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Mosley JD, Shelley JP, Dickson AL, Zanussi J, Daniel LL, Zheng NS, Bastarache L, Wei WQ, Shi M, Jarvik GP, Rosenthal EA, Khan A, Sherafati A, Kullo IJ, Walunas TL, Glessner J, Hakonarson H, Cox NJ, Roden DM, Frangakis SG, Vanderwerff B, Stein CM, Van Driest SL, Borinstein SC, Shu XO, Zawistowski M, Chung CP, Kawai VK. Clinical associations with a polygenic predisposition to benign lower white blood cell counts. Nat Commun 2024; 15:3384. [PMID: 38649760 PMCID: PMC11035609 DOI: 10.1038/s41467-024-47804-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 08/20/2023] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
Polygenic variation unrelated to disease contributes to interindividual variation in baseline white blood cell (WBC) counts, but its clinical significance is uncharacterized. We investigated the clinical consequences of a genetic predisposition toward lower WBC counts among 89,559 biobank participants from tertiary care centers using a polygenic score for WBC count (PGSWBC) comprising single nucleotide polymorphisms not associated with disease. A predisposition to lower WBC counts was associated with a decreased risk of identifying pathology on a bone marrow biopsy performed for a low WBC count (odds-ratio = 0.55 per standard deviation increase in PGSWBC [95%CI, 0.30-0.94], p = 0.04), an increased risk of leukopenia (a low WBC count) when treated with a chemotherapeutic (n = 1724, hazard ratio [HR] = 0.78 [0.69-0.88], p = 4.0 × 10-5) or immunosuppressant (n = 354, HR = 0.61 [0.38-0.99], p = 0.04). A predisposition to benign lower WBC counts was associated with an increased risk of discontinuing azathioprine treatment (n = 1,466, HR = 0.62 [0.44-0.87], p = 0.006). Collectively, these findings suggest that there are genetically predisposed individuals who are susceptible to escalations or alterations in clinical care that may be harmful or of little benefit.
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Affiliation(s)
- Jonathan D Mosley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - John P Shelley
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alyson L Dickson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jacy Zanussi
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Laura L Daniel
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Neil S Zheng
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Yale School of Medicine, New Haven, CT, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mingjian Shi
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gail P Jarvik
- Department of Genome Sciences, University of Washington Medical Center, Seattle, WA, USA
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA, USA
| | - Elisabeth A Rosenthal
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA, USA
| | - Atlas Khan
- Division of Nephrology, Dept of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Alborz Sherafati
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Theresa L Walunas
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Joseph Glessner
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nancy J Cox
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Stephan G Frangakis
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Brett Vanderwerff
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - C Michael Stein
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sara L Van Driest
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Scott C Borinstein
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiao-Ou Shu
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Matthew Zawistowski
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | | | - Vivian K Kawai
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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Yan C, Ong HH, Grabowska ME, Krantz MS, Su WC, Dickson AL, Peterson JF, Feng Q, Roden DM, Stein CM, Kerchberger VE, Malin BA, Wei WQ. Large language models facilitate the generation of electronic health record phenotyping algorithms. J Am Med Inform Assoc 2024:ocae072. [PMID: 38613820 DOI: 10.1093/jamia/ocae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/21/2024] [Accepted: 03/22/2024] [Indexed: 04/15/2024] Open
Abstract
OBJECTIVES Phenotyping is a core task in observational health research utilizing electronic health records (EHRs). Developing an accurate algorithm demands substantial input from domain experts, involving extensive literature review and evidence synthesis. This burdensome process limits scalability and delays knowledge discovery. We investigate the potential for leveraging large language models (LLMs) to enhance the efficiency of EHR phenotyping by generating high-quality algorithm drafts. MATERIALS AND METHODS We prompted four LLMs-GPT-4 and GPT-3.5 of ChatGPT, Claude 2, and Bard-in October 2023, asking them to generate executable phenotyping algorithms in the form of SQL queries adhering to a common data model (CDM) for three phenotypes (ie, type 2 diabetes mellitus, dementia, and hypothyroidism). Three phenotyping experts evaluated the returned algorithms across several critical metrics. We further implemented the top-rated algorithms and compared them against clinician-validated phenotyping algorithms from the Electronic Medical Records and Genomics (eMERGE) network. RESULTS GPT-4 and GPT-3.5 exhibited significantly higher overall expert evaluation scores in instruction following, algorithmic logic, and SQL executability, when compared to Claude 2 and Bard. Although GPT-4 and GPT-3.5 effectively identified relevant clinical concepts, they exhibited immature capability in organizing phenotyping criteria with the proper logic, leading to phenotyping algorithms that were either excessively restrictive (with low recall) or overly broad (with low positive predictive values). CONCLUSION GPT versions 3.5 and 4 are capable of drafting phenotyping algorithms by identifying relevant clinical criteria aligned with a CDM. However, expertise in informatics and clinical experience is still required to assess and further refine generated algorithms.
