1
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Thomas S, Lichtenberg T, Dang K, Fitzsimons M, Grossman RL, Kundra R, Lavery JA, Lenoue-Newton ML, Panageas KS, Sawyers C, Schultz ND, Sirintrapun SJ, Topaloglu U, Welch A, Yu T, Zehir A, Gardos S. Linked Entity Attribute Pair (LEAP): A Harmonization Framework for Data Pooling. JCO Clin Cancer Inform 2021; 4:691-699. [PMID: 32755461 PMCID: PMC7469618 DOI: 10.1200/cci.20.00037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Indexed: 11/20/2022] Open
Abstract
PURPOSE As data-sharing projects become increasingly frequent, so does the need to map data elements between multiple classification systems. A generic, robust, shareable architecture will result in increased efficiency and transparency of the mapping process, while upholding the integrity of the data. MATERIALS AND METHODS The American Association for Cancer Research’s Genomics Evidence Neoplasia Information Exchange (GENIE) collects clinical and genomic data for precision cancer medicine. As part of its commitment to open science, GENIE has partnered with the National Cancer Institute’s Genomic Data Commons (GDC) as a secondary repository. After initial efforts to submit data from GENIE to GDC failed, we realized the need for a solution to allow for the iterative mapping of data elements between dynamic classification systems. We developed the Linked Entity Attribute Pair (LEAP) database framework to store and manage the term mappings used to submit data from GENIE to GDC. RESULTS After creating and populating the LEAP framework, we identified 195 mappings from GENIE to GDC requiring remediation and observed a 28% reduction in effort to resolve these issues, as well as a reduction in inadvertent errors. These results led to a decrease in the time to map between OncoTree, the cancer type ontology used by GENIE, and International Classification of Disease for Oncology, 3rd Edition, used by GDC, from several months to less than 1 week. CONCLUSION The LEAP framework provides a streamlined mapping process among various classification systems and allows for reusability so that efforts to create or adjust mappings are straightforward. The ability of the framework to track changes over time streamlines the process to map data elements across various dynamic classification systems.
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Affiliation(s)
- Stacy Thomas
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Tara Lichtenberg
- Center for Translational Data Science, University of Chicago, Chicago, IL
| | | | - Michael Fitzsimons
- Center for Translational Data Science, University of Chicago, Chicago, IL.,University of Illinois at Chicago, Chicago, IL
| | - Robert L Grossman
- Center for Translational Data Science, University of Chicago, Chicago, IL
| | - Ritika Kundra
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jessica A Lavery
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Katherine S Panageas
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Charles Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nikolaus D Schultz
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Umit Topaloglu
- Cancer Biology, Wake Forest University School of Medicine, Winston Salem, NC
| | - Angelica Welch
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Stuart Gardos
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, NY
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Kundra R, Zhang H, Sheridan R, Sirintrapun SJ, Wang A, Ochoa A, Wilson M, Gross B, Sun Y, Madupuri R, Satravada BA, Reales D, Vakiani E, Al-Ahmadie HA, Dogan A, Arcila M, Zehir A, Maron S, Berger MF, Viaplana C, Janeway K, Ducar M, Sholl L, Dogan S, Bedard P, Surrey LF, Sanchez IH, Syed A, Rema AB, Chakravarty D, Suehnholz S, Nissan M, Iyer GV, Murali R, Bouvier N, Soslow RA, Hyman D, Younes A, Intlekofer A, Harding JJ, Carvajal RD, Sabbatini PJ, Abou-Alfa GK, Morris L, Janjigian YY, Gallagher MM, Soumerai TA, Mellinghoff IK, Hakimi AA, Fury M, Huse JT, Bagrodia A, Hameed M, Thomas S, Gardos S, Cerami E, Mazor T, Kumari P, Raman P, Shivdasani P, MacFarland S, Newman S, Waanders A, Gao J, Solit D, Schultz N. OncoTree: A Cancer Classification System for Precision Oncology. JCO Clin Cancer Inform 2021; 5:221-230. [PMID: 33625877 PMCID: PMC8240791 DOI: 10.1200/cci.20.00108] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [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: 08/07/2020] [Revised: 10/26/2020] [Accepted: 12/21/2020] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Cancer classification is foundational for patient care and oncology research. Systems such as International Classification of Diseases for Oncology (ICD-O), Systematized Nomenclature of Medicine Clinical Terms (SNOMED-CT), and National Cancer Institute Thesaurus (NCIt) provide large sets of cancer classification terminologies but they lack a dynamic modernized cancer classification platform that addresses the fast-evolving needs in clinical reporting of genomic sequencing results and associated oncology research. METHODS To meet these needs, we have developed OncoTree, an open-source cancer classification system. It is maintained by a cross-institutional committee of oncologists, pathologists, scientists, and engineers, accessible via an open-source Web user interface and an application programming interface. RESULTS OncoTree currently includes 868 tumor types across 32 organ sites. OncoTree has been adopted as the tumor classification system for American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE), a large genomic and clinical data-sharing consortium, and for clinical molecular testing efforts at Memorial Sloan Kettering Cancer Center and Dana-Farber Cancer Institute. It is also used by precision oncology tools such as OncoKB and cBioPortal for Cancer Genomics. CONCLUSION OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research.
