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Lysenkova Wiklander M, Arvidsson G, Bunikis I, Lundmark A, Raine A, Marincevic-Zuniga Y, Gezelius H, Bremer A, Feuk L, Ameur A, Nordlund J. A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing. Life Sci Alliance 2024; 7:e202302481. [PMID: 38777370 PMCID: PMC11111970 DOI: 10.26508/lsa.202302481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
The B-cell acute lymphoblastic leukemia (ALL) cell line REH, with the t(12;21) ETV6::RUNX1 translocation, is known to have a complex karyotype defined by a series of large-scale chromosomal rearrangements. Taken from a 15-yr-old at relapse, the cell line offers a practical model for the study of pediatric B-ALL. In recent years, short- and long-read DNA and RNA sequencing have emerged as a complement to karyotyping techniques in the resolution of structural variants in an oncological context. Here, we explore the integration of long-read PacBio and Oxford Nanopore whole-genome sequencing, IsoSeq RNA sequencing, and short-read Illumina sequencing to create a detailed genomic and transcriptomic characterization of the REH cell line. Whole-genome sequencing clarified the molecular traits of disrupted ALL-associated genes including CDKN2A, PAX5, BTG1, VPREB1, and TBL1XR1, as well as the glucocorticoid receptor NR3C1 Meanwhile, transcriptome sequencing identified seven fusion genes within the genomic breakpoints. Together, our extensive whole-genome investigation makes high-quality open-source data available to the leukemia genomics community.
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Affiliation(s)
- Mariya Lysenkova Wiklander
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Gustav Arvidsson
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Ignas Bunikis
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Anders Lundmark
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Amanda Raine
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Yanara Marincevic-Zuniga
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Henrik Gezelius
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Anna Bremer
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/01apvbh93 Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
| | - Lars Feuk
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Adam Ameur
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
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2
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Hodder A, Leiter SM, Kennedy J, Addy D, Ahmed M, Ajithkumar T, Allinson K, Ancliff P, Bailey S, Barnard G, Burke GAA, Burns C, Cano-Flanagan J, Chalker J, Coleman N, Cheng D, Clinch Y, Dryden C, Ghorashian S, Griffin B, Horan G, Hubank M, May P, McDerra J, Nagrecha R, Nicholson J, O'Connor D, Pavasovic V, Quaegebeur A, Rao A, Roberts T, Samarasinghe S, Stasevich I, Tadross JA, Trayers C, Trotman J, Vora A, Watkins J, Chitty LS, Bowdin S, Armstrong R, Murray MJ, Hook CE, Tarpey P, Vedi A, Bartram J, Behjati S. Benefits for children with suspected cancer from routine whole-genome sequencing. Nat Med 2024:10.1038/s41591-024-03056-w. [PMID: 38956197 DOI: 10.1038/s41591-024-03056-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/08/2024] [Indexed: 07/04/2024]
Abstract
Clinical whole-genome sequencing (WGS) has been shown to deliver potential benefits to children with cancer and to alter treatment in high-risk patient groups. It remains unknown whether offering WGS to every child with suspected cancer can change patient management. We collected WGS variant calls and clinical and diagnostic information from 281 children (282 tumors) across two English units (n = 152 from a hematology center, n = 130 from a solid tumor center) where WGS had become a routine test. Our key finding was that variants uniquely attributable to WGS changed the management in ~7% (20 out of 282) of cases while providing additional disease-relevant findings, beyond standard-of-care molecular tests, in 108 instances for 83 (29%) cases. Furthermore, WGS faithfully reproduced every standard-of-care molecular test (n = 738) and revealed several previously unknown genomic features of childhood tumors. We show that WGS can be delivered as part of routine clinical care to children with suspected cancer and can change clinical management by delivering unexpected genomic insights. Our experience portrays WGS as a clinically impactful assay for routine practice, providing opportunities for assay consolidation and for delivery of molecularly informed patient care.
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Affiliation(s)
- Angus Hodder
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Sarah M Leiter
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Jonathan Kennedy
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Dilys Addy
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Munaza Ahmed
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | | | - Kieren Allinson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Phil Ancliff
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Shivani Bailey
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Gemma Barnard
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - G A Amos Burke
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Charlotte Burns
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Danny Cheng
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | | | - Caryl Dryden
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Sara Ghorashian
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Blanche Griffin
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- North Thames Genomic Laboratory Hub, London, UK
| | - Gail Horan
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Michael Hubank
- North Thames Genomic Laboratory Hub, London, UK
- The Institute of Cancer Research, London, UK
| | - Phillippa May
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Joanna McDerra
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Rajvi Nagrecha
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - James Nicholson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - David O'Connor
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Vesna Pavasovic
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Annelies Quaegebeur
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Anupama Rao
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Thomas Roberts
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
| | | | - Iryna Stasevich
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - John A Tadross
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Claire Trayers
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jamie Trotman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
| | - Ajay Vora
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - James Watkins
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
| | - Lyn S Chitty
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- North Thames Genomic Laboratory Hub, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Sarah Bowdin
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
| | - Ruth Armstrong
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Matthew J Murray
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Catherine E Hook
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Patrick Tarpey
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- East Genomics Laboratory Hub, Cambridge, UK.
| | - Aditi Vedi
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
| | - Jack Bartram
- Great Ormond Street Hospital NHS Foundation Trust, London, UK.
- North Thames Genomic Laboratory Hub, London, UK.