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Affiliation(s)
- Chao Yan
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Henry H Ong
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Monika E Grabowska
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Matthew S Krantz
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Wu-Chen Su
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Alyson L Dickson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Josh F Peterson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - QiPing Feng
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Dan M Roden
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - C Michael Stein
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - V Eric Kerchberger
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Bradley A Malin
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
- Department of Computer Science, Vanderbilt University, Nashville, TN 37203, United States
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
- Department of Computer Science, Vanderbilt University, Nashville, TN 37203, United States
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Davogustto G, Wells QS, Harrell FE, Greene SJ, Roden DM, Stevenson LW. Impact of Insurance Status and Region on Angiotensin Receptor-Neprilysin Inhibitor Prescription During Heart Failure Hospitalizations. JACC Heart Fail 2024:S2213-1779(24)00161-6. [PMID: 38639698 DOI: 10.1016/j.jchf.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/26/2024] [Accepted: 02/06/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND An angiotensin receptor-neprilysin inhibitor (ARNI) is the preferred renin-angiotensin system (RAS) inhibitor for heart failure with reduced ejection fraction (HFrEF). Among eligible patients, insurance status and prescriber concern regarding out-of-pocket costs may constrain early initiation of ARNI and other new therapies. OBJECTIVES In this study, the authors sought to evaluate the association of insurance and other social determinants of health with ARNI initiation at discharge from HFrEF hospitalization. METHODS The authors analyzed ARNI initiation from January 2017 to June 2020 among patients with HFrEF eligible to receive RAS inhibitor at discharge from hospitals in the Get With The Guidelines-Heart Failure registry. The primary outcome was the proportion of ARNI prescription at discharge among those prescribed RAS inhibitor who were not on ARNI on admission. A logistic regression model was used to determine the association of insurance status, U.S. region, and their interaction, as well as self-reported race, with ARNI initiation at discharge. RESULTS From 42,766 admissions, 24,904 were excluded for absolute or relative contraindications to RAS inhibitors. RAS inhibitors were prescribed for 16,817 (94.2%) of remaining discharges, for which ARNI was prescribed in 1,640 (9.8%). Self-reported Black patients were less likely to be initiated on ARNI compared to self-reported White patients (OR: 0.64; 95% CI: 0.50-0.81). Compared to Medicare beneficiaries, patients with third-party insurance, Medicaid, or no insurance were less likely to be initiated on ARNI (OR: 0.47 [95% CI: 0.31-0.72], OR: 0.41 [95% CI: 0.25-0.67], and OR: 0.20 [95% CI: 0.08-0.47], respectively). ARNI therapy varied by hospital region, with lowest utilization in the Mountain region. An interaction was demonstrated between the impact of insurance disparities and hospital region. CONCLUSIONS Among patients hospitalized between 2017 and 2020 for HFrEF who were prescribed RAS inhibitor therapy at discharge, insurance status, geographic region, and self-reported race were associated with ARNI initiation.
