki 310-8512, Japan
| | - Shizuko Kakinuma
- Radiobiology for Children's Health Program, Research Center for Radiation Protection, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan; Radiation Effect Accumulation and Prevention Project, Fukushima Project Headquarters, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan.
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Stasevich I, Inglott S, Austin N, Chatters S, Chalker J, Addy D, Dryden C, Ancliff P, Ford A, Williams O, Kempski H. PAX5 alterations in genetically unclassified childhood Precursor B-cell acute lymphoblastic leukaemia. Br J Haematol 2015; 171:263-272. [PMID: 26115422 DOI: 10.1111/bjh.13543] [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] [Received: 03/09/2015] [Accepted: 05/12/2015] [Indexed: 11/29/2022]
Abstract
Here, we report a high incidence of PAX5 abnormalities observed in 32/68 (47%) of patients with genetically unclassified childhood precursor B-cell acute lymphoblastic leukaemia (pre-B ALL). Various deletions, gains, mutations and rearrangements of PAX5 comprised 45%, 12%, 29% and 14%, respectively, of the abnormalities found. 28% of patients showed more than one abnormality of the gene, implying bi-allelic impairment of PAX5. Novel PAX5-RHOXF2, PAX5-ELK3 and PAX5-CBFA2T2 rearrangements, which lead to aberrant expression of PAX5, were also identified. PAX5 rearrangements demonstrated a complex mechanism of formation including concurrent duplications/deletions of PAX5 and its partner genes. Finally, the splice variant c.1013-2A>G, seen in two patients with loss of one PAX5 allele, was confirmed to be germ-line in one patient and somatic in the other. PAX5 alterations were also found to be clinically associated with a higher white blood cell count (P = 0·015). These findings contribute to the knowledge of PAX5 alterations and their role in the pathogenesis of pre-B ALL.
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Affiliation(s)
- Irina Stasevich
- Haematology Cellular and Molecular Diagnostic Service, Great Ormond Street Hospital, London, UK.,Developmental Biology and Cancer (DBC), University College London-Institute of Child Health, London, UK
| | - Sarah Inglott
- Haematology Cellular and Molecular Diagnostic Service, Great Ormond Street Hospital, London, UK
| | - Nicola Austin
- Haematology Cellular and Molecular Diagnostic Service, Great Ormond Street Hospital, London, UK
| | - Steve Chatters
- Haematology Cellular and Molecular Diagnostic Service, Great Ormond Street Hospital, London, UK
| | - Jane Chalker
- Haematology Cellular and Molecular Diagnostic Service, Great Ormond Street Hospital, London, UK
| | - Dilys Addy
- Haematology Cellular and Molecular Diagnostic Service, Great Ormond Street Hospital, London, UK
| | - Carryl Dryden
- Haematology Cellular and Molecular Diagnostic Service, Great Ormond Street Hospital, London, UK
| | - Philip Ancliff
- Department of Haematology, Great Ormond Street Hospital, London, UK
| | - Anthony Ford
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Owen Williams
- Developmental Biology and Cancer (DBC), University College London-Institute of Child Health, London, UK
| | - Helena Kempski
- Haematology Cellular and Molecular Diagnostic Service, Great Ormond Street Hospital, London, UK.,Developmental Biology and Cancer (DBC), University College London-Institute of Child Health, London, UK
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37
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Barbosa TC, Terra-Granado E, Quezado Magalhães IM, Neves GR, Gadelha A, Guedes Filho GE, Souza MS, Melaragno R, Emerenciano M, Pombo-de-Oliveira MS. Frequency of copy number abnormalities in common genes associated with B-cell precursor acute lymphoblastic leukemia cytogenetic subtypes in Brazilian children. Cancer Genet 2015; 208:492-501. [PMID: 26277549 DOI: 10.1016/j.cancergen.2015.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 06/08/2015] [Accepted: 06/15/2015] [Indexed: 10/23/2022]
Abstract
Copy number alterations (CNAs) in genes committed to B-cell precursors have been associated with poor survival in subgroups of patients with B-cell precursor acute lymphoblastic leukemia (BCP-ALL). We investigated submicroscopic alterations in a series of 274 Brazilian children with BCP-ALL by multiplex ligation-dependent probe amplification and evaluated their correlation with clinical and laboratory features. The relevance of overlapping CNA abnormalities was also explored. Deletions/amplifications in at least one gene were identified in 83% of the total series. In children older than 2 years, there was a predominance of CNAs involving deletions in IKZF1, CDKN2A, and CDKN2B, whereas the pseudoautosomal region 1 (PAR1) had deletions that were found more frequently in infants (P <0.05). Based on the cytogenetic subgroups, favorable cytogenetic subgroups showed more deletions than other subgroups that occurred simultaneously, specifically ETV6 deletions (P <0.05). TCF3-PBX1 was frequently deleted in RB1, and an absence of deletions was observed in IKZF1 and genes localized to the PAR1 region. The results corroborate with previous genome-wide studies and aggregate new markers for risk stratification of BCP-ALL in Brazil.
