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Weng LC, Rämö JT, Jurgens SJ, Khurshid S, Chaffin M, Hall AW, Morrill VN, Wang X, Nauffal V, Sun YV, Beer D, Lee S, Nadkarni GN, Duong T, Wang B, Czuba T, Austin TR, Yoneda ZT, Friedman DJ, Clayton A, Hyman MC, Judy RL, Skanes AC, Orland KM, Treu TM, Oetjens MT, Alonso A, Soliman EZ, Lin H, Lunetta KL, van der Pals J, Issa TZ, Nafissi NA, May HT, Leong-Sit P, Roselli C, Choi SH, Khan HR, Knight S, Karlsson Linnér R, Bezzina CR, Ripatti S, Heckbert SR, Gaziano JM, Loos RJF, Psaty BM, Smith JG, Benjamin EJ, Arking DE, Rader DJ, Shah SH, Roden DM, Damrauer SM, Eckhardt LL, Roberts JD, Cutler MJ, Shoemaker MB, Haggerty CM, Cho K, Palotie A, Wilson PWF, Ellinor PT, Lubitz SA. The impact of common and rare genetic variants on bradyarrhythmia development. Nat Genet 2025; 57:53-64. [PMID: 39747593 PMCID: PMC11735381 DOI: 10.1038/s41588-024-01978-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 10/09/2024] [Indexed: 01/04/2025]
Abstract
To broaden our understanding of bradyarrhythmias and conduction disease, we performed common variant genome-wide association analyses in up to 1.3 million individuals and rare variant burden testing in 460,000 individuals for sinus node dysfunction (SND), distal conduction disease (DCD) and pacemaker (PM) implantation. We identified 13, 31 and 21 common variant loci for SND, DCD and PM, respectively. Four well-known loci (SCN5A/SCN10A, CCDC141, TBX20 and CAMK2D) were shared for SND and DCD, while others were more specific for SND or DCD. SND and DCD showed a moderate genetic correlation (rg = 0.63). Cardiomyocyte-expressed genes were enriched for contributions to DCD heritability. Rare-variant analyses implicated LMNA for all bradyarrhythmia phenotypes, SMAD6 and SCN5A for DCD and TTN, MYBPC3 and SCN5A for PM. These results show that variation in multiple genetic pathways (for example, ion channel function, cardiac developmental programs, sarcomeric structure and cellular homeostasis) appear critical to the development of bradyarrhythmias.
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Grants
- R01 HL141901 NHLBI NIH HHS
- R01 HL139738 NHLBI NIH HHS
- 18SFRN34250007 American Heart Association (American Heart Association, Inc.)
- TNE FANTASY 19CV03 Fondation Leducq
- R01 HL092577 NHLBI NIH HHS
- R01 HL105756 NHLBI NIH HHS
- R01 HL157635 NHLBI NIH HHS
- R01 HL139731 NHLBI NIH HHS
- U01 AG068221 NIA NIH HHS
- 23CDA1050571 American Heart Association (American Heart Association, Inc.)
- T32 HL007101 NHLBI NIH HHS
- R01 AG083735 NIA NIH HHS
- 18SFRN34110082 American Heart Association (American Heart Association, Inc.)
- 18SFRN34230127 American Heart Association (American Heart Association, Inc.)
- IK2 CX001780 CSRD VA
- 75N92019D00031 NHLBI NIH HHS
- K23 HL169839 NHLBI NIH HHS
- 03-007-2022-0035 Hartstichting (Dutch Heart Foundation)
- R21 HL175584 NHLBI NIH HHS
- R01 HL163987 NHLBI NIH HHS
- National Institutes of Health:R01HL139731 & R01HL157635
- Sigrid Juséliuksen Säätiö (Sigrid Jusélius Foundation)
- National Institutes of Health: K23HL169839
- National Institutes of Health: RO1HL092577
- National Institutes of Health: T32HL007101
- Swedish Heart-Lung Foundation (2022-0344, 2022-0345), the Swedish Research Council (2021-02273), the European Research Council (ERC-STG-2015-679242), Gothenburg University, Skane University Hospital, the Scania county, governmental funding of clinical research within the Swedish National Health Service, a generous donation from the Knut and Alice Wallenberg foundation to the Wallenberg Center for Molecular Medicine in Lund, and funding from the Swedish Research Council (Linnaeus grant Dnr 349-2006-237, Strategic Research Area Exodiab Dnr 2009-1039) and Swedish Foundation for Strategic Research (Dnr IRC15-0067) to the Lund University Diabetes Center.