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Affiliation(s)
- Giovanni Davogustto
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt School of Medicine, Nashville, Tennessee, USA.
| | - Quinn S Wells
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt School of Medicine, Nashville, Tennessee, USA
| | - Frank E Harrell
- Department of Biostatistics, Vanderbilt School of Medicine, Nashville, Tennessee, USA
| | - Stephen J Greene
- Duke Clinical Research Institute, Durham, North Carolina, USA; Division of Cardiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Dan M Roden
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt School of Medicine, Nashville, Tennessee, USA
| | - Lynne W Stevenson
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt School of Medicine, Nashville, Tennessee, USA
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Strayer N, Vessels T, Choi K, Zhang S, Li Y, Sharber B, Hsi RS, Bejan CA, Bick AG, Balko JM, Johnson DB, Wheless LE, Wells QS, Shah R, Philips EJ, Self WH, Pulley JM, Wilkins CH, Chen Q, Hartert T, Savona MR, Shyr Y, Roden DM, Smoller JW, Ruderfer DM, Xu Y. Interoperability of phenome-wide multimorbidity patterns: a comparative study of two large-scale EHR systems. medRxiv 2024:2024.03.28.24305045. [PMID: 38585743 PMCID: PMC10996752 DOI: 10.1101/2024.03.28.24305045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Background Electronic health records (EHR) are increasingly used for studying multimorbidities. However, concerns about accuracy, completeness, and EHRs being primarily designed for billing and administration raise questions about the consistency and reproducibility of EHR-based multimorbidity research. Methods Utilizing phecodes to represent the disease phenome, we analyzed pairwise comorbidity strengths using a dual logistic regression approach and constructed multimorbidity as an undirected weighted graph. We assessed the consistency of the multimorbidity networks within and between two major EHR systems at local (nodes and edges), meso (neighboring patterns), and global (network statistics) scales. We present case studies to identify disease clusters and uncover clinically interpretable disease relationships. We provide an interactive web tool and a knowledge base combing data from multiple sources for online multimorbidity analysis. Findings Analyzing data from 500,000 patients across Vanderbilt University Medical Center and Mass General Brigham health systems, we observed a strong correlation in disease frequencies ( Kendall's τ = 0.643) and comorbidity strengths (Pearson ρ = 0.79). Consistent network statistics across EHRs suggest a similar structure of multimorbidity networks at various scales. Comorbidity strengths and similarities of multimorbidity connection patterns align with the disease genetic correlations. Graph-theoretic analyses revealed a consistent core-periphery structure, implying efficient network clustering through threshold graph construction. Using hydronephrosis as a case study, we demonstrated the network's ability to uncover clinically relevant disease relationships and provide novel insights. Interpretation Our findings demonstrate the robustness of large-scale EHR data for studying complex disease interactions. The alignment of multimorbidity patterns with genetic data suggests the potential utility for uncovering shared etiology of diseases. The consistent core-periphery network structure offers a strategic approach to analyze disease clusters. This work also sets the stage for advanced disease modeling, with implications for precision medicine. Funding VUMC Biostatistics Development Award, UL1 TR002243, R21DK127075, R01HL140074, P50GM115305, R01CA227481.
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Affiliation(s)
- Nick Strayer
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Tess Vessels
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Digital Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Karmel Choi
- Psychiatric & Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston MA
- Center for Precision Psychiatry, Department of Psychiatry, Massachusetts General Hospital, Boston MA
| | - Siwei Zhang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yajing Li
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Brian Sharber
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ryan S Hsi
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Cosmin A Bejan
- Department of Biomedical informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alexander G. Bick
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Justin M Balko
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Douglas B Johnson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lee E Wheless
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Quinn S Wells
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ravi Shah
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Elizabeth J Philips
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - Wesley H Self
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jill M Pulley
- Department of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Consuelo H Wilkins
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qingxia Chen
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Tina Hartert
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Michael R Savona
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yu Shyr
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M Roden
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jordan W Smoller
- Psychiatric & Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston MA
- Center for Precision Psychiatry, Department of Psychiatry, Massachusetts General Hospital, Boston MA
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA
| | - Douglas M Ruderfer
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Digital Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical informatics, Vanderbilt University Medical Center, Nashville, TN, USA
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Landstrom AP, Chahal CAA, Roden DM, Ho CY, Shah SH. A Customizable and Peer-Reviewed Curriculum for Cardiovascular Genetics and Genomics. Circulation 2024; 149:902-904. [PMID: 38498607 DOI: 10.1161/circulationaha.123.067681] [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] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Affiliation(s)
- Andrew P Landstrom
- Department of Pediatrics, Division of Pediatric Cardiology, and Department of Cell Biology, Duke University School of Medicine, Durham, NC (A.P.L.)
| | - C Anwar A Chahal
- University of Pennsylvania, Department of Cardiology, Philadelphia (C.A.A.C.)