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Affiliation(s)
- Thayana Conceição Barbosa
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Eugenia Terra-Granado
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | | | | | | | | | | | | | - Mariana Emerenciano
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Maria S Pombo-de-Oliveira
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.
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KRAS and CREBBP mutations: a relapse-linked malicious liaison in childhood high hyperdiploid acute lymphoblastic leukemia. Leukemia 2015; 29:1656-67. [PMID: 25917266 PMCID: PMC4530204 DOI: 10.1038/leu.2015.107] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/16/2015] [Indexed: 12/24/2022]
Abstract
High hyperdiploidy defines the largest genetic entity of childhood acute lymphoblastic leukemia (ALL). Despite its relatively low recurrence risk, this subgroup generates a high proportion of relapses. The cause and origin of these relapses remains obscure. We therefore explored the mutational landscape in high hyperdiploid (HD) ALL with whole-exome (n=19) and subsequent targeted deep sequencing of 60 genes in 100 relapsing and 51 non-relapsing cases. We identified multiple clones at diagnosis that were primarily defined by a variety of mutations in receptor tyrosine kinase (RTK)/Ras pathway and chromatin-modifying genes. The relapse clones consisted of reappearing as well as new mutations, and overall contained more mutations. Although RTK/Ras pathway mutations were similarly frequent between diagnosis and relapse, both intergenic and intragenic heterogeneity was essentially lost at relapse. CREBBP mutations, however, increased from initially 18–30% at relapse, then commonly co-occurred with KRAS mutations (P<0.001) and these relapses appeared primarily early (P=0.012). Our results confirm the exceptional susceptibility of HD ALL to RTK/Ras pathway and CREBBP mutations, but, more importantly, suggest that mutant KRAS and CREBBP might cooperate and equip cells with the necessary capacity to evolve into a relapse-generating clone.
