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Kaivola K, Chia R, Ding J, Rasheed M, Fujita M, Menon V, Walton RL, Collins RL, Billingsley K, Brand H, Talkowski M, Zhao X, Dewan R, Stark A, Ray A, Solaiman S, Alvarez Jerez P, Malik L, Dawson TM, Rosenthal LS, Albert MS, Pletnikova O, Troncoso JC, Masellis M, Keith J, Black SE, Ferrucci L, Resnick SM, Tanaka T, Topol E, Torkamani A, Tienari P, Foroud TM, Ghetti B, Landers JE, Ryten M, Morris HR, Hardy JA, Mazzini L, D'Alfonso S, Moglia C, Calvo A, Serrano GE, Beach TG, Ferman T, Graff-Radford NR, Boeve BF, Wszolek ZK, Dickson DW, Chiò A, Bennett DA, De Jager PL, Ross OA, Dalgard CL, Gibbs JR, Traynor BJ, Scholz SW. Genome-wide structural variant analysis identifies risk loci for non-Alzheimer's dementias. CELL GENOMICS 2023; 3:100316. [PMID: 37388914 PMCID: PMC10300553 DOI: 10.1016/j.xgen.2023.100316] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/21/2023] [Accepted: 04/06/2023] [Indexed: 07/01/2023]
Abstract
We characterized the role of structural variants, a largely unexplored type of genetic variation, in two non-Alzheimer's dementias, namely Lewy body dementia (LBD) and frontotemporal dementia (FTD)/amyotrophic lateral sclerosis (ALS). To do this, we applied an advanced structural variant calling pipeline (GATK-SV) to short-read whole-genome sequence data from 5,213 European-ancestry cases and 4,132 controls. We discovered, replicated, and validated a deletion in TPCN1 as a novel risk locus for LBD and detected the known structural variants at the C9orf72 and MAPT loci as associated with FTD/ALS. We also identified rare pathogenic structural variants in both LBD and FTD/ALS. Finally, we assembled a catalog of structural variants that can be mined for new insights into the pathogenesis of these understudied forms of dementia.
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Affiliation(s)
- Karri Kaivola
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Ruth Chia
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Jinhui Ding
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Memoona Rasheed
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Masashi Fujita
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, New York, NY, USA
| | - Vilas Menon
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, New York, NY, USA
| | - Ronald L. Walton
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
| | - Ryan L. Collins
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T.), Cambridge, MA, USA
- Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kimberley Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
- Centre for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T.), Cambridge, MA, USA
- Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Michael Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T.), Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Xuefang Zhao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T.), Cambridge, MA, USA
| | - Ramita Dewan
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Ali Stark
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Anindita Ray
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Sultana Solaiman
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Pilar Alvarez Jerez
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
- Centre for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD, USA
| | - Laksh Malik
- Centre for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD, USA
| | - Ted M. Dawson
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Neuroregeneration and Stem Cell Programs, Institute of Cell Engineering, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Department of Pharmacology and Molecular Science, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Liana S. Rosenthal
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Marilyn S. Albert
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Olga Pletnikova
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University of Buffalo, Buffalo, NY, USA
- Department of Pathology (Neuropathology), Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Juan C. Troncoso
- Department of Pathology (Neuropathology), Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Mario Masellis
- Cognitive & Movement Disorders Clinic, Sunnybrook Health Sciences Centre, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
- Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON, Canada
- Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, University of Toronto, 2075 Bayview Avenue, Toronto, ON, Canada
- LC Campbell Cognitive Neurology Research Unit, Sunnybrook Research Institute, University of Toronto, 2075 Bayview Avenue, Toronto, ON, Canada
| | - Julia Keith
- Department of Anatomical Pathology, Sunnybrook Health Sciences Centre, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
| | - Sandra E. Black
- Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON, Canada
- Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, University of Toronto, 2075 Bayview Avenue, Toronto, ON, Canada
- LC Campbell Cognitive Neurology Research Unit, Sunnybrook Research Institute, University of Toronto, 2075 Bayview Avenue, Toronto, ON, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
- Heart and Stroke Foundation Canadian Partnership for Stroke Recovery, Sunnybrook Health Sciences Centre, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
| | - Luigi Ferrucci
- Longitudinal Studies Section, National Institute on Aging, Baltimore, MD, USA
| | - Susan M. Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Baltimore, MD, USA
| | - Toshiko Tanaka
- Longitudinal Studies Section, National Institute on Aging, Baltimore, MD, USA
| | - PROSPECT Consortium