- Center for Inherited Cardiovascular Diseases, WellSpan Health, Lancaster, PA (C.A.A.C.)
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN (C.A.A.C.)
- Barts Heart Centre, West Smithfield, London, UK (C.A.A.C.)
| | - Dan M Roden
- Department of Medicine, Department of Pharmacology, and Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN (D.M.R.)
| | - Carolyn Y Ho
- Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.Y.H.)
| | - Svati H Shah
- Division of Cardiology, Department of Medicine, and Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC (S.H.S.)
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El‐Harasis MA, Quintana JA, Martinez‐Parachini JR, Jackson GG, Varghese BT, Yoneda ZT, Murphy BS, Crawford DM, Tomasek K, Su YR, Wells QS, Roden DM, Michaud GF, Saavedra P, Estrada JC, Richardson TD, Kanagasundram AN, Shen ST, Montgomery JA, Ellis CR, Crossley GH, Eberl M, Gillet L, Ziegler A, Shoemaker MB. Recurrence After Atrial Fibrillation Ablation and Investigational Biomarkers of Cardiac Remodeling. J Am Heart Assoc 2024; 13:e031029. [PMID: 38471835 PMCID: PMC11010019 DOI: 10.1161/jaha.123.031029] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/23/2023] [Indexed: 03/14/2024]
Abstract
BACKGROUND Recurrence after atrial fibrillation (AF) ablation remains common. We evaluated the association between recurrence and levels of biomarkers of cardiac remodeling, and their ability to improve recurrence prediction when added to a clinical prediction model. METHODS AND RESULTS Blood samples collected before de novo catheter ablation were analyzed. Levels of bone morphogenetic protein-10, angiopoietin-2, fibroblast growth factor-23, insulin-like growth factor-binding protein-7, myosin-binding protein C3, growth differentiation factor-15, interleukin-6, N-terminal pro-brain natriuretic peptide, and high-sensitivity troponin T were measured. Recurrence was defined as ≥30 seconds of an atrial arrhythmia 3 to 12 months postablation. Multivariable logistic regression was performed using biomarker levels along with clinical covariates: APPLE score (Age >65 years, Persistent AF, imPaired eGFR [<60 ml/min/1.73m2], LA diameter ≥43 mm, EF <50%; which includes age, left atrial diameter, left ventricular ejection fraction, persistent atrial fibrillation, and estimated glomerular filtration rate), preablation rhythm, sex, height, body mass index, presence of an implanted continuous monitor, year of ablation, and additional linear ablation. A total of 1873 participants were included. A multivariable logistic regression showed an association between recurrence and levels of angiopoietin-2 (odds ratio, 1.08 [95% CI, 1.02-1.15], P=0.007) and interleukin-6 (odds ratio, 1.02 [95% CI, 1.003-1.03]; P=0.02). The area under the receiver operating characteristic curve of a model that only contained clinical predictors was 0.711. The addition of any of the 9 studied biomarkers to the predictive model did not result in a statistically significant improvement in the area under the receiver operating characteristic curve. CONCLUSIONS Higher angiopoietin-2 and interleukin-6 levels were associated with recurrence after atrial fibrillation ablation in multivariable modeling. However, the addition of biomarkers to a clinical prediction model did not significantly improve recurrence prediction.