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Affiliation(s)
- Ritika Kundra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hongxin Zhang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Robert Sheridan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Avery Wang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Angelica Ochoa
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Manda Wilson
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Benjamin Gross
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yichao Sun
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ramyasree Madupuri
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Baby A. Satravada
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Dalicia Reales
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Efsevia Vakiani
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ahmet Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Steven Maron
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F. Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering, New York, NY
| | - Cristina Viaplana
- Oncology Data Science (ODysSey Group), Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Katherine Janeway
- Pediatrics, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | | | - Lynette Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Department of Pathology, Harvard Medical School, Boston, MA
| | - Snjezana Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Philippe Bedard
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Lea F. Surrey
- Cancer Genomics Program, Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Aijaz Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Debyani Chakravarty
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sarah Suehnholz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Moriah Nissan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gopakumar V. Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rajmohan Murali
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nancy Bouvier
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Robert A. Soslow
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Andrew Intlekofer
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering, New York, NY
| | - James J. Harding
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | | | - Paul J. Sabbatini
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | | | - Luc Morris
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering, New York, NY
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering, New York, NY
- Department of Surgery, Memorial Sloan Kettering, New York, NY
| | - Yelena Y. Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Tara A. Soumerai
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Ingo K. Mellinghoff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering, New York, NY
| | - Abraham A. Hakimi
- Department of Urology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Jason T. Huse
- Departments of Pathology and Translational Molecular Pathology, University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Aditya Bagrodia
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Stacy Thomas
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Stuart Gardos
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ethan Cerami
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA
| | - Tali Mazor
- Knowledge Systems Group, Dana-Farber Cancer Institute, Boston, MA
| | - Priti Kumari
- Knowledge Systems Group, Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Suzanne MacFarland
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA
- University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Scott Newman
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN
| | | | - Jianjiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering, New York, NY
- Department of Medicine, Columbia University Medical Center, New York, NY
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering, New York, NY
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering, New York, NY
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3
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Bolton KL, Ptashkin RN, Gao T, Braunstein L, Devlin SM, Kelly D, Patel M, Berthon A, Syed A, Yabe M, Coombs CC, Caltabellotta NM, Walsh M, Offit K, Stadler Z, Mandelker D, Schulman J, Patel A, Philip J, Bernard E, Gundem G, Ossa JEA, Levine M, Martinez JSM, Farnoud N, Glodzik D, Li S, Robson ME, Lee C, Pharoah PDP, Stopsack KH, Spitzer B, Mantha S, Fagin J, Boucai L, Gibson CJ, Ebert BL, Young AL, Druley T, Takahashi K, Gillis N, Ball M, Padron E, Hyman DM, Baselga J, Norton L, Gardos S, Klimek VM, Scher H, Bajorin D, Paraiso E, Benayed R, Arcila ME, Ladanyi M, Solit DB, Berger MF, Tallman M, Garcia-Closas M, Chatterjee N, Diaz LA, Levine RL, Morton LM, Zehir A, Papaemmanuil E. Cancer therapy shapes the fitness landscape of clonal hematopoiesis. Nat Genet 2020; 52:1219-1226. [PMID: 33106634 PMCID: PMC7891089 DOI: 10.1038/s41588-020-00710-0] [Citation(s) in RCA: 312] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 09/02/2020] [Indexed: 01/30/2023]
Abstract
