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Hickey G, Monlong J, Ebler J, Novak AM, Eizenga JM, Gao Y, Marschall T, Li H, Paten B, Abel HJ, Antonacci-Fulton LL, Asri M, Baid G, Baker CA, Belyaeva A, Billis K, Bourque G, Buonaiuto S, Carroll A, Chaisson MJP, Chang PC, Chang XH, Cheng H, Chu J, Cody S, Colonna V, Cook DE, Cook-Deegan RM, Cornejo OE, Diekhans M, Doerr D, Ebert P, Ebler J, Eichler EE, Eizenga JM, Fairley S, Fedrigo O, Felsenfeld AL, Feng X, Fischer C, Flicek P, Formenti G, Frankish A, Fulton RS, Gao Y, Garg S, Garrison E, Garrison NA, Giron CG, Green RE, Groza C, Guarracino A, Haggerty L, Hall IM, Harvey WT, Haukness M, Haussler D, Heumos S, Hickey G, Hoekzema K, Hourlier T, Howe K, Jain M, Jarvis ED, Ji HP, Kenny EE, Koenig BA, Kolesnikov A, Korbel JO, Kordosky J, Koren S, Lee H, Lewis AP, Li H, Liao WW, Lu S, Lu TY, Lucas JK, Magalhães H, Marco-Sola S, Marijon P, Markello C, Marschall T, Martin FJ, McCartney A, McDaniel J, Miga KH, Mitchell MW, Monlong J, Mountcastle J, Munson KM, Mwaniki MN, Nattestad M, Novak AM, Nurk S, Olsen HE, Olson ND, Paten B, Pesout T, Phillippy AM, Popejoy AB, Porubsky D, Prins P, Puiu D, Rautiainen M, Regier AA, Rhie A, Sacco S, Sanders AD, Schneider VA, Schultz BI, Shafin K, Sibbesen JA, Sirén J, Smith MW, Sofia HJ, Tayoun ANA, Thibaud-Nissen F, Tomlinson C, Tricomi FF, Villani F, Vollger MR, Wagner J, Walenz B, Wang T, Wood JMD, Zimin AV, Zook JM. Pangenome graph construction from genome alignments with Minigraph-Cactus. Nat Biotechnol 2024; 42:663-673. [PMID: 37165083 PMCID: PMC10638906 DOI: 10.1038/s41587-023-01793-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [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: 10/06/2022] [Accepted: 04/18/2023] [Indexed: 05/12/2023]
Abstract
Pangenome references address biases of reference genomes by storing a representative set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles determined by variant callers can be used to construct pangenome graphs, but advances in long-read sequencing are leading to widely available, high-quality phased assemblies. Constructing a pangenome graph directly from assemblies, as opposed to variant calls, leverages the graph's ability to represent variation at different scales. Here we present the Minigraph-Cactus pangenome pipeline, which creates pangenomes directly from whole-genome alignments, and demonstrate its ability to scale to 90 human haplotypes from the Human Pangenome Reference Consortium. The method builds graphs containing all forms of genetic variation while allowing use of current mapping and genotyping tools. We measure the effect of the quality and completeness of reference genomes used for analysis within the pangenomes and show that using the CHM13 reference from the Telomere-to-Telomere Consortium improves the accuracy of our methods. We also demonstrate construction of a Drosophila melanogaster pangenome.
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Affiliation(s)
- Glenn Hickey
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
- These authors contributed equally: Glenn Hickey, Jean Monlong
| | - Jean Monlong
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
- These authors contributed equally: Glenn Hickey, Jean Monlong
| | - Jana Ebler
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Adam M. Novak
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Jordan M. Eizenga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Yan Gao
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Tobias Marschall
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | - Haley J. Abel
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Mobin Asri
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | - Carl A. Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Canadian Center for Computational Genomics, McGill University, Montreal, QC, Canada
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Silvia Buonaiuto
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | | | - Mark J. P. Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | | | - Xian H. Chang
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Haoyu Cheng
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Justin Chu
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sarah Cody
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Vincenza Colonna
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | | | - Robert M. Cook-Deegan
- Arizona State University, Barrett and O’Connor Washington Center, Washington, DC, USA
| | - Omar E. Cornejo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Daniel Doerr
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Peter Ebert
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Core Unit Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jana Ebler
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Jordan M. Eizenga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Susan Fairley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Adam L. Felsenfeld
- National Institutes of Health (NIH)–National Human Genome Research Institute, Bethesda, MD, USA
| | - Xiaowen Feng
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Christian Fischer
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Robert S. Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Yan Gao
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shilpa Garg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Copenhagen, Denmark
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Nanibaa’ A. Garrison
- Institute for Society and Genetics, College of Letters and Science, University of California, Los Angeles, Los Angeles, CA, USA
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Carlos Garcia Giron
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Richard E. Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
- Dovetail Genomics, Scotts Valley, CA, USA
| | - Cristian Groza
- Quantitative Life Sciences, McGill University, Montreal, QC, Canada
| | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Genomics Research Centre, Human Technopole, Milan, Italy
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ira M. Hall
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Genomic Health, Yale University School of Medicine, New Haven, CT, USA
| | - William T. Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - David Haussler
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Simon Heumos
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
- Biomedical Data Science, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Glenn Hickey
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
- These authors contributed equally: Glenn Hickey, Jean Monlong
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Miten Jain
- Northeastern University, Boston, MA, USA
| | - Erich D. Jarvis
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Hanlee P. Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Barbara A. Koenig
- Program in Bioethics and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | | | - Jan O. Korbel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Jennifer Kordosky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - HoJoon Lee
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Alexandra P. Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Wen-Wei Liao
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Genomic Health, Yale University School of Medicine, New Haven, CT, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Shuangjia Lu
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Tsung-Yu Lu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Julian K. Lucas
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Hugo Magalhães
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Santiago Marco-Sola
- Computer Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
- Departament d’Arquitectura de Computadors i Sistemes Operatius, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Pierre Marijon
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Charles Markello
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Tobias Marschall
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Fergal J. Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ann McCartney
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer McDaniel
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Karen H. Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | - Jean Monlong
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
- These authors contributed equally: Glenn Hickey, Jean Monlong
| | | | - Katherine M. Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | | | - Adam M. Novak
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hugh E. Olsen
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Nathan D. Olson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Trevor Pesout
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alice B. Popejoy
- Department of Public Health Sciences, University of California, Davis, Davis, CA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Daniela Puiu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Mikko Rautiainen
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Allison A. Regier
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Ashley D. Sanders
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Valerie A. Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Baergen I. Schultz
- National Institutes of Health (NIH)–National Human Genome Research Institute, Bethesda, MD, USA
| | | | - Jonas A. Sibbesen
- Center for Health Data Science, University of Copenhagen, Copenhagen, Denmark
| | - Jouni Sirén
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Michael W. Smith
- National Institutes of Health (NIH)–National Human Genome Research Institute, Bethesda, MD, USA
| | - Heidi J. Sofia
- National Institutes of Health (NIH)–National Human Genome Research Institute, Bethesda, MD, USA
| | - Ahmad N. Abou Tayoun
- Al Jalila Genomics Center of Excellence, Al Jalila Children’s Specialty Hospital, Dubai, UAE
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Francesca Floriana Tricomi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Mitchell R. Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | - Justin Wagner
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Brian Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ting Wang
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Aleksey V. Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Justin M. Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
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Gomez F, Fisk B, McMichael JF, Mosior M, Foltz JA, Skidmore ZL, Duncavage EJ, Miller CA, Abel H, Li YS, Russler-Germain DA, Krysiak K, Watkins MP, Ramirez CA, Schmidt A, Martins Rodrigues F, Trani L, Khanna A, Wagner JA, Fulton RS, Fronick CC, O'Laughlin MD, Schappe T, Cashen AF, Mehta-Shah N, Kahl BS, Walker J, Bartlett NL, Griffith M, Fehniger TA, Griffith OL. Ultra-Deep Sequencing Reveals the Mutational Landscape of Classical Hodgkin Lymphoma. Cancer Res Commun 2023; 3:2312-2330. [PMID: 37910143 PMCID: PMC10648575 DOI: 10.1158/2767-9764.crc-23-0140] [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] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/27/2023] [Accepted: 10/24/2023] [Indexed: 11/03/2023]
Abstract
The malignant Hodgkin and Reed Sternberg (HRS) cells of classical Hodgkin lymphoma (cHL) are scarce in affected lymph nodes, creating a challenge to detect driver somatic mutations. As an alternative to cell purification techniques, we hypothesized that ultra-deep exome sequencing would allow genomic study of HRS cells, thereby streamlining analysis and avoiding technical pitfalls. To test this, 31 cHL tumor/normal pairs were exome sequenced to approximately 1,000× median depth of coverage. An orthogonal error-corrected sequencing approach verified >95% of the discovered mutations. We identified mutations in genes novel to cHL including: CDH5 and PCDH7, novel stop gain mutations in IL4R, and a novel pattern of recurrent mutations in pathways regulating Hippo signaling. As a further application of our exome sequencing, we attempted to identify expressed somatic single-nucleotide variants (SNV) in single-nuclei RNA sequencing (snRNA-seq) data generated from a patient in our cohort. Our snRNA analysis identified a clear cluster of cells containing a somatic SNV identified in our deep exome data. This cluster has differentially expressed genes that are consistent with genes known to be dysregulated in HRS cells (e.g., PIM1 and PIM3). The cluster also contains cells with an expanded B-cell clonotype further supporting a malignant phenotype. This study provides proof-of-principle that ultra-deep exome sequencing can be utilized to identify recurrent mutations in HRS cells and demonstrates the feasibility of snRNA-seq in the context of cHL. These studies provide the foundation for the further analysis of genomic variants in large cohorts of patients with cHL. SIGNIFICANCE Our data demonstrate the utility of ultra-deep exome sequencing in uncovering somatic variants in Hodgkin lymphoma, creating new opportunities to define the genes that are recurrently mutated in this disease. We also show for the first time the successful application of snRNA-seq in Hodgkin lymphoma and describe the expression profile of a putative cluster of HRS cells in a single patient.
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Affiliation(s)
- Felicia Gomez
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
| | - Bryan Fisk
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Joshua F. McMichael
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Matthew Mosior
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Jennifer A. Foltz
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Zachary L. Skidmore
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Eric J. Duncavage
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - Christopher A. Miller
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Haley Abel
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Yi-Shan Li
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - David A. Russler-Germain
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Kilannin Krysiak
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - Marcus P. Watkins
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Cody A. Ramirez
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Alina Schmidt
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Fernanda Martins Rodrigues
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Lee Trani
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Ajay Khanna
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Julia A. Wagner
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Robert S. Fulton
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Catrina C. Fronick
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Michelle D. O'Laughlin
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Timothy Schappe
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Amanda F. Cashen
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Neha Mehta-Shah
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Brad S. Kahl
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Jason Walker
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Nancy L. Bartlett
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Malachi Griffith
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri
| | - Todd A. Fehniger
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
| | - Obi L. Griffith
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri
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3
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Iglesia MD, Jayasinghe RG, Chen S, Terekhanova NV, Herndon JM, Storrs E, Karpova A, Zhou DC, Al Deen NN, Shinkle AT, Lu RJH, Caravan W, Houston A, Zhao Y, Sato K, Lal P, Street C, Rodrigues FM, Southard-Smith AN, Targino da Costa ALN, Zhu H, Mo CK, Crowson L, Fulton RS, Wyczalkowski MA, Fronick CC, Fulton LA, Sun H, Davies SR, Appelbaum EL, Chasnoff SE, Carmody M, Brooks C, Liu R, Wendl MC, Oh C, Bender D, Cruchaga C, Harari O, Bredemeyer A, Lavine K, Bose R, Margenthaler J, Held JM, Achilefu S, Ademuyiwa F, Aft R, Ma C, Colditz GA, Ju T, Oh ST, Fitzpatrick J, Hwang ES, Shoghi KI, Chheda MG, Veis DJ, Chen F, Fields RC, Gillanders WE, Ding L. Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages. bioRxiv 2023:2023.10.31.565031. [PMID: 37961519 PMCID: PMC10634973 DOI: 10.1101/2023.10.31.565031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Breast cancer is a heterogeneous disease, and treatment is guided by biomarker profiles representing distinct molecular subtypes. Breast cancer arises from the breast ductal epithelium, and experimental data suggests breast cancer subtypes have different cells of origin within that lineage. The precise cells of origin for each subtype and the transcriptional networks that characterize these tumor-normal lineages are not established. In this work, we applied bulk, single-cell (sc), and single-nucleus (sn) multi-omic techniques as well as spatial transcriptomics and multiplex imaging on 61 samples from 37 breast cancer patients to show characteristic links in gene expression and chromatin accessibility between breast cancer subtypes and their putative cells of origin. We applied the PAM50 subtyping algorithm in tandem with bulk RNA-seq and snRNA-seq to reliably subtype even low-purity tumor samples and confirm promoter accessibility using snATAC. Trajectory analysis of chromatin accessibility and differentially accessible motifs clearly connected progenitor populations with breast cancer subtypes supporting the cell of origin for basal-like and luminal A and B tumors. Regulatory network analysis of transcription factors underscored the importance of BHLHE40 in luminal breast cancer and luminal mature cells, and KLF5 in basal-like tumors and luminal progenitor cells. Furthermore, we identify key genes defining the basal-like ( PRKCA , SOX6 , RGS6 , KCNQ3 ) and luminal A/B ( FAM155A , LRP1B ) lineages, with expression in both precursor and cancer cells and further upregulation in tumors. Exhausted CTLA4-expressing CD8+ T cells were enriched in basal-like breast cancer, suggesting altered means of immune dysfunction among breast cancer subtypes. We used spatial transcriptomics and multiplex imaging to provide spatial detail for key markers of benign and malignant cell types and immune cell colocation. These findings demonstrate analysis of paired transcription and chromatin accessibility at the single cell level is a powerful tool for investigating breast cancer lineage development and highlight transcriptional networks that define basal and luminal breast cancer lineages.
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4
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Abel HJ, Oetjen KA, Miller CA, Ramakrishnan SM, Day RB, Helton NM, Fronick CC, Fulton RS, Heath SE, Tarnawsky SP, Nonavinkere Srivatsan S, Duncavage EJ, Schroeder MC, Payton JE, Spencer DH, Walter MJ, Westervelt P, DiPersio JF, Ley TJ, Link DC. Genomic landscape of TP53-mutated myeloid malignancies. Blood Adv 2023; 7:4586-4598. [PMID: 37339484 PMCID: PMC10425686 DOI: 10.1182/bloodadvances.2023010156] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 03/08/2023] [Revised: 05/19/2023] [Accepted: 06/07/2023] [Indexed: 06/22/2023] Open
Abstract
TP53-mutated myeloid malignancies are associated with complex cytogenetics and extensive structural variants, which complicates detailed genomic analysis by conventional clinical techniques. We performed whole-genome sequencing (WGS) of 42 acute myeloid leukemia (AML)/myelodysplastic syndromes (MDS) cases with paired normal tissue to better characterize the genomic landscape of TP53-mutated AML/MDS. WGS accurately determines TP53 allele status, a key prognostic factor, resulting in the reclassification of 12% of cases from monoallelic to multihit. Although aneuploidy and chromothripsis are shared with most TP53-mutated cancers, the specific chromosome abnormalities are distinct to each cancer type, suggesting a dependence on the tissue of origin. ETV6 expression is reduced in nearly all cases of TP53-mutated AML/MDS, either through gene deletion or presumed epigenetic silencing. Within the AML cohort, mutations of NF1 are highly enriched, with deletions of 1 copy of NF1 present in 45% of cases and biallelic mutations in 17%. Telomere content is increased in TP53-mutated AMLs compared with other AML subtypes, and abnormal telomeric sequences were detected in the interstitial regions of chromosomes. These data highlight the unique features of TP53-mutated myeloid malignancies, including the high frequency of chromothripsis and structural variation, the frequent involvement of unique genes (including NF1 and ETV6) as cooperating events, and evidence for altered telomere maintenance.
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Affiliation(s)
- Haley J. Abel
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Karolyn A. Oetjen
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Christopher A. Miller
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Sai M. Ramakrishnan
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Ryan B. Day
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Nichole M. Helton
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Catrina C. Fronick
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Robert S. Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Sharon E. Heath
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Stefan P. Tarnawsky
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | | | - Eric J. Duncavage
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO
| | - Molly C. Schroeder
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO
| | - Jacqueline E. Payton
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO
| | - David H. Spencer
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO
| | - Matthew J. Walter
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Peter Westervelt
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - John F. DiPersio
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Timothy J. Ley
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Daniel C. Link
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
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5
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DeZern AE, Goll JB, Lindsley RC, Bejar R, Wilson SH, Hebert D, Deeg J, Zhang L, Gore S, Al Baghdadi T, Maciejewski J, Liu J, Padron E, Komrojki R, Saber W, Abel G, Kroft SH, Harrington A, Grimes T, Reed H, Fulton RS, DiFronzo NL, Gillis N, Sekeres MA, Walter MJ. Utility of targeted gene sequencing to differentiate myeloid malignancies from other cytopenic conditions. Blood Adv 2023; 7:3749-3759. [PMID: 36947201 PMCID: PMC10368770 DOI: 10.1182/bloodadvances.2022008578] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 07/18/2022] [Revised: 02/13/2023] [Accepted: 02/24/2023] [Indexed: 03/23/2023] Open
Abstract
The National Heart, Lung, and Blood Institute-funded National MDS Natural History Study (NCT02775383) is a prospective cohort study enrolling patients with cytopenia with suspected myelodysplastic syndromes (MDS) to evaluate factors associated with disease. Here, we sequenced 53 genes in bone marrow samples harvested from 1298 patients diagnosed with myeloid malignancy, including MDS and non-MDS myeloid malignancy or alternative marrow conditions with cytopenia based on concordance between independent histopathologic reviews (local, centralized, and tertiary to adjudicate disagreements when needed). We developed a novel 2-stage diagnostic classifier based on mutational profiles in 18 of 53 sequenced genes that were sufficient to best predict a diagnosis of myeloid malignancy and among those with a predicted myeloid malignancy, predict whether they had MDS. The classifier achieved a positive predictive value (PPV) of 0.84 and negative predictive value (NPV) of 0.8 with an area under the receiver operating characteristic curve (AUROC) of 0.85 when classifying patients as having myeloid vs no myeloid malignancy based on variant allele frequencies (VAFs) in 17 genes and a PPV of 0.71 and NPV of 0.64 with an AUROC of 0.73 when classifying patients as having MDS vs non-MDS malignancy based on VAFs in 10 genes. We next assessed how this approach could complement histopathology to improve diagnostic accuracy. For 99 of 139 (71%) patients (PPV of 0.83 and NPV of 0.65) with local and centralized histopathologic disagreement in myeloid vs no myeloid malignancy, the classifier-predicted diagnosis agreed with the tertiary pathology review (considered the internal gold standard).
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Affiliation(s)
| | | | | | | | | | | | - Joachim Deeg
- Fred Hutchison Cancer Research Center, Seattle, WA
| | | | - Steven Gore
- National Cancer Institute, National Institutes of Health, Rockville, MD
| | | | | | | | | | | | - Wael Saber
- Center for International Blood and Marrow Transplant Research, Milwaukee, WI
| | | | | | | | | | | | - Robert S. Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Nancy L. DiFronzo
- National Institutes of Health, National Heart, Lung, and Blood Institute, Bethesda, MD
| | | | | | - Matthew J. Walter
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO
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6
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Liao WW, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas JK, Monlong J, Abel HJ, Buonaiuto S, Chang XH, Cheng H, Chu J, Colonna V, Eizenga JM, Feng X, Fischer C, Fulton RS, Garg S, Groza C, Guarracino A, Harvey WT, Heumos S, Howe K, Jain M, Lu TY, Markello C, Martin FJ, Mitchell MW, Munson KM, Mwaniki MN, Novak AM, Olsen HE, Pesout T, Porubsky D, Prins P, Sibbesen JA, Sirén J, Tomlinson C, Villani F, Vollger MR, Antonacci-Fulton LL, Baid G, Baker CA, Belyaeva A, Billis K, Carroll A, Chang PC, Cody S, Cook DE, Cook-Deegan RM, Cornejo OE, Diekhans M, Ebert P, Fairley S, Fedrigo O, Felsenfeld AL, Formenti G, Frankish A, Gao Y, Garrison NA, Giron CG, Green RE, Haggerty L, Hoekzema K, Hourlier T, Ji HP, Kenny EE, Koenig BA, Kolesnikov A, Korbel JO, Kordosky J, Koren S, Lee H, Lewis AP, Magalhães H, Marco-Sola S, Marijon P, McCartney A, McDaniel J, Mountcastle J, Nattestad M, Nurk S, Olson ND, Popejoy AB, Puiu D, Rautiainen M, Regier AA, Rhie A, Sacco S, Sanders AD, Schneider VA, Schultz BI, Shafin K, Smith MW, Sofia HJ, Abou Tayoun AN, Thibaud-Nissen F, Tricomi FF, Wagner J, Walenz B, Wood JMD, Zimin AV, Bourque G, Chaisson MJP, Flicek P, Phillippy AM, Zook JM, Eichler EE, Haussler D, Wang T, Jarvis ED, Miga KH, Garrison E, Marschall T, Hall IM, Li H, Paten B. A draft human pangenome reference. Nature 2023; 617:312-324. [PMID: 37165242 PMCID: PMC10172123 DOI: 10.1038/s41586-023-05896-x] [Citation(s) in RCA: 163] [Impact Index Per Article: 163.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 02/28/2023] [Indexed: 05/12/2023]
Abstract
Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.