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Affiliation(s)
- Majd A. El‐Harasis
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Joseph A. Quintana
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | | | - Gregory G. Jackson
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Bibin T. Varghese
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Zachary T. Yoneda
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Brittany S. Murphy
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Diane M. Crawford
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Kelsey Tomasek
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Yan Ru Su
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Quinn S. Wells
- Departments of Medicine, Pharmacology, and Biomedical InformaticsVanderbilt University Medical CenterNashvilleTN
| | - Dan M. Roden
- Departments of Medicine, Pharmacology, and Biomedical InformaticsVanderbilt University Medical CenterNashvilleTN
| | - Gregory F. Michaud
- Division of Cardiovascular Medicine, Massachusetts General HospitalBostonMA
| | - Pablo Saavedra
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Juan Carlos Estrada
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Travis D. Richardson
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | | | - Sharon T. Shen
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Jay A. Montgomery
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Christopher R. Ellis
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - George H. Crossley
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
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7
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Wada Y, Wang L, Hall LD, Yang T, Short LL, Solus JF, Glazer AM, Roden DM. The electrophysiologic effects of KCNQ1 extend beyond expression of IKs: evidence from genetic and pharmacologic block. Cardiovasc Res 2024:cvae042. [PMID: 38442735 DOI: 10.1093/cvr/cvae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/06/2023] [Revised: 01/22/2024] [Accepted: 02/01/2024] [Indexed: 03/07/2024] Open
Abstract
AIMS While variants in KCNQ1 are the commonest cause of the congenital long QT syndrome, we and others find only a small IKs in cardiomyocytes from human induced pluripotent stem cells (iPSC-CMs) or human ventricular myocytes. METHODS AND RESULTS We studied population control iPSC-CMs and iPSC-CMs from a patient with Jervell and Lange-Nielsen (JLN) syndrome due to compound heterozygous loss of function KCNQ1 variants. We compared the effects of pharmacologic IKs block to those of genetic KCNQ1 ablation, using JLN cells, cells homozygous for the KCNQ1 loss of function allele G643S, or siRNAs reducing KCNQ1 expression. We also studied the effects of two blockers of IKr, the other major cardiac repolarizing current, in the setting of pharmacologic or genetic ablation of KCNQ1: moxifloxacin, associated with a very low risk of drug-induced long QT, and dofetilide, a high-risk drug.In control cells, a small IKs was readily recorded but pharmacologic IKs block produced no change in action potential duration at 90% repolarization (APD90). By contrast, in cells with genetic ablation of KCNQ1 (JLN), baseline APD90 was markedly prolonged compared with control cells (469 ± 20 vs. 310 ± 16 ms). JLN cells displayed increased sensitivity to acute IKr block: the concentration (μM) of moxifloxacin required to prolong APD90 100 msec was 237.4 (median, IQR 100.6-391.6, n = 7) in population cells versus 23.7 (17.3-28.7, n = 11) in JLN cells. In control cells, chronic moxifloxacin exposure (300μM) mildly prolonged APD90 (10%) and increased IKs, while chronic exposure to dofetilide (5 nM) produced greater prolongation (67%) and no increase in IKs. However, in the siRNA-treated cells, moxifloxacin did not increase IKs, and markedly prolonged APD90. CONCLUSION Our data strongly suggest that KCNQ1 expression modulates baseline cardiac repolarization, and the response to IKr block, through mechanisms beyond simply generating IKs. TRANSLATIONAL PERSPECTIVE Mutations in KCNQ1 - whose expression generates IKs - are the major cause of long QT syndrome. We report here that while pharmacologic IKs block in human cardiomyocytes generates minimal change in repolarization, suppressing KCNQ1 expression markedly increases both baseline repolarization duration and sensitivity to some (but not all) specific IKr blockers. Thus, beyond simply generating IKs, KCNQ1 subserves critical additional role(s) in repolarization control at baseline and in response to IKr block. Our findings imply that assessment of arrhythmic risk in individual patients and by drugs requires a framework that extends beyond a simple one gene-one ion current paradigm.