Acquired mutations are pervasive across normal tissues. However, understanding of the processes that drive transformation of certain clones to cancer is limited. Here we study this phenomenon in the context of clonal hematopoiesis (CH) and the development of therapy-related myeloid neoplasms (tMNs). We find that mutations are selected differentially based on exposures. Mutations in ASXL1 are enriched in current or former smokers, whereas cancer therapy with radiation, platinum and topoisomerase II inhibitors preferentially selects for mutations in DNA damage response genes (TP53, PPM1D, CHEK2). Sequential sampling provides definitive evidence that DNA damage response clones outcompete other clones when exposed to certain therapies. Among cases in which CH was previously detected, the CH mutation was present at tMN diagnosis. We identify the molecular characteristics of CH that increase risk of tMN. The increasing implementation of clinical sequencing at diagnosis provides an opportunity to identify patients at risk of tMN for prevention strategies.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Antineoplastic Agents/pharmacology
- Cell Transformation, Neoplastic/drug effects
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/radiation effects
- Child
- Child, Preschool
- Clonal Evolution
- Clonal Hematopoiesis/drug effects
- Clonal Hematopoiesis/genetics
- Cohort Studies
- Female
- Genetic Fitness
- Humans
- Infant
- Infant, Newborn
- Leukemia, Myeloid/genetics
- Male
- Middle Aged
- Models, Biological
- Mutation
- Neoplasms/drug therapy
- Neoplasms/radiotherapy
- Neoplasms, Second Primary/genetics
- Selection, Genetic
- Young Adult
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Affiliation(s)
- Kelly L Bolton
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryan N Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Teng Gao
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lior Braunstein
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sean M Devlin
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Kelly
- Department of Information Systems, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Minal Patel
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Antonin Berthon
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aijazuddin Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mariko Yabe
- Department of Pathology, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Catherine C Coombs
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicole M Caltabellotta
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mike Walsh
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zsofia Stadler
- Department of Medicine, Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jessica Schulman
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Akshar Patel
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John Philip
- Department of Health Informatics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elsa Bernard
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gunes Gundem
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juan E Arango Ossa
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Max Levine
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Noushin Farnoud
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dominik Glodzik
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sonya Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark E Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Choonsik Lee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paul D P Pharoah
- Department of Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
- Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Konrad H Stopsack
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Barbara Spitzer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simon Mantha
- Department of Medicine, Hematology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James Fagin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laura Boucai
- Department of Medicine, Endocrinology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Andrew L Young
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Todd Druley
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Koichi Takahashi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nancy Gillis
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
- Department of Malignant Hematology, Moffitt Cancer Center, Tampa, FL, USA
| | - Markus Ball
- Department of Malignant Hematology, Moffitt Cancer Center, Tampa, FL, USA
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Eric Padron
- Department of Malignant Hematology, Moffitt Cancer Center, Tampa, FL, USA
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Jose Baselga
- Research & Development, AstraZeneca, Milton, Cambridge, UK
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Stuart Gardos
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Virginia M Klimek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Howard Scher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Dean Bajorin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Eder Paraiso
- Department of Medicine, Endocrinology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Strategy & Innovation, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Endocrinology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Endocrinology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martin Tallman
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Montserrat Garcia-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nilanjan Chatterjee