- US Department of Veterans Affairs Clinical Research and Development award IK2-CX001780
- National Institutes of Health: R01HL163987-01 and R01HL139738-01
- Academy of Finland Centre of Excellence in Complex Disease Genetics (grant no. 312074 and 336824)
- National Institutes of Health: R01HL139731, R01HL157635, and RO1HL092577 European Union: MAESTRIA 965286
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Affiliation(s)
- Lu-Chen Weng
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | - Joel T Rämö
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sean J Jurgens
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Experimental Cardiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Shaan Khurshid
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Telemachus and Irene Demoulas Family Foundation Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA
| | - Mark Chaffin
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amelia Weber Hall
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Valerie N Morrill
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xin Wang
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Victor Nauffal
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
- Cardiovascular Medicine Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Yan V Sun
- VA Atlanta Healthcare System, Decatur, GA, USA
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | | | - Simon Lee
- Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | | | - ThuyVy Duong
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Biqi Wang
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Tomasz Czuba
- The Wallenberg Laboratory/Department of Molecular and Clinical Medicine, Institute of Medicine, Gothenburg University, Gothenburg, Sweden
- Department of Cardiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Thomas R Austin
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Zachary T Yoneda
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Daniel J Friedman
- Division of Cardiology, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Anne Clayton
- Intermountain Heart Institute, Intermountain Medical Center, Murray, UT, USA
| | - Matthew C Hyman
- Division of Cardiac Electrophysiology, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Renae L Judy
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Allan C Skanes
- Section of Cardiac Electrophysiology, Division of Cardiology, Department of Medicine, Western University, London, Ontario, Canada
| | - Kate M Orland
- Department of Medicine, Division of Cardiovascular Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Matthew T Oetjens
- Autism and Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | - Alvaro Alonso
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Elsayed Z Soliman
- Epidemiological Cardiology Research Center, Section on Cardiovascular Medicine, Department of Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Honghuang Lin
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Jesper van der Pals
- Department of Cardiology, Clinical Sciences, Lund University and Skane University Hospital, Lund, Sweden
| | - Tariq Z Issa
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Navid A Nafissi
- Division of Cardiology, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Heidi T May
- Intermountain Heart Institute, Intermountain Medical Center, Murray, UT, USA
| | - Peter Leong-Sit
- Section of Cardiac Electrophysiology, Division of Cardiology, Department of Medicine, Western University, London, Ontario, Canada
| | - Carolina Roselli
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Seung Hoan Choi
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Habib R Khan
- Section of Cardiac Electrophysiology, Western University, London, Ontario, Canada
| | - Stacey Knight
- Intermountain Heart Institute, Intermountain Medical Center, Murray, UT, USA
- Department of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Richard Karlsson Linnér
- Autism and Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
- Department of Economics, Leiden Law School, Leiden University, Leiden, The Netherlands
| | - Connie R Bezzina
- Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Heart Center, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Susan R Heckbert
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - J Michael Gaziano
- VA Boston Healthcare System, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA, USA
| | - J Gustav Smith
- The Wallenberg Laboratory/Department of Molecular and Clinical Medicine, Institute of Medicine, Gothenburg University, Gothenburg, Sweden
- Department of Cardiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Cardiology, Clinical Sciences, Lund University and Skane University Hospital, Lund, Sweden
- Wallenberg Center for Molecular Medicine and Lund University Diabetes Center, Lund University, Lund, Sweden
| | - Emelia J Benjamin
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
- NHLBI and BU's Framingham Heart Study, Framingham, MA, USA
| | - Dan E Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel J Rader
- Departments of Medicine and Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Svati H Shah
- Division of Cardiology, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Dan M Roden
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - Scott M Damrauer
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics and Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lee L Eckhardt
- Department of Medicine, Division of Cardiovascular Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Jason D Roberts
- Section of Cardiac Electrophysiology, Division of Cardiology, Department of Medicine, Western University, London, Ontario, Canada
| | - Michael J Cutler
- Intermountain Heart Institute, Intermountain Medical Center, Murray, UT, USA
| | - M Benjamin Shoemaker
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christopher M Haggerty
- Heart Institute, Geisinger, Danville, PA, USA
- Department of Translational Data Science and Informatics, Geisinger, Danville, PA, USA
| | - Kelly Cho
- VA Boston Healthcare System, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- The Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Department of Neurology and Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Peter W F Wilson
- VA Atlanta Healthcare System, Decatur, GA, USA
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Telemachus and Irene Demoulas Family Foundation Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA
| | - Steven A Lubitz
- Telemachus and Irene Demoulas Family Foundation Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA.