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
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3
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Pagliaro L, Chen SJ, Herranz D, Mecucci C, Harrison CJ, Mullighan CG, Zhang M, Chen Z, Boissel N, Winter SS, Roti G. Acute lymphoblastic leukaemia. Nat Rev Dis Primers 2024; 10:41. [PMID: 38871740 DOI: 10.1038/s41572-024-00525-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/01/2024] [Indexed: 06/15/2024]
Abstract
Acute lymphoblastic leukaemia (ALL) is a haematological malignancy characterized by the uncontrolled proliferation of immature lymphoid cells. Over past decades, significant progress has been made in understanding the biology of ALL, resulting in remarkable improvements in its diagnosis, treatment and monitoring. Since the advent of chemotherapy, ALL has been the platform to test for innovative approaches applicable to cancer in general. For example, the advent of omics medicine has led to a deeper understanding of the molecular and genetic features that underpin ALL. Innovations in genomic profiling techniques have identified specific genetic alterations and mutations that drive ALL, inspiring new therapies. Targeted agents, such as tyrosine kinase inhibitors and immunotherapies, have shown promising results in subgroups of patients while minimizing adverse effects. Furthermore, the development of chimeric antigen receptor T cell therapy represents a breakthrough in ALL treatment, resulting in remarkable responses and potential long-term remissions. Advances are not limited to treatment modalities alone. Measurable residual disease monitoring and ex vivo drug response profiling screening have provided earlier detection of disease relapse and identification of exceptional responders, enabling clinicians to adjust treatment strategies for individual patients. Decades of supportive and prophylactic care have improved the management of treatment-related complications, enhancing the quality of life for patients with ALL.
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Affiliation(s)
- Luca Pagliaro
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Translational Hematology and Chemogenomics (THEC), University of Parma, Parma, Italy
- Hematology and BMT Unit, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Sai-Juan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Daniel Herranz
- Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Cristina Mecucci
- Department of Medicine, Hematology and Clinical Immunology, University of Perugia, Perugia, Italy
| | - Christine J Harrison
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ming Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Nicolas Boissel
- Hôpital Saint-Louis, APHP, Institut de Recherche Saint-Louis, Université Paris Cité, Paris, France
| | - Stuart S Winter
- Children's Minnesota Cancer and Blood Disorders Program, Minneapolis, MN, USA
| | - Giovanni Roti
- Department of Medicine and Surgery, University of Parma, Parma, Italy.
- Translational Hematology and Chemogenomics (THEC), University of Parma, Parma, Italy.
- Hematology and BMT Unit, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy.
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4
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Hu Z, Jia Z, Liu J, Mao A, Han H, Gu Z. MD-ALL: an integrative platform for molecular diagnosis of B-acute lymphoblastic leukemia. Haematologica 2024; 109:1741-1754. [PMID: 37981856 PMCID: PMC11141650 DOI: 10.3324/haematol.2023.283706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 11/06/2023] [Indexed: 11/21/2023] Open
Abstract
B-acute lymphoblastic leukemia (B-ALL) consists of dozens of subtypes defined by distinct gene expression profiles (GEP) and various genetic lesions. With the application of transcriptome sequencing (RNA sequencing [RNA-seq]), multiple novel subtypes have been identified, which lead to an advanced B-ALL classification and risk-stratification system. However, the complexity of analyzing RNA-seq data for B-ALL classification hinders the implementation of the new B-ALL taxonomy. Here, we introduce Molecular Diagnosis of Acute Lymphoblastic Leukemia (MD-ALL), an integrative platform featuring sensitive and accurate B-ALL classification based on GEP and sentinel genetic alterations from RNA-seq data. In this study, we systematically analyzed 2,955 B-ALL RNA-seq samples and generated a reference dataset representing all the reported B-ALL subtypes. Using multiple machine learning algorithms, we identified the feature genes and then established highly sensitive and accurate models for B-ALL classification using either bulk or single-cell RNA-seq data. Importantly, this platform integrates multiple aspects of key genetic lesions acquired from RNA-seq data, which include sequence mutations, large-scale copy number variations, and gene rearrangements, to perform comprehensive and definitive B-ALL classification. Through validation in a hold-out cohort of 974 samples, our models demonstrated superior performance for B-ALL classification compared with alternative tools. Moreover, to ensure accessibility and user-friendly navigation even for users with limited or no programming background, we developed an interactive graphical user interface for this MD-ALL platform, using the R Shiny package. In summary, MD-ALL is a user-friendly B-ALL classification platform designed to enable integrative, accurate, and comprehensive B-ALL subtype classification. MD-ALL is available from https://github.com/gu-lab20/MD-ALL.
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Affiliation(s)
- Zunsong Hu
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA; Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA
| | - Zhilian Jia
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA; Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA
| | - Jiangyue Liu
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, Duarte, CA, USA; Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA
| | - Allen Mao
- Research Informatics, City of Hope National Medical Center, Duarte, CA
| | - Helen Han
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA; Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA
| | - Zhaohui Gu
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA; Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA.
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5
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de Boer EN, Vroom V, Scheper AJ, Johansson LF, Bosscher L, Rietema N, Commandeur-Jan SZ, Knoers NVAM, Sikkema-Raddatz B, van den Berg E, van Diemen CC. Cas9-directed long-read sequencing to resolve optical genome mapping findings in leukemia diagnostics. Sci Rep 2024; 14:8508. [PMID: 38605095 PMCID: PMC11009395 DOI: 10.1038/s41598-024-59092-6] [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: 08/30/2023] [Accepted: 04/08/2024] [Indexed: 04/13/2024] Open
Abstract
Leukemias are genetically heterogeneous and diagnostics therefore includes various standard-of-care (SOC) techniques, including karyotyping, SNP-array and FISH. Optical genome mapping (OGM) may replace these as it detects different types of structural aberrations simultaneously and additionally detects much smaller aberrations (500 bp vs 5-10 Mb with karyotyping). However, its resolution may still be too low to define clinical relevance of aberrations when they are located between two OGM labels or when labels are not distinct enough. Here, we test the potential of Cas9-directed long-read sequencing (LRS) as an additional technique to resolve such potentially relevant new findings. From an internal Bionano implementation study we selected ten OGM calls that could not be validated with SOC methods. Per variant we designed crRNAs for Cas9 enrichment, prepared libraries and sequenced them on a MinION/GridION device. We could confirm all aberrations and, importantly, the actual breakpoints of the OGM calls were located between 0.2 and 5.5 kb of the OGM-estimated breakpoints, confirming the high reliability of OGM. Furthermore, we show examples of redefinition of aberrations between labels that enable judgment of clinical relevance. Our results suggest that Cas9-directed LRS can be a relevant and flexible secondary technique in diagnostic workflows including OGM.