- Department of Biostatistics, Bloomberg School of Public Health Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Luis A Diaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Program in Precision Interception and Prevention, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Solid Tumor Division, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ross L Levine
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Elli Papaemmanuil
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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4
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Bolton KL, Ptashkin RN, Gao T, Braunstein L, Devlin SM, Patel M, Berthon A, Syed A, Yabe M, Coombs C, Caltabellotta NM, Walsh M, Offit K, Stadler Z, Lee C, Pharoah P, Stopsack KH, Spitzer B, Mantha S, Fagin J, Boucai L, Gibson CJ, Ebert B, Young AL, Druley T, Takahashi K, Gillis N, Ball M, Padron E, Hyman D, Baselga J, Norton L, Gardos S, Klimek V, Scher H, Bajorin D, Paraiso E, Benayed R, Arcilla M, Ladanyi M, Solit D, Berger M, Tallman M, Garcia-Closas M, Chatterjee N, Diaz L, Levine R, Morton L, Zehir A, Papaemmanuil E. Abstract 5703: Oncologic therapy shapes the fitness landscape of clonal hematopoiesis. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-5703] [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
Recent studies among healthy individuals show evidence of somatic mutations in leukemia-associated genes, referred to as clonal hematopoiesis (CH). To determine the relationship between CH and oncologic therapy we collected sequential blood samples from 525 cancer patients (median sampling interval time = 23 months, range: 6-53 months) of whom 61% received cytotoxic therapy or external beam radiation therapy and 39% received either targeted/immunotherapy or were untreated. Samples were sequenced using deep targeted capture-based platforms. To determine whether CH mutational features were associated with tMN risk, we performed Cox proportional hazards regression on 9,549 cancer patients exposed to oncologic therapy of whom 75 cases developed tMN (median time to transformation=26 months). To further compare the genetic and clonal relationships between tMN and the proceeding CH, we analyzed 35 cases for which paired samples were available. We compared the growth rate of the variant allele fraction (VAF) of CH clones across treatment modalities and in untreated patients. A significant increase in the growth rate of CH mutations was seen in DDR genes among those receiving cytotoxic (p=0.03) or radiation therapy (p=0.02) during the follow-up period compared to patients who did not receive therapy. Similar growth rates among treated and untreated patients were seen for non-DDR CH genes such as DNMT3A. Increasing cumulative exposure to cytotoxic therapy (p=0.01) and external beam radiation therapy (2x10-8) resulted in higher growth rates for DDR CH mutations. Among 34 subjects with at least two CH mutations in which one mutation was in a DDR gene and one in a non-DDR gene, we studied competing clonal dynamics for multiple gene mutations within the same patient. The risk of tMN was positively associated with CH in a known myeloid neoplasm driver mutation (HR=6.9, p<10-6), and increased with the total number of mutations and clone size. The strongest associations were observed for mutations in TP53 and for CH with mutations in spliceosome genes (SRSF2, U2AF1 and SF3B1). Lower hemoglobin, lower platelet counts, lower neutrophil counts, higher red cell distribution width and higher mean corpuscular volume were all positively associated with increased tMN risk. Among 35 cases for which paired samples were available, in 19 patients (59%), we found evidence of at least one of these mutations at the time of pre-tMN sequencing and in 13 (41%), we identified two or more in the pre-tMN sample. In all cases the dominant clone at tMN transformation was defined by a mutation seen at CH Our serial sampling data provide clear evidence that oncologic therapy strongly selects for clones with mutations in the DDR genes and that these clones have limited competitive fitness, in the absence of cytotoxic or radiation therapy. We further validate the relevance of CH as a predictor and precursor of tMN in cancer patients. We show that CH mutations detected prior to tMN diagnosis were consistently part of the dominant clone at tMN diagnosis and demonstrate that oncologic therapy directly promotes clones with mutations in genes associated with chemo-resistant disease such as TP53.
Citation Format: Kelly L. Bolton, Ryan N. Ptashkin, Teng Gao, Lior Braunstein, Sean M. Devlin, Minal Patel, Antonin Berthon, Aijazuddin Syed, Mariko Yabe, Catherine Coombs, Nicole M. Caltabellotta, Mike Walsh, Ken Offit, Zsofia Stadler, Choonsik Lee, Paul Pharoah, Konrad H. Stopsack, Barbara Spitzer, Simon Mantha, James Fagin, Laura Boucai, Christopher J. Gibson, Benjamin Ebert, Andrew L. Young, Todd Druley, Koichi Takahashi, Nancy Gillis, Markus Ball, Eric Padron, David Hyman, Jose Baselga, Larry Norton, Stuart Gardos, Virginia Klimek, Howard Scher, Dean Bajorin, Eder Paraiso, Ryma Benayed, Maria Arcilla, Marc Ladanyi, David Solit, Michael Berger, Martin Tallman, Montserrat Garcia-Closas, Nilanjan Chatterjee, Luis Diaz, Ross Levine, Lindsay Morton, Ahmet Zehir, Elli Papaemmanuil. Oncologic therapy shapes the fitness landscape of clonal hematopoiesis [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5703.