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Karrman K, Castor A, Behrendtz M, Forestier E, Olsson L, Ehinger M, Biloglav A, Fioretos T, Paulsson K, Johansson B. Deep sequencing and SNP array analyses of pediatric T-cell acute lymphoblastic leukemia reveal NOTCH1 mutations in minor subclones and a high incidence of uniparental isodisomies affecting CDKN2A. J Hematol Oncol 2015; 8:42. [PMID: 25903014 PMCID: PMC4412034 DOI: 10.1186/s13045-015-0138-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/13/2015] [Indexed: 12/22/2022] Open
Abstract
Background Pediatric T-cell acute lymphoblastic leukemia (T-ALL) is a genetically heterogeneous disease that arises in a multistep fashion through acquisition of several genetic aberrations, subsequently giving rise to a malignant, clonal expansion of T-lymphoblasts. The aim of the present study was to identify additional as well as cooperative genetic events in T-ALL. Methods A population-based pediatric T-ALL series comprising 47 cases was investigated by SNP array and deep sequencing analyses of 75 genes, in order to ascertain pathogenetically pertinent aberrations and to identify cooperative events. Results The majority (92%) of cases harbored copy number aberrations/uniparental isodisomies (UPIDs), with a median of three changes (range 0–11) per case. The genes recurrently deleted comprised CDKN2A, CDKN2B, LEF1, PTEN, RBI, and STIL. No case had a whole chromosome UPID; in fact, literature data show that this is a rare phenomenon in T-ALL. However, segmental UPIDs (sUPIDs) were seen in 42% of our cases, with most being sUPID9p that always were associated with homozygous CDKN2A deletions, with a heterozygous deletion occurring prior to the sUPID9p in all instances. Among the 75 genes sequenced, 14 (19%) were mutated in 28 (72%) of 39 analyzed cases. The genes targeted are involved in signaling transduction, epigenetic regulation, and transcription. In some cases, NOTCH1 mutations were seen in minor subclones and lost at relapse; thus, such mutations can be secondary events. Conclusions Deep sequencing and SNP array analyses of T-ALL revealed lack of wUPIDs, a high proportion of sUPID9p targeting CDKN2A, NOTCH1 mutations in subclones, and recurrent mutations of genes involved in signaling transduction, epigenetic regulation, and transcription. Electronic supplementary material The online version of this article (doi:10.1186/s13045-015-0138-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kristina Karrman
- Department of Clinical Genetics, University and Regional Laboratories, Region Skåne, SE-221 85, Lund, Sweden. .,Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.
| | - Anders Castor
- Department of Pediatrics, Skåne University Hospital, Lund University, Lund, Sweden.
| | - Mikael Behrendtz
- Department of Pediatrics, Linköping University Hospital, Linköping, Sweden.
| | - Erik Forestier
- Department of Medical Biosciences, Clinical Genetics, Umeå University, Umeå, Sweden.
| | - Linda Olsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.
| | - Mats Ehinger
- Department of Pathology, University and Regional Laboratories, Region Skåne, Lund, Sweden.
| | - Andrea Biloglav
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.
| | - Thoas Fioretos
- Department of Clinical Genetics, University and Regional Laboratories, Region Skåne, SE-221 85, Lund, Sweden. .,Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.
| | - Kajsa Paulsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.
| | - Bertil Johansson
- Department of Clinical Genetics, University and Regional Laboratories, Region Skåne, SE-221 85, Lund, Sweden. .,Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.
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40
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Roberts KG, Mullighan CG. Genomics in acute lymphoblastic leukaemia: insights and treatment implications. Nat Rev Clin Oncol 2015; 12:344-57. [PMID: 25781572 DOI: 10.1038/nrclinonc.2015.38] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Acute lymphoblastic leukaemia (ALL) is the commonest childhood cancer and an important cause of morbidity from haematological malignancies in adults. In the past several years, we have witnessed major advances in the understanding of the genetic basis of ALL. Genome-wide profiling studies, including microarray analysis and genome sequencing, have helped identify multiple key cellular pathways that are frequently mutated in ALL such as lymphoid development, tumour suppression, cytokine receptors, kinase and Ras signalling, and chromatin remodeling. These studies have characterized new subtypes of ALL, notably Philadelphia chromosome-like ALL, which is a high-risk subtype characterized by a diverse range of alterations that activate cytokine receptors or tyrosine kinases amenable to inhibition with approved tyrosine kinase inhibitors. Genomic profiling has also enabled the identification of inherited genetic variants of ALL that influence the risk of leukaemia development, and characterization of the relationship between genetic variants, clonal heterogeneity and the risk of relapse. Many of these findings are of direct clinical relevance and ongoing studies implementing clinical sequencing in leukaemia diagnosis and management have great potential to improve the outcome of patients with high-risk ALL.