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Affiliation(s)
- Eddy N de Boer
- Department of Genetics, University of Groningen, University Medical Center Groningen, CB51, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.
| | - Vincent Vroom
- Department of Genetics, University of Groningen, University Medical Center Groningen, CB51, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Arjen J Scheper
- Department of Genetics, University of Groningen, University Medical Center Groningen, CB51, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Lennart F Johansson
- Department of Genetics, University of Groningen, University Medical Center Groningen, CB51, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Laura Bosscher
- Department of Genetics, University of Groningen, University Medical Center Groningen, CB51, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Nettie Rietema
- Department of Genetics, University of Groningen, University Medical Center Groningen, CB51, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Sabrina Z Commandeur-Jan
- Department of Genetics, University of Groningen, University Medical Center Groningen, CB51, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Nine V A M Knoers
- Department of Genetics, University of Groningen, University Medical Center Groningen, CB51, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Birgit Sikkema-Raddatz
- Department of Genetics, University of Groningen, University Medical Center Groningen, CB51, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Eva van den Berg
- Department of Genetics, University of Groningen, University Medical Center Groningen, CB51, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Cleo C van Diemen
- Department of Genetics, University of Groningen, University Medical Center Groningen, CB51, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
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6
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Mosquera Orgueira A, Krali O, Pérez Míguez C, Peleteiro Raíndo A, Díaz Arias JÁ, González Pérez MS, Pérez Encinas MM, Fernández Sanmartín M, Sinnet D, Heyman M, Lönnerholm G, Norén-Nyström U, Schmiegelow K, Nordlund J. Refining risk prediction in pediatric acute lymphoblastic leukemia through DNA methylation profiling. Clin Epigenetics 2024; 16:49. [PMID: 38549146 PMCID: PMC10976833 DOI: 10.1186/s13148-024-01662-6] [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: 12/01/2023] [Accepted: 03/16/2024] [Indexed: 04/02/2024] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most prevalent cancer in children, and despite considerable progress in treatment outcomes, relapses still pose significant risks of mortality and long-term complications. To address this challenge, we employed a supervised machine learning technique, specifically random survival forests, to predict the risk of relapse and mortality using array-based DNA methylation data from a cohort of 763 pediatric ALL patients treated in Nordic countries. The relapse risk predictor (RRP) was constructed based on 16 CpG sites, demonstrating c-indexes of 0.667 and 0.677 in the training and test sets, respectively. The mortality risk predictor (MRP), comprising 53 CpG sites, exhibited c-indexes of 0.751 and 0.754 in the training and test sets, respectively. To validate the prognostic value of the predictors, we further analyzed two independent cohorts of Canadian (n = 42) and Nordic (n = 384) ALL patients. The external validation confirmed our findings, with the RRP achieving a c-index of 0.667 in the Canadian cohort, and the RRP and MRP achieving c-indexes of 0.529 and 0.621, respectively, in an independent Nordic cohort. The precision of the RRP and MRP models improved when incorporating traditional risk group data, underscoring the potential for synergistic integration of clinical prognostic factors. The MRP model also enabled the definition of a risk group with high rates of relapse and mortality. Our results demonstrate the potential of DNA methylation as a prognostic factor and a tool to refine risk stratification in pediatric ALL. This may lead to personalized treatment strategies based on epigenetic profiling.
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Affiliation(s)
- Adrián Mosquera Orgueira
- Department of Hematology, University Hospital of Santiago de Compostela, Compostela, Spain.
- Health Research Institute of Santiago de Compostela, Compostela, Spain.
| | - Olga Krali
- Department of Medical Sciences, Molecular Precision Medicine, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Andrés Peleteiro Raíndo
- Department of Hematology, University Hospital of Santiago de Compostela, Compostela, Spain
- Health Research Institute of Santiago de Compostela, Compostela, Spain
| | - José Ángel Díaz Arias
- Department of Hematology, University Hospital of Santiago de Compostela, Compostela, Spain
- Health Research Institute of Santiago de Compostela, Compostela, Spain
| | - Marta Sonia González Pérez
- Department of Hematology, University Hospital of Santiago de Compostela, Compostela, Spain
- Health Research Institute of Santiago de Compostela, Compostela, Spain
| | - Manuel Mateo Pérez Encinas
- Department of Hematology, University Hospital of Santiago de Compostela, Compostela, Spain
- Health Research Institute of Santiago de Compostela, Compostela, Spain
| | - Manuel Fernández Sanmartín
- Health Research Institute of Santiago de Compostela, Compostela, Spain
- Department of Pediatric Medicine, University Hospital of Santiago de Compostela, Santiago de Compostela, Spain
| | - Daniel Sinnet
- Research Center, CHU Sainte-Justine, Montréal, Canada
- Department of Pediatrics, Université de Montréal, Montreal, Canada
| | - Mats Heyman
- Childhood Cancer Research Unit, Karolinska Institutet, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
- For the Nordic Society of Pediatric Hematology and Oncology (NOPHO), Stockholm, Sweden
| | - Gudmar Lönnerholm
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
- For the Nordic Society of Pediatric Hematology and Oncology (NOPHO), Stockholm, Sweden
| | - Ulrika Norén-Nyström
- Department of Clinical Sciences, Pediatrics, Umeå University, Umeå, Sweden
- For the Nordic Society of Pediatric Hematology and Oncology (NOPHO), Stockholm, Sweden
| | - Kjeld Schmiegelow
- Pediatrics and Adolescent Medicine, Rigshospitalet, and the Medical Faculty, Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- For the Nordic Society of Pediatric Hematology and Oncology (NOPHO), Stockholm, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Precision Medicine, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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7