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5
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Bhagawati M, Paul S, Agarwal S, Protogeron A, Sfikakis PP, Kitas GD, Khanna NN, Ruzsa Z, Sharma AM, Tomazu O, Turk M, Faa G, Tsoulfas G, Laird JR, Rathore V, Johri AM, Viskovic K, Kalra M, Balestrieri A, Nicolaides A, Singh IM, Chaturvedi S, Paraskevas KI, Fouda MM, Saba L, Suri JS. Cardiovascular disease/stroke risk stratification in deep learning framework: a review. Cardiovasc Diagn Ther 2023; 13:557-598. [PMID: 37405023 PMCID: PMC10315429 DOI: 10.21037/cdt-22-438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 05/17/2023] [Indexed: 07/06/2023]
Abstract
The global mortality rate is known to be the highest due to cardiovascular disease (CVD). Thus, preventive, and early CVD risk identification in a non-invasive manner is vital as healthcare cost is increasing day by day. Conventional methods for risk prediction of CVD lack robustness due to the non-linear relationship between risk factors and cardiovascular events in multi-ethnic cohorts. Few recently proposed machine learning-based risk stratification reviews without deep learning (DL) integration. The proposed study focuses on CVD risk stratification by the use of techniques mainly solo deep learning (SDL) and hybrid deep learning (HDL). Using a PRISMA model, 286 DL-based CVD studies were selected and analyzed. The databases included were Science Direct, IEEE Xplore, PubMed, and Google Scholar. This review is focused on different SDL and HDL architectures, their characteristics, applications, scientific and clinical validation, along with plaque tissue characterization for CVD/stroke risk stratification. Since signal processing methods are also crucial, the study further briefly presented Electrocardiogram (ECG)-based solutions. Finally, the study presented the risk due to bias in AI systems. The risk of bias tools used were (I) ranking method (RBS), (II) region-based map (RBM), (III) radial bias area (RBA), (IV) prediction model risk of bias assessment tool (PROBAST), and (V) risk of bias in non-randomized studies-of interventions (ROBINS-I). The surrogate carotid ultrasound image was mostly used in the UNet-based DL framework for arterial wall segmentation. Ground truth (GT) selection is vital for reducing the risk of bias (RoB) for CVD risk stratification. It was observed that the convolutional neural network (CNN) algorithms were widely used since the feature extraction process was automated. The ensemble-based DL techniques for risk stratification in CVD are likely to supersede the SDL and HDL paradigms. Due to the reliability, high accuracy, and faster execution on dedicated hardware, these DL methods for CVD risk assessment are powerful and promising. The risk of bias in DL methods can be best reduced by considering multicentre data collection and clinical evaluation.
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Affiliation(s)
- Mrinalini Bhagawati
- Department of Biomedical Engineering, North-Eastern Hill University, Shillong, India
| | - Sudip Paul
- Department of Biomedical Engineering, North-Eastern Hill University, Shillong, India
| | - Sushant Agarwal
- Advanced Knowledge Engineering Centre, GBTI, Roseville, CA, USA
- Department of Computer Science Engineering, PSIT, Kanpur, India
| | - Athanasios Protogeron
- Department of Cardiovascular Prevention & Research Unit Clinic & Laboratory of Pathophysiology, National and Kapodistrian University of Athens, Athens, Greece
| | - Petros P. Sfikakis
- Rheumatology Unit, National Kapodistrian University of Athens, Athens, Greece
| | - George D. Kitas
- Arthritis Research UK Centre for Epidemiology, Manchester University, Manchester, UK
| | - Narendra N. Khanna
- Department of Cardiology, Indraprastha APOLLO Hospitals, New Delhi, India
| | | | - Aditya M. Sharma
- Division of Cardiovascular Medicine, University of Virginia, Charlottesville, VA, USA
| | - Omerzu Tomazu
- Department of Neurology, University Medical Centre Maribor, Maribor, Slovenia
| | - Monika Turk
- The Hanse-Wissenschaftskolleg Institute for Advanced Study, Delmenhorst, Germany
| | - Gavino Faa
- Department of Pathology, A.O.U., di Cagliari -Polo di Monserrato s.s, Cagliari, Italy
| | - George Tsoulfas
- Aristoteleion University of Thessaloniki, Thessaloniki, Greece
| | - John R. Laird
- Cardiology Department, St. Helena Hospital, St. Helena, CA, USA
| | - Vijay Rathore
- Nephrology Department, Kaiser Permanente, Sacramento, CA, USA
| | - Amer M. Johri
- Department of Medicine, Division of Cardiology, Queen’s University, Kingston, Canada
| | | | - Manudeep Kalra
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Antonella Balestrieri
- Department of Radiology, Azienda Ospedaliero Universitaria (A.O.U.), Cagliari, Italy
| | - Andrew Nicolaides
- Vascular Screening and Diagnostic Centre, University of Nicosia Medical School, Nicosia, Cyprus
| | - Inder M. Singh
- Stroke Diagnostic and Monitoring Division, AtheroPoint™, Roseville, CA, USA
| | - Seemant Chaturvedi
- Department of Neurology & Stroke Program, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kosmas I. Paraskevas
- Department of Vascular Surgery, Central Clinic of Athens, N. Iraklio, Athens, Greece
| | | | - Luca Saba
- Department of Radiology, Azienda Ospedaliero Universitaria (A.O.U.), Cagliari, Italy
| | - Jasjit S. Suri
- Stroke Diagnostic and Monitoring Division, AtheroPoint™, Roseville, CA, USA
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