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Affiliation(s)
- Kathryn G Roberts
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 342, Memphis, TN 38105, USA
| | - Charles G Mullighan
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 342, Memphis, TN 38105, USA
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41
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Impact of IKZF1 deletions on long-term outcomes of allo-SCT following imatinib-based chemotherapy in adult Philadelphia chromosome-positive ALL. Bone Marrow Transplant 2014; 50:354-62. [DOI: 10.1038/bmt.2014.281] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 10/29/2014] [Accepted: 11/03/2014] [Indexed: 11/08/2022]
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42
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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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43
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Wan TSK. Cancer cytogenetics: methodology revisited. Ann Lab Med 2014; 34:413-25. [PMID: 25368816 PMCID: PMC4215412 DOI: 10.3343/alm.2014.34.6.413] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 07/31/2014] [Accepted: 10/06/2014] [Indexed: 01/14/2023] Open
Abstract
The Philadelphia chromosome was the first genetic abnormality discovered in cancer (in 1960), and it was found to be consistently associated with CML. The description of the Philadelphia chromosome ushered in a new era in the field of cancer cytogenetics. Accumulating genetic data have been shown to be intimately associated with the diagnosis and prognosis of neoplasms; thus, karyotyping is now considered a mandatory investigation for all newly diagnosed leukemias. The development of FISH in the 1980s overcame many of the drawbacks of assessing the genetic alterations in cancer cells by karyotyping. Karyotyping of cancer cells remains the gold standard since it provides a global analysis of the abnormalities in the entire genome of a single cell. However, subsequent methodological advances in molecular cytogenetics based on the principle of FISH that were initiated in the early 1990s have greatly enhanced the efficiency and accuracy of karyotype analysis by marrying conventional cytogenetics with molecular technologies. In this review, the development, current utilization, and technical pitfalls of both the conventional and molecular cytogenetics approaches used for cancer diagnosis over the past five decades will be discussed.
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Affiliation(s)
- Thomas S. K. Wan
- Haematology Division, Department of Pathology, The University of Hong Kong, Hong Kong
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44
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Nowak D, Liem NLM, Mossner M, Klaumünzer M, Papa RA, Nowak V, Jann JC, Akagi T, Kawamata N, Okamoto R, Thoennissen NH, Kato M, Sanada M, Hofmann WK, Ogawa S, Marshall GM, Lock RB, Koeffler HP. Variegated clonality and rapid emergence of new molecular lesions in xenografts of acute lymphoblastic leukemia are associated with drug resistance. Exp Hematol 2014; 43:32-43.e1-35. [PMID: 25450514 DOI: 10.1016/j.exphem.2014.09.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 08/18/2014] [Accepted: 09/19/2014] [Indexed: 01/22/2023]
Abstract
The use of genome-wide copy-number analysis and massive parallel sequencing has revolutionized the understanding of the clonal architecture of pediatric acute lymphoblastic leukemia (ALL) by demonstrating that this disease is composed of highly variable clonal ancestries following the rules of Darwinian selection. The current study aimed to analyze the molecular composition of childhood ALL biopsies and patient-derived xenografts with particular emphasis on mechanisms associated with acquired chemoresistance. Genomic DNA from seven primary pediatric ALL patient samples, 29 serially passaged xenografts, and six in vivo selected chemoresistant xenografts were analyzed with 250K single-nucleotide polymorphism arrays. Copy-number analysis of non-drug-selected xenografts confirmed a highly variable molecular pattern of variegated subclones. Whereas primary patient samples from initial diagnosis displayed a mean of 5.7 copy-number alterations per sample, serially passaged xenografts contained a mean of 8.2 and chemoresistant xenografts a mean of 10.5 copy-number alterations per sample, respectively. Resistance to cytarabine was explained by a new homozygous deletion of the DCK gene, whereas methotrexate resistance was associated with monoallelic deletion of FPGS and mutation of the remaining allele. This study demonstrates that selecting for chemoresistance in xenografted human ALL cells can reveal novel mechanisms associated with drug resistance.
