1
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Gundem G, Levine MF, Roberts SS, Cheung IY, Medina-Martínez JS, Feng Y, Arango-Ossa JE, Chadoutaud L, Rita M, Asimomitis G, Zhou J, You D, Bouvier N, Spitzer B, Solit DB, Dela Cruz F, LaQuaglia MP, Kushner BH, Modak S, Shukla N, Iacobuzio-Donahue CA, Kung AL, Cheung NKV, Papaemmanuil E. Clonal evolution during metastatic spread in high-risk neuroblastoma. Nat Genet 2023:10.1038/s41588-023-01395-x. [PMID: 37169874 DOI: 10.1038/s41588-023-01395-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/12/2023] [Indexed: 05/13/2023]
Abstract
Patients with high-risk neuroblastoma generally present with widely metastatic disease and often relapse despite intensive therapy. As most studies to date focused on diagnosis-relapse pairs, our understanding of the genetic and clonal dynamics of metastatic spread and disease progression remain limited. Here, using genomic profiling of 470 sequential and spatially separated samples from 283 patients, we characterize subtype-specific genetic evolutionary trajectories from diagnosis through progression and end-stage metastatic disease. Clonal tracing timed disease initiation to embryogenesis. Continuous acquisition of structural variants at disease-defining loci (MYCN, TERT, MDM2-CDK4) followed by convergent evolution of mutations targeting shared pathways emerged as the predominant feature of progression. At diagnosis metastatic clones were already established at distant sites where they could stay dormant, only to cause relapses years later and spread via metastasis-to-metastasis and polyclonal seeding after therapy.
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Affiliation(s)
- Gunes Gundem
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Max F Levine
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stephen S Roberts
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irene Y Cheung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juan S Medina-Martínez
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yi Feng
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juan E Arango-Ossa
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Loic Chadoutaud
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mathieu Rita
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Georgios Asimomitis
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joe Zhou
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daoqi You
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nancy Bouvier
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Barbara Spitzer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, New York, NY, USA
| | - Filemon Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael P LaQuaglia
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brian H Kushner
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shakeel Modak
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christine A Iacobuzio-Donahue
- The David M. Rubenstein Center for Pancreatic Cancer Research, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew L Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nai-Kong V Cheung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elli Papaemmanuil
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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3
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Tazi Y, Arango-Ossa JE, Zhou Y, Bernard E, Thomas I, Gilkes A, Freeman S, Pradat Y, Johnson SJ, Hills R, Dillon R, Levine MF, Leongamornlert D, Butler A, Ganser A, Bullinger L, Döhner K, Ottmann O, Adams R, Döhner H, Campbell PJ, Burnett AK, Dennis M, Russell NH, Devlin SM, Huntly BJP, Papaemmanuil E. Unified classification and risk-stratification in Acute Myeloid Leukemia. Nat Commun 2022; 13:4622. [PMID: 35941135 PMCID: PMC9360033 DOI: 10.1038/s41467-022-32103-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/11/2022] [Indexed: 02/02/2023] Open
Abstract
Clinical recommendations for Acute Myeloid Leukemia (AML) classification and risk-stratification remain heavily reliant on cytogenetic findings at diagnosis, which are present in <50% of patients. Using comprehensive molecular profiling data from 3,653 patients we characterize and validate 16 molecular classes describing 100% of AML patients. Each class represents diverse biological AML subgroups, and is associated with distinct clinical presentation, likelihood of response to induction chemotherapy, risk of relapse and death over time. Secondary AML-2, emerges as the second largest class (24%), associates with high-risk disease, poor prognosis irrespective of flow Minimal Residual Disease (MRD) negativity, and derives significant benefit from transplantation. Guided by class membership we derive a 3-tier risk-stratification score that re-stratifies 26% of patients as compared to standard of care. This results in a unified framework for disease classification and risk-stratification in AML that relies on information from cytogenetics and 32 genes. Last, we develop an open-access patient-tailored clinical decision support tool.
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Grants
- MC_PC_17230 Medical Research Council
- BRC-1215-20014 Department of Health
- 203151/Z/16/Z Wellcome Trust
- MR-R009708-1 Medical Research Council
- C18680/A25508 Cancer Research UK
- 29806 Cancer Research UK
- 25350 Cancer Research UK
- P30 CA008748 NCI NIH HHS
- Wellcome Trust
- 25508 Cancer Research UK
- 25643 Cancer Research UK
- MR/R009708/1 Medical Research Council
- C49940/A25117 Cancer Research UK
- 205254/Z/16/Z Wellcome Trust
- E.P. is a Josie Robertson Investigator and is supported by the European Hematology Association, American Society of Hematology, Gabrielle’s Angels Foundation, V Foundation and The Geoffrey Beene Foundation and is a Damon Runyon Rachleff Innovator fellow. Work in the BJPH lab is funded by Cancer Research UK (C18680/A25508), the European Research Council (647685), MRC (MR-R009708-1), the Kay Kendall Leukaemia Fund (KKL1243), the Wellcome Trust (205254/Z/16/Z) and the Cancer Research UK Cambridge Major Centre (C49940/A25117). This research was supported by the NIHR Cambridge Biomedical Research Centre (BRC-1215-20014), and was funded in part, by the Wellcome Trust who supported the Wellcome - MRC Cambridge Stem Cell Institute (203151/Z/16/Z). The views expressed are those of the authors and not necessarily those of the NIHR or the Department of Health and Social Care. L.B., H.D. and B.J.P.H. are supported by the HARMONY Alliance (IMI Project No. 116026; https://www.harmony-alliance.eu/). The UK-NCRI AML working group trials were supported with research grants from the Medical Research Council (MRC), Cancer Research UK (CRUK), Blood Cancer UK and Cardiff University. We would like to thank all patients and investigators for their participation in the trials and the study.