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Kubota H, Ueno H, Tasaka K, Isobe T, Saida S, Kato I, Umeda K, Hiwatari M, Hasegawa D, Imamura T, Kakiuchi N, Nannya Y, Ogawa S, Hiramatsu H, Takita J. RNA-seq-based miRNA signature as an independent predictor of relapse in pediatric B-cell acute lymphoblastic leukemia. Blood Adv 2024; 8:1258-1271. [PMID: 38127276 PMCID: PMC10918494 DOI: 10.1182/bloodadvances.2023011583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/21/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023] Open
Abstract
ABSTRACT Aberrant micro-RNA (miRNA) expression profiles have been associated with disease progression and clinical outcome in pediatric cancers. However, few studies have analyzed genome-wide dysregulation of miRNAs and messenger RNAs (mRNAs) in pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL). To identify novel prognostic factors, we comprehensively investigated miRNA and mRNA sequencing (miRNA-seq and mRNA-seq) data in pediatric BCP-ALL samples with poor outcome. We analyzed 180 patients, including 43 matched pairs at diagnosis and relapse. Consensus clustering of miRNA expression data revealed a distinct profile characterized by mainly downregulation of miRNAs (referred to as an miR-low cluster [MLC]). The MLC profile was not associated with any known genetic subgroups. Intriguingly, patients classified as MLC had significantly shorter event-free survival (median 21 vs 33 months; log-rank P = 3 ×10-5). Furthermore, this poor prognosis was retained even in hyperdiploid ALL. This poor prognostic MLC profiling was confirmed in the validation cohort. Notably, non-MLC profiling at diagnosis (n = 9 of 23; Fisher exact test, P = .039) often changed into MLC profiling at relapse for the same patient. Integrated analysis of miRNA-seq and mRNA-seq data revealed that the transcriptional profile of MLC was characterized by enrichment of MYC target and oxidative phosphorylation genes, reduced intron retention, and low expression of DICER1. Thus, our miRNA-mRNA integration approach yielded a truly unbiased molecular stratification of pediatric BCP-ALL cases based on a novel prognostic miRNA signature, which may lead to better clinical outcomes.
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Affiliation(s)
- Hirohito Kubota
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroo Ueno
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keiji Tasaka
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomoya Isobe
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Hematology, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Satoshi Saida
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Itaru Kato
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Katsutsugu Umeda
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mitsuteru Hiwatari
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Pediatrics, School of Medicine, Teikyo University, Tokyo, Japan
| | - Daiichiro Hasegawa
- Department of Hematology and Oncology, Hyogo Prefectural Kobe Children Hospital, Hyogo, Japan
| | - Toshihiko Imamura
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Nobuyuki Kakiuchi
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- The Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Division of Hematopoietic Disease Control, Institute of Medical Science, The University of Tokyo, Tokyo, 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 (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Hidefumi Hiramatsu
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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8
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Cho YU. The role of next-generation sequencing in hematologic malignancies. Blood Res 2024; 59:11. [PMID: 38485897 PMCID: PMC10917716 DOI: 10.1007/s44313-024-00010-0] [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: 01/17/2024] [Accepted: 02/13/2024] [Indexed: 03/18/2024] Open
Abstract
Next-generation sequencing (NGS) allows high-throughput detection of molecular changes in tumors. Over the past 15 years, NGS has rapidly evolved from a promising research tool to a core component of the clinical laboratory. Sequencing of tumor cells provides an important step in detecting somatic driver mutations that not only characterize the disease but also influence treatment decisions. For patients with hematologic malignancies, NGS has been used for accurate classification and diagnosis based on genetic alterations. The recently revised World Health Organization classification and the European LeukemiaNet recommendations for acute myeloid leukemia consider genetic abnormalities as a top priority for diagnosis, prognostication, monitoring of measurable residual disease, and treatment choice. This review aims to present the role and utility of various NGS approaches for the diagnosis, treatment, and follow-up of hemato-oncology patients.
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Affiliation(s)
- Young-Uk Cho
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, 05505, Korea.
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9
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Xiang L, Wang Y, Pan W. Importance of Rare Gene Alterations in the Prognosis of B-Cell Acute Lymphoblastic Leukemia. Turk J Haematol 2024; 41:49-50. [PMID: 38174667 PMCID: PMC10918399 DOI: 10.4274/tjh.galenos.2024.2023.0400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 01/04/2024] [Indexed: 01/05/2024] Open
Affiliation(s)
- Li Xiang
- Zhejiang Provincial People’s Hospital Bijie Hospital, Department of Science and Education, Bijie, China
| | - Yongliang Wang
- Xinchang Hospital Affiliated to Wenzhou Medical University, Department of Thoracic Surgery, Xinchang, China
| | - Wei Pan
- Haiyan People’s Hospital, Department of Clinical Laboratory, Haiyan, China
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10
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Behrens YL, Pietzsch S, Antić Ž, Zhang Y, Bergmann AK. The landscape of cytogenetic and molecular genetic methods in diagnostics for hematologic neoplasia. Best Pract Res Clin Haematol 2024; 37:101539. [PMID: 38490767 DOI: 10.1016/j.beha.2024.101539] [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: 12/05/2023] [Accepted: 01/28/2024] [Indexed: 03/17/2024]
Abstract
Improvements made during the last decades in the management of patients with hematologic neoplasia have resulted in increase of overall survival. These advancements have become possible through progress in our understanding of genetic basis of different hematologic malignancies and their role in the current risk-adapted treatment protocols. In this review, we provide an overview of current cytogenetic and molecular genetic methods, commonly used in the genetic characterization of hematologic malignancies, describe the current developments in the cytogenetic and molecular diagnostics, and give an outlook into their future development. Furthermore, we give a brief overview of the most important public databases and guidelines for sequence variant interpretation.