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Affiliation(s)
- Wen-Wei Liao
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Genomic Health, Yale University School of Medicine, New Haven, CT, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Mobin Asri
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Jana Ebler
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Daniel Doerr
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Marina Haukness
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Glenn Hickey
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Shuangjia Lu
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Genomic Health, Yale University School of Medicine, New Haven, CT, USA
| | - Julian K Lucas
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Jean Monlong
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Haley J Abel
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Silvia Buonaiuto
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | - Xian H Chang
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Haoyu Cheng
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Justin Chu
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Vincenza Colonna
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jordan M Eizenga
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Xiaowen Feng
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Christian Fischer
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Robert S Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Shilpa Garg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Copenhagen, Denmark
| | - Cristian Groza
- Quantitative Life Sciences, McGill University, Montréal, Québec, Canada
| | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Genomics Research Centre, Human Technopole, Milan, Italy
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Simon Heumos
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
- Biomedical Data Science, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Miten Jain
- Northeastern University, Boston, MA, USA
| | - Tsung-Yu Lu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Charles Markello
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Adam M Novak
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Hugh E Olsen
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Trevor Pesout
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jonas A Sibbesen
- Center for Health Data Science, University of Copenhagen, Copenhagen, Denmark
| | - Jouni Sirén
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | | | | | - Carl A Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | | | - Sarah Cody
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Robert M Cook-Deegan
- Barrett and O'Connor Washington Center, Arizona State University, Washington, DC, USA
| | - Omar E Cornejo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Mark Diekhans
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Peter Ebert
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
- Core Unit Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Susan Fairley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Adam L Felsenfeld
- National Institutes of Health (NIH)-National Human Genome Research Institute, Bethesda, MD, USA
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yan Gao
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nanibaa' A Garrison
- Institute for Society and Genetics, College of Letters and Science, University of California, Los Angeles, CA, USA
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Carlos Garcia Giron
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
- Dovetail Genomics, Scotts Valley, CA, USA
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Hanlee P Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Barbara A Koenig
- Program in Bioethics and Institute for Human Genetics, University of California, San Francisco, CA, USA
| | | | - Jan O Korbel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jennifer Kordosky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - HoJoon Lee
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Hugo Magalhães
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Santiago Marco-Sola
- Computer Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
- Departament d'Arquitectura de Computadors i Sistemes Operatius, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Pierre Marijon
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Ann McCartney
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer McDaniel
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | | | - Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nathan D Olson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Alice B Popejoy
- Department of Public Health Sciences, University of California, Davis, CA, USA
| | - Daniela Puiu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Mikko Rautiainen
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Allison A Regier
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Ashley D Sanders
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Valerie A Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Baergen I Schultz
- National Institutes of Health (NIH)-National Human Genome Research Institute, Bethesda, MD, USA
| | | | - Michael W Smith
- National Institutes of Health (NIH)-National Human Genome Research Institute, Bethesda, MD, USA
| | - Heidi J Sofia
- National Institutes of Health (NIH)-National Human Genome Research Institute, Bethesda, MD, USA
| | - Ahmad N Abou Tayoun
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai, UAE
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Francesca Floriana Tricomi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Justin Wagner
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Brian Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Aleksey V Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Canadian Center for Computational Genomics, McGill University, Montréal, Québec, Canada
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Justin M Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - David Haussler
- Genomics Institute, University of California, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Ting Wang
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Erich D Jarvis
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Karen H Miga
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
| | - Tobias Marschall
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany.
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany.
| | - Ira M Hall
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
- Center for Genomic Health, Yale University School of Medicine, New Haven, CT, USA.
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Benedict Paten
- Genomics Institute, University of California, Santa Cruz, CA, USA.
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7
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Slade MJ, Ghasemi R, O'Laughlin M, Burton T, Fulton RS, Abel HJ, Duncavage EJ, Ley TJ, Jacoby MA, Spencer DH. Persistent Molecular Disease in Adult Patients With AML Evaluated With Whole-Exome and Targeted Error-Corrected DNA Sequencing. JCO Precis Oncol 2023; 7:e2200559. [PMID: 37079859 PMCID: PMC10530963 DOI: 10.1200/po.22.00559] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 10/07/2022] [Revised: 02/03/2023] [Accepted: 03/01/2023] [Indexed: 04/22/2023] Open
Abstract
PURPOSE Persistent molecular disease (PMD) after induction chemotherapy predicts relapse in AML. In this study, we used whole-exome sequencing (WES) and targeted error-corrected sequencing to assess the frequency and mutational patterns of PMD in 30 patients with AML. MATERIALS AND METHODS The study cohort included 30 patients with adult AML younger than 65 years who were uniformly treated with standard induction chemotherapy. Tumor/normal WES was performed for all patients at presentation. PMD analysis was evaluated in bone marrow samples obtained during clinicopathologic remission using repeat WES and analysis of patient-specific mutations and error-corrected sequencing of 40 recurrently mutated AML genes (MyeloSeq). RESULTS WES for patient-specific mutations detected PMD in 63% of patients (19/30) using a minimum variant allele fraction (VAF) of 2.5%. In comparison, MyeloSeq identified persistent mutations above 0.1% VAF in 77% of patients (23/30). PMD was usually present at relatively high levels (>2.5% VAFs), such that WES and MyeloSeq agreed for 73% of patients despite differences in detection limits. Mutations in DNMT3A, ASXL1, and TET2 (ie, DTA mutations) were persistent in 16 of 17 patients, but WES also detected non-DTA mutations in 14 of these patients, which for some patients distinguished residual AML cells from clonal hematopoiesis. Surprisingly, MyeloSeq detected additional variants not identified at presentation in 73% of patients that were consistent with new clonal cell populations after chemotherapy. CONCLUSION PMD and clonal hematopoiesis are both common in patients with AML in first remission. These findings demonstrate the importance of baseline testing for accurate interpretation of mutation-based tumor monitoring assays for patients with AML and highlight the need for clinical trials to determine whether these complex mutation patterns correlate with clinical outcomes in AML.
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Affiliation(s)
- Michael J. Slade
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Reza Ghasemi
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Michelle O'Laughlin
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Tasha Burton
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Robert S. Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Haley J. Abel
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Eric J. Duncavage
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Timothy J. Ley
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Meagan A. Jacoby
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - David H. Spencer
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
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Abel HJ, Oetjen KA, Miller CA, Ramakrishnan SM, Day RB, Helton NM, Fronick CC, Fulton RS, Heath SE, Tarnawsky SP, Srivatsan SN, Duncavage EJ, Schroeder MC, Payton JE, Spencer DH, Walter MJ, Westervelt P, DiPersio JF, Ley TJ, Link DC. Genomic landscape of TP53 -mutated myeloid malignancies. medRxiv 2023:2023.01.10.23284322. [PMID: 36711871 PMCID: PMC9882519 DOI: 10.1101/2023.01.10.23284322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
TP53 -mutated myeloid malignancies are most frequently associated with complex cytogenetics. The presence of complex and extensive structural variants complicates detailed genomic analysis by conventional clinical techniques. We performed whole genome sequencing of 42 AML/MDS cases with paired normal tissue to characterize the genomic landscape of TP53 -mutated myeloid malignancies. The vast majority of cases had multi-hit involvement at the TP53 genetic locus (94%), as well as aneuploidy and chromothripsis. Chromosomal patterns of aneuploidy differed significantly from TP53 -mutated cancers arising in other tissues. Recurrent structural variants affected regions that include ETV6 on chr12p, RUNX1 on chr21, and NF1 on chr17q. Most notably for ETV6 , transcript expression was low in cases of TP53 -mutated myeloid malignancies both with and without structural rearrangements involving chromosome 12p. Telomeric content is increased in TP53 -mutated AML/MDS compared other AML subtypes, and telomeric content was detected adjacent to interstitial regions of chromosomes. The genomic landscape of TP53 -mutated myeloid malignancies reveals recurrent structural variants affecting key hematopoietic transcription factors and telomeric repeats that are generally not detected by panel sequencing or conventional cytogenetic analyses. Key Points WGS comprehensively determines TP53 mutation status, resulting in the reclassification of 12% of cases from mono-allelic to multi-hit Chromothripsis is more frequent than previously appreciated, with a preference for specific chromosomes ETV6 is deleted in 45% of cases, with evidence for epigenetic suppression in non-deleted cases NF1 is mutated in 48% of cases, with multi-hit mutations in 17% of these cases TP53 -mutated AML/MDS is associated with altered telomere content compared with other AMLs.
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Affiliation(s)
- Haley J. Abel
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | - Karolyn A. Oetjen
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | - Christopher A. Miller
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | - Sai M. Ramakrishnan
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | - Ryan B. Day
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | - Nichole M. Helton
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | | | - Robert S. Fulton
- McDonnell Genome Institute, Washington University School of Medicine
| | - Sharon E. Heath
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | - Stefan P. Tarnawsky
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | | | - Eric J. Duncavage
- Department of Pathology & Immunology, Washington University School of Medicine
| | - Molly C. Schroeder
- Department of Pathology & Immunology, Washington University School of Medicine
| | | | - David H. Spencer
- Division of Oncology, Department of Medicine, Washington University School of Medicine
- McDonnell Genome Institute, Washington University School of Medicine
- Department of Pathology & Immunology, Washington University School of Medicine
| | - Matthew J. Walter
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | - Peter Westervelt
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | - John F. DiPersio
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | - Timothy J. Ley
- Division of Oncology, Department of Medicine, Washington University School of Medicine
| | - Daniel C. Link
- Division of Oncology, Department of Medicine, Washington University School of Medicine
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9
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Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Spellman PT, Wedge DC, Van Loo P, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Gonzalez S, Rubanova Y, Macintyre G, Adams DJ, Anur P, Beroukhim R, Boutros PC, Bowtell DD, Campbell PJ, Cao S, Christie EL, Cmero M, Cun Y, Dawson KJ, Demeulemeester J, Donmez N, Drews RM, Eils R, Fan Y, Fittall M, Garsed DW, Getz G, Ha G, Imielinski M, Jerman L, Ji Y, Kleinheinz K, Lee J, Lee-Six H, Livitz DG, Malikic S, Markowetz F, Martincorena I, Mitchell TJ, Mustonen V, Oesper L, Peifer M, Peto M, Raphael BJ, Rosebrock D, Sahinalp SC, Salcedo A, Schlesner M, Schumacher S, Sengupta S, Shi R, Shin SJ, Spiro O, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Stein LD, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Vázquez-García I, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Vembu S, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Wheeler DA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Yang TP, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Yao X, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Yuan K, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Zhu H, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Wang W, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Morris QD, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Spellman PT, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Wedge DC, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Van Loo P, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Spellman PT, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Wedge DC, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Van Loo P, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Aaltonen LA, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Abascal F, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Abeshouse A, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Aburatani H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Adams DJ, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Agrawal N, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Ahn KS, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Ahn SM, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Aikata H, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Akbani R, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Akdemir KC, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Al-Ahmadie H, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Al-Sedairy ST, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Al-Shahrour F, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Alawi M, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Albert M, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Aldape K, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Alexandrov LB, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Ally A, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Alsop K, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Alvarez EG, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Amary F, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Amin SB, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Aminou B, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ammerpohl O, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Anderson MJ, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Ang Y, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Antonello D, von Mering C, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV. Author Correction: The evolutionary history of 2,658 cancers. Nature 2023; 614:E42. [PMID: 36697833 PMCID: PMC9931577 DOI: 10.1038/s41586-022-05601-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Wellcome Sanger Institute, Cambridge, UK.
| | - Clemency Jolly
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Ignaty Leshchiner
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Stefan C. Dentro
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK
| | - Santiago Gonzalez
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Daniel Rosebrock
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Thomas J. Mitchell
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Yulia Rubanova
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Pavana Anur
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - Kaixian Yu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Maxime Tarabichi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Amit Deshwar
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Jeff Wintersinger
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Kortine Kleinheinz
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, Heidelberg, Germany
| | - Ignacio Vázquez-García
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Kerstin Haase
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Lara Jerman
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK ,grid.8954.00000 0001 0721 6013University of Ljubljana, Ljubljana, Slovenia
| | - Subhajit Sengupta
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA
| | - Geoff Macintyre
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Salem Malikic
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Nilgun Donmez
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Dimitri G. Livitz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Marek Cmero
- grid.1008.90000 0001 2179 088XUniversity of Melbourne, Melbourne, Victoria Australia ,grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute, Melbourne, Victoria Australia
| | - Jonas Demeulemeester
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.5596.f0000 0001 0668 7884University of Leuven, Leuven, Belgium
| | - Steven Schumacher
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Yu Fan
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xiaotong Yao
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Juhee Lee
- grid.205975.c0000 0001 0740 6917University of California Santa Cruz, Santa Cruz, CA USA
| | - Matthias Schlesner
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul C. Boutros
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, Ontario Canada ,grid.19006.3e0000 0000 9632 6718University of California, Los Angeles, CA USA
| | - David D. Bowtell
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, Victoria Australia
| | - Hongtu Zhu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Gad Getz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA USA ,grid.32224.350000 0004 0386 9924Department of Pathology, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Marcin Imielinski
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Rameen Beroukhim
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - S. Cenk Sahinalp
- grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada ,grid.411377.70000 0001 0790 959XIndiana University, Bloomington, IN USA
| | - Yuan Ji
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822The University of Chicago, Chicago, IL USA
| | - Martin Peifer
- grid.6190.e0000 0000 8580 3777University of Cologne, Cologne, Germany
| | - Florian Markowetz
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ville Mustonen
- grid.7737.40000 0004 0410 2071University of Helsinki, Helsinki, Finland
| | - Ke Yuan
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK ,grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Wenyi Wang
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Quaid D. Morris
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | | | - Paul T. Spellman
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - David C. Wedge
- grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK ,grid.454382.c0000 0004 7871 7212Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, UK. .,University of Leuven, Leuven, Belgium.
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Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, Wu K, Yang H, Fonseca NA, Kahles A, Lehmann KV, Urban L, Soulette CM, Shiraishi Y, Liu F, He Y, Demircioğlu D, Davidson NR, Calabrese C, Zhang J, Perry MD, Xiang Q, Greger L, Li S, Liu D, Stark SG, Zhang F, Amin SB, Bailey P, Chateigner A, Cortés-Ciriano I, Craft B, Erkek S, Frenkel-Morgenstern M, Goldman M, Hoadley KA, Hou Y, Huska MR, Khurana E, Kilpinen H, Korbel JO, Lamaze FC, Li C, Li X, Li X, Liu X, Marin MG, Markowski J, Nandi T, Nielsen MM, Ojesina AI, Pan-Hammarström Q, Park PJ, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Pedamallu CS, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pedersen JS, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Siebert R, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Su H, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Tan P, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Teh BT, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Wang J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Waszak SM, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Xiong H, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Yakneen S, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Ye C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Yung C, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Zhang X, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Zheng L, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Zhu J, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, 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Viksna J, Göke J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Rätsch G, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Schwarz RF, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Stegle O, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Zhang Z, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Aaltonen LA, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Abascal F, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Abeshouse A, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Aburatani H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, 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Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, 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Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV. Author Correction: Genomic basis for RNA alterations in cancer. Nature 2023; 614:E37. [PMID: 36697831 PMCID: PMC9931574 DOI: 10.1038/s41586-022-05596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Claudia Calabrese
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Natalie R. Davidson
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medical College, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Deniz Demircioğlu
- grid.4280.e0000 0001 2180 6431National University of Singapore, Singapore, Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Nuno A. Fonseca
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Yao He
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - André Kahles
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Kjong-Van Lehmann
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Fenglin Liu
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Yuichi Shiraishi
- grid.26999.3d0000 0001 2151 536XThe University of Tokyo, Minato-ku, Japan
| | - Cameron M. Soulette
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Lara Urban
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Liliana Greger
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Siliang Li
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Dongbing Liu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Marc D. Perry
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.266102.10000 0001 2297 6811University of California, San Francisco, San Francisco, CA USA
| | - Qian Xiang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Fan Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Junjun Zhang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Peter Bailey
- grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Serap Erkek
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Katherine A. Hoadley
- grid.10698.360000000122483208The University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Yong Hou
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Matthew R. Huska
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Helena Kilpinen
- grid.83440.3b0000000121901201University College London, London, UK
| | - Jan O. Korbel
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maximillian G. Marin
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Julia Markowski
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Tannistha Nandi
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Qiang Pan-Hammarström
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.4714.60000 0004 1937 0626Karolinska Institutet, Stockholm, Sweden
| | - Chandra Sekhar Pedamallu
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Reiner Siebert
- grid.410712.10000 0004 0473 882XUlm University and Ulm University Medical Center, Ulm, Germany
| | - Stefan G. Stark
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Hong Su
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Patrick Tan
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, Singapore
| | - Sebastian M. Waszak
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Christina Yung
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Shida Zhu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Philip Awadalla
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada
| | - Chad J. Creighton
- grid.39382.330000 0001 2160 926XBaylor College of Medicine, Houston, TX USA
| | - Matthew Meyerson
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | | | - Kui Wu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Huanming Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China
| | | | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Angela N. Brooks
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - Jonathan Göke
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745National Cancer Centre Singapore, Singapore, Singapore
| | - Gunnar Rätsch
- ETH Zurich, Zurich, Switzerland. .,Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,University Hospital Zurich, Zurich, Switzerland.
| | - Roland F. Schwarz
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), partner site Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Stegle
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zemin Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
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Jarvis ED, Formenti G, Rhie A, Guarracino A, Yang C, Wood J, Tracey A, Thibaud-Nissen F, Vollger MR, Porubsky D, Cheng H, Asri M, Logsdon GA, Carnevali P, Chaisson MJP, Chin CS, Cody S, Collins J, Ebert P, Escalona M, Fedrigo O, Fulton RS, Fulton LL, Garg S, Gerton JL, Ghurye J, Granat A, Green RE, Harvey W, Hasenfeld P, Hastie A, Haukness M, Jaeger EB, Jain M, Kirsche M, Kolmogorov M, Korbel JO, Koren S, Korlach J, Lee J, Li D, Lindsay T, Lucas J, Luo F, Marschall T, Mitchell MW, McDaniel J, Nie F, Olsen HE, Olson ND, Pesout T, Potapova T, Puiu D, Regier A, Ruan J, Salzberg SL, Sanders AD, Schatz MC, Schmitt A, Schneider VA, Selvaraj S, Shafin K, Shumate A, Stitziel NO, Stober C, Torrance J, Wagner J, Wang J, Wenger A, Xiao C, Zimin AV, Zhang G, Wang T, Li H, Garrison E, Haussler D, Hall I, Zook JM, Eichler EE, Phillippy AM, Paten B, Howe K, Miga KH. Semi-automated assembly of high-quality diploid human reference genomes. Nature 2022; 611:519-531. [PMID: 36261518 PMCID: PMC9668749 DOI: 10.1038/s41586-022-05325-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 09/06/2022] [Indexed: 01/01/2023]
Abstract
The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society1,2. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals3,4. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome5. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity6. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1% of the length of CHM13. Nearly 48% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.
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Affiliation(s)
- Erich D. Jarvis
- grid.134907.80000 0001 2166 1519Vertebrate Genome Laboratory, The Rockefeller University, New York, NY USA ,grid.413575.10000 0001 2167 1581Howard Hughes Medical Institute, Chevy Chase, MD USA
| | - Giulio Formenti
- grid.134907.80000 0001 2166 1519Vertebrate Genome Laboratory, The Rockefeller University, New York, NY USA
| | - Arang Rhie
- grid.94365.3d0000 0001 2297 5165Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Andrea Guarracino
- grid.510779.d0000 0004 9414 6915Genomics Research Centre, Human Technopole, Viale Rita Levi-Montalcini, Milan, Italy
| | - Chentao Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China
| | - Jonathan Wood
- grid.10306.340000 0004 0606 5382Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Alan Tracey
- grid.10306.340000 0004 0606 5382Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Francoise Thibaud-Nissen
- grid.94365.3d0000 0001 2297 5165National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD USA
| | - Mitchell R. Vollger
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA USA
| | - David Porubsky
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA USA
| | - Haoyu Cheng
- grid.65499.370000 0001 2106 9910Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA USA
| | - Mobin Asri
- grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA USA
| | - Glennis A. Logsdon
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA USA
| | - Paolo Carnevali
- grid.507326.50000 0004 6090 4941Chan Zuckerberg Initiative, Redwood City, CA USA
| | - Mark J. P. Chaisson
- grid.42505.360000 0001 2156 6853Quantitative and Computational Biology, University of Southern California, Los Angeles, CA USA
| | | | - Sarah Cody
- grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO USA
| | - Joanna Collins
- grid.10306.340000 0004 0606 5382Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Peter Ebert
- grid.411327.20000 0001 2176 9917Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Merly Escalona
- grid.205975.c0000 0001 0740 6917Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA USA
| | - Olivier Fedrigo
- grid.134907.80000 0001 2166 1519Vertebrate Genome Laboratory, The Rockefeller University, New York, NY USA
| | - Robert S. Fulton
- grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO USA
| | - Lucinda L. Fulton
- grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO USA
| | - Shilpa Garg
- grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jennifer L. Gerton
- grid.250820.d0000 0000 9420 1591Stowers Institute for Medical Research, Kansas City, MO USA
| | - Jay Ghurye
- grid.504403.6Dovetail Genomics, Scotts Valley, CA USA
| | | | - Richard E. Green
- grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA USA
| | - William Harvey
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA USA
| | - Patrick Hasenfeld
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Alex Hastie
- grid.470262.50000 0004 0473 1353Bionano Genomics, San Diego, CA USA
| | - Marina Haukness
- grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA USA
| | - Erich B. Jaeger
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA USA
| | - Miten Jain
- grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA USA
| | - Melanie Kirsche
- grid.21107.350000 0001 2171 9311Department of Computer Science, Johns Hopkins University, Baltimore, MD USA
| | - Mikhail Kolmogorov
- grid.266100.30000 0001 2107 4242Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA USA
| | - Jan O. Korbel
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Sergey Koren
- grid.94365.3d0000 0001 2297 5165Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Jonas Korlach
- grid.423340.20000 0004 0640 9878Pacific Biosciences, Menlo Park, CA USA
| | - Joyce Lee
- grid.470262.50000 0004 0473 1353Bionano Genomics, San Diego, CA USA
| | - Daofeng Li
- grid.4367.60000 0001 2355 7002Department of Genetics, Washington University School of Medicine, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
| | - Tina Lindsay
- grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO USA
| | - Julian Lucas
- grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA USA
| | - Feng Luo
- grid.26090.3d0000 0001 0665 0280School of Computing, Clemson University, Clemson, SC USA
| | - Tobias Marschall
- grid.411327.20000 0001 2176 9917Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Matthew W. Mitchell
- grid.282012.b0000 0004 0627 5048Coriell Institute for Medical Research, Camden, NJ USA
| | - Jennifer McDaniel
- grid.94225.38000000012158463XMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD USA
| | - Fan Nie
- grid.216417.70000 0001 0379 7164Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
| | - Hugh E. Olsen
- grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA USA
| | - Nathan D. Olson
- grid.94225.38000000012158463XMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD USA
| | - Trevor Pesout
- grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA USA
| | - Tamara Potapova
- grid.250820.d0000 0000 9420 1591Stowers Institute for Medical Research, Kansas City, MO USA
| | - Daniela Puiu
- grid.21107.350000 0001 2171 9311Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD USA
| | - Allison Regier
- grid.511991.40000 0004 4910 5831DNAnexus, Mountain View, CA USA
| | - Jue Ruan
- grid.410727.70000 0001 0526 1937Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Steven L. Salzberg
- grid.21107.350000 0001 2171 9311Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD USA
| | - Ashley D. Sanders
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Michael C. Schatz
- grid.21107.350000 0001 2171 9311Department of Computer Science, Johns Hopkins University, Baltimore, MD USA
| | | | - Valerie A. Schneider
- grid.94365.3d0000 0001 2297 5165National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD USA
| | | | - Kishwar Shafin
- grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA USA
| | - Alaina Shumate
- grid.21107.350000 0001 2171 9311Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD USA
| | - Nathan O. Stitziel
- grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Department of Genetics, Washington University School of Medicine, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Cardiovascular Division, John T. Milliken Department of Internal Medicine, Washington University School of Medicine, St. Louis, USA
| | - Catherine Stober
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - James Torrance
- grid.10306.340000 0004 0606 5382Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Justin Wagner
- grid.94225.38000000012158463XMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD USA
| | - Jianxin Wang
- grid.216417.70000 0001 0379 7164Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
| | - Aaron Wenger
- grid.423340.20000 0004 0640 9878Pacific Biosciences, Menlo Park, CA USA
| | - Chuanle Xiao
- grid.12981.330000 0001 2360 039XState Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Aleksey V. Zimin
- grid.21107.350000 0001 2171 9311Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD USA
| | - Guojie Zhang
- grid.13402.340000 0004 1759 700XCenter for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Ting Wang
- grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Department of Genetics, Washington University School of Medicine, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO USA
| | - Heng Li
- grid.65499.370000 0001 2106 9910Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA USA
| | - Erik Garrison
- grid.267301.10000 0004 0386 9246Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN USA
| | - David Haussler
- grid.413575.10000 0001 2167 1581Howard Hughes Medical Institute, Chevy Chase, MD USA ,grid.205975.c0000 0001 0740 6917Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA USA
| | - Ira Hall
- grid.47100.320000000419368710Yale School of Medicine, New Haven, CT USA
| | - Justin M. Zook
- grid.94225.38000000012158463XMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD USA
| | - Evan E. Eichler
- grid.413575.10000 0001 2167 1581Howard Hughes Medical Institute, Chevy Chase, MD USA ,grid.34477.330000000122986657Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA USA
| | - Adam M. Phillippy
- grid.94365.3d0000 0001 2297 5165Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Benedict Paten
- grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA USA
| | - Kerstin Howe
- grid.10306.340000 0004 0606 5382Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Karen H. Miga
- grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA USA
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12
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Li S, Yao JC, Oetjen KA, Krambs JR, Xia J, Zhang J, Schmidt AP, Helton NM, Fulton RS, Heath SE, Turnbull IR, Mbalaviele G, Ley TJ, Walter MJ, Link DC. IL-1β expression in bone marrow dendritic cells is induced by TLR2 agonists and regulates HSC function. Blood 2022; 140:1607-1620. [PMID: 35675516 PMCID: PMC9707400 DOI: 10.1182/blood.2022016084] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 02/24/2022] [Accepted: 05/14/2022] [Indexed: 12/14/2022] Open
Abstract
Hematopoietic stem/progenitor cells (HSPCs) reside in localized microenvironments, or niches, in the bone marrow that provide key signals regulating their activity. A fundamental property of hematopoiesis is the ability to respond to environmental cues such as inflammation. How these cues are transmitted to HSPCs within hematopoietic niches is not well established. Here, we show that perivascular bone marrow dendritic cells (DCs) express a high basal level of Toll-like receptor-1 (TLR1) and TLR2. Systemic treatment with a TLR1/2 agonist induces HSPC expansion and mobilization. It also induces marked alterations in the bone marrow microenvironment, including a decrease in osteoblast activity and sinusoidal endothelial cell numbers. TLR1/2 agonist treatment of mice in which Myd88 is deleted specifically in DCs using Zbtb46-Cre show that the TLR1/2-induced expansion of multipotent HPSCs, but not HSPC mobilization or alterations in the bone marrow microenvironment, is dependent on TLR1/2 signaling in DCs. Interleukin-1β (IL-1β) is constitutively expressed in both murine and human DCs and is further induced after TLR1/2 stimulation. Systemic TLR1/2 agonist treatment of Il1r1-/- mice show that TLR1/2-induced HSPC expansion is dependent on IL-1β signaling. Single-cell RNA-sequencing of low-risk myelodysplastic syndrome bone marrow revealed that IL1B and TLR1 expression is increased in DCs. Collectively, these data suggest a model in which TLR1/2 stimulation of DCs induces secretion of IL-1β and other inflammatory cytokines into the perivascular niche, which in turn, regulates multipotent HSPCs. Increased DC TLR1/2 signaling may contribute to altered HSPC function in myelodysplastic syndrome by increasing local IL-1β expression.