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Affiliation(s)
- Daniel Nowak
- Division of Hematology and Oncology, Cedars Sinai Medical Center, University of California, Los Angeles, School of Medicine, Los Angeles, CA, United States; Department of Hematology and Oncology, Medical Faculty Mannheim of the University of Heidelberg, Heidelberg, Germany.
| | - Natalia L M Liem
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, University of New South Wales, Sydney, Australia
| | - Maximilian Mossner
- Department of Hematology and Oncology, Medical Faculty Mannheim of the University of Heidelberg, Heidelberg, Germany
| | - Marion Klaumünzer
- Department of Hematology and Oncology, Medical Faculty Mannheim of the University of Heidelberg, Heidelberg, Germany
| | - Rachael A Papa
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, University of New South Wales, Sydney, Australia
| | - Verena Nowak
- Division of Hematology and Oncology, Cedars Sinai Medical Center, University of California, Los Angeles, School of Medicine, Los Angeles, CA, United States; Department of Hematology and Oncology, Medical Faculty Mannheim of the University of Heidelberg, Heidelberg, Germany
| | - Johann C Jann
- Department of Hematology and Oncology, Medical Faculty Mannheim of the University of Heidelberg, Heidelberg, Germany
| | - Tadayuki Akagi
- Department of Stem Cell Biology, Graduate School of Medical Science, Kanazawa University, Ishikawa, Japan
| | - Norihiko Kawamata
- Division of Hematology and Oncology, Cedars Sinai Medical Center, University of California, Los Angeles, School of Medicine, Los Angeles, CA, United States
| | - Ryoko Okamoto
- Division of Hematology and Oncology, Cedars Sinai Medical Center, University of California, Los Angeles, School of Medicine, Los Angeles, CA, United States
| | - Nils H Thoennissen
- Division of Hematology and Oncology, Cedars Sinai Medical Center, University of California, Los Angeles, School of Medicine, Los Angeles, CA, United States
| | - Motohiro Kato
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masashi Sanada
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Wolf-Karsten Hofmann
- Department of Hematology and Oncology, Medical Faculty Mannheim of the University of Heidelberg, Heidelberg, Germany
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Glenn M Marshall
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, Australia
| | - Richard B Lock
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, University of New South Wales, Sydney, Australia
| | - H Phillip Koeffler
- Division of Hematology and Oncology, Cedars Sinai Medical Center, University of California, Los Angeles, School of Medicine, Los Angeles, CA, United States; National University of Singapore, Singapore, Singapore
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45
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Tao J, Zhang X, Lancet J, Bennett JM, Cai L, Papenhausen P, Moscinski L, Zhang L. Concurrence of B-lymphoblastic leukemia and myeloproliferative neoplasm with copy neutral loss of heterozygosity at chromosome 1p harboring a MPL W515S mutation. Cancer Genet 2014; 207:489-94. [PMID: 25453399 DOI: 10.1016/j.cancergen.2014.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 09/24/2014] [Accepted: 10/02/2014] [Indexed: 02/07/2023]
Abstract
B-lymphoblastic leukemia (B-ALL) is a neoplasm of precursors committed to B-cell lineage, whereas myeloproliferative neoplasm (MPN) is a clonal proliferation derived from myeloid stem cells. Concurrent B-ALL with MPN is uncommon except in the presence of abnormalities of the PDGFRA, PDGFRB, or FGFR1 genes or the BCR-ABL1 fusion gene. Herein, we describe a rare concurrence, B-ALL with MPN without the aforementioned genetic aberrations, in a 64-year-old male patient. The patient was initially diagnosed with B-ALL with normal karyotype and responded well to aggressive chemotherapy but had sustained leukocytosis and splenomegaly. The posttreatment restaging bone marrow was free of B-ALL but remained hypercellular with myeloid predominance. Using a single nucleotide polymorphism microarray study, we identified a copy neutral loss of heterozygosity at the terminus of 1p in the bone marrow samples taken at diagnosis and again at remission, 49% and 100%, respectively. Several additional genetic abnormalities were present in the initial marrow sample but not in the remission marrow samples. Retrospective molecular studies detected a MPL W515S homozygous mutation in both the initial and remission marrows for B-ALL, at 30-40% and 80% dosage effect, respectively. In summary, we present a case of concurrent B-ALL and MPN and demonstrate a stepwise cytogenetic and molecular approach to the final diagnosis.