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Affiliation(s)
- Yvonne Lisa Behrens
- Department of Human Genetics, Hannover Medical School, 30625, Hannover, Germany
| | - Stefan Pietzsch
- Department of Human Genetics, Hannover Medical School, 30625, Hannover, Germany
| | - Željko Antić
- Department of Human Genetics, Hannover Medical School, 30625, Hannover, Germany
| | - Yanming Zhang
- Cytogenetics Laboratory, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anke K Bergmann
- Department of Human Genetics, Hannover Medical School, 30625, Hannover, Germany.
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11
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Jang MA. Genomic technologies for detecting structural variations in hematologic malignancies. Blood Res 2024; 59:1. [PMID: 38485792 PMCID: PMC10903520 DOI: 10.1007/s44313-024-00001-1] [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: 12/05/2023] [Accepted: 12/18/2023] [Indexed: 03/18/2024] Open
Abstract
Genomic structural variations in myeloid, lymphoid, and plasma cell neoplasms can provide key diagnostic, prognostic, and therapeutic information while elucidating the underlying disease biology. Several molecular diagnostic approaches play a central role in evaluating hematological malignancies. Traditional cytogenetic diagnostic assays, such as chromosome banding and fluorescence in situ hybridization, are essential components of the current diagnostic workup that guide clinical care for most hematologic malignancies. However, each assay has inherent limitations, including limited resolution for detecting small structural variations and low coverage, and can only detect alterations in the target regions. Recently, the rapid expansion and increasing availability of novel and comprehensive genomic technologies have led to their use in clinical laboratories for clinical management and translational research. This review aims to describe the clinical relevance of structural variations in hematologic malignancies and introduce genomic technologies that may facilitate personalized tumor characterization and treatment.
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Affiliation(s)
- Mi-Ae Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul, 06351, Korea.
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12
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Paolino J, Tsai HK, Harris MH, Pikman Y. IKZF1 Alterations and Therapeutic Targeting in B-Cell Acute Lymphoblastic Leukemia. Biomedicines 2024; 12:89. [PMID: 38255194 PMCID: PMC10813044 DOI: 10.3390/biomedicines12010089] [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: 11/21/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
IKZF1 encodes the transcription factor IKAROS, a zinc finger DNA-binding protein with a key role in lymphoid lineage development. IKAROS plays a critical role in the development of lineage-restricted mature lymphocytes. Deletions within IKZF1 in B-cell acute lymphoblastic leukemia (B-ALL) lead to a loss of normal IKAROS function, conferring leukemic stem cell properties, including self-renewal and subsequent uncontrolled growth. IKZF1 deletions are associated with treatment resistance and inferior outcomes. Early identification of IKZF1 deletions in B-ALL may inform the intensification of therapy and other potential treatment strategies to improve outcomes in this high-risk leukemia.
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Affiliation(s)
- Jonathan Paolino
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Harrison K. Tsai
- Department of Pathology, Boston Children’s Hospital, Boston, MA 02115, USA (M.H.H.)
| | - Marian H. Harris
- Department of Pathology, Boston Children’s Hospital, Boston, MA 02115, USA (M.H.H.)
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
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13
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Aplan P, Bertoli R, Chung YJ, Difilippantonio M, Wokasch A, Marasco M, Klimaszewski H, Garber S, Zhu Y, Walker R, Cao D, Doroshow J, Meltzer P. 5-Aza-4'-thio-2'-deoxycytidine induces C>G transversions in a specific trinucleotide context and leads to acute lymphoid leukemia. RESEARCH SQUARE 2023:rs.3.rs-3186246. [PMID: 38168433 PMCID: PMC10760231 DOI: 10.21203/rs.3.rs-3186246/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
DNA methyltransferase inhibitors (DNMTi), most commonly cytidine analogs, are compounds that are used clinically to decrease 5'-cytosine methylation, with the aim of re-expression of tumor suppressor genes. We used a murine pre-clinical model of myelodysplastic syndrome based on transplantation of cells expressing a NUP98::HOXD13 transgene to investigate 5-Aza-4'-thio-2'-deoxycytidine (Aza TdCyd or ATC), a thiol substituted DNMTi, as a potential therapy. We found that ATC treatment led to lymphoid leukemia in wild-type recipient cells; further study revealed that healthy mice treated with ATC also developed lymphoid leukemia. Whole exome sequencing revealed thousands of acquired mutations, almost all of which were C > G transversions in a previously unrecognized, specific 5'-NCG-3' context. These mutations involved dozens of genes well-known to be involved in human lymphoid leukemia, such as Notch1, Pten, Pax5, Trp53 , and Nf1 . Treatment of human cells in vitro showed thousands of acquired C > G transversions in a similar context. Deletion of Dck , the rate-limiting enzyme for the cytidine salvage pathway, eliminated C > G transversions. Taken together, these findings demonstrate that DNMTi can be potent mutagens in human and mouse cells, both in vitro and in vivo .
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14
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Tueur G, Quessada J, De Bie J, Cuccuini W, Toujani S, Lefebvre C, Luquet I, Michaux L, Lafage-Pochitaloff M. Cytogenetics in the management of B-cell acute lymphoblastic leukemia: Guidelines from the Groupe Francophone de Cytogénétique Hématologique (GFCH). Curr Res Transl Med 2023; 71:103434. [PMID: 38064905 DOI: 10.1016/j.retram.2023.103434] [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: 07/09/2023] [Revised: 10/20/2023] [Accepted: 11/22/2023] [Indexed: 12/26/2023]
Abstract
Cytogenetic analysis is mandatory at initial assessment of B-cell acute lymphoblastic leukemia (B-ALL) due to its diagnostic and prognostic value. Results from chromosome banding analysis and complementary FISH are taken into account in therapeutic protocols and further completed by other techniques (RT-PCR, SNP-array, MLPA, NGS, OGM). Indeed, new genomic entities have been identified by NGS, mostly RNA sequencing, such as Ph-like ALL that can benefit from targeted therapy. Here, we have attempted to establish cytogenetic guidelines by reviewing the most recent published data including the novel 5th World Health Organization and International Consensus Classifications. We also focused on newly described cytogenomic entities and indicate alternative diagnostic tools such as NGS technology, as its importance is vastly increasing in the diagnostic setting.