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Affiliation(s)
- Yuko Wada
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN. U.S.A
| | - Lili Wang
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN. U.S.A
| | - Lynn D Hall
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN. U.S.A
| | - Tao Yang
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN. U.S.A
| | - Laura L Short
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN. U.S.A
| | - Joseph F Solus
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN. U.S.A
| | - Andrew M Glazer
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN. U.S.A
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN. U.S.A
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN. U.S.A
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Bick AG, Metcalf GA, Mayo KR, Lichtenstein L, Rura S, Carroll RJ, Musick A, Linder JE, Jordan IK, Nagar SD, Sharma S, Meller R, Basford M, Boerwinkle E, Cicek MS, Doheny KF, Eichler EE, Gabriel S, Gibbs RA, Glazer D, Harris PA, Jarvik GP, Philippakis A, Rehm HL, Roden DM, Thibodeau SN, Topper S, Blegen AL, Wirkus SJ, Wagner VA, Meyer JG, Cicek MS, Muzny DM, Venner E, Mawhinney MZ, Griffith SML, Hsu E, Ling H, Adams MK, Walker K, Hu J, Doddapaneni H, Kovar CL, Murugan M, Dugan S, Khan Z, Boerwinkle E, Lennon NJ, Austin-Tse C, Banks E, Gatzen M, Gupta N, Henricks E, Larsson K, McDonough S, Harrison SM, Kachulis C, Lebo MS, Neben CL, Steeves M, Zhou AY, Smith JD, Frazar CD, Davis CP, Patterson KE, Wheeler MM, McGee S, Lockwood CM, Shirts BH, Pritchard CC, Murray ML, Vasta V, Leistritz D, Richardson MA, Buchan JG, Radhakrishnan A, Krumm N, Ehmen BW, Schwartz S, Aster MMT, Cibulskis K, Haessly A, Asch R, Cremer A, Degatano K, Shergill A, Gauthier LD, Lee SK, Hatcher A, Grant GB, Brandt GR, Covarrubias M, Banks E, Able A, Green AE, Carroll RJ, Zhang J, Condon HR, Wang Y, Dillon MK, Albach CH, Baalawi W, Choi SH, Wang X, Rosenthal EA, Ramirez AH, Lim S, Nambiar S, Ozenberger B, Wise AL, Lunt C, Ginsburg GS, Denny JC. Genomic data in the All of Us Research Program. Nature 2024; 627:340-346. [PMID: 38374255 PMCID: PMC10937371 DOI: 10.1038/s41586-023-06957-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/08/2023] [Indexed: 02/21/2024]
Abstract
Comprehensively mapping the genetic basis of human disease across diverse individuals is a long-standing goal for the field of human genetics1-4. The All of Us Research Program is a longitudinal cohort study aiming to enrol a diverse group of at least one million individuals across the USA to accelerate biomedical research and improve human health5,6. Here we describe the programme's genomics data release of 245,388 clinical-grade genome sequences. This resource is unique in its diversity as 77% of participants are from communities that are historically under-represented in biomedical research and 46% are individuals from under-represented racial and ethnic minorities. All of Us identified more than 1 billion genetic variants, including more than 275 million previously unreported genetic variants, more than 3.9 million of which had coding consequences. Leveraging linkage between genomic data and the longitudinal electronic health record, we evaluated 3,724 genetic variants associated with 117 diseases and found high replication rates across both participants of European ancestry and participants of African ancestry. Summary-level data are publicly available, and individual-level data can be accessed by researchers through the All of Us Researcher Workbench using a unique data passport model with a median time from initial researcher registration to data access of 29 hours. We anticipate that this diverse dataset will advance the promise of genomic medicine for all.