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Affiliation(s)
| | | | - Teng Gao
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Minal Patel
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Mariko Yabe
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Mike Walsh
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ken Offit
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Choonsik Lee
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Paul Pharoah
- 3University of Cambridge, Cambridge, United Kingdom
| | | | | | - Simon Mantha
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - James Fagin
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Laura Boucai
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | | | | | | | - David Hyman
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jose Baselga
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Larry Norton
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Stuart Gardos
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Howard Scher
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Dean Bajorin
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Eder Paraiso
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryma Benayed
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria Arcilla
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - David Solit
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | - Luis Diaz
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ross Levine
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ahmet Zehir
- 1Memorial Sloan Kettering Cancer Center, New York, NY
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Bolton K, Ptashkin R, Braunstein L, Gao T, Devlin SM, Kelly D, Coombs C, Patel M, Moarii M, Bernard E, Berthon A, Boucai L, Glodzik D, Martin A, Stadler Z, Walsh M, Mandelker D, Patel A, Schulman J, Gundem G, Syed A, Arcila M, Solit DB, Robson ME, Ladanyi M, Lee C, Philip J, Bajorin D, Garcia-Closas M, Gardos S, Hyman D, Tallman M, Yabe M, Offit K, Scher H, Klimek V, Diaz L, Chatterjee N, Berger MF, Morton L, Levine R, Zehir A, Papaemmanuil E. Abstract LB-304: Oncologic therapy for solid tumors alters the risk of clonal hematopoiesis. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-lb-304] [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
Solid tumor patients often suffer from cytopenias and are at risk for therapy-related myeloid neoplasms (tMN). Somatic mutations in leukemia-associated genes can occur in normal healthy individuals, referred to as clonal hematopoiesis (CH). CH is associated with cytopenias, risk of leukemia and cardiovascular disease. We and others have shown that CH is frequent in cancer patients. Characterization of the relationship between exposure to specific oncologic regimens and CH and how these relate to cytopenias and tMN risk would inform treatment decisions and tMN prevention strategies.
To determine the relationship between CH and oncologic therapy we interrogated CH in a cohort of 9045 solid tumor patients. Subjects were sequenced using a targeted panel of cancer-associated mutations used to screen tumor samples against a blood control sample. Mutation detection was performed on blood-derived sequencing data using the matched tumor as a comparator and accounted for background sequencing error rates.
CH was identified in 23% of patients. In multivariate regression analyses adjusted by age, CH was more often found in current smokers (OR=1.20, 95%CI=1.07-1.35, p<0.001) and less often found in Asians compared to Whites (OR=0.72, 95%CI=0.56-0.89, p<0.001). Smoking was associated with CH mutations in ASXL1 (OR=3.75, 95%CI=2.73-5.17, p<0.001). There was a higher proportion of patients with CH among those who had received chemotherapy (OR=1.14, 95%CI=1.02-1.26, p=0.02) and those who had received external beam radiation therapy (OR=1.45, 95%CI=1.28-1.63, p<0.001) prior to blood collection. Mutations in the DNA repair/cell cycle pathway (including TP53, PPM1D and CHEK2) were more common among patients who received chemotherapy and radiation therapy prior to IMPACT testing compared to those who were treatment naïve (p<0.001). Exposure to prior cytotoxic chemotherapy (OR=1.20, 95%CI=1.02-1.30; p=0.007) and radiation therapy (OR=1.6, 95%CI=1.4-1.9, p<0.001) was associated with having CH while exposure to immunotherapy and targeted therapy was not. Increasing cumulative dose of chemotherapy overall and cytotoxic therapy was associated with a higher likelihood of CH (p=0.015 and p=0.007 respectively). There was evidence of specific gene, treatment and dosage effects. To further examine the relationship between oncologic therapy and clonal evolution of CH, we collected 375 sequential samples at least 18 months apart. T mean change in VAF of CH mutations per year was found to increase by 0.17% in patients who did not receive further therapy during the follow-up time and 0.49% in those who were exposed to cytotoxic chemotherapy. A subset of patients with CH were consented to germline testing for cancer predisposition genes (N=6368). We observe a higher rate of CH among patients with a germline mutation in the cell cycle/DNA repair pathway (i.e. TP53) when compared to patients without germline mutations (OR=3.7, 95% CI: 1.35-9.35, p-value=0.01).
CH is frequent in solid tumor patients and can be reliably detected when a matched tumor normal targeted gene sequencing approach is performed. Beyond age, CH is strongly associated with race, smoking and importantly prior exposure to oncologic therapy with evidence of specific treatment effects. Screening of CH in cancer cohorts is critical to the development of future clinical guidelines and risk-adapted prevention strategies for tMN.
Note: This abstract was not presented at the meeting.