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Affiliation(s)
- Giulia Tueur
- Laboratoire d'hématologie, Hôpital Avicenne, AP-HP, Bobigny 93000, France
| | - Julie Quessada
- Laboratoire de Cytogénétique Hématologique, Département d'Hématologie, CHU Timone, APHM, Aix Marseille Université, Marseille 13005, France; CRCM, Inserm UMR1068, CNRS UMR7258, Aix Marseille Université U105, Institut Paoli Calmettes, Marseille 13009, France
| | - Jolien De Bie
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, Leuven 3000, Belgium
| | - Wendy Cuccuini
- Laboratoire d'Hématologie, Unité de Cytogénétique, Hôpital Saint-Louis, AP-HP, Paris 75010, France
| | - Saloua Toujani
- Service de cytogénétique et biologie cellulaire, CHU de Rennes, Rennes 35033, France
| | - Christine Lefebvre
- Unité de Génétique des Hémopathies, Service d'Hématologie Biologique, CHU Grenoble Alpes, Grenoble 38000, France
| | - Isabelle Luquet
- Laboratoire d'Hématologie, CHU Toulouse (IUCT-O), Toulouse 31000, France
| | - Lucienne Michaux
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, Leuven 3000, Belgium; Katholieke Universiteit Leuven, Leuven 3000, Belgium
| | - Marina Lafage-Pochitaloff
- Laboratoire de Cytogénétique Hématologique, Département d'Hématologie, CHU Timone, APHM, Aix Marseille Université, Marseille 13005, France.
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15
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van Outersterp I, van der Velden VH, Hoogeveen PG, Vaitkevičienė GE, Sonneveld E, van Haaften G, Kuiper RP, zur Stadt U, Escherich G, Boer JM, den Boer ML. ABL-class Genomic Breakpoint Q-PCR: A Patient-specific Approach for MRD Monitoring in Acute Lymphoblastic Leukemia. Hemasphere 2023; 7:e967. [PMID: 37736661 PMCID: PMC10511034 DOI: 10.1097/hs9.0000000000000967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/03/2023] [Indexed: 09/23/2023] Open
Affiliation(s)
| | - Vincent H.J. van der Velden
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Patricia G. Hoogeveen
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Goda E. Vaitkevičienė
- Faculty of Medicine, Vilnius University, Lithuania
- Center for Pediatric Oncology and Hematology, Vilnius University Hospital Santaros Klinikos, Lithuania
| | - Edwin Sonneveld
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Dutch Childhood Oncology Group, Utrecht, The Netherlands
| | - Gijs van Haaften
- Department of Genetics, University Medical Center Utrecht, The Netherlands
| | - Roland P. Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Genetics, University Medical Center Utrecht, The Netherlands
| | - Udo zur Stadt
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg Eppendorf, Germany
| | - Gabriele Escherich
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg Eppendorf, Germany
| | - Judith M. Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Monique L. den Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pediatric Oncology and Hematology, Erasmus MC - Sophia Children’s Hospital, Rotterdam, The Netherlands
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16
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Thomson AJ, Rehn JA, Heatley SL, Eadie LN, Page EC, Schutz C, McClure BJ, Sutton R, Dalla-Pozza L, Moore AS, Greenwood M, Kotecha RS, Fong CY, Yong ASM, Yeung DT, Breen J, White DL. Reproducible Bioinformatics Analysis Workflows for Detecting IGH Gene Fusions in B-Cell Acute Lymphoblastic Leukaemia Patients. Cancers (Basel) 2023; 15:4731. [PMID: 37835427 PMCID: PMC10571859 DOI: 10.3390/cancers15194731] [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: 09/15/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
B-cell acute lymphoblastic leukaemia (B-ALL) is characterised by diverse genomic alterations, the most frequent being gene fusions detected via transcriptomic analysis (mRNA-seq). Due to its hypervariable nature, gene fusions involving the Immunoglobulin Heavy Chain (IGH) locus can be difficult to detect with standard gene fusion calling algorithms and significant computational resources and analysis times are required. We aimed to optimize a gene fusion calling workflow to achieve best-case sensitivity for IGH gene fusion detection. Using Nextflow, we developed a simplified workflow containing the algorithms FusionCatcher, Arriba, and STAR-Fusion. We analysed samples from 35 patients harbouring IGH fusions (IGH::CRLF2 n = 17, IGH::DUX4 n = 15, IGH::EPOR n = 3) and assessed the detection rates for each caller, before optimizing the parameters to enhance sensitivity for IGH fusions. Initial results showed that FusionCatcher and Arriba outperformed STAR-Fusion (85-89% vs. 29% of IGH fusions reported). We found that extensive filtering in STAR-Fusion hindered IGH reporting. By adjusting specific filtering steps (e.g., read support, fusion fragments per million total reads), we achieved a 94% reporting rate for IGH fusions with STAR-Fusion. This analysis highlights the importance of filtering optimization for IGH gene fusion events, offering alternative workflows for difficult-to-detect high-risk B-ALL subtypes.
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Affiliation(s)
- Ashlee J. Thomson
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.A.R.); (S.L.H.); (L.N.E.); (E.C.P.); (B.J.M.); (A.S.M.Y.); (D.T.Y.); (D.L.W.)
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia;
| | - Jacqueline A. Rehn
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.A.R.); (S.L.H.); (L.N.E.); (E.C.P.); (B.J.M.); (A.S.M.Y.); (D.T.Y.); (D.L.W.)