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Affiliation(s)
- Sidan Li
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO
- Hematology Oncology Center, Beijing Children’s Hospital, National Center for Children’s Health, Capital Medial University, Beijing, China
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Juo-Chin Yao
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO
| | - Karolyn A. Oetjen
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO
| | - Joseph R. Krambs
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO
| | - Jun Xia
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO
| | - Jingzhu Zhang
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO
| | - Amy P. Schmidt
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO
| | - Nichole M. Helton
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO
| | - Robert S. Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Sharon E. Heath
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO
| | - Isaiah R. Turnbull
- Department of Surgery, Washington University School of Medicine, St. Louis, MO
| | - Gabriel Mbalaviele
- Division of Bone and Mineral Disease, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO
| | - Timothy J. Ley
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO
| | - Matthew J. Walter
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO
| | - Daniel C. Link
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO
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13
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Cui Zhou D, Jayasinghe RG, Chen S, Herndon JM, Iglesia MD, Navale P, Wendl MC, Caravan W, Sato K, Storrs E, Mo CK, Liu J, Southard-Smith AN, Wu Y, Naser Al Deen N, Baer JM, Fulton RS, Wyczalkowski MA, Liu R, Fronick CC, Fulton LA, Shinkle A, Thammavong L, Zhu H, Sun H, Wang LB, Li Y, Zuo C, McMichael JF, Davies SR, Appelbaum EL, Robbins KJ, Chasnoff SE, Yang X, Reeb AN, Oh C, Serasanambati M, Lal P, Varghese R, Mashl JR, Ponce J, Terekhanova NV, Yao L, Wang F, Chen L, Schnaubelt M, Lu RJH, Schwarz JK, Puram SV, Kim AH, Song SK, Shoghi KI, Lau KS, Ju T, Chen K, Chatterjee D, Hawkins WG, Zhang H, Achilefu S, Chheda MG, Oh ST, Gillanders WE, Chen F, DeNardo DG, Fields RC, Ding L. Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer. Nat Genet 2022; 54:1390-1405. [PMID: 35995947 PMCID: PMC9470535 DOI: 10.1038/s41588-022-01157-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [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: 09/24/2021] [Accepted: 07/13/2022] [Indexed: 12/13/2022]
Abstract
Pancreatic ductal adenocarcinoma is a lethal disease with limited treatment options and poor survival. We studied 83 spatial samples from 31 patients (11 treatment-naïve and 20 treated) using single-cell/nucleus RNA sequencing, bulk-proteogenomics, spatial transcriptomics and cellular imaging. Subpopulations of tumor cells exhibited signatures of proliferation, KRAS signaling, cell stress and epithelial-to-mesenchymal transition. Mapping mutations and copy number events distinguished tumor populations from normal and transitional cells, including acinar-to-ductal metaplasia and pancreatic intraepithelial neoplasia. Pathology-assisted deconvolution of spatial transcriptomic data identified tumor and transitional subpopulations with distinct histological features. We showed coordinated expression of TIGIT in exhausted and regulatory T cells and Nectin in tumor cells. Chemo-resistant samples contain a threefold enrichment of inflammatory cancer-associated fibroblasts that upregulate metallothioneins. Our study reveals a deeper understanding of the intricate substructure of pancreatic ductal adenocarcinoma tumors that could help improve therapy for patients with this disease.
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Affiliation(s)
- Daniel Cui Zhou
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Reyka G Jayasinghe
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Siqi Chen
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - John M Herndon
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Michael D Iglesia
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Pooja Navale
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St Louis, St Louis, MO, USA
| | - Michael C Wendl
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
- Department of Genetics, Washington University in St Louis, St Louis, MO, USA
- Department of Mathematics, Washington University in St Louis, St Louis, MO, USA
| | - Wagma Caravan
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Kazuhito Sato
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Erik Storrs
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Chia-Kuei Mo
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Jingxian Liu
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Austin N Southard-Smith
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Yige Wu
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Nataly Naser Al Deen
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - John M Baer
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St Louis, St Louis, MO, USA
| | - Robert S Fulton
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Ruiyang Liu
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Catrina C Fronick
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Lucinda A Fulton
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Andrew Shinkle
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Lisa Thammavong
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Houxiang Zhu
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Hua Sun
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Liang-Bo Wang
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Yize Li
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Chong Zuo
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Joshua F McMichael
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Sherri R Davies
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
| | | | - Keenan J Robbins
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Sara E Chasnoff
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
| | - Xiaolu Yang
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Ashley N Reeb
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Department of Otolaryngology-Head & Neck Surgery, Washington University in St Louis, St Louis, MO, USA
| | - Clara Oh
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Mamatha Serasanambati
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Preet Lal
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Rajees Varghese
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Jay R Mashl
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Jennifer Ponce
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Nadezhda V Terekhanova
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Lijun Yao
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Fang Wang
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lijun Chen
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael Schnaubelt
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rita Jui-Hsien Lu
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Julie K Schwarz
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
- Department of Radiation Oncology, Washington University in St Louis, St Louis, MO, USA
- Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, MO, USA
| | - Sidharth V Puram
- Department of Otolaryngology-Head & Neck Surgery, Washington University in St Louis, St Louis, MO, USA
| | - Albert H Kim
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
- Department of Neurological Surgery, Washington University in St Louis, St Louis, MO, USA
| | - Sheng-Kwei Song
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Department of Radiology, Washington University in St Louis, St Louis, MO, USA
| | - Kooresh I Shoghi
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Department of Radiology, Washington University in St Louis, St Louis, MO, USA
| | - Ken S Lau
- Department of Cell and Developmental Biology and Epithelial Biology Center, Vanderbilt University School of Medicine, Vanderbilt, TN, USA
| | - Tao Ju
- Department of Computer Science and Engineering, Washington University in St Louis, St Louis, MO, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Deyali Chatterjee
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - William G Hawkins
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Samuel Achilefu
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Department of Radiology, Washington University in St Louis, St Louis, MO, USA
| | - Milan G Chheda
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Stephen T Oh
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St Louis, St Louis, MO, USA
| | - William E Gillanders
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Feng Chen
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - David G DeNardo
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA.
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University in St Louis, St Louis, MO, USA.
| | - Ryan C Fields
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA.
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA.
| | - Li Ding
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA.
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA.
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA.
- Department of Genetics, Washington University in St Louis, St Louis, MO, USA.
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14
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Banes GL, Fountain ED, Karklus A, Fulton RS, Antonacci-Fulton L, Nelson JO. Nine out of ten samples were mistakenly switched by The Orang-utan Genome Consortium. Sci Data 2022; 9:485. [PMID: 35961988 PMCID: PMC9374732 DOI: 10.1038/s41597-022-01602-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 01/12/2021] [Accepted: 06/24/2022] [Indexed: 12/20/2022] Open
Abstract
The Sumatran orang-utan (Pongo abelii) reference genome was first published in 2011, in conjunction with ten re-sequenced genomes from unrelated wild-caught individuals. Together, these published data have been utilized in almost all great ape genomic studies, plus in much broader comparative genomic research. Here, we report that the original sequencing Consortium inadvertently switched nine of the ten samples and/or resulting re-sequenced genomes, erroneously attributing eight of these to the wrong source individuals. Among them is a genome from the recently identified Tapanuli (P. tapanuliensis) species: thus, this genome was sequenced and published a full six years prior to the species’ description. Sex was wrongly assigned to five known individuals; the numbers in one sample identifier were swapped; and the identifier for another sample most closely resembles that of a sample from another individual entirely. These errors have been reproduced in countless subsequent manuscripts, with noted implications for studies reliant on data from known individuals.
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Affiliation(s)
- Graham L Banes
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, 1220 Capitol Court, Madison, WI, 53715, USA. .,School of Veterinary Medicine, University of Wisconsin-Madison, 2015 Linden Drive, Madison, WI, 53706, USA. .,The Orang-utan Conservation Genetics Project, Madison, WI, 53715, USA.
| | - Emily D Fountain
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, 1220 Capitol Court, Madison, WI, 53715, USA.,The Orang-utan Conservation Genetics Project, Madison, WI, 53715, USA
| | - Alyssa Karklus
- School of Veterinary Medicine, University of Wisconsin-Madison, 2015 Linden Drive, Madison, WI, 53706, USA.,The Orang-utan Conservation Genetics Project, Madison, WI, 53715, USA
| | - Robert S Fulton
- McDonnell Genome Institute at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, MO, 63108, USA
| | - Lucinda Antonacci-Fulton
- McDonnell Genome Institute at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, MO, 63108, USA
| | - Joanne O Nelson
- McDonnell Genome Institute at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, MO, 63108, USA
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15
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Menssen AJ, Khanna A, Miller CA, Nonavinkere Srivatsan S, Chang GS, Shao J, Robinson J, O'Laughlin M, Fronick CC, Fulton RS, Brendel K, Heath SE, Saba R, Welch JS, Spencer DH, Payton JE, Westervelt P, DiPersio JF, Link DC, Schuelke MJ, Jacoby MA, Duncavage EJ, Ley TJ, Walter MJ. Convergent Clonal Evolution of Signaling Gene Mutations Is a Hallmark of Myelodysplastic Syndrome Progression. Blood Cancer Discov 2022; 3:330-345. [PMID: 35709710 PMCID: PMC9338759 DOI: 10.1158/2643-3230.bcd-21-0155] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 08/26/2021] [Revised: 02/21/2022] [Accepted: 05/06/2022] [Indexed: 12/17/2022] Open
Abstract
Progression from myelodysplastic syndromes (MDS) to secondary acute myeloid leukemia (AML) is associated with the acquisition and expansion of subclones. Our understanding of subclone evolution during progression, including the frequency and preferred order of gene mutation acquisition, remains incomplete. Sequencing of 43 paired MDS and secondary AML samples identified at least one signaling gene mutation in 44% of MDS and 60% of secondary AML samples, often below the level of standard sequencing detection. In addition, 19% of MDS and 47% of secondary AML patients harbored more than one signaling gene mutation, almost always in separate, coexisting subclones. Signaling gene mutations demonstrated diverse patterns of clonal evolution during disease progression, including acquisition, expansion, persistence, and loss of mutations, with multiple patterns often coexisting in the same patient. Multivariate analysis revealed that MDS patients who had a signaling gene mutation had a higher risk of AML progression, potentially providing a biomarker for progression. SIGNIFICANCE Subclone expansion is a hallmark of progression from MDS to secondary AML. Subclonal signaling gene mutations are common at MDS (often at low levels), show complex and convergent patterns of clonal evolution, and are associated with future progression to secondary AML. See related article by Guess et al., p. 316 (33). See related commentary by Romine and van Galen, p. 270. This article is highlighted in the In This Issue feature, p. 265.
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Affiliation(s)
- Andrew J. Menssen
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Ajay Khanna
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Christopher A. Miller
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Sridhar Nonavinkere Srivatsan
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Gue Su Chang
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Jin Shao
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Joshua Robinson
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Michele O'Laughlin
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Catrina C. Fronick
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Robert S. Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Kimberly Brendel
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Sharon E. Heath
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Raya Saba
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - John S. Welch
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - David H. Spencer
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - Jacqueline E. Payton
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Peter Westervelt
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - John F. DiPersio
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - Daniel C. Link
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - Matthew J. Schuelke
- Division of Biostatistics, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Meagan A. Jacoby
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - Eric J. Duncavage
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Timothy J. Ley
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - Matthew J. Walter
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
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16
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Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Chen NC, Cheng H, Chin CS, Chow W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PG, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, Marschall T, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, Schneider VA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sović I, Storer JM, Streets A, Sullivan BA, Thibaud-Nissen F, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti U, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O’Neill RJ, Timp W, Zook JM, Schatz MC, Eichler EE, Miga KH, Phillippy AM. The complete sequence of a human genome. Science 2022; 376:44-53. [PMID: 35357919 PMCID: PMC9186530 DOI: 10.1126/science.abj6987] [Citation(s) in RCA: 875] [Impact Index Per Article: 437.5] [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] [Indexed: 12/11/2022]
Abstract
Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion-base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.
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Affiliation(s)
- Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | - Mikko Rautiainen
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | - Andrey V. Bzikadze
- Graduate Program in Bioinformatics and Systems Biology, University of California, San Diego; La Jolla, CA, USA
| | - Alla Mikheenko
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University; Saint Petersburg, Russia
| | - Mitchell R. Vollger
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
| | - Nicolas Altemose
- Department of Bioengineering, University of California, Berkeley; Berkeley, CA, USA
| | - Lev Uralsky
- Sirius University of Science and Technology; Sochi, Russia
- Vavilov Institute of General Genetics; Moscow, Russia
| | - Ariel Gershman
- Department of Molecular Biology and Genetics, Johns Hopkins University; Baltimore, MD, USA
| | - Sergey Aganezov
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
| | - Savannah J. Hoyt
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
| | - Glennis A. Logsdon
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
| | - Michael Alonge
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
| | | | | | - Gerard G. Bouffard
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Shelise Y. Brooks
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Gina V. Caldas
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA, USA
| | - Nae-Chyun Chen
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
| | - Haoyu Cheng
- Department of Data Sciences, Dana-Farber Cancer Institute; Boston, MA
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA
| | | | | | | | - Philip C. Dishuck
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
| | - Richard Durbin
- Wellcome Sanger Institute; Cambridge, UK
- Department of Genetics, University of Cambridge; Cambridge, UK
| | - Tatiana Dvorkina
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University; Saint Petersburg, Russia
| | | | - Giulio Formenti
- Laboratory of Neurogenetics of Language and The Vertebrate Genome Lab, The Rockefeller University; New York, NY, USA
- Howard Hughes Medical Institute; Chevy Chase, MD, USA
| | - Robert S. Fulton
- Department of Genetics, Washington University School of Medicine; St. Louis, MO, USA
| | | | - Erik Garrison
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
- University of Tennessee Health Science Center; Memphis, TN, USA
| | - Patrick G.S. Grady
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
| | | | - Ira M. Hall
- Department of Genetics, Yale University School of Medicine; New Haven, CT, USA
| | - Nancy F. Hansen
- Comparative Genomics Analysis Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Gabrielle A. Hartley
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
| | | | | | - Chirag Jain
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
- Department of Computational and Data Sciences, Indian Institute of Science; Bangalore KA, India
| | - Miten Jain
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
| | - Erich D. Jarvis
- Laboratory of Neurogenetics of Language and The Vertebrate Genome Lab, The Rockefeller University; New York, NY, USA
- Howard Hughes Medical Institute; Chevy Chase, MD, USA
| | | | - Melanie Kirsche
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
| | - Mikhail Kolmogorov
- Department of Computer Science and Engineering, University of California, San Diego; San Diego, CA, USA
| | | | - Milinn Kremitzki
- McDonnell Genome Institute, Washington University in St. Louis; St. Louis, MO, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute; Boston, MA
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA
| | - Valerie V. Maduro
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Tobias Marschall
- Heinrich Heine University Düsseldorf, Medical Faculty, Institute for Medical Biometry and Bioinformatics; Düsseldorf, Germany
| | - Ann M. McCartney
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | - Jennifer McDaniel
- Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
| | - Danny E. Miller
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children’s Hospital; Seattle, WA, USA
| | - James C. Mullikin
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
- Comparative Genomics Analysis Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Eugene W. Myers
- Max-Planck Institute of Molecular Cell Biology and Genetics; Dresden, Germany
| | - Nathan D. Olson
- Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
| | | | - Pavel A. Pevzner
- Department of Computer Science and Engineering, University of California, San Diego; San Diego, CA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
| | - Tamara Potapova
- Stowers Institute for Medical Research; Kansas City, MO, USA
| | - Evgeny I. Rogaev
- Sirius University of Science and Technology; Sochi, Russia
- Vavilov Institute of General Genetics; Moscow, Russia
- Department of Psychiatry, University of Massachusetts Medical School; Worcester, MA, USA
- Faculty of Biology, Lomonosov Moscow State University; Moscow, Russia
| | | | - Steven L. Salzberg
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, USA
| | - Valerie A. Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD, USA
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine; Houston TX, USA
| | - Kishwar Shafin
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
| | - Colin J. Shew
- Genome Center, MIND Institute, Department of Biochemistry and Molecular Medicine, University of California, Davis; CA, USA
| | - Alaina Shumate
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, USA
| | - Ying Sims
- Wellcome Sanger Institute; Cambridge, UK
| | | | - Daniela C. Soto
- Genome Center, MIND Institute, Department of Biochemistry and Molecular Medicine, University of California, Davis; CA, USA
| | - Ivan Sović
- Pacific Biosciences; Menlo Park, CA, USA
- Digital BioLogic d.o.o.; Ivanić-Grad, Croatia
| | | | - Aaron Streets
- Department of Bioengineering, University of California, Berkeley; Berkeley, CA, USA
- Chan Zuckerberg Biohub; San Francisco, CA, USA
| | - Beth A. Sullivan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine; Durham, NC, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD, USA
| | | | - Justin Wagner
- Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
| | - Brian P. Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | | | | | - Chunlin Xiao
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD, USA
| | - Stephanie M. Yan
- Department of Biology, Johns Hopkins University; Baltimore, MD, USA
| | - Alice C. Young
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Samantha Zarate
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
| | - Urvashi Surti
- Department of Pathology, University of Pittsburgh; Pittsburgh, PA, USA
| | - Rajiv C. McCoy
- Department of Biology, Johns Hopkins University; Baltimore, MD, USA
| | - Megan Y. Dennis
- Genome Center, MIND Institute, Department of Biochemistry and Molecular Medicine, University of California, Davis; CA, USA
| | - Ivan A. Alexandrov
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University; Saint Petersburg, Russia
- Vavilov Institute of General Genetics; Moscow, Russia
- Research Center of Biotechnology of the Russian Academy of Sciences; Moscow, Russia
| | - Jennifer L. Gerton
- Stowers Institute for Medical Research; Kansas City, MO, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical School; Kansas City, MO, USA
| | - Rachel J. O’Neill
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
| | - Winston Timp
- Department of Molecular Biology and Genetics, Johns Hopkins University; Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, USA
| | - Justin M. Zook
- Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
- Department of Biology, Johns Hopkins University; Baltimore, MD, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
- Howard Hughes Medical Institute; Chevy Chase, MD, USA
| | - Karen H. Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, CA, USA
| | - Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
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17
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Miller CA, Walker JR, Jensen TL, Hooper WF, Fulton RS, Painter JS, Sekeres MA, Ley TJ, Spencer DH, Goll JB, Walter MJ. Failure to Detect Mutations in U2AF1 due to Changes in the GRCh38 Reference Sequence. J Mol Diagn 2022; 24:219-223. [PMID: 35041928 PMCID: PMC8950341 DOI: 10.1016/j.jmoldx.2021.10.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/30/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022] Open
Abstract
The U2AF1 gene is a core part of mRNA splicing machinery and frequently contains somatic mutations that contribute to oncogenesis in myelodysplastic syndrome, acute myeloid leukemia, and other cancers. A change introduced in the GRCh38 version of the human reference build prevents detection of mutations in this gene, and others, by variant calling pipelines. This study describes the problem in detail and shows that a modified GRCh38 reference build with unchanged coordinates can be used to ameliorate the issue.