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, New York, NY, USA
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T.), Cambridge, MA, USA
- Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA, USA
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
- Centre for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Neuroregeneration and Stem Cell Programs, Institute of Cell Engineering, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Department of Pharmacology and Molecular Science, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University of Buffalo, Buffalo, NY, USA
- Department of Pathology (Neuropathology), Johns Hopkins University Medical Center, Baltimore, MD, USA
- Cognitive & Movement Disorders Clinic, Sunnybrook Health Sciences Centre, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
- Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON, Canada
- Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, University of Toronto, 2075 Bayview Avenue, Toronto, ON, Canada
- LC Campbell Cognitive Neurology Research Unit, Sunnybrook Research Institute, University of Toronto, 2075 Bayview Avenue, Toronto, ON, Canada
- Department of Anatomical Pathology, Sunnybrook Health Sciences Centre, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
- Heart and Stroke Foundation Canadian Partnership for Stroke Recovery, Sunnybrook Health Sciences Centre, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
- Longitudinal Studies Section, National Institute on Aging, Baltimore, MD, USA
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Baltimore, MD, USA
- Scripps Research Translational Institute, Scripps Research, La Jolla, CA, USA
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, University College London, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
- UCL Movement Disorders Centre, University College London, London, UK
- UK Dementia Research Institute, Department of Neurogenerative Disease and Reta Lila Weston Institute, London, UK
- Institute of Advanced Study, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Maggiore della Carita University Hospital, Novara, Italy
- Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy
- Azienda Ospedaliero Universitaria Città, della Salute e della Scienza, Corso Bramante, 88, Turin, Italy
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
- Department of Psychiatry and Psychology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
- Department of Neurology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
- Center for Sleep Medicine, Mayo Clinic, Rochester, MN, USA
- Institute of Cognitive Sciences and Technologies, C.N.R., Via S. Martino della Battaglia, 44, Rome, Italy
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- RNA Therapeutics Laboratory, Therapeutics Development Branch, National Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Eric Topol
- Scripps Research Translational Institute, Scripps Research, La Jolla, CA, USA
| | - Ali Torkamani
- Scripps Research Translational Institute, Scripps Research, La Jolla, CA, USA
| | - Pentti Tienari
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
| | - Tatiana M. Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - John E. Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Mina Ryten
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, University College London, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - Huw R. Morris
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
- UCL Movement Disorders Centre, University College London, London, UK
| | - John A. Hardy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
- UCL Movement Disorders Centre, University College London, London, UK
- UK Dementia Research Institute, Department of Neurogenerative Disease and Reta Lila Weston Institute, London, UK
- Institute of Advanced Study, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | | | - Sandra D'Alfonso
- Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | - Cristina Moglia
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy
- Azienda Ospedaliero Universitaria Città, della Salute e della Scienza, Corso Bramante, 88, Turin, Italy
| | - Andrea Calvo
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy
- Azienda Ospedaliero Universitaria Città, della Salute e della Scienza, Corso Bramante, 88, Turin, Italy
| | - Geidy E. Serrano
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Thomas G. Beach
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Tanis Ferman
- Department of Psychiatry and Psychology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
| | | | | | - Zbigniew K. Wszolek
- Institute of Cognitive Sciences and Technologies, C.N.R., Via S. Martino della Battaglia, 44, Rome, Italy
| | - Dennis W. Dickson
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
| | - Adriano Chiò
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy
- Azienda Ospedaliero Universitaria Città, della Salute e della Scienza, Corso Bramante, 88, Turin, Italy
- Institute of Cognitive Sciences and Technologies, C.N.R., Via S. Martino della Battaglia, 44, Rome, Italy
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, New York, NY, USA
| | - Owen A. Ross
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
| | - Clifton L. Dalgard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - J. Raphael Gibbs
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Bryan J. Traynor
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
- RNA Therapeutics Laboratory, Therapeutics Development Branch, National Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Sonja W. Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
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