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Affiliation(s)
- Yanis Tazi
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Computational Biology and Medicine PhD Program, Weill Cornell Medicine of Cornell University and Rockefeller University, New York, NY, USA
- The Rockefeller University, New York, NY, USA
| | - Juan E Arango-Ossa
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yangyu Zhou
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elsa Bernard
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ian Thomas
- Centre for Trials Research, School of Medicine, Cardiff University, Cardiff, UK
| | - Amanda Gilkes
- Department of Haematology, School of Medicine, Cardiff University, Cardiff, UK
| | - Sylvie Freeman
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Yoann Pradat
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sean J Johnson
- Centre for Trials Research, School of Medicine, Cardiff University, Cardiff, UK
| | - Robert Hills
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Richard Dillon
- Department of Medical and Molecular Genetics, King's College, London, UK
| | - Max F Levine
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Leongamornlert
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Adam Butler
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Lars Bullinger
- Department of Hematology, Oncology, and Tumorimmunology, Campus Virchow Klinikum, Berlin, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Konstanze Döhner
- Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Oliver Ottmann
- Department of Haematology, School of Medicine, Cardiff University, Cardiff, UK
| | - Richard Adams
- Centre for Trials Research, School of Medicine, Cardiff University, Cardiff, UK
| | - Hartmut Döhner
- Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Alan K Burnett
- Visiting Professor University of Glasgow, formerly Cardiff University, Cardiff, UK
| | | | - Nigel H Russell
- Department of Haematology, Nottingham University Hospital, Nottingham, UK
| | - Sean M Devlin
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brian J P Huntly
- Department of Haematology and Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Elli Papaemmanuil
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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4
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Shukla N, Levine MF, Gundem G, Domenico D, Spitzer B, Bouvier N, Arango-Ossa JE, Glodzik D, Medina-Martínez JS, Bhanot U, Gutiérrez-Abril J, Zhou Y, Fiala E, Stockfisch E, Li S, Rodriguez-Sanchez MI, O'Donohue T, Cobbs C, Roehrl MHA, Benhamida J, Iglesias Cardenas F, Ortiz M, Kinnaman M, Roberts S, Ladanyi M, Modak S, Farouk-Sait S, Slotkin E, Karajannis MA, Dela Cruz F, Glade Bender J, Zehir A, Viale A, Walsh MF, Kung AL, Papaemmanuil E. Feasibility of whole genome and transcriptome profiling in pediatric and young adult cancers. Nat Commun 2022; 13:2485. [PMID: 35585047 PMCID: PMC9117241 DOI: 10.1038/s41467-022-30233-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 04/21/2022] [Indexed: 02/07/2023] Open
Abstract
The utility of cancer whole genome and transcriptome sequencing (cWGTS) in oncology is increasingly recognized. However, implementation of cWGTS is challenged by the need to deliver results within clinically relevant timeframes, concerns about assay sensitivity, reporting and prioritization of findings. In a prospective research study we develop a workflow that reports comprehensive cWGTS results in 9 days. Comparison of cWGTS to diagnostic panel assays demonstrates the potential of cWGTS to capture all clinically reported mutations with comparable sensitivity in a single workflow. Benchmarking identifies a minimum of 80× as optimal depth for clinical WGS sequencing. Integration of germline, somatic DNA and RNA-seq data enable data-driven variant prioritization and reporting, with oncogenic findings reported in 54% more patients than standard of care. These results establish key technical considerations for the implementation of cWGTS as an integrated test in clinical oncology. Cancer whole-genome and transcriptome sequencing (cWGTS) has been challenging to implement in clinical settings. Here, the authors develop a workflow to deliver robust cWGTS analyses and reports within clinically-relevant timeframes for paediatric, adolescent and young adult solid tumour patients.