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Affiliation(s)
- Christopher A. Miller
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri,Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri,Address correspondence to Christopher A. Miller, Ph.D., Division of Oncology, Washington University School of Medicine, 660 S. Euclid Ave, Campus Box 8007, St. Louis, MO 63110.
| | - Jason R. Walker
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | | | | | - Robert S. Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | | | - Mikkael A. Sekeres
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami School of Medicine, Miami, Florida
| | - Timothy J. Ley
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri,Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - David H. Spencer
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri,Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | | | - Matthew J. Walter
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri,Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
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18
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Wilson ER, Helton NM, Heath SE, Fulton RS, Payton JE, Welch JS, Walter MJ, Westervelt P, DiPersio JF, Link DC, Miller CA, Ley TJ, Spencer DH. Focal disruption of DNA methylation dynamics at enhancers in IDH-mutant AML cells. Leukemia 2022; 36:935-945. [PMID: 34873300 PMCID: PMC8979817 DOI: 10.1038/s41375-021-01476-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 11/01/2021] [Accepted: 11/15/2021] [Indexed: 12/17/2022]
Abstract
Recurrent mutations in IDH1 or IDH2 in acute myeloid leukemia (AML) are associated with increased DNA methylation, but the genome-wide patterns of this hypermethylation phenotype have not been comprehensively studied in AML samples. We analyzed whole-genome bisulfite sequencing data from 15 primary AML samples with IDH1 or IDH2 mutations, which identified ~4000 focal regions that were uniquely hypermethylated in IDHmut samples vs. normal CD34+ cells and other AMLs. These regions had modest hypermethylation in AMLs with biallelic TET2 mutations, and levels of 5-hydroxymethylation that were diminished in IDH and TET-mutant samples, indicating that this hypermethylation results from inhibition of TET-mediated demethylation. Focal hypermethylation in IDHmut AMLs occurred at regions with low methylation in CD34+ cells, implying that DNA methylation and demethylation are active at these loci. AML samples containing IDH and DNMT3AR882 mutations were significantly less hypermethylated, suggesting that IDHmut-associated hypermethylation is mediated by DNMT3A. IDHmut-specific hypermethylation was highly enriched for enhancers that form direct interactions with genes involved in normal hematopoiesis and AML, including MYC and ETV6. These results suggest that focal hypermethylation in IDH-mutant AML occurs by altering the balance between DNA methylation and demethylation, and that disruption of these pathways at enhancers may contribute to AML pathogenesis.
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Affiliation(s)
- Elisabeth R. Wilson
- grid.4367.60000 0001 2355 7002Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St. Louis, MO USA
| | - Nichole M. Helton
- grid.4367.60000 0001 2355 7002Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St. Louis, MO USA
| | - Sharon E. Heath
- grid.4367.60000 0001 2355 7002Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St. Louis, MO USA
| | - Robert S. Fulton
- grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University, St. Louis, MO USA
| | - Jacqueline E. Payton
- grid.4367.60000 0001 2355 7002Department of Pathology and Immunology, Washington University, St. Louis, MO USA
| | - John S. Welch
- grid.4367.60000 0001 2355 7002Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St. Louis, MO USA
| | - Matthew J. Walter
- grid.4367.60000 0001 2355 7002Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St. Louis, MO USA
| | - Peter Westervelt
- grid.4367.60000 0001 2355 7002Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St. Louis, MO USA
| | - John F. DiPersio
- grid.4367.60000 0001 2355 7002Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St. Louis, MO USA
| | - Daniel C. Link
- grid.4367.60000 0001 2355 7002Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St. Louis, MO USA
| | - Christopher A. Miller
- grid.4367.60000 0001 2355 7002Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University, St. Louis, MO USA
| | - Timothy J. Ley
- grid.4367.60000 0001 2355 7002Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St. Louis, MO USA
| | - David H. Spencer
- grid.4367.60000 0001 2355 7002Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Department of Pathology and Immunology, Washington University, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University, St. Louis, MO USA
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19
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Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Della Valle G, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AFA, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordoñez GR, López-Otín C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, RoyChoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, de Jong PJ, Weinstock GM, Rogers J, Mardis ER, Gibbs RA, Wilson RK. Author Correction: Comparative and demographic analysis of orang-utan genomes. Nature 2022; 608:E36. [PMID: 35962045 PMCID: PMC9402433 DOI: 10.1038/s41586-022-04799-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Devin P. Locke
- grid.4367.60000 0001 2355 7002The Genome Center at Washington University, Washington University School of Medicine, Saint Louis, Missouri USA
| | - LaDeana W. Hillier
- grid.4367.60000 0001 2355 7002The Genome Center at Washington University, Washington University School of Medicine, Saint Louis, Missouri USA
| | - Wesley C. Warren
- grid.4367.60000 0001 2355 7002The Genome Center at Washington University, Washington University School of Medicine, Saint Louis, Missouri USA
| | - Kim C. Worley
- grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas USA
| | - Lynne V. Nazareth
- grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas USA
| | - Donna M. Muzny
- grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas USA
| | - Shiaw-Pyng Yang
- grid.4367.60000 0001 2355 7002The Genome Center at Washington University, Washington University School of Medicine, Saint Louis, Missouri USA
| | - Zhengyuan Wang
- grid.4367.60000 0001 2355 7002The Genome Center at Washington University, Washington University School of Medicine, Saint Louis, Missouri USA
| | - Asif T. Chinwalla
- grid.4367.60000 0001 2355 7002The Genome Center at Washington University, Washington University School of Medicine, Saint Louis, Missouri USA
| | - Pat Minx
- grid.4367.60000 0001 2355 7002The Genome Center at Washington University, Washington University School of Medicine, Saint Louis, Missouri USA
| | - Makedonka Mitreva
- grid.4367.60000 0001 2355 7002The Genome Center at Washington University, Washington University School of Medicine, Saint Louis, Missouri USA
| | - Lisa Cook
- grid.4367.60000 0001 2355 7002The Genome Center at Washington University, Washington University School of Medicine, Saint Louis, Missouri USA
| | - Kim D. Delehaunty
- grid.4367.60000 0001 2355 7002The Genome Center at Washington University, Washington University School of Medicine, Saint Louis, Missouri USA
| | - Catrina Fronick
- grid.4367.60000 0001 2355 7002The Genome Center at Washington University, Washington University School of Medicine, Saint Louis, Missouri USA
| | - Heather Schmidt
- grid.4367.60000 0001 2355 7002The Genome Center at Washington University, Washington University School of Medicine, Saint Louis, Missouri USA
| | - Lucinda A. Fulton
- grid.4367.60000 0001 2355 7002The Genome Center at Washington University, Washington University School of Medicine, Saint Louis, Missouri USA
| | - Robert S. Fulton
- grid.4367.60000 0001 2355 7002The Genome Center at Washington University, Washington University School of Medicine, Saint Louis, Missouri USA
| | - Joanne O. Nelson
- grid.4367.60000 0001 2355 7002The Genome Center at Washington University, Washington University School of Medicine, Saint Louis, Missouri USA
| | - Vincent Magrini
- grid.4367.60000 0001 2355 7002The Genome Center at Washington University, Washington University School of Medicine, Saint Louis, Missouri USA
| | - Craig Pohl
- grid.4367.60000 0001 2355 7002The Genome Center at Washington University, Washington University School of Medicine, Saint Louis, Missouri USA
| | - Tina A. Graves
- grid.4367.60000 0001 2355 7002The Genome Center at Washington University, Washington University School of Medicine, Saint Louis, Missouri USA
| | - Chris Markovic
- grid.4367.60000 0001 2355 7002The Genome Center at Washington University, Washington University School of Medicine, Saint Louis, Missouri USA
| | - Andy Cree
- grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas USA
| | - Huyen H. Dinh
- grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas USA
| | - Jennifer Hume
- grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas USA
| | - Christie L. Kovar
- grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas USA
| | - Gerald R. Fowler
- grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas USA
| | - Gerton Lunter
- grid.4991.50000 0004 1936 8948MRC Functional Genomics Unit and Department of Physiology, Anatomy and Genetics, University of Oxford, Le Gros Clark Building, Oxford, UK ,grid.270683.80000 0004 0641 4511Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Stephen Meader
- grid.4991.50000 0004 1936 8948MRC Functional Genomics Unit and Department of Physiology, Anatomy and Genetics, University of Oxford, Le Gros Clark Building, Oxford, UK
| | - Andreas Heger
- grid.4991.50000 0004 1936 8948MRC Functional Genomics Unit and Department of Physiology, Anatomy and Genetics, University of Oxford, Le Gros Clark Building, Oxford, UK
| | - Chris P. Ponting
- grid.4991.50000 0004 1936 8948MRC Functional Genomics Unit and Department of Physiology, Anatomy and Genetics, University of Oxford, Le Gros Clark Building, Oxford, UK
| | - Tomas Marques-Bonet
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington USA ,grid.5612.00000 0001 2172 2676IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, Barcelona, Spain
| | - Can Alkan
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington USA
| | - Lin Chen
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington USA
| | - Ze Cheng
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington USA
| | - Jeffrey M. Kidd
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington USA
| | - Evan E. Eichler
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington USA ,grid.413575.10000 0001 2167 1581Howard Hughes Medical Institute, Seattle, Washington USA
| | - Simon White
- grid.10306.340000 0004 0606 5382Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Stephen Searle
- grid.10306.340000 0004 0606 5382Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Albert J. Vilella
- grid.52788.300000 0004 0427 7672European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge UK
| | - Yuan Chen
- grid.52788.300000 0004 0427 7672European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge UK
| | - Paul Flicek
- grid.52788.300000 0004 0427 7672European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge UK
| | - Jian Ma
- grid.205975.c0000 0001 0740 6917Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California USA ,grid.35403.310000 0004 1936 9991Present Address: Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois USA
| | - Brian Raney
- grid.205975.c0000 0001 0740 6917Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California USA
| | - Bernard Suh
- grid.205975.c0000 0001 0740 6917Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California USA
| | - Richard Burhans
- grid.29857.310000 0001 2097 4281Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania, USA
| | - Javier Herrero
- grid.52788.300000 0004 0427 7672European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge UK
| | - David Haussler
- grid.205975.c0000 0001 0740 6917Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California USA
| | - Rui Faria
- grid.5612.00000 0001 2172 2676IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, Barcelona, Spain ,grid.5808.50000 0001 1503 7226CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Olga Fernando
- grid.5612.00000 0001 2172 2676IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, Barcelona, Spain ,grid.10772.330000000121511713Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Fleur Darré
- grid.5612.00000 0001 2172 2676IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, Barcelona, Spain
| | - Domènec Farré
- grid.5612.00000 0001 2172 2676IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, Barcelona, Spain
| | - Elodie Gazave
- grid.5612.00000 0001 2172 2676IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, Barcelona, Spain
| | - Meritxell Oliva
- grid.5612.00000 0001 2172 2676IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, Barcelona, Spain
| | - Arcadi Navarro
- grid.5612.00000 0001 2172 2676IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, Barcelona, Spain ,grid.425902.80000 0000 9601 989XICREA (Institució Catalana de Recerca i Estudis Avançats) and INB (Instituto Nacional de Bioinformática) PRBB, Doctor Aiguader, 88, Barcelona, Spain
| | - Roberta Roberto
- grid.7644.10000 0001 0120 3326Department of Biology, University of Bari, Bari, Italy
| | - Oronzo Capozzi
- grid.7644.10000 0001 0120 3326Department of Biology, University of Bari, Bari, Italy
| | | | - Giuliano Della Valle
- grid.6292.f0000 0004 1757 1758Department of Biology, University of Bologna, Bologna, Italy
| | - Stefania Purgato
- grid.6292.f0000 0004 1757 1758Department of Biology, University of Bologna, Bologna, Italy
| | - Mariano Rocchi
- grid.7644.10000 0001 0120 3326Department of Biology, University of Bari, Bari, Italy
| | - Miriam K. Konkel
- grid.64337.350000 0001 0662 7451Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana USA
| | - Jerilyn A. Walker
- grid.64337.350000 0001 0662 7451Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana USA
| | - Brygg Ullmer
- grid.64337.350000 0001 0662 7451Center for Computation and Technology, Department of Computer Sciences, Louisiana State University, Baton Rouge, Louisiana USA
| | - Mark A. Batzer
- grid.64337.350000 0001 0662 7451Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana USA
| | - Arian F. A. Smit
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, Seattle, Washington USA
| | - Robert Hubley
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, Seattle, Washington USA
| | - Claudio Casola
- grid.411377.70000 0001 0790 959XDepartment of Biology and School of Informatics and Computing, Indiana University, Bloomington, Indiana USA
| | - Daniel R. Schrider
- grid.411377.70000 0001 0790 959XDepartment of Biology and School of Informatics and Computing, Indiana University, Bloomington, Indiana USA
| | - Matthew W. Hahn
- grid.411377.70000 0001 0790 959XDepartment of Biology and School of Informatics and Computing, Indiana University, Bloomington, Indiana USA
| | - Victor Quesada
- grid.10863.3c0000 0001 2164 6351Instituto Universitario de Oncologia, Departamento de Bioquimica y Biologia Molecular, Universidad de Oviedo, Oviedo, Spain
| | - Xose S. Puente
- grid.10863.3c0000 0001 2164 6351Instituto Universitario de Oncologia, Departamento de Bioquimica y Biologia Molecular, Universidad de Oviedo, Oviedo, Spain
| | - Gonzalo R. Ordoñez
- grid.10863.3c0000 0001 2164 6351Instituto Universitario de Oncologia, Departamento de Bioquimica y Biologia Molecular, Universidad de Oviedo, Oviedo, Spain
| | - Carlos López-Otín
- grid.10863.3c0000 0001 2164 6351Instituto Universitario de Oncologia, Departamento de Bioquimica y Biologia Molecular, Universidad de Oviedo, Oviedo, Spain
| | - Tomas Vinar
- grid.7634.60000000109409708Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynska Dolina, Bratislava, Slovakia
| | - Brona Brejova
- grid.7634.60000000109409708Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynska Dolina, Bratislava, Slovakia
| | - Aakrosh Ratan
- grid.29857.310000 0001 2097 4281Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania, USA
| | - Robert S. Harris
- grid.29857.310000 0001 2097 4281Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania, USA
| | - Webb Miller
- grid.29857.310000 0001 2097 4281Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania, USA
| | - Carolin Kosiol
- Institut für Populations genetik, Vetmeduni Vienna, Wien, Austria
| | - Heather A. Lawson
- grid.4367.60000 0001 2355 7002Department of Anatomy and Neurobiology, Washington University School of Medicine, Saint Louis, Missouri USA
| | - Vikas Taliwal
- grid.5386.8000000041936877XDepartment of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York USA
| | - André L. Martins
- grid.5386.8000000041936877XDepartment of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York USA
| | - Adam Siepel
- grid.5386.8000000041936877XDepartment of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York USA
| | - Arindam RoyChoudhury
- grid.21729.3f0000000419368729Department of Biostatistics, Columbia University, New York, New York USA
| | - Xin Ma
- grid.5386.8000000041936877XDepartment of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York USA
| | - Jeremiah Degenhardt
- grid.5386.8000000041936877XDepartment of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York USA
| | - Carlos D. Bustamante
- grid.168010.e0000000419368956Department of Genetics, Stanford University, Stanford, California USA
| | - Ryan N. Gutenkunst
- grid.134563.60000 0001 2168 186XDepartment of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona USA
| | - Thomas Mailund
- grid.7048.b0000 0001 1956 2722Bioinformatics Research Centre, Aarhus University, Aarhus C, Denmark
| | - Julien Y. Dutheil
- grid.7048.b0000 0001 1956 2722Bioinformatics Research Centre, Aarhus University, Aarhus C, Denmark
| | - Asger Hobolth
- grid.7048.b0000 0001 1956 2722Bioinformatics Research Centre, Aarhus University, Aarhus C, Denmark
| | - Mikkel H. Schierup
- grid.7048.b0000 0001 1956 2722Bioinformatics Research Centre, Aarhus University, Aarhus C, Denmark
| | - Oliver A. Ryder
- grid.452788.40000 0004 0458 5309San Diego Zoo’s Institute for Conservation Research, Escondido, California USA
| | - Yuko Yoshinaga
- grid.414016.60000 0004 0433 7727Children’s Hospital Oakland Research Institute, Oakland, California USA
| | - Pieter J. de Jong
- grid.414016.60000 0004 0433 7727Children’s Hospital Oakland Research Institute, Oakland, California USA
| | - George M. Weinstock
- grid.4367.60000 0001 2355 7002The Genome Center at Washington University, Washington University School of Medicine, Saint Louis, Missouri USA
| | - Jeffrey Rogers
- grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas USA
| | - Elaine R. Mardis
- grid.4367.60000 0001 2355 7002The Genome Center at Washington University, Washington University School of Medicine, Saint Louis, Missouri USA
| | - Richard A. Gibbs
- grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas USA
| | - Richard K. Wilson
- grid.4367.60000 0001 2355 7002The Genome Center at Washington University, Washington University School of Medicine, Saint Louis, Missouri USA
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Duncavage EJ, Schroeder MC, O'Laughlin M, Wilson R, MacMillan S, Bohannon A, Kruchowski S, Garza J, Du F, Hughes AEO, Robinson J, Hughes E, Heath SE, Baty JD, Neidich J, Christopher MJ, Jacoby MA, Uy GL, Fulton RS, Miller CA, Payton JE, Link DC, Walter MJ, Westervelt P, DiPersio JF, Ley TJ, Spencer DH. Genome Sequencing as an Alternative to Cytogenetic Analysis in Myeloid Cancers. N Engl J Med 2021; 384:924-935. [PMID: 33704937 PMCID: PMC8130455 DOI: 10.1056/nejmoa2024534] [Citation(s) in RCA: 139] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Genomic analysis is essential for risk stratification in patients with acute myeloid leukemia (AML) or myelodysplastic syndromes (MDS). Whole-genome sequencing is a potential replacement for conventional cytogenetic and sequencing approaches, but its accuracy, feasibility, and clinical utility have not been demonstrated. METHODS We used a streamlined whole-genome sequencing approach to obtain genomic profiles for 263 patients with myeloid cancers, including 235 patients who had undergone successful cytogenetic analysis. We adapted sample preparation, sequencing, and analysis to detect mutations for risk stratification using existing European Leukemia Network (ELN) guidelines and to minimize turnaround time. We analyzed the performance of whole-genome sequencing by comparing our results with findings from cytogenetic analysis and targeted sequencing. RESULTS Whole-genome sequencing detected all 40 recurrent translocations and 91 copy-number alterations that had been identified by cytogenetic analysis. In addition, we identified new clinically reportable genomic events in 40 of 235 patients (17.0%). Prospective sequencing of samples obtained from 117 consecutive patients was performed in a median of 5 days and provided new genetic information in 29 patients (24.8%), which changed the risk category for 19 patients (16.2%). Standard AML risk groups, as defined by sequencing results instead of cytogenetic analysis, correlated with clinical outcomes. Whole-genome sequencing was also used to stratify patients who had inconclusive results by cytogenetic analysis into risk groups in which clinical outcomes were measurably different. CONCLUSIONS In our study, we found that whole-genome sequencing provided rapid and accurate genomic profiling in patients with AML or MDS. Such sequencing also provided a greater diagnostic yield than conventional cytogenetic analysis and more efficient risk stratification on the basis of standard risk categories. (Funded by the Siteman Cancer Research Fund and others.).
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Affiliation(s)
- Eric J Duncavage
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - Molly C Schroeder
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - Michele O'Laughlin
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - Roxanne Wilson
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - Sandra MacMillan
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - Andrew Bohannon
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - Scott Kruchowski
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - John Garza
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - Feiyu Du
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - Andrew E O Hughes
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - Josh Robinson
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - Emma Hughes
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - Sharon E Heath
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - Jack D Baty
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - Julie Neidich
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - Matthew J Christopher
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - Meagan A Jacoby
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - Geoffrey L Uy
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - Robert S Fulton
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - Christopher A Miller
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - Jacqueline E Payton
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - Daniel C Link
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - Matthew J Walter
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - Peter Westervelt
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - John F DiPersio
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - Timothy J Ley
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
| | - David H Spencer
- From the Department of Pathology and Immunology (E.J.D., M.C.S., A.E.O.H., J.N., J.E.P., D.H.S.), McDonnell Genome Institute (M.O., R.W., S.M., A.B., S.K., J.G., F.D., R.S.F., D.H.S.), and the Divisions of Oncology (J.R., E.H., S.E.H., M.J.C., M.A.J., G.L.U., C.A.M., D.C.L., M.J.W., P.W., J.F.D., T.J.L., D.H.S.) and Biostatistics (J.D.B.), Department of Medicine, Washington University School of Medicine, St. Louis
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21
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Lalli MA, Langmade JS, Chen X, Fronick CC, Sawyer CS, Burcea LC, Wilkinson MN, Fulton RS, Heinz M, Buchser WJ, Head RD, Mitra RD, Milbrandt J. Rapid and Extraction-Free Detection of SARS-CoV-2 from Saliva by Colorimetric Reverse-Transcription Loop-Mediated Isothermal Amplification. Clin Chem 2021; 67:415-424. [PMID: 33098427 PMCID: PMC7665435 DOI: 10.1093/clinchem/hvaa267] [Citation(s) in RCA: 164] [Impact Index Per Article: 54.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/08/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Rapid, reliable, and widespread testing is required to curtail the ongoing COVID-19 pandemic. Current gold-standard nucleic acid tests are hampered by supply shortages in critical reagents including nasal swabs, RNA extraction kits, personal protective equipment, instrumentation, and labor. METHODS To overcome these challenges, we developed a rapid colorimetric assay using reverse-transcription loop-mediated isothermal amplification (RT-LAMP) optimized on human saliva samples without an RNA purification step. We describe the optimization of saliva pretreatment protocols to enable analytically sensitive viral detection by RT-LAMP. We optimized the RT-LAMP reaction conditions and implemented high-throughput unbiased methods for assay interpretation. We tested whether saliva pretreatment could also enable viral detection by conventional reverse-transcription quantitative polymerase chain reaction (RT-qPCR). Finally, we validated these assays on clinical samples. RESULTS The optimized saliva pretreatment protocol enabled analytically sensitive extraction-free detection of SARS-CoV-2 from saliva by colorimetric RT-LAMP or RT-qPCR. In simulated samples, the optimized RT-LAMP assay had a limit of detection of 59 (95% confidence interval: 44-104) particle copies per reaction. We highlighted the flexibility of LAMP assay implementation using 3 readouts: naked-eye colorimetry, spectrophotometry, and real-time fluorescence. In a set of 30 clinical saliva samples, colorimetric RT-LAMP and RT-qPCR assays performed directly on pretreated saliva samples without RNA extraction had accuracies greater than 90%. CONCLUSIONS Rapid and extraction-free detection of SARS-CoV-2 from saliva by colorimetric RT-LAMP is a simple, sensitive, and cost-effective approach with broad potential to expand diagnostic testing for the virus causing COVID-19.