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia;
| | - Susan L. Heatley
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.A.R.); (S.L.H.); (L.N.E.); (E.C.P.); (B.J.M.); (A.S.M.Y.); (D.T.Y.); (D.L.W.)
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia;
- Australian and New Zealand Children’s Oncology Group (ANZCHOG), Clayton, VIC 3168, Australia
| | - Laura N. Eadie
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.A.R.); (S.L.H.); (L.N.E.); (E.C.P.); (B.J.M.); (A.S.M.Y.); (D.T.Y.); (D.L.W.)
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia;
| | - Elyse C. Page
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.A.R.); (S.L.H.); (L.N.E.); (E.C.P.); (B.J.M.); (A.S.M.Y.); (D.T.Y.); (D.L.W.)
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia;
| | - Caitlin Schutz
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia;
| | - Barbara J. McClure
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.A.R.); (S.L.H.); (L.N.E.); (E.C.P.); (B.J.M.); (A.S.M.Y.); (D.T.Y.); (D.L.W.)
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia;
| | - Rosemary Sutton
- Molecular Diagnostics, Children’s Cancer Institute, Kensington, NSW 2750, Australia;
| | - Luciano Dalla-Pozza
- The Cancer Centre for Children, The Children’s Hospital at Westmead, Westmead, NSW 2145, Australia;
| | - Andrew S. Moore
- Oncology Service, Children’s Health Queensland Hospital and Health Service, Brisbane, QLD 4101, Australia;
- Child Health Research Centre, The University of Queensland, Brisbane, QLD 4000, Australia
| | - Matthew Greenwood
- Department of Haematology and Transfusion Services, Royal North Shore Hospital, Sydney, NSW 2065, Australia;
- Faculty of Health and Medicine, University of Sydney, Sydney, NSW 2006, Australia
| | - Rishi S. Kotecha
- Department of Clinical Haematology, Oncology, Blood and Marrow Transplantation, Perth Children’s Hospital, Perth, WA 6009, Australia;
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia
- Curtin Medical School, Curtin University, Perth, WA 6845, Australia
| | - Chun Y. Fong
- Department of Clinical Haematology, Austin Health, Heidelberg, VIC 3083, Australia;
| | - Agnes S. M. Yong
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.A.R.); (S.L.H.); (L.N.E.); (E.C.P.); (B.J.M.); (A.S.M.Y.); (D.T.Y.); (D.L.W.)
- South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia
- Division of Pathology & Laboratory, University of Western Australia Medical School, Perth, WA 6009, Australia
- Department of Haematology, Royal Perth Hospital, Perth, WA 6000, Australia
| | - David T. Yeung
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.A.R.); (S.L.H.); (L.N.E.); (E.C.P.); (B.J.M.); (A.S.M.Y.); (D.T.Y.); (D.L.W.)
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia;
- Haematology Department, Royal Adelaide Hospital and SA Pathology, Adelaide, SA 5000, Australia
| | - James Breen
- Black Ochre Data Labs, Indigenous Genomics, Telethon Kids Institute, Adelaide, SA 5000, Australia
- James Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Deborah L. White
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.A.R.); (S.L.H.); (L.N.E.); (E.C.P.); (B.J.M.); (A.S.M.Y.); (D.T.Y.); (D.L.W.)
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia;
- Australian and New Zealand Children’s Oncology Group (ANZCHOG), Clayton, VIC 3168, Australia
- Australian Genomics Health Alliance (AGHA), The Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
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17
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Gao Q, Ryan SL, Iacobucci I, Ghate PS, Cranston RE, Schwab C, Elsayed AH, Shi L, Pounds S, Lei S, Baviskar P, Pei D, Cheng C, Bashton M, Sinclair P, Bentley DR, Ross MT, Kingsbury Z, James T, Roberts KG, Devidas M, Fan Y, Chen W, Chang TC, Wu G, Carroll A, Heerema N, Valentine V, Valentine M, Yang W, Yang JJ, Moorman AV, Harrison CJ, Mullighan CG. The genomic landscape of acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21. Blood 2023; 142:711-723. [PMID: 37216686 PMCID: PMC10460677 DOI: 10.1182/blood.2022019094] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 04/06/2023] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Intrachromosomal amplification of chromosome 21 defines a subtype of high-risk childhood acute lymphoblastic leukemia (iAMP21-ALL) characterized by copy number changes and complex rearrangements of chromosome 21. The genomic basis of iAMP21-ALL and the pathogenic role of the region of amplification of chromosome 21 to leukemogenesis remains incompletely understood. In this study, using integrated whole genome and transcriptome sequencing of 124 patients with iAMP21-ALL, including rare cases arising in the context of constitutional chromosomal aberrations, we identified subgroups of iAMP21-ALL based on the patterns of copy number alteration and structural variation. This large data set enabled formal delineation of a 7.8 Mb common region of amplification harboring 71 genes, 43 of which were differentially expressed compared with non-iAMP21-ALL ones, including multiple genes implicated in the pathogenesis of acute leukemia (CHAF1B, DYRK1A, ERG, HMGN1, and RUNX1). Using multimodal single-cell genomic profiling, including single-cell whole genome sequencing of 2 cases, we documented clonal heterogeneity and genomic evolution, demonstrating that the acquisition of the iAMP21 chromosome is an early event that may undergo progressive amplification during disease ontogeny. We show that UV-mutational signatures and high mutation load are characteristic secondary genetic features. Although the genomic alterations of chromosome 21 are variable, these integrated genomic analyses and demonstration of an extended common minimal region of amplification broaden the definition of iAMP21-ALL for more precise diagnosis using cytogenetic or genomic methods to inform clinical management.