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Affiliation(s)
- N Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M F Levine
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - G Gundem
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - D Domenico
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - B Spitzer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - N Bouvier
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J E Arango-Ossa
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - D Glodzik
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J S Medina-Martínez
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - U Bhanot
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Precision Pathology Biobanking Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J Gutiérrez-Abril
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Y Zhou
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - E Fiala
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - E Stockfisch
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Li
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - T O'Donohue
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - C Cobbs
- Integrated Genomics Operation Core, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M H A Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Precision Pathology Biobanking Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - F Iglesias Cardenas
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Ortiz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Kinnaman
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Roberts
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Modak
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Farouk-Sait
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - E Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M A Karajannis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - F Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J Glade Bender
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Viale
- Integrated Genomics Operation Core, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M F Walsh
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A L Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - E Papaemmanuil
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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5
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Medina-Martínez JS, Arango-Ossa JE, Levine MF, Zhou Y, Gundem G, Kung AL, Papaemmanuil E. Isabl Platform, a digital biobank for processing multimodal patient data. BMC Bioinformatics 2020; 21:549. [PMID: 33256603 PMCID: PMC7708092 DOI: 10.1186/s12859-020-03879-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 11/13/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The widespread adoption of high throughput technologies has democratized data generation. However, data processing in accordance with best practices remains challenging and the data capital often becomes siloed. This presents an opportunity to consolidate data assets into digital biobanks-ecosystems of readily accessible, structured, and annotated datasets that can be dynamically queried and analysed. RESULTS We present Isabl, a customizable plug-and-play platform for the processing of multimodal patient-centric data. Isabl's architecture consists of a relational database (Isabl DB), a command line client (Isabl CLI), a RESTful API (Isabl API) and a frontend web application (Isabl Web). Isabl supports automated deployment of user-validated pipelines across the entire data capital. A full audit trail is maintained to secure data provenance, governance and ensuring reproducibility of findings. CONCLUSIONS As a digital biobank, Isabl supports continuous data utilization and automated meta analyses at scale, and serves as a catalyst for research innovation, new discoveries, and clinical translation.
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Affiliation(s)
| | | | - Max F Levine
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yangyu Zhou
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gunes Gundem
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew L Kung
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
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6
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Medina-Martínez JS, Arango-Ossa JE, Gundem G, Levine MF, Patel M, Farnoud NR, Yellapantula VD, Teng G, Mccarter JG, Bernard E, Rapaport F, Glodzik D, Levine RL, Kung A, Papaemmanuil E. Abstract 5105: A plug-and-play infrastructure for scalable bioinformatics operations. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-5105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Genome profiling represents a critical pillar for clinical, translational, and basic research studies. Hospitals, core facilities, and research enterprises invest significant resources to generate genomic data sets. Yet, data management and analysis is frequently manual, which demands significant operator time and often results in siloed resources rendering them as single-use assets. Centralization of the genomic capital in a framework that enables automated processing, metadata integration and continuous interrogation maximizes return for investment and serves as the critical catalyst for research innovation, clinical translation and reproducible research. We developed Isabl, a plug-and-play infrastructure for scalable bioinformatics operations. Isabl provides solutions for databasing, assets management, tracking, automated and reproducible data processing. Dynamic reporting and meta-analysis across data assets is enabled.
Isabl is built on four main components. First, an individual-centric and extensible relational database with tracking support for samples (temporal, spatial, aliquot), experimental data (assays, platforms, sequencing runs), cohorts (clinical trials, research projects) and versioned bioinformatics applications (assembly aware, tools, results). Second, the database is exposed through a fully featured RESTful API that enables horizontal integration with information systems such as sequencing cores LIMS, variant visualization platforms like cBioPortal, and where applicable, clinical and biospecimen institutional databases. Third, a Software Development Kit (SDK) built for Next Generation Sequencing assets management. The SDK enables automated execution of data import and language-agnostic bioinformatics applications (alignment, variant calling, post-processing) with support for cohort and individual level reporting features. Furthermore, the SDK facilitates dynamic retrieval of results using vertical and horizontal queries (individual and cohort level, respectively). Lastly, Isabl comes with a Single Page Web Application that fosters user interaction with multidisciplinary teams (i.e. researchers, project coordinators, engineers, clinicians) facilitating tracking of analyses, results visualization, and dynamic query processing.
Isabl is currently supporting the Memorial Sloan Kettering Genome Pediatrics Precision Medicine Initiative, a prototype platform that delivers integrated, real-time automated reporting of clinical targeted gene re-sequencing, research whole genome and transcriptome profiling data; as well as linked data from pre-clinical models (i.e. PDX) and single cells studies. As an open-source tool, Isabl democratizes access to a purpose built, automated, scalable and fully integrable bioinformatics architecture. Isabl will be available at https://github.com/isabl-io.
Citation Format: Juan S. Medina-Martínez, Juan E. Arango-Ossa, Gunes Gundem, Max F. Levine, Minal Patel, Noushin R. Farnoud, Venkata D. Yellapantula, Gao Teng, Joseph G. Mccarter, Elsa Bernard, Franck Rapaport, Dominik Glodzik, Ross L. Levine, Andrew Kung, Elli Papaemmanuil. A plug-and-play infrastructure for scalable bioinformatics operations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5105.
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Affiliation(s)
| | | | - Gunes Gundem
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Max F. Levine
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Minal Patel
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Gao Teng
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Elsa Bernard
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Andrew Kung
- 1Memorial Sloan Kettering Cancer Center, New York, NY
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