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Affiliation(s)
- Matthew A Lalli
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Joshua S Langmade
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Xuhua Chen
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Catrina C Fronick
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Christopher S Sawyer
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Lauren C Burcea
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Michael N Wilkinson
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Robert S Fulton
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Michael Heinz
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - William J Buchser
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Richard D Head
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Robi D Mitra
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Jeffrey Milbrandt
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
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22
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Lalli MA, Langmade SJ, Chen X, Fronick CC, Sawyer CS, Burcea LC, Wilkinson MN, Fulton RS, Heinz M, Buchser WJ, Head RD, Mitra RD, Milbrandt J. Rapid and extraction-free detection of SARS-CoV-2 from saliva with colorimetric LAMP. medRxiv 2020. [PMID: 32511508 DOI: 10.1101/2020.05.07.20093542] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Rapid, reliable, and widespread testing is required to curtail the ongoing COVID-19 pandemic. Current gold standard nucleic acid tests are hampered by supply shortages in critical reagents including nasal swabs, RNA extraction kits, personal protective equipment (PPE), instrumentation, and labor. Here we present an approach to overcome these challenges with the development of a rapid colorimetric assay using reverse-transcription loop-mediated isothermal amplification (RT-LAMP) optimized on human saliva samples without an RNA purification step. We describe our optimizations of the LAMP reaction and saliva pretreatment protocols that enabled rapid and sensitive detection of < 102 viral genomes per reaction in contrived saliva controls. Moreover, our saliva pretreatment protocol enabled sensitive viral detection by conventional quantitative reverse transcription polymerase chain reaction (qRT-PCR) without RNA extraction. We validated the high performance of these assays on clinical samples and demonstrate a promising approach to overcome the current bottlenecks limiting widespread testing.
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23
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Dang HX, Krasnick BA, White BS, Grossman JG, Strand MS, Zhang J, Cabanski CR, Miller CA, Fulton RS, Goedegebuure SP, Fronick CC, Griffith M, Larson DE, Goetz BD, Walker JR, Hawkins WG, Strasberg SM, Linehan DC, Lim KH, Lockhart AC, Mardis ER, Wilson RK, Ley TJ, Maher CA, Fields RC. The clonal evolution of metastatic colorectal cancer. Sci Adv 2020; 6:eaay9691. [PMID: 32577507 PMCID: PMC7286679 DOI: 10.1126/sciadv.aay9691] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 04/10/2020] [Indexed: 06/11/2023]
Abstract
Tumor heterogeneity and evolution drive treatment resistance in metastatic colorectal cancer (mCRC). Patient-derived xenografts (PDXs) can model mCRC biology; however, their ability to accurately mimic human tumor heterogeneity is unclear. Current genomic studies in mCRC have limited scope and lack matched PDXs. Therefore, the landscape of tumor heterogeneity and its impact on the evolution of metastasis and PDXs remain undefined. We performed whole-genome, deep exome, and targeted validation sequencing of multiple primary regions, matched distant metastases, and PDXs from 11 patients with mCRC. We observed intricate clonal heterogeneity and evolution affecting metastasis dissemination and PDX clonal selection. Metastasis formation followed both monoclonal and polyclonal seeding models. In four cases, metastasis-seeding clones were not identified in any primary region, consistent with a metastasis-seeding-metastasis model. PDXs underrepresented the subclonal heterogeneity of parental tumors. These suggest that single sample tumor sequencing and current PDX models may be insufficient to guide precision medicine.
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Affiliation(s)
- Ha X. Dang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
- The Alvin J. Siteman Comprehensive Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Bradley A. Krasnick
- The Alvin J. Siteman Comprehensive Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Surgery, Washington University in St. Louis, St. Louis, MO, USA
- Barnes-Jewish Hospital, St. Louis, MO, USA
| | | | - Julie G. Grossman
- The Alvin J. Siteman Comprehensive Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Surgery, Washington University in St. Louis, St. Louis, MO, USA
- Barnes-Jewish Hospital, St. Louis, MO, USA
| | - Matthew S. Strand
- The Alvin J. Siteman Comprehensive Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Surgery, Washington University in St. Louis, St. Louis, MO, USA
- Barnes-Jewish Hospital, St. Louis, MO, USA
| | - Jin Zhang
- Department of Radiation Oncology, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Christopher A. Miller
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Robert S. Fulton
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - S. Peter Goedegebuure
- The Alvin J. Siteman Comprehensive Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Surgery, Washington University in St. Louis, St. Louis, MO, USA
- Barnes-Jewish Hospital, St. Louis, MO, USA
| | - Catrina C. Fronick
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Malachi Griffith
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | - David E. Larson
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Brian D. Goetz
- The Alvin J. Siteman Comprehensive Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Jason R. Walker
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - William G. Hawkins
- The Alvin J. Siteman Comprehensive Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Surgery, Washington University in St. Louis, St. Louis, MO, USA
- Barnes-Jewish Hospital, St. Louis, MO, USA
| | - Steven M. Strasberg
- The Alvin J. Siteman Comprehensive Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Surgery, Washington University in St. Louis, St. Louis, MO, USA
- Barnes-Jewish Hospital, St. Louis, MO, USA
| | - David C. Linehan
- Department of Surgery and The Wilmot Cancer Institute, University of Rochester School of Medicine, Rochester, NY, USA
| | - Kian H. Lim
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - A. Craig Lockhart
- Division of Medical Oncology, Department of Medicine, The Sylvester Comprehensive Cancer Center, University of Miami School of Medicine, Miami, FL, USA
| | - Elaine R. Mardis
- Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Richard K. Wilson
- Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Timothy J. Ley
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
- The Alvin J. Siteman Comprehensive Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Christopher A. Maher
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
- The Alvin J. Siteman Comprehensive Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Ryan C. Fields
- The Alvin J. Siteman Comprehensive Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Surgery, Washington University in St. Louis, St. Louis, MO, USA
- Barnes-Jewish Hospital, St. Louis, MO, USA
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Aaltonen LA, Abascal F, Abeshouse A, Aburatani H, Adams DJ, Agrawal N, Ahn KS, Ahn SM, Aikata H, Akbani R, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, von Mering C. Pan-cancer analysis of whole genomes. Nature 2020; 578:82-93. [PMID: 32025007 PMCID: PMC7025898 DOI: 10.1038/s41586-020-1969-6] [Citation(s) in RCA: 1435] [Impact Index Per Article: 358.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.
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Locke AE, Steinberg KM, Chiang CWK, Service SK, Havulinna AS, Stell L, Pirinen M, Abel HJ, Chiang CC, Fulton RS, Jackson AU, Kang CJ, Kanchi KL, Koboldt DC, Larson DE, Nelson J, Nicholas TJ, Pietilä A, Ramensky V, Ray D, Scott LJ, Stringham HM, Vangipurapu J, Welch R, Yajnik P, Yin X, Eriksson JG, Ala-Korpela M, Järvelin MR, Männikkö M, Laivuori H, Dutcher SK, Stitziel NO, Wilson RK, Hall IM, Sabatti C, Palotie A, Salomaa V, Laakso M, Ripatti S, Boehnke M, Freimer NB. Author Correction: Exome sequencing of Finnish isolates enhances rare-variant association power. Nature 2019; 575:E4. [PMID: 31686056 DOI: 10.1038/s41586-019-1726-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An Amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Adam E Locke
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.,McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA.,Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Karyn Meltz Steinberg
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA.,Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - Charleston W K Chiang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.,Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.,Quantitative and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Susan K Service
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Aki S Havulinna
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,National Institute for Health and Welfare, Helsinki, Finland
| | - Laurel Stell
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Department of Public Health, University of Helsinki, Helsinki, Finland.,Helsinki Institute for Information Technology HIIT and Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Haley J Abel
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA.,Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Colby C Chiang
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Robert S Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA.,Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Anne U Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Chul Joo Kang
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Krishna L Kanchi
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel C Koboldt
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA.,The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - David E Larson
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA.,Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Joanne Nelson
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Thomas J Nicholas
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA.,USTAR Center for Genetic Discovery and Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Arto Pietilä
- National Institute for Health and Welfare, Helsinki, Finland
| | - Vasily Ramensky
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.,Federal State Institution "National Medical Research Center for Preventive Medicine" of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Debashree Ray
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Departments of Epidemiology and Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Laura J Scott
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Heather M Stringham
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jagadish Vangipurapu
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Ryan Welch
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Pranav Yajnik
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Xianyong Yin
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Johan G Eriksson
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland.,Department of General Practice and Primary Health Care, University of Helsinki, Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Mika Ala-Korpela
- Systems Epidemiology, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.,Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, University of Oulu, Oulu, Finland.,NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland.,Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK.,Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol, UK.,Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Faculty of Medicine, Nursing and Health Sciences, The Alfred Hospital, Monash University, Melbourne, Victoria, Australia
| | - Marjo-Riitta Järvelin
- Biocenter Oulu, University of Oulu, Oulu, Finland.,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Unit of Primary Health Care, Oulu University Hospital, Oulu, Finland.,Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK.,Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK
| | - Minna Männikkö
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Northern Finland Birth Cohorts, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Hannele Laivuori
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Department of Obstetrics and Gynecology, Tampere University Hospital and University of Tampere, Faculty of Medicine and Health Technology, Tampere, Finland
| | | | - Susan K Dutcher
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA.,Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Nathan O Stitziel
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA.,Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA.,The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Ira M Hall
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.,McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Chiara Sabatti
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.,Department of Statistics, Stanford University, Stanford, CA, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Analytical and Translational Genetics Unit (ATGU), Psychiatric & Neurodevelopmental Genetics Unit, Departments of Psychiatry and Neurology, Massachusetts General Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, Finland
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland.,Department of Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Department of Public Health, University of Helsinki, Helsinki, Finland.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA.
| | - Nelson B Freimer
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.
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Locke AE, Steinberg KM, Chiang CWK, Service SK, Havulinna AS, Stell L, Pirinen M, Abel HJ, Chiang CC, Fulton RS, Jackson AU, Kang CJ, Kanchi KL, Koboldt DC, Larson DE, Nelson J, Nicholas TJ, Pietilä A, Ramensky V, Ray D, Scott LJ, Stringham HM, Vangipurapu J, Welch R, Yajnik P, Yin X, Eriksson JG, Ala-Korpela M, Järvelin MR, Männikkö M, Laivuori H, Dutcher SK, Stitziel NO, Wilson RK, Hall IM, Sabatti C, Palotie A, Salomaa V, Laakso M, Ripatti S, Boehnke M, Freimer NB. Exome sequencing of Finnish isolates enhances rare-variant association power. Nature 2019; 572:323-328. [PMID: 31367044 PMCID: PMC6697530 DOI: 10.1038/s41586-019-1457-z] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [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: 11/05/2018] [Accepted: 07/02/2019] [Indexed: 12/30/2022]
Abstract
Exome-sequencing studies have generally been underpowered to identify deleterious alleles with a large effect on complex traits as such alleles are mostly rare. Because the population of northern and eastern Finland has expanded considerably and in isolation following a series of bottlenecks, individuals of these populations have numerous deleterious alleles at a relatively high frequency. Here, using exome sequencing of nearly 20,000 individuals from these regions, we investigate the role of rare coding variants in clinically relevant quantitative cardiometabolic traits. Exome-wide association studies for 64 quantitative traits identified 26 newly associated deleterious alleles. Of these 26 alleles, 19 are either unique to or more than 20 times more frequent in Finnish individuals than in other Europeans and show geographical clustering comparable to Mendelian disease mutations that are characteristic of the Finnish population. We estimate that sequencing studies of populations without this unique history would require hundreds of thousands to millions of participants to achieve comparable association power.
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Affiliation(s)
- Adam E Locke
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Karyn Meltz Steinberg
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - Charleston W K Chiang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Quantitative and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Susan K Service
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Aki S Havulinna
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Helsinki, Finland
| | - Laurel Stell
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Helsinki Institute for Information Technology HIIT and Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Haley J Abel
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Colby C Chiang
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Robert S Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Anne U Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Chul Joo Kang
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Krishna L Kanchi
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel C Koboldt
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - David E Larson
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Joanne Nelson
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Thomas J Nicholas
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- USTAR Center for Genetic Discovery and Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Arto Pietilä
- National Institute for Health and Welfare, Helsinki, Finland
| | - Vasily Ramensky
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
- Federal State Institution "National Medical Research Center for Preventive Medicine" of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Debashree Ray
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Departments of Epidemiology and Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Laura J Scott
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Heather M Stringham
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jagadish Vangipurapu
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Ryan Welch
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Pranav Yajnik
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Xianyong Yin
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Johan G Eriksson
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Department of General Practice and Primary Health Care, University of Helsinki, Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Mika Ala-Korpela
- Systems Epidemiology, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, University of Oulu, Oulu, Finland
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Faculty of Medicine, Nursing and Health Sciences, The Alfred Hospital, Monash University, Melbourne, Victoria, Australia
| | - Marjo-Riitta Järvelin
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Unit of Primary Health Care, Oulu University Hospital, Oulu, Finland
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK
| | - Minna Männikkö
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Northern Finland Birth Cohorts, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Hannele Laivuori
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Obstetrics and Gynecology, Tampere University Hospital and University of Tampere, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Susan K Dutcher
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Nathan O Stitziel
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Ira M Hall
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Chiara Sabatti
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Analytical and Translational Genetics Unit (ATGU), Psychiatric & Neurodevelopmental Genetics Unit, Departments of Psychiatry and Neurology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, Finland
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA.
| | - Nelson B Freimer
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.
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27
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Robinson KM, Yang W, Karol SE, Kornegay N, Jay D, Cheng C, Choi JK, Campana D, Pui CH, Wood B, Borowitz MJ, Gastier-Foster J, Larsen EC, Winick N, Carroll WL, Loh ML, Raetz EA, Hunger SP, Devidas M, Mardis ER, Fulton RS, Relling MV, Jeha S. No evidence that G6PD deficiency affects the efficacy or safety of daunorubicin in acute lymphoblastic leukemia induction therapy. Pediatr Blood Cancer 2019; 66:e27681. [PMID: 30848065 PMCID: PMC6518412 DOI: 10.1002/pbc.27681] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/07/2019] [Accepted: 02/11/2019] [Indexed: 02/02/2023]
Abstract
BACKGROUND/OBJECTIVES Anthracyclines are used in induction therapy of pediatric acute lymphoblastic leukemia (ALL) and are known to generate oxidative stress; whether this translates into enhanced antileukemic activity or hemolytic effects in patients with glucose-6-phosphate dehydrogenase (G6PD) deficiency is unknown. DESIGN/METHODS Among 726 pediatric patients with newly diagnosed ALL treated at St. Jude Children's Research Hospital, 22 had deficient G6PD activity. We compared the prevalence of positive minimal residual disease (MRD) ≥1% at Day 15/Day 19 of induction or ≥0.01% at Day 42/Day 46 (end of induction) and the number of red blood cell (RBC) transfusions after daunorubicin in induction between patients with or without G6PD deficiency, adjusting for ALL risk group, treatment protocol, age, and gender. RESULTS There was no difference in Day 15/19 (P = 1) or end of induction MRD (P = 0.76) nor in the number of RBC transfusions (P = 0.73); the lack of association with MRD was confirmed in a dataset of 1192 newly diagnosed male patients enrolled in a Children's Oncology Group trial (P = 0.78). CONCLUSION We found no evidence that G6PD deficiency affects daunorubicin activity during induction treatment for ALL.
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Affiliation(s)
- Katherine M. Robinson
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN
| | - Seth E. Karol
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Nancy Kornegay
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN
| | - Dennis Jay
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN
| | - John K. Choi
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Dario Campana
- Department of Paediatrics, National University of Singapore, Singapore
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Brent Wood
- Department of Laboratory Medicine, Seattle Children’s Hospital, Seattle, WA
| | - Michael J. Borowitz
- Department of Hematologic Pathology, John’s Hopkins University, Baltimore, MD
| | | | - Eric C. Larsen
- Department of Pediatric Hematology-Oncology, Maine Medical Center, Scarborough, ME
| | - Naomi Winick
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX
| | - William L. Carroll
- Perlmutter Cancer Center, Department of Pediatrics, NYU Langone Medical Center, New York, New York
| | - Mignon L. Loh
- Department of Pediatrics, Benioff Children’s Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Elizabeth A. Raetz
- Perlmutter Cancer Center, Department of Pediatrics, NYU Langone Medical Center, New York, New York
| | - Stephen P. Hunger
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA
| | | | - Elaine R. Mardis
- The Ohio State University and Nationwide Children’s Hospital, Columbus, Ohio
| | - Robert S. Fulton
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Mary V. Relling
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN
| | - Sima Jeha
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN
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28
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Christopher MJ, Petti AA, Rettig MP, Miller CA, Chendamarai E, Duncavage EJ, Klco JM, Helton NM, O'Laughlin M, Fronick CC, Fulton RS, Wilson RK, Wartman LD, Welch JS, Heath SE, Baty JD, Payton JE, Graubert TA, Link DC, Walter MJ, Westervelt P, Ley TJ, DiPersio JF. Immune Escape of Relapsed AML Cells after Allogeneic Transplantation. N Engl J Med 2018; 379:2330-2341. [PMID: 30380364 PMCID: PMC6322675 DOI: 10.1056/nejmoa1808777] [Citation(s) in RCA: 280] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND As consolidation therapy for acute myeloid leukemia (AML), allogeneic hematopoietic stem-cell transplantation provides a benefit in part by means of an immune-mediated graft-versus-leukemia effect. We hypothesized that the immune-mediated selective pressure imposed by allogeneic transplantation may cause distinct patterns of tumor evolution in relapsed disease. METHODS We performed enhanced exome sequencing on paired samples obtained at initial presentation with AML and at relapse from 15 patients who had a relapse after hematopoietic stem-cell transplantation (with transplants from an HLA-matched sibling, HLA-matched unrelated donor, or HLA-mismatched unrelated donor) and from 20 patients who had a relapse after chemotherapy. We performed RNA sequencing and flow cytometry on a subgroup of these samples and on additional samples for validation. RESULTS On exome sequencing, the spectrum of gained and lost mutations observed with relapse after transplantation was similar to the spectrum observed with relapse after chemotherapy. Specifically, relapse after transplantation was not associated with the acquisition of previously unknown AML-specific mutations or structural variations in immune-related genes. In contrast, RNA sequencing of samples obtained at relapse after transplantation revealed dysregulation of pathways involved in adaptive and innate immunity, including down-regulation of major histocompatibility complex (MHC) class II genes ( HLA-DPA1, HLA-DPB1, HLA-DQB1, and HLA-DRB1) to levels that were 3 to 12 times lower than the levels seen in paired samples obtained at presentation. Flow cytometry and immunohistochemical analysis confirmed decreased expression of MHC class II at relapse in 17 of 34 patients who had a relapse after transplantation. Evidence suggested that interferon-γ treatment could rapidly reverse this phenotype in AML blasts in vitro. CONCLUSIONS AML relapse after transplantation was not associated with the acquisition of relapse-specific mutations in immune-related genes. However, it was associated with dysregulation of pathways that may influence immune function, including down-regulation of MHC class II genes, which are involved in antigen presentation. These epigenetic changes may be reversible with appropriate therapy. (Funded by the National Cancer Institute and others.).
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MESH Headings
- Adolescent
- Adult
- Aged
- Down-Regulation
- Epigenesis, Genetic
- Female
- Flow Cytometry
- Genes, MHC Class II/physiology
- Hematopoietic Stem Cell Transplantation
- Humans
- Immunity/genetics
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/immunology
- Leukemia, Myeloid, Acute/pathology
- Male
- Middle Aged
- Mutation
- RNA, Neoplasm/analysis
- Recurrence
- Sequence Analysis, RNA
- T-Lymphocytes/immunology
- Transplantation, Homologous
- Exome Sequencing
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Affiliation(s)
- Matthew J Christopher
- From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.)
| | - Allegra A Petti
- From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.)
| | - Michael P Rettig
- From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.)
| | - Christopher A Miller
- From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.)
| | - Ezhilarasi Chendamarai
- From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.)
| | - Eric J Duncavage
- From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.)
| | - Jeffery M Klco
- From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.)
| | - Nicole M Helton
- From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.)
| | - Michelle O'Laughlin
- From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.)
| | - Catrina C Fronick
- From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.)
| | - Robert S Fulton
- From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.)
| | - Richard K Wilson
- From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.)
| | - Lukas D Wartman
- From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.)
| | - John S Welch
- From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.)
| | - Sharon E Heath
- From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.)
| | - Jack D Baty
- From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.)
| | - Jacqueline E Payton
- From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.)
| | - Timothy A Graubert
- From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.)
| | - Daniel C Link
- From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.)
| | - Matthew J Walter
- From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.)
| | - Peter Westervelt
- From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.)
| | - Timothy J Ley
- From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.)
| | - John F DiPersio
- From the Division of Oncology, Department of Internal Medicine (M.J.C., A.A.P., M.P.R., C.A.M., E.C., N.M.H., L.D.W., J.S.W., S.E.H., D.C.L., M.J.W., P.W., T.J.L., J.F.D.), the McDonnell Genome Institute (A.A.P., C.A.M., M.O., C.C.F., R.S.F., L.D.W., T.J.L.), the Department of Pathology and Immunology (E.J.D., J.E.P.), and the Division of Biostatistics (J.D.B.), Washington University in St. Louis, St. Louis; the Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN (J.M.K.); the Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH (R.K.W.); and the Center for Cancer Research, Massachusetts General Hospital, Boston (T.A.G.)
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29
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Gubin MM, Esaulova E, Ward JP, Malkova ON, Runci D, Wong P, Noguchi T, Arthur CD, Meng W, Alspach E, Medrano RFV, Fronick C, Fehlings M, Newell EW, Fulton RS, Sheehan KCF, Oh ST, Schreiber RD, Artyomov MN. High-Dimensional Analysis Delineates Myeloid and Lymphoid Compartment Remodeling during Successful Immune-Checkpoint Cancer Therapy. Cell 2018; 175:1014-1030.e19. [PMID: 30343900 DOI: 10.1016/j.cell.2018.09.030] [Citation(s) in RCA: 219] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 07/13/2018] [Accepted: 09/13/2018] [Indexed: 12/23/2022]
Abstract
Although current immune-checkpoint therapy (ICT) mainly targets lymphoid cells, it is associated with a broader remodeling of the tumor micro-environment. Here, using complementary forms of high-dimensional profiling, we define differences across all hematopoietic cells from syngeneic mouse tumors during unrestrained tumor growth or effective ICT. Unbiased assessment of gene expression of tumor-infiltrating cells by single-cell RNA sequencing (scRNAseq) and longitudinal assessment of cellular protein expression by mass cytometry (CyTOF) revealed significant remodeling of both the lymphoid and myeloid intratumoral compartments. Surprisingly, we observed multiple subpopulations of monocytes/macrophages, distinguishable by the markers CD206, CX3CR1, CD1d, and iNOS, that change over time during ICT in a manner partially dependent on IFNγ. Our data support the hypothesis that this macrophage polarization/activation results from effects on circulatory monocytes and early macrophages entering tumors, rather than on pre-polarized mature intratumoral macrophages.