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Affiliation(s)
- Jiangchuan Tao
- Department of Hematopathology and Laboratory Medicine, H. Lee Moffitt Cancer Center and Research Institute and the University of South Florida, Tampa, FL, USA
| | - Xiaohui Zhang
- Department of Hematopathology and Laboratory Medicine, H. Lee Moffitt Cancer Center and Research Institute and the University of South Florida, Tampa, FL, USA
| | - Jeffrey Lancet
- Department of Hematopathology and Laboratory Medicine, H. Lee Moffitt Cancer Center and Research Institute and the University of South Florida, Tampa, FL, USA
| | - John M Bennett
- Department of Pathology, University of Rochester Medical Center, School of Medicine and Dentistry, Rochester, NY, USA
| | - Li Cai
- Departments of Cytogenetics and Molecular Oncology Lab, Integrated Oncology-Laboratory Corporation of America, RTP, Winston-Salem, NC, USA
| | - Peter Papenhausen
- Departments of Cytogenetics and Molecular Oncology Lab, Integrated Oncology-Laboratory Corporation of America, RTP, Winston-Salem, NC, USA
| | - Lynn Moscinski
- Department of Hematopathology and Laboratory Medicine, H. Lee Moffitt Cancer Center and Research Institute and the University of South Florida, Tampa, FL, USA
| | - Ling Zhang
- Department of Hematopathology and Laboratory Medicine, H. Lee Moffitt Cancer Center and Research Institute and the University of South Florida, Tampa, FL, USA.
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Fazio G, Daniele G, Cazzaniga V, Impera L, Severgnini M, Iacobucci I, Galbiati M, Leszl A, Cifola I, De Bellis G, Bresciani P, Martinelli G, Basso G, Biondi A, Storlazzi CT, Cazzaniga G. Three novel fusion transcripts of the paired box 5 gene in B-cell precursor acute lymphoblastic leukemia. Haematologica 2014; 100:e14-7. [PMID: 25304615 DOI: 10.3324/haematol.2014.112193] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Grazia Fazio
- Centro Ricerca Tettamanti, Clinica Pediatrica, Dipartimento di Scienze della Salute, Università di Milano-Bicocca, Ospedale S. Gerardo/Fondazione MBBM, Monza
| | - Giulia Daniele
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro", Bari
| | - Valeria Cazzaniga
- Centro Ricerca Tettamanti, Clinica Pediatrica, Dipartimento di Scienze della Salute, Università di Milano-Bicocca, Ospedale S. Gerardo/Fondazione MBBM, Monza
| | - Luciana Impera
- Dept. of Emergency and Organ Transplantation, Hematology - University of Bari, Bari
| | - Marco Severgnini
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Milano
| | - Ilaria Iacobucci
- Institute of Hematology "L. e A. Seragnoli", Dep. of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna
| | - Marta Galbiati
- Centro Ricerca Tettamanti, Clinica Pediatrica, Dipartimento di Scienze della Salute, Università di Milano-Bicocca, Ospedale S. Gerardo/Fondazione MBBM, Monza
| | - Anna Leszl
- Laboratorio di Oncoematologia, Dipartimento di Pediatria Università Padova, Padova
| | - Ingrid Cifola
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Milano
| | - Gianluca De Bellis
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Milano
| | - Paola Bresciani
- Department of Medical and Surgical Sciences, Azienda Ospedaliero-Universitaria Policlinico, University of Modena and Reggio Emilia, Modena, Italy
| | - Giovanni Martinelli
- Institute of Hematology "L. e A. Seragnoli", Dep. of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna
| | - Giuseppe Basso
- Laboratorio di Oncoematologia, Dipartimento di Pediatria Università Padova, Padova
| | - Andrea Biondi
- Centro Ricerca Tettamanti, Clinica Pediatrica, Dipartimento di Scienze della Salute, Università di Milano-Bicocca, Ospedale S. Gerardo/Fondazione MBBM, Monza
| | | | - Giovanni Cazzaniga
- Centro Ricerca Tettamanti, Clinica Pediatrica, Dipartimento di Scienze della Salute, Università di Milano-Bicocca, Ospedale S. Gerardo/Fondazione MBBM, Monza
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Aly RM, Ghazy HF. Prognostic significance of MSI2 predicts unfavorable outcome in adult B-acute lymphoblastic leukemia. Int J Lab Hematol 2014; 37:272-8. [PMID: 25090928 DOI: 10.1111/ijlh.12284] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 06/26/2014] [Indexed: 12/24/2022]