Citation Format: Kelly Bolton, Ryan Ptashkin, Lior Braunstein, Teng Gao, Sean M. Devlin, Daniel Kelly, Catherine Coombs, Minal Patel, Matahi Moarii, Elsa Bernard, Antonin Berthon, Laura Boucai, Dominik Glodzik, Axel Martin, Zsofia Stadler, Michael Walsh, Diana Mandelker, Akshar Patel, Jessica Schulman, Gunes Gundem, Aijazuddin Syed, Maria Arcila, David B. Solit, Mark E. Robson, Marc Ladanyi, Choonsik Lee, John Philip, Dean Bajorin, Montserrat Garcia-Closas, Stuart Gardos, David Hyman, Martin Tallman, Mariko Yabe, Kenneth Offit, Howard Scher, Virginia Klimek, Luis Diaz, Nilanjan Chatterjee, Michael F. Berger, Lindsay Morton, Ross Levine, Ahmet Zehir, Elli Papaemmanuil. Oncologic therapy for solid tumors alters the risk of clonal hematopoiesis [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 LB-304.
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Affiliation(s)
- Kelly Bolton
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryan Ptashkin
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Teng Gao
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Daniel Kelly
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Minal Patel
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Elsa Bernard
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Laura Boucai
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Axel Martin
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Michael Walsh
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Akshar Patel
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Gunes Gundem
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Maria Arcila
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Marc Ladanyi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - John Philip
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Dean Bajorin
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Stuart Gardos
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - David Hyman
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Mariko Yabe
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kenneth Offit
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Howard Scher
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Luis Diaz
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Ross Levine
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- 1Memorial Sloan Kettering Cancer Center, New York, NY
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Epstein AS, Soff GA, Capanu M, Crosbie C, Shah MA, Kelsen DP, Denton B, Gardos S, O'Reilly EM. Analysis of incidence and clinical outcomes in patients with thromboembolic events and invasive exocrine pancreatic cancer. Cancer 2011; 118:3053-61. [PMID: 21989534 DOI: 10.1002/cncr.26600] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 06/16/2011] [Accepted: 06/23/2011] [Indexed: 02/06/2023]
Abstract
BACKGROUND Pancreatic adenocarcinoma is among the most common malignancies associated with thromboembolic events (TEs); however, reported incidence figures vary significantly and contain small patient cohorts. Pancreatic cancer-specific thrombosis studies examining the correlation between clinical variables, including thrombosis timing and the impact of thrombosis on survival, have not been reported. METHODS Survival analyses were performed relating to the development and timing of a TE in 1915 patients administered chemotherapy at Memorial Sloan-Kettering Cancer Center with invasive exocrine pancreatic cancer from January 1, 2000 to December 31, 2009. TE timing, relative to clinical parameters including laboratory data, erythropoietin-stimulating agent use, and body mass index (BMI), were also analyzed. RESULTS A thrombosis was identified in 690 (36%) patients. After adjusting for patients with pancreatic surgery and thrombosis (n = 127), developing a TE significantly increased the risk of death (hazard ratio [HR], 2.6; 95% confidence interval [CI], 2.3-2.8; P < .01). Patients with an early TE (within 1.5 months from pancreatic cancer diagnosis) had a significantly higher risk of death (HR, 2.1; 95% CI, 1.7-2.5; P < .01) compared with patients with late TE or no TE. Erythropoietin-stimulating agent use and an elevated international normalized ratio were associated with significantly shorter time to thrombosis. Low BMI was associated with significantly longer time to thrombosis. CONCLUSIONS TEs are common in exocrine pancreatic cancer, with coagulopathy, erythropoietin-stimulating agent use, and underweight BMI influencing thrombosis timing. TEs, particularly early ones, confer a significantly worse prognosis, suggesting a biological significance, underscoring the relevance of ongoing prophylaxis trials, and raising the question of whether early TEs should be considered a stratification factor for clinical trials.
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Affiliation(s)
- Andrew S Epstein
- Department of Medicine, Division of Gastrointestinal Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
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Epstein AS, Crosbie C, Gardos S, Soff GA, Shah MA, Kelsen DP, O’Reilly EM. A single-institution (MSKCC) analysis of incidence and clinical outcomes in patients with thromboembolic events and exocrine pancreas cancer. J Clin Oncol 2010. [DOI: 10.1200/jco.2010.28.15_suppl.4062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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