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Affiliation(s)
- Matthew M Gubin
- Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Ekaterina Esaulova
- Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA; Computer Technologies Department, ITMO University, Saint Petersburg, 197110, Russia
| | - Jeffrey P Ward
- Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA; Division of Oncology, Department of Medicine, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Olga N Malkova
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniele Runci
- Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Pamela Wong
- Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Takuro Noguchi
- Department of Comprehensive Cancer Therapy, Shinshu University School of Medicine 3-1-1 Asahi, Matsumoto Nagano, 390-8621, Japan
| | - Cora D Arthur
- Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Wei Meng
- Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Elise Alspach
- Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Ruan F V Medrano
- Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Catrina Fronick
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St. Louis, MO 63108, USA
| | - Michael Fehlings
- Agency for Science, Technology and Research (A(∗)STAR), Singapore Immunology Network (SIgN), 8 A Biomedical Grove, Singapore, 138648, Singapore
| | - Evan W Newell
- Agency for Science, Technology and Research (A(∗)STAR), Singapore Immunology Network (SIgN), 8 A Biomedical Grove, Singapore, 138648, Singapore
| | - Robert S Fulton
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St. Louis, MO 63108, USA
| | - Kathleen C F Sheehan
- Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Stephen T Oh
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA; Division of Hematology, Washington University School of Medicine, 660 S. Euclid Ave., Campus Box 8125, St. Louis, MO 63110, USA
| | - Robert D Schreiber
- Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
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30
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Wagner AH, Devarakonda S, Skidmore ZL, Krysiak K, Ramu A, Trani L, Kunisaki J, Masood A, Waqar SN, Spies NC, Morgensztern D, Waligorski J, Ponce J, Fulton RS, Maggi LB, Weber JD, Watson MA, O'Conor CJ, Ritter JH, Olsen RR, Cheng H, Mukhopadhyay A, Can I, Cessna MH, Oliver TG, Mardis ER, Wilson RK, Griffith M, Griffith OL, Govindan R. Recurrent WNT pathway alterations are frequent in relapsed small cell lung cancer. Nat Commun 2018; 9:3787. [PMID: 30224629 PMCID: PMC6141466 DOI: 10.1038/s41467-018-06162-9] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [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: 02/02/2018] [Accepted: 08/13/2018] [Indexed: 12/27/2022] Open
Abstract
Nearly all patients with small cell lung cancer (SCLC) eventually relapse with chemoresistant disease. The molecular mechanisms driving chemoresistance in SCLC remain un-characterized. Here, we describe whole-exome sequencing of paired SCLC tumor samples procured at diagnosis and relapse from 12 patients, and unpaired relapse samples from 18 additional patients. Multiple somatic copy number alterations, including gains in ABCC1 and deletions in MYCL, MSH2, and MSH6, are identifiable in relapsed samples. Relapse samples also exhibit recurrent mutations and loss of heterozygosity in regulators of WNT signaling, including CHD8 and APC. Analysis of RNA-sequencing data shows enrichment for an ASCL1-low expression subtype and WNT activation in relapse samples. Activation of WNT signaling in chemosensitive human SCLC cell lines through APC knockdown induces chemoresistance. Additionally, in vitro-derived chemoresistant cell lines demonstrate increased WNT activity. Overall, our results suggest WNT signaling activation as a mechanism of chemoresistance in relapsed SCLC.
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Affiliation(s)
- Alex H Wagner
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Siddhartha Devarakonda
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | - Zachary L Skidmore
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Kilannin Krysiak
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Avinash Ramu
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Lee Trani
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Jason Kunisaki
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Ashiq Masood
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
- Saint Luke's Health System, Kansas City, MO, USA
| | - Saiama N Waqar
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | - Nicholas C Spies
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Daniel Morgensztern
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | - Jason Waligorski
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Jennifer Ponce
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Robert S Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Leonard B Maggi
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
- ICCE Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jason D Weber
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
- ICCE Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Mark A Watson
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | - Christopher J O'Conor
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jon H Ritter
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Rachelle R Olsen
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT, 84112, USA
| | - Haixia Cheng
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT, 84112, USA
| | - Anandaroop Mukhopadhyay
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT, 84112, USA
| | - Ismail Can
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT, 84112, USA
| | - Melissa H Cessna
- Intermountain Healthcare BioRepository and Department of Pathology, Intermountain Healthcare, Salt Lake City, UT, 84103, USA
| | - Trudy G Oliver
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT, 84112, USA
| | - Elaine R Mardis
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Nationwide Children's Hospital, Columbus, OH, USA
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Nationwide Children's Hospital, Columbus, OH, USA
| | - Malachi Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA.
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Obi L Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA.
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Ramaswamy Govindan
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA.
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31
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Duncavage EJ, Jacoby MA, Chang GS, Miller CA, Edwin N, Shao J, Elliott K, Robinson J, Abel H, Fulton RS, Fronick CC, O'Laughlin M, Heath SE, Brendel K, Saba R, Wartman LD, Christopher MJ, Pusic I, Welch JS, Uy GL, Link DC, DiPersio JF, Westervelt P, Ley TJ, Trinkaus K, Graubert TA, Walter MJ. Mutation Clearance after Transplantation for Myelodysplastic Syndrome. N Engl J Med 2018; 379:1028-1041. [PMID: 30207916 PMCID: PMC6309244 DOI: 10.1056/nejmoa1804714] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Allogeneic hematopoietic stem-cell transplantation is the only curative treatment for patients with myelodysplastic syndrome (MDS). The molecular predictors of disease progression after transplantation are unclear. METHODS We sequenced bone marrow and skin samples from 90 adults with MDS who underwent allogeneic hematopoietic stem-cell transplantation after a myeloablative or reduced-intensity conditioning regimen. We detected mutations before transplantation using enhanced exome sequencing, and we evaluated mutation clearance by using error-corrected sequencing to genotype mutations in bone marrow samples obtained 30 days after transplantation. In this exploratory study, we evaluated the association of a mutation detected after transplantation with disease progression and survival. RESULTS Sequencing identified at least one validated somatic mutation before transplantation in 86 of 90 patients (96%); 32 of these patients (37%) had at least one mutation with a maximum variant allele frequency of at least 0.5% (equivalent to 1 heterozygous mutant cell in 100 cells) 30 days after transplantation. Patients with disease progression had mutations with a higher maximum variant allele frequency at 30 days than those who did not (median maximum variant allele frequency, 0.9% vs. 0%; P<0.001). The presence of at least one mutation with a variant allele frequency of at least 0.5% at day 30 was associated with a higher risk of progression (53.1% vs. 13.0%; conditioning regimen-adjusted hazard ratio, 3.86; 95% confidence interval [CI], 1.96 to 7.62; P<0.001) and a lower 1-year rate of progression-free survival than the absence of such a mutation (31.3% vs. 59.3%; conditioning regimen-adjusted hazard ratio for progression or death, 2.22; 95% CI, 1.32 to 3.73; P=0.005). The rate of progression-free survival was lower among patients who had received a reduced-intensity conditioning regimen and had at least one persistent mutation with a variant allele frequency of at least 0.5% at day 30 than among patients with other combinations of conditioning regimen and mutation status (P≤0.001). Multivariate analysis confirmed that patients who had a mutation with a variant allele frequency of at least 0.5% detected at day 30 had a higher risk of progression (hazard ratio, 4.48; 95% CI, 2.21 to 9.08; P<0.001) and a lower 1-year rate of progression-free survival than those who did not (hazard ratio for progression or death, 2.39; 95% CI, 1.40 to 4.09; P=0.002). CONCLUSIONS The risk of disease progression was higher among patients with MDS in whom persistent disease-associated mutations were detected in the bone marrow 30 days after transplantation than among those in whom these mutations were not detected. (Funded by the Leukemia and Lymphoma Society and others.).
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Affiliation(s)
- Eric J Duncavage
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Meagan A Jacoby
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Gue Su Chang
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Christopher A Miller
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Natasha Edwin
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Jin Shao
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Kevin Elliott
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Joshua Robinson
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Haley Abel
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Robert S Fulton
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Catrina C Fronick
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Michelle O'Laughlin
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Sharon E Heath
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Kimberly Brendel
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Raya Saba
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Lukas D Wartman
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Matthew J Christopher
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Iskra Pusic
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - John S Welch
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Geoffrey L Uy
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Daniel C Link
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - John F DiPersio
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Peter Westervelt
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Timothy J Ley
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Kathryn Trinkaus
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Timothy A Graubert
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
| | - Matthew J Walter
- From the Department of Pathology and Immunology (E.J.D.), the Department of Medicine, Division of Oncology (M.A.J., C.A.M., N.E., J.S., K.E., J.R., S.E.H., K.B., L.D.W., M.J.C., I.P., J.S.W., G.L.U., D.C.L., J.F.D., P.W., T.J.L., M.J.W.), the McDonnell Genome Institute (G.S.C., C.A.M., H.A., R.S.F., C.C.F., M.O.), the Department of Medicine, Division of Hospital Medicine (R.S.), and Siteman Biostatistics Shared Resource, Siteman Cancer Center (K.T.), Washington University School of Medicine in St. Louis, St. Louis; and Massachusetts General Hospital Cancer Center, Boston (T.A.G.)
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Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Cantsilieris S, Meyerson OS, Underwood JG, Nelson BJ, Chaisson MJP, Dougherty ML, Munson KM, Hastie AR, Diekhans M, Hormozdiari F, Lorusso N, Hoekzema K, Qiu R, Clark K, Raja A, Welch AE, Sorensen M, Baker C, Fulton RS, Armstrong J, Graves-Lindsay TA, Denli AM, Hoppe ER, Hsieh P, Hill CM, Pang AWC, Lee J, Lam ET, Dutcher SK, Gage FH, Warren WC, Shendure J, Haussler D, Schneider VA, Cao H, Ventura M, Wilson RK, Paten B, Pollen A, Eichler EE. High-resolution comparative analysis of great ape genomes. Science 2018; 360:eaar6343. [PMID: 29880660 PMCID: PMC6178954 DOI: 10.1126/science.aar6343] [Citation(s) in RCA: 225] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 04/02/2018] [Indexed: 12/22/2022]
Abstract
Genetic studies of human evolution require high-quality contiguous ape genome assemblies that are not guided by the human reference. We coupled long-read sequence assembly and full-length complementary DNA sequencing with a multiplatform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies. By comparing these with two long-read de novo human genome assemblies and a gorilla genome assembly, we characterized lineage-specific and shared great ape genetic variation ranging from single- to mega-base pair-sized variants. We identified ~17,000 fixed human-specific structural variants identifying genic and putative regulatory changes that have emerged in humans since divergence from nonhuman apes. Interestingly, these variants are enriched near genes that are down-regulated in human compared to chimpanzee cerebral organoids, particularly in cells analogous to radial glial neural progenitors.
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Affiliation(s)
- Zev N Kronenberg
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ian T Fiddes
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Gordon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Shwetha Murali
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Stuart Cantsilieris
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Olivia S Meyerson
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jason G Underwood
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Pacific Biosciences (PacBio) of California, Inc., Menlo Park, CA 94025, USA
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Mark J P Chaisson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Computational Biology and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA
| | - Max L Dougherty
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Fereydoun Hormozdiari
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA 95817, USA
| | - Nicola Lorusso
- Department of Biology, University of Bari, Aldo Moro, Bari 70121, Italy
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ruolan Qiu
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Karen Clark
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Archana Raja
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - AnneMarie E Welch
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Melanie Sorensen
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Carl Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Robert S Fulton
- Departments of Medicine and Genetics, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Joel Armstrong
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Tina A Graves-Lindsay
- Departments of Medicine and Genetics, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Ahmet M Denli
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Emma R Hoppe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - PingHsun Hsieh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Christopher M Hill
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | - Joyce Lee
- Bionano Genomics, San Diego, CA 92121, USA
| | | | - Susan K Dutcher
- Departments of Medicine and Genetics, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Fred H Gage
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Wesley C Warren
- Departments of Medicine and Genetics, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - David Haussler
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Valerie A Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Han Cao
- Bionano Genomics, San Diego, CA 92121, USA
| | - Mario Ventura
- Department of Biology, University of Bari, Aldo Moro, Bari 70121, Italy
| | - Richard K Wilson
- Departments of Medicine and Genetics, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Alex Pollen
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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Miller CA, Dahiya S, Li T, Fulton RS, Smyth MD, Dunn GP, Rubin JB, Mardis ER. Resistance-promoting effects of ependymoma treatment revealed through genomic analysis of multiple recurrences in a single patient. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a002444. [PMID: 29440180 PMCID: PMC5880262 DOI: 10.1101/mcs.a002444] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 12/26/2017] [Indexed: 12/11/2022] Open
Abstract
As in other brain tumors, multiple recurrences after complete resection and irradiation of supratentorial ependymoma are common and frequently result in patient death. This standard-of-care treatment was established in the pregenomic era without the ability to evaluate the effect that mutagenic therapies may exert on tumor evolution and in promoting resistance, recurrence, and death. We seized a rare opportunity to characterize treatment effects and the evolution of a single patient's ependymoma across four recurrences after different therapies. A combination of high-depth whole-genome and exome-based DNA sequencing of germline and tumor specimens, RNA sequencing of tumor specimens, and advanced computational analyses were used. Treatment with radiation and chemotherapies resulted in a substantial increase in mutational burden and diversification of the tumor subclonal architecture without eradication of the founding clone. Notable somatic alterations included a MEN1 driver, several epigenetic modifiers, and therapy-induced mutations that impacted multiple other cancer-relevant pathways and altered the neoantigen landscape. These genomic data provided new mechanistic insights into the genesis of ependymoma and pathways of resistance. They also revealed that radiation and chemotherapy were significant forces in shaping the increased subclonal complexity of each tumor recurrence while also failing to eradicate the founding clone. This raises the question of whether standard-of-care treatments have similar consequences in other patients with ependymoma and other types of brain tumors. If so, the perspective obtained by real-time genomic characterization of a tumor may be essential for making effective patient-specific and adaptive clinical decisions.
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Affiliation(s)
- Christopher A Miller
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri 63110, USA.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Sonika Dahiya
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Tiandao Li
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Robert S Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Matthew D Smyth
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Gavin P Dunn
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Joshua B Rubin
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Elaine R Mardis
- Institute for Genomic Medicine, Nationwide Children's Hospital, and The Ohio State University College of Medicine, Columbus, Ohio 43205, USA
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34
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White BS, Lanc I, O'Neal J, Gupta H, Fulton RS, Schmidt H, Fronick C, Belter EA, Fiala M, King J, Ahmann GJ, DeRome M, Mardis ER, Vij R, DiPersio JF, Levy J, Auclair D, Tomasson MH. A multiple myeloma-specific capture sequencing platform discovers novel translocations and frequent, risk-associated point mutations in IGLL5. Blood Cancer J 2018; 8:35. [PMID: 29563506 PMCID: PMC5862875 DOI: 10.1038/s41408-018-0062-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [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: 07/21/2017] [Revised: 12/10/2017] [Accepted: 12/18/2017] [Indexed: 12/28/2022] Open
Abstract
Multiple myeloma (MM) is a disease of copy number variants (CNVs), chromosomal translocations, and single-nucleotide variants (SNVs). To enable integrative studies across these diverse mutation types, we developed a capture-based sequencing platform to detect their occurrence in 465 genes altered in MM and used it to sequence 95 primary tumor-normal pairs to a mean depth of 104×. We detected cases of hyperdiploidy (23%), deletions of 1p (8%), 6q (21%), 8p (17%), 14q (16%), 16q (22%), and 17p (4%), and amplification of 1q (19%). We also detected IGH and MYC translocations near expected frequencies and non-silent SNVs in NRAS (24%), KRAS (21%), FAM46C (17%), TP53 (9%), DIS3 (9%), and BRAF (3%). We discovered frequent mutations in IGLL5 (18%) that were mutually exclusive of RAS mutations and associated with increased risk of disease progression (p = 0.03), suggesting that IGLL5 may be a stratifying biomarker. We identified novel IGLL5/IGH translocations in two samples. We subjected 15 of the pairs to ultra-deep sequencing (1259×) and found that although depth correlated with number of mutations detected (p = 0.001), depth past ~300× added little. The platform provides cost-effective genomic analysis for research and may be useful in individualizing treatment decisions in clinical settings.
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Affiliation(s)
- Brian S White
- Department of Medicine, Washington University School of Medicine, St. Louis, 63110, MO, USA.,Sage Bionetworks, Seattle, WA, 91809, USA
| | - Irena Lanc
- Department of Medicine, Washington University School of Medicine, St. Louis, 63110, MO, USA
| | - Julie O'Neal
- Department of Medicine, Washington University School of Medicine, St. Louis, 63110, MO, USA
| | - Harshath Gupta
- Department of Medicine, Washington University School of Medicine, St. Louis, 63110, MO, USA
| | - Robert S Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63108, MO, USA
| | - Heather Schmidt
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63108, MO, USA
| | - Catrina Fronick
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63108, MO, USA
| | - Edward A Belter
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63108, MO, USA
| | - Mark Fiala
- Department of Medicine, Washington University School of Medicine, St. Louis, 63110, MO, USA
| | - Justin King
- Department of Medicine, Washington University School of Medicine, St. Louis, 63110, MO, USA
| | - Greg J Ahmann
- Division of Hematology-Oncology, Mayo Clinic, Rochester, 55905, MN, USA
| | - Mary DeRome
- Multiple Myeloma Research Foundation, Norwalk, CT, 06851, USA
| | - Elaine R Mardis
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63108, MO, USA.,Genomics Institute, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Ravi Vij
- Department of Medicine, Washington University School of Medicine, St. Louis, 63110, MO, USA
| | - John F DiPersio
- Department of Medicine, Washington University School of Medicine, St. Louis, 63110, MO, USA
| | - Joan Levy
- Multiple Myeloma Research Foundation, Norwalk, CT, 06851, USA.,Chordoma Foundation, Durham, NC, 27702, USA
| | - Daniel Auclair
- Multiple Myeloma Research Foundation, Norwalk, CT, 06851, USA
| | - Michael H Tomasson
- Department of Medicine, Washington University School of Medicine, St. Louis, 63110, MO, USA. .,Division of Hematology, Oncology and Bone Marrow Transplantation, 5204 MERF, University of Iowa, Iowa City, IA, 52242, USA.
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35
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Jacoby MA, Duncavage EJ, Chang GS, Miller CA, Shao J, Elliott K, Robinson J, Fulton RS, Fronick CC, O'Laughlin M, Heath SE, Pusic I, Welch JS, Link DC, DiPersio JF, Westervelt P, Ley TJ, Graubert TA, Walter MJ. Subclones dominate at MDS progression following allogeneic hematopoietic cell transplant. JCI Insight 2018. [PMID: 29515031 DOI: 10.1172/jci.insight.98962] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Allogeneic hematopoietic cell transplantation (alloHCT) is a potentially curative treatment for myelodysplastic syndromes (MDS), but patients who relapse after transplant have poor outcomes. In order to understand the contribution of tumor clonal evolution to disease progression,we applied exome and error-corrected targeted sequencing coupled with copy number analysis to comprehensively define changes in the clonal architecture of MDS in response to therapy using 51 serially acquired tumor samples from 9 patients who progressed after an alloHCT. We show that small subclones before alloHCT can drive progression after alloHCT. Notably, at least one subclone expanded or emerged at progression in all patients. Newly acquired structural variants (SVs) were present in an emergent/expanding subclone in 8 of 9 patients at progression, implicating the acquisition of SVs as important late subclonal progression events. In addition, pretransplant therapy with azacitidine likely influenced the mutation spectrum and evolution of emergent subclones after alloHCT. Although subclone evolution is common, founding clone mutations are always present at progression and could be detected in the bone marrow as early as 30 and/or 100 days after alloHCT in 6 of 8 (75%) patients, often prior to clinical progression. In conclusion, MDS progression after alloHCT is characterized by subclonal expansion and evolution, which can be influenced by pretransplant therapy.
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Affiliation(s)
| | | | - Gue Su Chang
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Christopher A Miller
- Department of Medicine, Division of Oncology.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jin Shao
- Department of Medicine, Division of Oncology
| | | | | | - Robert S Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Catrina C Fronick
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michelle O'Laughlin
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | | | - Iskra Pusic
- Department of Medicine, Division of Oncology
| | | | | | | | | | | | - Timothy A Graubert
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts, USA
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36
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Ainscough BJ, Griffith M, Coffman AC, Wagner AH, Kunisaki J, Choudhary MN, McMichael JF, Fulton RS, Wilson RK, Griffith OL, Mardis ER. DoCM: a database of curated mutations in cancer. Nat Methods 2018; 13:806-7. [PMID: 27684579 DOI: 10.1038/nmeth.4000] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Benjamin J Ainscough
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA.,Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Malachi Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA.,Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Adam C Coffman
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Alex H Wagner
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA.,Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jason Kunisaki
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Mayank Nk Choudhary
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Joshua F McMichael
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Robert S Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA.,Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA.,Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Obi L Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA.,Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Elaine R Mardis
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA.,Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
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37
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Cooper ML, Choi J, Staser K, Ritchey JK, Devenport JM, Eckardt K, Rettig MP, Wang B, Eissenberg LG, Ghobadi A, Gehrs LN, Prior JL, Achilefu S, Miller CA, Fronick CC, O'Neal J, Gao F, Weinstock DM, Gutierrez A, Fulton RS, DiPersio JF. An "off-the-shelf" fratricide-resistant CAR-T for the treatment of T cell hematologic malignancies. Leukemia 2018; 32:1970-1983. [PMID: 29483708 PMCID: PMC6102094 DOI: 10.1038/s41375-018-0065-5] [Citation(s) in RCA: 246] [Impact Index Per Article: 41.0] [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: 12/18/2017] [Revised: 01/22/2018] [Accepted: 02/01/2018] [Indexed: 12/27/2022]
Abstract
T cell malignancies represent a group of hematologic cancers with high rates of relapse and mortality in patients for whom no effective targeted therapies exist. The shared expression of target antigens between chimeric antigen receptor (CAR) T cells and malignant T cells has limited the development of CAR-T because of unintended CAR-T fratricide and an inability to harvest sufficient autologous T cells. Here we describe a fratricide resistant ‘off-the-shelf’ CAR-T (or UCART7) that targets CD7+ T cell malignancies and, through CRISPR/Cas9 gene editing, lacks both CD7 and T cell receptor alpha chain (TRAC) expression. UCART7 demonstrates efficacy against human T cell acute lymphoblastic leukemia (T-ALL) cell lines and primary T-ALL in vitro and in vivo without the induction of xenogeneic GvHD. Fratricide resistant, allo-tolerant ‘off-the-shelf’ CAR-T represents a strategy for treatment of relapsed and refractory T-ALL and non-Hodgkin’s T cell lymphoma without a requirement for autologous T cells.