Abstract
INTRODUCTION The Musashi-2 gene (MSI2) is implicated in leukemogenesis, and high MSI2 expression has been associated with decreased survival in acute myeloid leukemia (AML) and acute lymphoid leukemia (ALL), suggesting its use as a new prognostic marker. We aimed to validate the prognostic significance of MSI2 in ALL. METHODS MSI2 expression was measured by real-time polymerase chain reaction in 140 adult B-ALL patients and compared to controls. RESULTS MSI2 expression level in patients was significantly higher when compared to the control group (P = 0.001). High MSI2 expression did not correlate with the clinical characteristics of patients. However, patients with high MSI2 expression had significantly lower incidence of complete remission (CR) (P = 0.03), inferior overall survival (P = 0.018), and shorter disease-free survival (P = 0.001). Multivariate analysis revealed that high MSI2 expression was an independent prognostic factor for adult BCR-ABL1-negative B-ALL patients. CONCLUSION These results confirm the association of MSI2 expression with outcome in adult B-ALL and demonstrate the utility of MSI2 as a clinical prognostic biomarker.
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Affiliation(s)
- R M Aly
- Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
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48
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IGF2BP1: a novel IGH translocation partner in B acute lymphoblastic leukemia. Cancer Genet 2014; 207:332-4. [PMID: 25195122 DOI: 10.1016/j.cancergen.2014.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/15/2014] [Accepted: 07/18/2014] [Indexed: 11/22/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common form of childhood malignancy. Detecting and characterizing recurrent translocations is critical for ALL diagnosis and treatment. IGH (immunoglobulin heavy chain) rearrangements are relatively common in lymphoproliferative disorders, including ALL. Here we report a 16-year-old boy who was diagnosed with B acute lymphoblastic leukemia. Chromosome analysis showed a t(14;17)(q32;q21) with an additional copy of the derivative chromosome 14. IGH rearrangement was confirmed by concurrent FISH analysis. Chromosomal microarray analysis (CMA) showed the breakpoint at the 5 prime end of the IGF2BP1 gene located at 17q21.32. To the best of our knowledge, this is the first report of ALL with a 14;17 translocation resulting in an IGH-IGF2BP1 fusion; however, previous studies have implicated a role for up-regulation of IGF2BP1 in ALL.
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Chiaretti S, Gianfelici V, Ceglie G, Foà R. Genomic characterization of acute leukemias. Med Princ Pract 2014; 23:487-506. [PMID: 24968698 PMCID: PMC5586934 DOI: 10.1159/000362793] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Accepted: 04/10/2014] [Indexed: 01/09/2023] Open
Abstract
Over the past two decades, hematologic malignancies have been extensively evaluated due to the introduction of powerful technologies, such as conventional karyotyping, FISH analysis, gene and microRNA expression profiling, array comparative genomic hybridization and SNP arrays, and next-generation sequencing (including whole-exome sequencing and RNA-seq). These analyses have allowed for the refinement of the mechanisms underlying the leukemic transformation in several oncohematologic disorders and, more importantly, they have permitted the definition of novel prognostic algorithms aimed at stratifying patients at the onset of disease and, consequently, treating them in the most appropriate manner. Furthermore, the identification of specific molecular markers is opening the door to targeted and personalized medicine. The most important findings on novel acquisitions in the context of acute lymphoblastic leukemia of both B and T lineage and de novo acute myeloid leukemia are described in this review.