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Affiliation(s)
- Qingsong Gao
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Sarra L Ryan
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, United Kingdom
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Pankaj S Ghate
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Ruth E Cranston
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, United Kingdom
| | - Claire Schwab
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, United Kingdom
| | - Abdelrahman H Elsayed
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | - Lei Shi
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | - Shaohua Lei
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
- Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, Memphis, TN
| | | | - Deqing Pei
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | - Matthew Bashton
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, United Kingdom
| | - Paul Sinclair
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, United Kingdom
| | - David R Bentley
- Illumina Cambridge, Ltd, Illumina Centre, Great Abingdon, Cambridge, United Kingdom
| | - Mark T Ross
- Illumina Cambridge, Ltd, Illumina Centre, Great Abingdon, Cambridge, United Kingdom
| | - Zoya Kingsbury
- Illumina Cambridge, Ltd, Illumina Centre, Great Abingdon, Cambridge, United Kingdom
| | - Terena James
- Illumina Cambridge, Ltd, Illumina Centre, Great Abingdon, Cambridge, United Kingdom
| | - Kathryn G Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
- Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, Memphis, TN
| | - Meenakshi Devidas
- Department of Global Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN
| | - Wenan Chen
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN
| | - Andrew Carroll
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Nyla Heerema
- Department of Pathology, The Ohio State University, Columbus, OH
| | - Virginia Valentine
- Cytogenetics Shared Resource, St. Jude Children's Research Hospital, Memphis, TN
| | - Marcus Valentine
- Cytogenetics Shared Resource, St. Jude Children's Research Hospital, Memphis, TN
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Anthony V Moorman
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, United Kingdom
| | - Christine J Harrison
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle upon Tyne, United Kingdom
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
- Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, Memphis, TN
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18
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Leongamornlert D, Gutiérrez-Abril J, Lee S, Barretta E, Creasey T, Gundem G, Levine MF, Arango-Ossa JE, Liosis K, Medina-Martinez JS, Zuborne Alapi K, Kirkwood AA, Clifton-Hadley L, Patrick P, Jones D, O’Neill L, Butler AP, Harrison CJ, Campbell P, Patel B, Moorman AV, Fielding AK, Papaemmanuil E. Diagnostic utility of whole genome sequencing in adults with B-other acute lymphoblastic leukemia. Blood Adv 2023; 7:3862-3873. [PMID: 36867579 PMCID: PMC10405200 DOI: 10.1182/bloodadvances.2022008992] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/12/2023] [Indexed: 03/04/2023] Open
Abstract
Genomic profiling during the diagnosis of B-cell precursor acute lymphoblastic leukemia (BCP-ALL) in adults is used to guide disease classification, risk stratification, and treatment decisions. Patients for whom diagnostic screening fails to identify disease-defining or risk-stratifying lesions are classified as having B-other ALL. We screened a cohort of 652 BCP-ALL cases enrolled in UKALL14 to identify and perform whole genome sequencing (WGS) of paired tumor-normal samples. For 52 patients with B-other, we compared the WGS findings with data from clinical and research cytogenetics. WGS identified a cancer-associated event in 51 of 52 patients, including an established subtype defining genetic alterations that were previously missed with standard-of-care (SoC) genetics in 5 of them. Of the 47 true B-other ALL, we identified a recurrent driver in 87% (41). A complex karyotype via cytogenetics emerges as a heterogeneous group, including distinct genetic alterations associated with either favorable (DUX4-r) or poor outcomes (MEF2D-r and IGK::BCL2). For a subset of 31 cases, we integrated the findings from RNA sequencing (RNA-seq) analysis to include fusion gene detection and classification based on gene expression. Compared with RNA-seq, WGS was sufficient to detect and resolve recurrent genetic subtypes; however, RNA-seq can provide orthogonal validation of findings. In conclusion, we demonstrated that WGS can identify clinically relevant genetic abnormalities missed with SoC testing as well as identify leukemia driver events in virtually all cases of B-other ALL.
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Affiliation(s)
- Daniel Leongamornlert
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Jesús Gutiérrez-Abril
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - SooWah Lee
- Department of Haematology, University College London (UCL) Cancer Institute, London, United Kingdom
| | - Emilio Barretta
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Thomas Creasey
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Gunes Gundem
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Max F. Levine
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Juan E. Arango-Ossa
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Konstantinos Liosis
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Juan S. Medina-Martinez
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Krisztina Zuborne Alapi
- Department of Haematology, University College London (UCL) Cancer Institute, London, United Kingdom
| | - Amy A. Kirkwood
- Cancer Research UK & UCL Cancer Trials Centre, UCL Cancer Institute, UCL, London, United Kingdom
| | - Laura Clifton-Hadley
- Cancer Research UK & UCL Cancer Trials Centre, UCL Cancer Institute, UCL, London, United Kingdom
| | - Pip Patrick
- Cancer Research UK & UCL Cancer Trials Centre, UCL Cancer Institute, UCL, London, United Kingdom
| | - David Jones
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Laura O’Neill
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Adam P. Butler
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Christine J. Harrison
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Peter Campbell
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Bela Patel
- Department of Haemato-Oncology, Barts Cancer Institute, Queen Mary University, London, United Kingdom
| | - Anthony V. Moorman
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Adele K. Fielding
- Department of Haematology, University College London (UCL) Cancer Institute, London, United Kingdom
| | - Elli Papaemmanuil
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
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19
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Robbe P, Schuh A. Genomic Stratification of Hematological Malignancies. Hemasphere 2023; 7:e902. [PMID: 37251914 PMCID: PMC10219718 DOI: 10.1097/hs9.0000000000000902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 04/25/2023] [Indexed: 05/31/2023] Open
Affiliation(s)
- Pauline Robbe
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Anna Schuh
- Department of Oncology, University of Oxford, United Kingdom
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20
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Multi-Omic Approaches to Classify, Predict, and Treat Acute Leukemias. Cancers (Basel) 2023; 15:cancers15041049. [PMID: 36831391 PMCID: PMC9954455 DOI: 10.3390/cancers15041049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer, in which nearly 5% of the cases are diagnosed before the first year of age [...].
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