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Affiliation(s)
- Matthew L Cooper
- Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Jaebok Choi
- Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Karl Staser
- Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Internal Medicine, Division of Dermatology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Julie K Ritchey
- Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jessica M Devenport
- Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Kayla Eckardt
- Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Michael P Rettig
- Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Bing Wang
- Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Linda G Eissenberg
- Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Armin Ghobadi
- Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Leah N Gehrs
- Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Julie L Prior
- Mallinckrodt Institute of Radiology, Washington University in St. Louis School of Medicine, St. Louis, MO, 63110, USA
| | - Samuel Achilefu
- Mallinckrodt Institute of Radiology, Washington University in St. Louis School of Medicine, St. Louis, MO, 63110, USA
| | - Christopher A Miller
- Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Catrina C Fronick
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Julie O'Neal
- Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Feng Gao
- Department of Surgery, Division of Public Health Sciences, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - David M Weinstock
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Alejandro Gutierrez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02215, USA
| | - Robert S Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - John F DiPersio
- Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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38
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Wong TN, Miller CA, Jotte MRM, Bagegni N, Baty JD, Schmidt AP, Cashen AF, Duncavage EJ, Helton NM, Fiala M, Fulton RS, Heath SE, Janke M, Luber K, Westervelt P, Vij R, DiPersio JF, Welch JS, Graubert TA, Walter MJ, Ley TJ, Link DC. Cellular stressors contribute to the expansion of hematopoietic clones of varying leukemic potential. Nat Commun 2018; 9:455. [PMID: 29386642 PMCID: PMC5792556 DOI: 10.1038/s41467-018-02858-0] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [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: 09/28/2017] [Accepted: 01/04/2018] [Indexed: 01/22/2023] Open
Abstract
Hematopoietic clones harboring specific mutations may expand over time. However, it remains unclear how different cellular stressors influence this expansion. Here we characterize clonal hematopoiesis after two different cellular stressors: cytotoxic therapy and hematopoietic transplantation. Cytotoxic therapy results in the expansion of clones carrying mutations in DNA damage response genes, including TP53 and PPM1D. Analyses of sorted populations show that these clones are typically multilineage and myeloid-biased. Following autologous transplantation, most clones persist with stable chimerism. However, DNMT3A mutant clones often expand, while PPM1D mutant clones often decrease in size. To assess the leukemic potential of these expanded clones, we genotyped 134 t-AML/t-MDS samples. Mutations in non-TP53 DNA damage response genes are infrequent in t-AML/t-MDS despite several being commonly identified after cytotoxic therapy. These data suggest that different hematopoietic stressors promote the expansion of distinct long-lived clones, carrying specific mutations, whose leukemic potential depends partially on the mutations they harbor. Cellular stressors can impact clonal hematopoiesis. Here, the authors explore the impact of cytotoxic therapy and hematopoietic transplantation on clonal expansion, suggesting different stressors can promote expansion of distinct long-lived clones.
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Affiliation(s)
- Terrence N Wong
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Christopher A Miller
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Matthew R M Jotte
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Nusayba Bagegni
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jack D Baty
- Division of Biostatistics, Washington University, St. Louis, MO, 63110, USA
| | - Amy P Schmidt
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Amanda F Cashen
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | - Eric J Duncavage
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Nichole M Helton
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Mark Fiala
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Robert S Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Sharon E Heath
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Megan Janke
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Kierstin Luber
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Peter Westervelt
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | - Ravi Vij
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | - John F DiPersio
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | - John S Welch
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | | | - Matthew J Walter
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | - Timothy J Ley
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | - Daniel C Link
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA. .,Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA.
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39
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Grigsby P, Elhammali A, Ruiz F, Markovina S, McLellan MD, Miller CA, Chundury A, Ta NAL, Rashmi R, Pfeifer JD, Fulton RS, DeWees T, Schwarz JK. Clinical outcomes and differential effects of PI3K pathway mutation in obese versus non-obese patients with cervical cancer. Oncotarget 2017; 9:4061-4073. [PMID: 29423104 PMCID: PMC5790521 DOI: 10.18632/oncotarget.23664] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/13/2017] [Indexed: 12/12/2022] Open
Abstract
The purpose of this study was to evaluate the effect of obesity and obesity-associated factors on the outcomes of patients with cervical cancer. Outcomes were evaluated in 591 patients with FIGO Ib to IV cervical cancer treated uniformly with definitive radiation. Patients were stratified into 3 groups based upon pretreatment Body Mass Index (BMI): A ≤ 18.5; B 18.6 – 34.9; and C ≥ 35. The 5-year freedom from failure rates were 58, 59, and 73% for BMI groups A, B, and C (p = 0.01). Overall survival rates were 50, 59, and 68%, respectively (p = 0.02). High expression of phosphorylated AKT (pAKT) was associated with poor outcomes only in non-obese patients. Obese patients with PI3K pathway mutant tumors had a trend toward favorable outcomes, while a similar effect was not observed in non-obese patients. Compared to similar tumors from non-obese hosts, PIK3CA and PTEN mutant tumors from obese patients failed to express high levels of phosphorylated AKT and its downstream targets. These results show that patients with obesity at the time of diagnosis of cervical cancer exhibit improved outcomes after radiation. PI3K/AKT pathway mutations are common in obese patients, but are not associated with activation of AKT signaling.
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Affiliation(s)
- Perry Grigsby
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA.,Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.,Division of Nuclear Medicine, Mallinckrodt Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Adnan Elhammali
- Department of Radiation Oncology, MD Anderson Cancer Center, University of Texas Health Science Center, Houston, TX, USA
| | - Fiona Ruiz
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Stephanie Markovina
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA.,Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael D McLellan
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Christopher A Miller
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Anupama Chundury
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ngoc-Anh L Ta
- Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Ramachandran Rashmi
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - John D Pfeifer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.,Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO, USA
| | - Robert S Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Todd DeWees
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Julie K Schwarz
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA.,Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.,Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
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40
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Griffith OL, Chan SR, Griffith M, Krysiak K, Skidmore ZL, Hundal J, Allen JA, Arthur CD, Runci D, Bugatti M, Miceli AP, Schmidt H, Trani L, Kanchi KL, Miller CA, Larson DE, Fulton RS, Vermi W, Wilson RK, Schreiber RD, Mardis ER. Truncating Prolactin Receptor Mutations Promote Tumor Growth in Murine Estrogen Receptor-Alpha Mammary Carcinomas. Cell Rep 2017; 17:249-260. [PMID: 27681435 DOI: 10.1016/j.celrep.2016.08.076] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 05/27/2016] [Accepted: 08/23/2016] [Indexed: 10/20/2022] Open
Abstract
Estrogen receptor alpha-positive (ERα+) luminal tumors are the most frequent subtype of breast cancer. Stat1(-/-) mice develop mammary tumors that closely recapitulate the biological characteristics of this cancer subtype. To identify transforming events that contribute to tumorigenesis, we performed whole genome sequencing of Stat1(-/-) primary mammary tumors and matched normal tissues. This investigation identified somatic truncating mutations affecting the prolactin receptor (PRLR) in all tumor and no normal samples. Targeted sequencing confirmed the presence of these mutations in precancerous lesions, indicating that this is an early event in tumorigenesis. Functional evaluation of these heterozygous mutations in Stat1(-/-) mouse embryonic fibroblasts showed that co-expression of truncated and wild-type PRLR led to aberrant STAT3 and STAT5 activation downstream of the receptor, cellular transformation in vitro, and tumor formation in vivo. In conclusion, truncating mutations of PRLR promote tumor growth in a model of human ERα+ breast cancer and warrant further investigation.
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Affiliation(s)
- Obi L Griffith
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave., St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, 660 S Euclid Ave., St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University School of Medicine, 4921 Parkview Pl., St. Louis, MO 63110, USA
| | - Szeman Ruby Chan
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S Euclid Ave., St. Louis, MO 63110, USA
| | - Malachi Griffith
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave., St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University School of Medicine, 4921 Parkview Pl., St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, 660 S Euclid Ave., St. Louis, MO 63110, USA
| | - Kilannin Krysiak
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave., St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, 660 S Euclid Ave., St. Louis, MO 63110, USA
| | - Zachary L Skidmore
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave., St. Louis, MO 63108, USA
| | - Jasreet Hundal
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave., St. Louis, MO 63108, USA
| | - Julie A Allen
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S Euclid Ave., St. Louis, MO 63110, USA
| | - Cora D Arthur
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S Euclid Ave., St. Louis, MO 63110, USA
| | - Daniele Runci
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S Euclid Ave., St. Louis, MO 63110, USA
| | - Mattia Bugatti
- Section of Pathology, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Piazza del Mercato, 15, 25121 Brescia, Italy
| | - Alexander P Miceli
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S Euclid Ave., St. Louis, MO 63110, USA
| | - Heather Schmidt
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave., St. Louis, MO 63108, USA
| | - Lee Trani
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave., St. Louis, MO 63108, USA
| | - Krishna-Latha Kanchi
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave., St. Louis, MO 63108, USA
| | - Christopher A Miller
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave., St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, 660 S Euclid Ave., St. Louis, MO 63110, USA
| | - David E Larson
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave., St. Louis, MO 63108, USA; Department of Genetics, Washington University School of Medicine, 660 S Euclid Ave., St. Louis, MO 63110, USA
| | - Robert S Fulton
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave., St. Louis, MO 63108, USA; Department of Genetics, Washington University School of Medicine, 660 S Euclid Ave., St. Louis, MO 63110, USA
| | - William Vermi
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S Euclid Ave., St. Louis, MO 63110, USA; Section of Pathology, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Piazza del Mercato, 15, 25121 Brescia, Italy
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave., St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, 660 S Euclid Ave., St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University School of Medicine, 4921 Parkview Pl., St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, 660 S Euclid Ave., St. Louis, MO 63110, USA
| | - Robert D Schreiber
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S Euclid Ave., St. Louis, MO 63110, USA; Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, 425 S Euclid Ave., St. Louis, MO 63110, USA.
| | - Elaine R Mardis
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave., St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, 660 S Euclid Ave., St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University School of Medicine, 4921 Parkview Pl., St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, 660 S Euclid Ave., St. Louis, MO 63110, USA.
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Zhang J, Griffith M, Miller CA, Griffith OL, Spencer DH, Walker JR, Magrini V, McGrath SD, Ly A, Helton NM, Trissal M, Link DC, Dang HX, Larson DE, Kulkarni S, Cordes MG, Fronick CC, Fulton RS, Klco JM, Mardis ER, Ley TJ, Wilson RK, Maher CA. Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes. Exp Hematol 2017; 55:19-33. [PMID: 28760689 DOI: 10.1016/j.exphem.2017.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/20/2017] [Accepted: 07/25/2017] [Indexed: 01/29/2023]
Abstract
To detect diverse and novel RNA species comprehensively, we compared deep small RNA and RNA sequencing (RNA-seq) methods applied to a primary acute myeloid leukemia (AML) sample. We were able to discover previously unannotated small RNAs using deep sequencing of a library method using broader insert size selection. We analyzed the long noncoding RNA (lncRNA) landscape in AML by comparing deep sequencing from multiple RNA-seq library construction methods for the sample that we studied and then integrating RNA-seq data from 179 AML cases. This identified lncRNAs that are completely novel, differentially expressed, and associated with specific AML subtypes. Our study revealed the complexity of the noncoding RNA transcriptome through a combined strategy of strand-specific small RNA and total RNA-seq. This dataset will serve as an invaluable resource for future RNA-based analyses.
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Affiliation(s)
- Jin Zhang
- The McDonnell Genome Institute, Washington University, St. Louis, MO; Department of Medicine, Washington University, St. Louis, MO; Siteman Cancer Center, Washington University, St. Louis, MO
| | - Malachi Griffith
- The McDonnell Genome Institute, Washington University, St. Louis, MO; Siteman Cancer Center, Washington University, St. Louis, MO; Department of Genetics, Washington University, St. Louis, MO
| | - Christopher A Miller
- The McDonnell Genome Institute, Washington University, St. Louis, MO; Department of Medicine, Washington University, St. Louis, MO
| | - Obi L Griffith
- The McDonnell Genome Institute, Washington University, St. Louis, MO; Department of Medicine, Washington University, St. Louis, MO; Siteman Cancer Center, Washington University, St. Louis, MO; Department of Genetics, Washington University, St. Louis, MO
| | - David H Spencer
- Department of Medicine, Washington University, St. Louis, MO
| | - Jason R Walker
- The McDonnell Genome Institute, Washington University, St. Louis, MO
| | - Vincent Magrini
- Nationwide Children's Hospital, Institute for Genomic Medicine, Columbus, OH
| | - Sean D McGrath
- Nationwide Children's Hospital, Institute for Genomic Medicine, Columbus, OH
| | - Amy Ly
- The McDonnell Genome Institute, Washington University, St. Louis, MO
| | | | - Maria Trissal
- Department of Medicine, Washington University, St. Louis, MO
| | - Daniel C Link
- Department of Medicine, Washington University, St. Louis, MO
| | - Ha X Dang
- The McDonnell Genome Institute, Washington University, St. Louis, MO; Department of Medicine, Washington University, St. Louis, MO; Siteman Cancer Center, Washington University, St. Louis, MO
| | - David E Larson
- The McDonnell Genome Institute, Washington University, St. Louis, MO; Department of Genetics, Washington University, St. Louis, MO
| | | | - Matthew G Cordes
- The McDonnell Genome Institute, Washington University, St. Louis, MO
| | - Catrina C Fronick
- The McDonnell Genome Institute, Washington University, St. Louis, MO
| | - Robert S Fulton
- The McDonnell Genome Institute, Washington University, St. Louis, MO
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Elaine R Mardis
- Nationwide Children's Hospital, Institute for Genomic Medicine, Columbus, OH
| | - Timothy J Ley
- The McDonnell Genome Institute, Washington University, St. Louis, MO; Department of Medicine, Washington University, St. Louis, MO; Siteman Cancer Center, Washington University, St. Louis, MO; Department of Genetics, Washington University, St. Louis, MO
| | - Richard K Wilson
- Nationwide Children's Hospital, Institute for Genomic Medicine, Columbus, OH
| | - Christopher A Maher
- The McDonnell Genome Institute, Washington University, St. Louis, MO; Department of Medicine, Washington University, St. Louis, MO; Siteman Cancer Center, Washington University, St. Louis, MO; Department of Biomedical Engineering, Washington University, St. Louis, MO.
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42
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Cui J, Diogo D, Stahl EA, Canhao H, Mariette X, Greenberg JD, Okada Y, Pappas DA, Fulton RS, Tak PP, Nurmohamed MT, Lee A, Larson DE, Kurreeman F, Deluca TL, O'Laughlin M, Fronick CC, Fulton LL, Mardis ER, van der Horst-Bruinsma IE, Wolbink GJ, Gregersen PK, Kremer JM, Crusius JBA, de Vries N, Huizinga TWJ, Fonseca JE, Miceli-Richard C, Karlson EW, Coenen MJH, Barton A, Plenge RM, Raychaudhuri S. Brief Report: The Role of Rare Protein-Coding Variants in Anti-Tumor Necrosis Factor Treatment Response in Rheumatoid Arthritis. Arthritis Rheumatol 2017; 69:735-741. [PMID: 27788309 DOI: 10.1002/art.39966] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 10/20/2016] [Indexed: 12/29/2022]
Abstract
OBJECTIVE In many rheumatoid arthritis (RA) patients, disease is controlled with anti-tumor necrosis factor (anti-TNF) biologic therapies. However, in a significant number of patients, the disease fails to respond to anti-TNF therapy. We undertook the present study to examine the hypothesis that rare and low-frequency genetic variants might influence response to anti-TNF treatment. METHODS We sequenced the coding region of 750 genes in 1,094 RA patients of European ancestry who were treated with anti-TNF. After quality control, 690 genes were included in the analysis. We applied single-variant association and gene-based association tests to identify variants associated with anti-TNF treatment response. In addition, given the key mechanistic role of TNF, we performed gene set analyses of 27 TNF pathway genes. RESULTS We identified 14,420 functional variants, of which 6,934 were predicted as nonsynonymous 2,136 of which were further predicted to be "damaging." Despite the fact that the study was well powered, no single variant or gene showed study-wide significant association with change in the outcome measures disease activity or European League Against Rheumatism response. Intriguingly, we observed 3 genes, of 27 with nominal signals of association (P < 0.05), that were involved in the TNF signaling pathway. However, when we performed a rigorous gene set enrichment analysis based on association P value ranking, we observed no evidence of enrichment of association at genes involved in the TNF pathway (Penrichment = 0.15, based on phenotype permutations). CONCLUSION Our findings suggest that rare and low-frequency protein-coding variants in TNF signaling pathway genes or other genes do not contribute substantially to anti-TNF treatment response in patients with RA.
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Affiliation(s)
- Jing Cui
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Dorothee Diogo
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, and Broad Institute, Cambridge, Massachusetts
| | - Eli A Stahl
- Mount Sinai School of Medicine, New York, New York
| | | | - Xavier Mariette
- Université Paris Sud, INSERM U1184, Center for Immunology of Viral Infections and Autoimmune Diseases, Bicêtre Hospital, AP-HP, Paris, France
| | | | - Yukinori Okada
- Osaka University Graduate School of Medicine, Osaka, Japan
| | | | - Robert S Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Paul P Tak
- University of Amsterdam, Amsterdam, The Netherlands
| | | | - Annette Lee
- Feinstein Institute for Medical Research, Manhasset, New York
| | - David E Larson
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Fina Kurreeman
- Leiden University Medical Centre, Leiden, The Netherlands
| | - Tracie L Deluca
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Michelle O'Laughlin
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Catrina C Fronick
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Lucinda L Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Elaine R Mardis
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | | | - Gert-Jan Wolbink
- Amsterdam Rheumatology and Immunology Center, Reade, Amsterdam, The Netherlands
| | | | - Joel M Kremer
- Albany Medical College and the Center for Rheumatology, Albany, New York
| | | | | | | | | | | | | | | | - Anne Barton
- Centre for Musculoskeletal Research, University of Manchester and Central Manchester NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Robert M Plenge
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, and Broad Institute, Cambridge, Massachusetts
| | - Soumya Raychaudhuri
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, Broad Institute, Cambridge, Massachusetts, and Centre for Musculoskeletal Research, University of Manchester and Central Manchester NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
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43
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Krysiak K, Ramirez C, Gomez F, Miller CA, Fulton RS, Kreisel F, Cashen AF, Bartlett NL, Ruano A, Hsi ED, Griffith M, Griffith OL, Fehniger TA. Abstract 2444: Recurrent mutations and clinical outcomes in patients with follicular lymphoma. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-2444] [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
Follicular lymphoma (FL), the most common indolent non-Hodgkin lymphoma (NHL), is associated with a highly heterogeneous clinical course. The genetic landscape of FL is less understood than other B-cell NHLs such as chronic lymphocytic leukemia and diffuse large B-cell lymphoma. With ongoing clinical trials using therapies targeting B cell receptor signaling (e.g., ibrutinib) in FL, recurrent mutations could impact the interpretation of these trial outcomes and the identification of specific patient subpopulations that have increased or decreased clinical benefit.
To identify novel recurrent mutations in FL, we designed a large custom capture lymphoma-related gene panel (WUSM-LP) and queried 113 predominantly treatment-naïve FL samples. To design the WUSM-LP reagent (NimbleGen), we targeted the coding regions of 1716 genes identified in exome sequencing data from a cohort of 24 patients (28 samples) with FL combined with genes recurrently mutated in B-cell non-Hodgkin lymphoma in the literature (Krysiak K et al., Blood, 2016). Previously, we applied the WUSM-LP to the discovery cohort and an additional 81, primarily treatment-naïve, FL samples. Using mutations identified in these 105 individuals, we identified 39 significantly mutated genes (SMGs). These included well-characterized genes in FL (e.g., KMT2D, EZH2, TNFRSF14), and identified novel mutations (BTK, HVCN1, and others) thereby expanding the repertoire of mutations affecting genes in the BCR signaling pathway, SWI/SNF complex and histone family. Including novel BTK mutations, we identified 23 (22%) individuals harboring mutations that likely up-regulate signaling downstream of BTK, potentially affecting response rates to BTK-targeting therapies at the point of FL diagnosis.
We also focused on the subset FL patients (N=59) that were sequenced within 1 year of front-line therapy in order to identify clinical associations between recurrent mutations and clinical outcomes, comparing mutation status of SMGs to progression-free survival (PFS) rates. Improved PFS was observed in patients harboring HVCN1 mutations (p<0.05) in the treated cohort. CREBBP mutations were associated with significantly reduced PFS (p<0.05).
Since our initial analysis, we have completed sequencing of an additional 174 FL samples with clinical data available. Confirming our earlier observations with an independent cohort, we observed 9 TNFAIP3 truncating, 18 CARD11 coiled-coil domain, 4 BCL10 truncating and 8 BTK mutations in these samples. These mutations affect 18.4% of FL patients in this cohort, are likely to up-regulate NFkappaB signaling and may impact ibrutinib sensitivity. With the additional power of 8 HVCN1 and 110 CREBBP mutations we have identified, we will evaluate the previously identified associations. The analyses of recurrent mutations and clinical correlations in this combined cohort of nearly 300 FL patients are ongoing and will be presented.
Citation Format: Kilannin Krysiak, Cody Ramirez, Felicia Gomez, Christopher A. Miller, Robert S. Fulton, Friederike Kreisel, Amanda F. Cashen, Nancy L. Bartlett, Ana Ruano, Eric D. Hsi, Malachi Griffith, Obi L. Griffith, Todd A. Fehniger. Recurrent mutations and clinical outcomes in patients with follicular lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2444. doi:10.1158/1538-7445.AM2017-2444
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Affiliation(s)
| | - Cody Ramirez
- 1Washington University in Saint Louis, Saint Louis, MO
| | - Felicia Gomez
- 1Washington University in Saint Louis, Saint Louis, MO
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44
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Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, Fulton RS, Kremitzki M, Magrini V, Markovic C, McGrath S, Steinberg KM, Auger K, Chow W, Collins J, Harden G, Hubbard T, Pelan S, Simpson JT, Threadgold G, Torrance J, Wood JM, Clarke L, Koren S, Boitano M, Peluso P, Li H, Chin CS, Phillippy AM, Durbin R, Wilson RK, Flicek P, Eichler EE, Church DM. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Res 2017; 27:849-864. [PMID: 28396521 PMCID: PMC5411779 DOI: 10.1101/gr.213611.116] [Citation(s) in RCA: 501] [Impact Index Per Article: 71.6] [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: 07/29/2016] [Accepted: 03/14/2017] [Indexed: 11/24/2022]
Abstract
The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009; it reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures, and localization of previously orphaned sequences. We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues. For the first time, the reference assembly contains sequence-based representations for the centromeres. We also expanded the number of alternate loci to create a reference that provides a more robust representation of human population variation. We demonstrate that the updates render the reference an improved annotation substrate, alter read alignments in unchanged regions, and impact variant interpretation at clinically relevant loci. We additionally evaluated a collection of new de novo long-read haploid assemblies and conclude that although the new assemblies compare favorably to the reference with respect to continuity, error rate, and gene completeness, the reference still provides the best representation for complex genomic regions and coding sequences. We assert that the collected updates in GRCh38 make the newer assembly a more robust substrate for comprehensive analyses that will promote our understanding of human biology and advance our efforts to improve health.