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Affiliation(s)
- Sabina Chiaretti
- Division of Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Rome, Italy
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50
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Hemmat M, Chen W, Anguiano A, Naggar ME, Racke FK, Jones D, Wang Y, Strom CM, Chang K, Boyar FZ. Submicroscopic deletion of 5q involving tumor suppressor genes (CTNNA1, HSPA9) and copy neutral loss of heterozygosity associated with TET2 and EZH2 mutations in a case of MDS with normal chromosome and FISH results. Mol Cytogenet 2014; 7:35. [PMID: 25177364 PMCID: PMC4149311 DOI: 10.1186/1755-8166-7-35] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Accepted: 05/19/2014] [Indexed: 12/24/2022] Open
Abstract
Advances in genome-wide molecular cytogenetics allow identification of novel submicroscopic DNA copy number alterations (aCNAs) and copy-neutral loss of heterozygosity (cnLOH) resulting in homozygosity for known gene mutations in myeloid neoplasms. We describe the use of an oligo-SNP array for genomic profiling of aCNA and cnLOH, together with sequence analysis of recurrently mutated genes, in a patient with myelodysplastic syndrome (MDS) presenting with normal karyotype and FISH results. Oligo-SNP array analysis revealed a hemizygous deletion of 896 kb at chromosome 5q31.2, representing the smallest 5q deletion reported to date. The deletion involved multiple genes, including two tumor suppressor candidate genes (CTNNA1 and HSPA9) that are associated with MDS/AML. The SNP-array study also detected 3 segments of somatic cnLOH: one involved the entire long arm of chromosome 4; the second involved the distal half of the long arm of chromosome 7, and the third encompassed the entire chromosome 22 (UPD 22). Sequence analysis revealed mutations in TET2 (4q), EZH2 (7q), ASXL1 (20q11.21), and RUNX1 (21q22.3). Coincidently, TET2 and EZH2 were located at segments of cnLOH resulting in their homozygosity. Loss of heterozygosity affecting these two chromosomes and mutations in TET2 and EZH2 are indicative of a myelodysplastic syndrome with a poor prognosis. Deletion of the tumor suppressor genes CTNNA1 and HSPA9 is also likely to contribute to a poor prognosis. Furthermore, the original cnLOHs in multiple chromosomes and additional cnLOH 14q in the follow-up study suggest genetic evolution of the disease and poor prognosis. This study attests to the fact that some patients with a myelodysplastic syndrome who exhibit a normal karyotype may have underlying genetic abnormalities detectable by chromosomal microarray and/or targeted mutation analyses.
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Affiliation(s)
- Morteza Hemmat
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, 92675 San Juan Capistrano, CA, USA
| | - Weina Chen
- University of Texas southwestern Medical Center, 5323 Harry Hines Blvd, 75235 Dallas, TX, USA
| | - Arturo Anguiano
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, 92675 San Juan Capistrano, CA, USA
| | - Mohammed El Naggar
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, 92675 San Juan Capistrano, CA, USA
| | - Frederick K Racke
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, 92675 San Juan Capistrano, CA, USA
| | - Dan Jones
- Quest Diagnostics Nichols Institute, 14225 Newbrook Drive, 20151 Chantilly, VA, USA
| | - Yongbao Wang
- Quest Diagnostics Nichols Institute, 14225 Newbrook Drive, 20151 Chantilly, VA, USA
| | - Charles M Strom
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, 92675 San Juan Capistrano, CA, USA
| | - Karl Chang
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, 92675 San Juan Capistrano, CA, USA
| | - Fatih Z Boyar
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, 92675 San Juan Capistrano, CA, USA
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