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Affiliation(s)
- Valerie A Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Tina Graves-Lindsay
- McDonnell Genome Institute at Washington University, St. Louis, Missouri 63018, USA
| | - Kerstin Howe
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Nathan Bouk
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Hsiu-Chuan Chen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Paul A Kitts
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Derek Albracht
- McDonnell Genome Institute at Washington University, St. Louis, Missouri 63018, USA
| | - Robert S Fulton
- McDonnell Genome Institute at Washington University, St. Louis, Missouri 63018, USA
| | - Milinn Kremitzki
- McDonnell Genome Institute at Washington University, St. Louis, Missouri 63018, USA
| | - Vincent Magrini
- McDonnell Genome Institute at Washington University, St. Louis, Missouri 63018, USA
| | - Chris Markovic
- McDonnell Genome Institute at Washington University, St. Louis, Missouri 63018, USA
| | - Sean McGrath
- McDonnell Genome Institute at Washington University, St. Louis, Missouri 63018, USA
| | | | - Kate Auger
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - William Chow
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Joanna Collins
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Glenn Harden
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Timothy Hubbard
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Sarah Pelan
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Jared T Simpson
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Glen Threadgold
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - James Torrance
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Jonathan M Wood
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Sergey Koren
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | - Paul Peluso
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Heng Li
- Broad Institute, Cambridge, Massachusetts 02142, USA
| | | | - Adam M Phillippy
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Richard K Wilson
- McDonnell Genome Institute at Washington University, St. Louis, Missouri 63018, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
| | - Deanna M Church
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
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Purkait S, Miller CA, Kumar A, Sharma V, Pathak P, Jha P, Sharma MC, Suri V, Suri A, Sharma B, Fulton RS, Kale SS, Dahiya S, Sarkar C. ATRX in Diffuse Gliomas With its Mosaic/Heterogeneous Expression in a Subset. Brain Pathol 2017; 27:138-145. [PMID: 26833422 PMCID: PMC8029305 DOI: 10.1111/bpa.12364] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/24/2016] [Indexed: 12/25/2022] Open
Abstract
This study aims (1) to evaluate ATRX expression in different grades and subtypes of gliomas and correlate with other hallmark genetic alterations, (2) to identify and characterize mosaic/heterogeneous staining in gliomas in terms of mutation status. One hundred seventy six cases of glioma were assessed for ATRX immunohistochemistry and subdivided into positive, negative and mosaic/heterogeneous staining patterns. Five cases with heterogeneous staining were further subjected to next generation sequencing. Higher frequency of ATRX immune-negativity was detected in grade II/III astrocytic, oligoastrocytic tumors and secondary glioblastomas (GBMs), while infrequent in primary GBMs and rare in oligodendrogliomas. Loss of expression was significantly associated with IDH1 and/or TP53 mutation, while mutually exclusive with 1p/19q codeletion. Mosaic/heterogeneous staining was detected exclusively in GBMs (21.2%). Two different types of mosaic staining were identified (1) Admixture of positive and negative nuclei or intermixed mosaic and (2) Separate fragments with positive and negative/intermixed mosaic staining. ATRX mutation was identified in 2/5 (40%) cases with mosaic staining while one case showed DAXX mutation. All these cases were characterized by distinctly separate immune-negative and positive/intermixed foci. Hence, it is suggested that cases with heterogeneous staining (especially those with distinctly negative fragments) should be subjected to mutation analysis.
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Affiliation(s)
- Suvendu Purkait
- Department of PathologyAll India Institute of Medical Sciences (AIIMS)New DelhiIndia
| | | | - Anupam Kumar
- Department of PathologyAll India Institute of Medical Sciences (AIIMS)New DelhiIndia
| | - Vikas Sharma
- Department of PathologyAll India Institute of Medical Sciences (AIIMS)New DelhiIndia
| | - Pankaj Pathak
- Department of PathologyAll India Institute of Medical Sciences (AIIMS)New DelhiIndia
| | - Prerana Jha
- Department of PathologyAll India Institute of Medical Sciences (AIIMS)New DelhiIndia
| | - Mehar Chand Sharma
- Department of PathologyAll India Institute of Medical Sciences (AIIMS)New DelhiIndia
| | - Vaishali Suri
- Department of PathologyAll India Institute of Medical Sciences (AIIMS)New DelhiIndia
| | - Ashish Suri
- Department of NeurosurgeryAll India Institute of Medical Sciences (AIIMS)New DelhiIndia
| | - B.S. Sharma
- Department of NeurosurgeryAll India Institute of Medical Sciences (AIIMS)New DelhiIndia
| | - Robert S. Fulton
- McDonnell Genome Institute, Washington University School of MedicineSt. LouisMO
| | - Shashank Sharad Kale
- Department of NeurosurgeryAll India Institute of Medical Sciences (AIIMS)New DelhiIndia
| | - Sonika Dahiya
- Department of Pathology and ImmunologyWashington University School of MedicineSt. LouisMO
| | - Chitra Sarkar
- Department of PathologyAll India Institute of Medical Sciences (AIIMS)New DelhiIndia
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Spencer DH, Russler-Germain DA, Ketkar S, Helton NM, Lamprecht TL, Fulton RS, Fronick CC, O'Laughlin M, Heath SE, Shinawi M, Westervelt P, Payton JE, Wartman LD, Welch JS, Wilson RK, Walter MJ, Link DC, DiPersio JF, Ley TJ. CpG Island Hypermethylation Mediated by DNMT3A Is a Consequence of AML Progression. Cell 2017; 168:801-816.e13. [PMID: 28215704 DOI: 10.1016/j.cell.2017.01.021] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/21/2016] [Accepted: 01/19/2017] [Indexed: 12/11/2022]
Abstract
DNMT3A mutations occur in ∼25% of acute myeloid leukemia (AML) patients. The most common mutation, DNMT3AR882H, has dominant negative activity that reduces DNA methylation activity by ∼80% in vitro. To understand the contribution of DNMT3A-dependent methylation to leukemogenesis, we performed whole-genome bisulfite sequencing of primary leukemic and non-leukemic cells in patients with or without DNMT3AR882 mutations. Non-leukemic hematopoietic cells with DNMT3AR882H displayed focal methylation loss, suggesting that hypomethylation antedates AML. Although virtually all AMLs with wild-type DNMT3A displayed CpG island hypermethylation, this change was not associated with gene silencing and was essentially absent in AMLs with DNMT3AR882 mutations. Primary hematopoietic stem cells expanded with cytokines were hypermethylated in a DNMT3A-dependent manner, suggesting that hypermethylation may be a response to, rather than a cause of, cellular proliferation. Our findings suggest that hypomethylation is an initiating phenotype in AMLs with DNMT3AR882, while DNMT3A-dependent CpG island hypermethylation is a consequence of AML progression.
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Affiliation(s)
- David H Spencer
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; The McDonnell Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - David A Russler-Germain
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shamika Ketkar
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nichole M Helton
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tamara L Lamprecht
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Robert S Fulton
- The McDonnell Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - Catrina C Fronick
- The McDonnell Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - Michelle O'Laughlin
- The McDonnell Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - Sharon E Heath
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marwan Shinawi
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Peter Westervelt
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jacqueline E Payton
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lukas D Wartman
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; The McDonnell Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - John S Welch
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Richard K Wilson
- The McDonnell Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - Matthew J Walter
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Daniel C Link
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - John F DiPersio
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Timothy J Ley
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; The McDonnell Genome Institute, Washington University, St. Louis, MO 63110, USA.
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47
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Hoadley KA, Siegel MB, Kanchi KL, Miller CA, Ding L, Zhao W, He X, Parker JS, Wendl MC, Fulton RS, Demeter RT, Wilson RK, Carey LA, Perou CM, Mardis ER. Correction: Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases. PLoS Med 2017; 14:e1002222. [PMID: 28068332 PMCID: PMC5221755 DOI: 10.1371/journal.pmed.1002222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pmed.1002174.].
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48
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Hoadley KA, Siegel MB, Kanchi KL, Miller CA, Ding L, Zhao W, He X, Parker JS, Wendl MC, Fulton RS, Demeter RT, Wilson RK, Carey LA, Perou CM, Mardis ER. Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases. PLoS Med 2016; 13:e1002174. [PMID: 27923045 PMCID: PMC5140046 DOI: 10.1371/journal.pmed.1002174] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 10/12/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Metastasis is the main cause of cancer patient deaths and remains a poorly characterized process. It is still unclear when in tumor progression the ability to metastasize arises and whether this ability is inherent to the primary tumor or is acquired well after primary tumor formation. Next-generation sequencing and analytical methods to define clonal heterogeneity provide a means for identifying genetic events and the temporal relationships between these events in the primary and metastatic tumors within an individual. METHODS AND FINDINGS We performed DNA whole genome and mRNA sequencing on two primary tumors, each with either four or five distinct tissue site-specific metastases, from two individuals with triple-negative/basal-like breast cancers. As evidenced by their case histories, each patient had an aggressive disease course with abbreviated survival. In each patient, the overall gene expression signatures, DNA copy number patterns, and somatic mutation patterns were highly similar across each primary tumor and its associated metastases. Almost every mutation found in the primary was found in a metastasis (for the two patients, 52/54 and 75/75). Many of these mutations were found in every tumor (11/54 and 65/75, respectively). In addition, each metastasis had fewer metastatic-specific events and shared at least 50% of its somatic mutation repertoire with the primary tumor, and all samples from each patient grouped together by gene expression clustering analysis. TP53 was the only mutated gene in common between both patients and was present in every tumor in this study. Strikingly, each metastasis resulted from multiclonal seeding instead of from a single cell of origin, and few of the new mutations, present only in the metastases, were expressed in mRNAs. Because of the clinical differences between these two patients and the small sample size of our study, the generalizability of these findings will need to be further examined in larger cohorts of patients. CONCLUSIONS Our findings suggest that multiclonal seeding may be common amongst basal-like breast cancers. In these two patients, mutations and DNA copy number changes in the primary tumors appear to have had a biologic impact on metastatic potential, whereas mutations arising in the metastases were much more likely to be passengers.
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Affiliation(s)
- Katherine A. Hoadley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Marni B. Siegel
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Krishna L. Kanchi
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Christopher A. Miller
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Li Ding
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Wei Zhao
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Xiaping He
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Joel S. Parker
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Michael C. Wendl
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
- Department of Mathematics, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Robert S. Fulton
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Ryan T. Demeter
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Richard K. Wilson
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Lisa A. Carey
- Division of Hematology-Oncology, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Charles M. Perou
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Elaine R. Mardis
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
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49
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Zhang J, McCastlain K, Yoshihara H, Xu B, Chang Y, Churchman ML, Wu G, Li Y, Wei L, Iacobucci I, Liu Y, Qu C, Wen J, Edmonson M, Payne-Turner D, Kaufmann KB, Takayanagi SI, Wienholds E, Waanders E, Ntziachristos P, Bakogianni S, Wang J, Aifantis I, Roberts KG, Ma J, Song G, Easton J, Mulder HL, Chen X, Newman S, Ma X, Rusch M, Gupta P, Boggs K, Vadodaria B, Dalton J, Liu Y, Valentine ML, Ding L, Lu C, Fulton RS, Fulton L, Tabib Y, Ochoa K, Devidas M, Pei D, Cheng C, Yang J, Evans WE, Relling MV, Pui CH, Jeha S, Harvey RC, Chen IML, Willman CL, Marcucci G, Bloomfield CD, Kohlschmidt J, Mrózek K, Paietta E, Tallman MS, Stock W, Foster MC, Racevskis J, Rowe JM, Luger S, Kornblau SM, Shurtleff SA, Raimondi SC, Mardis ER, Wilson RK, Dick JE, Hunger SP, Loh ML, Downing JR, Mullighan CG. Deregulation of DUX4 and ERG in acute lymphoblastic leukemia. Nat Genet 2016; 48:1481-1489. [PMID: 27776115 PMCID: PMC5144107 DOI: 10.1038/ng.3691] [Citation(s) in RCA: 206] [Impact Index Per Article: 25.8] [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: 04/18/2016] [Accepted: 09/09/2016] [Indexed: 12/25/2022]
Abstract
Chromosomal rearrangements deregulating hematopoietic transcription factors are common in acute lymphoblastic leukemia (ALL). Here we show that deregulation of the homeobox transcription factor gene DUX4 and the ETS transcription factor gene ERG is a hallmark of a subtype of B-progenitor ALL that comprises up to 7% of B-ALL. DUX4 rearrangement and overexpression was present in all cases and was accompanied by transcriptional deregulation of ERG, expression of a novel ERG isoform, ERGalt, and frequent ERG deletion. ERGalt uses a non-canonical first exon whose transcription was initiated by DUX4 binding. ERGalt retains the DNA-binding and transactivation domains of ERG, but it inhibits wild-type ERG transcriptional activity and is transforming. These results illustrate a unique paradigm of transcription factor deregulation in leukemia in which DUX4 deregulation results in loss of function of ERG, either by deletion or induced expression of an isoform that is a dominant-negative inhibitor of wild-type ERG function.
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Affiliation(s)
- Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Kelly McCastlain
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Hiroki Yoshihara
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Beisi Xu
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Yunchao Chang
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | | | - Gang Wu
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Yongjin Li
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Lei Wei
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Yu Liu
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Chunxu Qu
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Ji Wen
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Michael Edmonson
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | | | - Kerstin B. Kaufmann
- Princess Margaret Cancer Centre, University Health Network and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Shin-ichiro Takayanagi
- Princess Margaret Cancer Centre, University Health Network and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Oncology Research Laboratories, Kyowa Hakko Kirin Co., Ltd., Machida-shi, Tokyo, 194-8533, Japan
| | - Erno Wienholds
- Princess Margaret Cancer Centre, University Health Network and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Esmé Waanders
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
- Department of Human Genetics, Radboud University Medical Center and Radboud Center for Molecular Life Sciences, Nijmegen, the Netherlands
| | | | - Sofia Bakogianni
- Department of Pathology, New York University School of Medicine, New York, NY
| | - Jingjing Wang
- Department of Pathology, New York University School of Medicine, New York, NY
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, NY
- Howard Hughes Medical Institute, New York, NY
| | - Kathryn G. Roberts
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Jing Ma
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Guangchun Song
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - John Easton
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Heather L. Mulder
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Scott Newman
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Pankaj Gupta
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Kristy Boggs
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Bhavin Vadodaria
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - James Dalton
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Yanling Liu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Marcus L Valentine
- Cytogenetics Core Facility, St. Jude Children’s Research Hospital, Memphis, TN
| | - Li Ding
- McDonnell Genome Institute, Washington University, St Louis, MO
| | - Charles Lu
- McDonnell Genome Institute, Washington University, St Louis, MO
| | | | - Lucinda Fulton
- McDonnell Genome Institute, Washington University, St Louis, MO
| | - Yashodhan Tabib
- McDonnell Genome Institute, Washington University, St Louis, MO
| | - Kerri Ochoa
- McDonnell Genome Institute, Washington University, St Louis, MO
| | - Meenakshi Devidas
- Department of Biostatistics, Colleges of Medicine, Public Health & Health Profession, University of Florida, Gainesville, FL
| | - 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
| | - Jun Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - William E. Evans
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Mary V. Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Sima Jeha
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Richard C. Harvey
- Department of Pathology, The Cancer Research and Treatment Center, University of New Mexico, Albuquerque, NM
| | - I-Ming L Chen
- Department of Pathology, The Cancer Research and Treatment Center, University of New Mexico, Albuquerque, NM
| | - Cheryl L. Willman
- Department of Pathology, The Cancer Research and Treatment Center, University of New Mexico, Albuquerque, NM
| | | | | | | | - Krzysztof Mrózek
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | | | | | - Wendy Stock
- University of Chicago Medical Center, Chicago, IL
| | - Matthew C. Foster
- Division of Hematology/Oncology, University of North Carolina, Chapel Hill, NC
| | - Janis Racevskis
- Department of Medicine (Oncology), Albert Einstein College of Medicine, Montefiore Medical Center, New York, NY
| | - Jacob M. Rowe
- Department of Pediatrics, Children’s Hospital of Philadelphia and the University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Selina Luger
- Department of Pediatrics, Benioff Children’s Hospital, University of California at San Francisco, San Francisco, CA
| | - Steven M. Kornblau
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Sheila A Shurtleff
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Susana C. Raimondi
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | | | | | - John E. Dick
- Princess Margaret Cancer Centre, University Health Network and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Stephen P Hunger
- Department of Pediatrics, Children’s Hospital of Philadelphia and the University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Mignon L. Loh
- Department of Pediatrics, Benioff Children’s Hospital, University of California at San Francisco, San Francisco, CA
| | - James R. Downing
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
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50
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Welch JS, Petti AA, Miller CA, Fronick CC, O'Laughlin M, Fulton RS, Wilson RK, Baty JD, Duncavage EJ, Tandon B, Lee YS, Wartman LD, Uy GL, Ghobadi A, Tomasson MH, Pusic I, Romee R, Fehniger TA, Stockerl-Goldstein KE, Vij R, Oh ST, Abboud CN, Cashen AF, Schroeder MA, Jacoby MA, Heath SE, Luber K, Janke MR, Hantel A, Khan N, Sukhanova MJ, Knoebel RW, Stock W, Graubert TA, Walter MJ, Westervelt P, Link DC, DiPersio JF, Ley TJ. TP53 and Decitabine in Acute Myeloid Leukemia and Myelodysplastic Syndromes. N Engl J Med 2016; 375:2023-2036. [PMID: 27959731 PMCID: PMC5217532 DOI: 10.1056/nejmoa1605949] [Citation(s) in RCA: 596] [Impact Index Per Article: 74.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND The molecular determinants of clinical responses to decitabine therapy in patients with acute myeloid leukemia (AML) or myelodysplastic syndromes (MDS) are unclear. METHODS We enrolled 84 adult patients with AML or MDS in a single-institution trial of decitabine to identify somatic mutations and their relationships to clinical responses. Decitabine was administered at a dose of 20 mg per square meter of body-surface area per day for 10 consecutive days in monthly cycles. We performed enhanced exome or gene-panel sequencing in 67 of these patients and serial sequencing at multiple time points to evaluate patterns of mutation clearance in 54 patients. An extension cohort included 32 additional patients who received decitabine in different protocols. RESULTS Of the 116 patients, 53 (46%) had bone marrow blast clearance (<5% blasts). Response rates were higher among patients with an unfavorable-risk cytogenetic profile than among patients with an intermediate-risk or favorable-risk cytogenetic profile (29 of 43 patients [67%] vs. 24 of 71 patients [34%], P<0.001) and among patients with TP53 mutations than among patients with wild-type TP53 (21 of 21 [100%] vs. 32 of 78 [41%], P<0.001). Previous studies have consistently shown that patients with an unfavorable-risk cytogenetic profile and TP53 mutations who receive conventional chemotherapy have poor outcomes. However, in this study of 10-day courses of decitabine, neither of these risk factors was associated with a lower rate of overall survival than the rate of survival among study patients with intermediate-risk cytogenetic profiles. CONCLUSIONS Patients with AML and MDS who had cytogenetic abnormalities associated with unfavorable risk, TP53 mutations, or both had favorable clinical responses and robust (but incomplete) mutation clearance after receiving serial 10-day courses of decitabine. Although these responses were not durable, they resulted in rates of overall survival that were similar to those among patients with AML who had an intermediate-risk cytogenetic profile and who also received serial 10-day courses of decitabine. (Funded by the National Cancer Institute and others; ClinicalTrials.gov number, NCT01687400 .).
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MESH Headings
- 5-Methylcytosine/analysis
- Adult
- Aged
- Aged, 80 and over
- Antimetabolites, Antineoplastic/administration & dosage
- Antimetabolites, Antineoplastic/adverse effects
- Azacitidine/administration & dosage
- Azacitidine/adverse effects
- Azacitidine/analogs & derivatives
- Biomarkers, Tumor/analysis
- Bone Marrow/chemistry
- Bone Marrow/pathology
- Decitabine
- Exome
- Female
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/mortality
- Male
- Middle Aged
- Mutation
- Myelodysplastic Syndromes/drug therapy
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/mortality
- Prospective Studies
- Risk Factors
- Survival Rate
- Tumor Suppressor Protein p53/genetics
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Affiliation(s)
- John S Welch
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Allegra A Petti
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Christopher A Miller
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Catrina C Fronick
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Michelle O'Laughlin
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Robert S Fulton
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Richard K Wilson
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Jack D Baty
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Eric J Duncavage
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Bevan Tandon
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Yi-Shan Lee
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Lukas D Wartman
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Geoffrey L Uy
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Armin Ghobadi
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Michael H Tomasson
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Iskra Pusic
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Rizwan Romee
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Todd A Fehniger
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Keith E Stockerl-Goldstein
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Ravi Vij
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Stephen T Oh
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Camille N Abboud
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Amanda F Cashen
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Mark A Schroeder
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Meagan A Jacoby
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Sharon E Heath
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Kierstin Luber
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Megan R Janke
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Andrew Hantel
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Niloufer Khan
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Madina J Sukhanova
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Randall W Knoebel
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Wendy Stock
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Timothy A Graubert
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Matthew J Walter
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Peter Westervelt
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Daniel C Link
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - John F DiPersio
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
| | - Timothy J Ley
- the Department of Internal Medicine, Division of Oncology (J.S.W., L.D.W., G.L.U., A.G., M.H.T., I.P., R.R., T.A.F., K.E.S.-G., R.V., S.T.O., C.N.A., A.F.C., M.A.S., M.A.J., S.E.H., K.L., M.R.J., M.J.W., P.W., D.C.L., J.F.D., T.J.L.), and the Division of Biostatistics (J.D.B.), and the Department of Pathology and Immunology (E.J.D., B.T., Y.-S.L.), Washington University School of Medicine, and McDonnell Genome Institute, Washington University in St. Louis (A.A.P., C.A.M., C.C.F., M.O., R.S.F., R.K.W., L.D.W., T.J.L.) - both in St. Louis; the Departments of Internal Medicine (A.H., N.K., M.J.S., W.S.) and Pharmacy (R.W.K.), University of Chicago, Chicago; and the Department of Internal Medicine (T.A.G.), Massachusetts General Hospital, Boston
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