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9
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Yan C, Ong HH, Grabowska ME, Krantz MS, Su WC, Dickson AL, Peterson JF, Feng Q, Roden DM, Stein CM, Kerchberger VE, Malin BA, Wei WQ. Large Language Models Facilitate the Generation of Electronic Health Record Phenotyping Algorithms. medRxiv 2024:2023.12.19.23300230. [PMID: 38196578 PMCID: PMC10775330 DOI: 10.1101/2023.12.19.23300230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Objectives Phenotyping is a core task in observational health research utilizing electronic health records (EHRs). Developing an accurate algorithm demands substantial input from domain experts, involving extensive literature review and evidence synthesis. This burdensome process limits scalability and delays knowledge discovery. We investigate the potential for leveraging large language models (LLMs) to enhance the efficiency of EHR phenotyping by generating high-quality algorithm drafts. Materials and Methods We prompted four LLMs-GPT-4 and GPT-3.5 of ChatGPT, Claude 2, and Bard-in October 2023, asking them to generate executable phenotyping algorithms in the form of SQL queries adhering to a common data model (CDM) for three phenotypes (i.e., type 2 diabetes mellitus, dementia, and hypothyroidism). Three phenotyping experts evaluated the returned algorithms across several critical metrics. We further implemented the top-rated algorithms and compared them against clinician-validated phenotyping algorithms from the Electronic Medical Records and Genomics (eMERGE) network. Results GPT-4 and GPT-3.5 exhibited significantly higher overall expert evaluation scores in instruction following, algorithmic logic, and SQL executability, when compared to Claude 2 and Bard. Although GPT-4 and GPT-3.5 effectively identified relevant clinical concepts, they exhibited immature capability in organizing phenotyping criteria with the proper logic, leading to phenotyping algorithms that were either excessively restrictive (with low recall) or overly broad (with low positive predictive values). Conclusion GPT versions 3.5 and 4 are capable of drafting phenotyping algorithms by identifying relevant clinical criteria aligned with a CDM. However, expertise in informatics and clinical experience is still required to assess and further refine generated algorithms.
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Affiliation(s)
- Chao Yan
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Henry H. Ong
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Monika E. Grabowska
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Matthew S. Krantz
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Wu-Chen Su
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Alyson L. Dickson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Josh F. Peterson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - QiPing Feng
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Dan M. Roden
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - C. Michael Stein
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - V. Eric Kerchberger
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Bradley A. Malin
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
- Department of Computer Science, Vanderbilt University, Nashville, TN
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
- Department of Computer Science, Vanderbilt University, Nashville, TN
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10
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Yan C, Grabowska ME, Dickson AL, Li B, Wen Z, Roden DM, Michael Stein C, Embí PJ, Peterson JF, Feng Q, Malin BA, Wei WQ. Leveraging generative AI to prioritize drug repurposing candidates for Alzheimer's disease with real-world clinical validation. NPJ Digit Med 2024; 7:46. [PMID: 38409350 PMCID: PMC10897392 DOI: 10.1038/s41746-024-01038-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024] Open
Abstract
Drug repurposing represents an attractive alternative to the costly and time-consuming process of new drug development, particularly for serious, widespread conditions with limited effective treatments, such as Alzheimer's disease (AD). Emerging generative artificial intelligence (GAI) technologies like ChatGPT offer the promise of expediting the review and summary of scientific knowledge. To examine the feasibility of using GAI for identifying drug repurposing candidates, we iteratively tasked ChatGPT with proposing the twenty most promising drugs for repurposing in AD, and tested the top ten for risk of incident AD in exposed and unexposed individuals over age 65 in two large clinical datasets: (1) Vanderbilt University Medical Center and (2) the All of Us Research Program. Among the candidates suggested by ChatGPT, metformin, simvastatin, and losartan were associated with lower AD risk in meta-analysis. These findings suggest GAI technologies can assimilate scientific insights from an extensive Internet-based search space, helping to prioritize drug repurposing candidates and facilitate the treatment of diseases.
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Affiliation(s)
- Chao Yan
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Monika E Grabowska
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alyson L Dickson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Zhexing Wen
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - C Michael Stein
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Peter J Embí
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Josh F Peterson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - QiPing Feng
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bradley A Malin
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA.
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11
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Glazer AM, Yang T, Li B, Page D, Fouda M, Wada Y, Lancaster MC, O’Neill MJ, Muhammad A, Gao X, Ackerman MJ, Sanatani S, Ruben PC, Roden DM. Multifocal Ectopic Purkinje Premature Contractions due to neutralization of an SCN5A negative charge: structural insights into the gating pore hypothesis. bioRxiv 2024:2024.02.13.580021. [PMID: 38405820 PMCID: PMC10888965 DOI: 10.1101/2024.02.13.580021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Background We identified a novel SCN5A variant, E171Q, in a neonate with very frequent ectopy and reduced ejection fraction which normalized after arrhythmia suppression by flecainide. This clinical picture is consistent with multifocal ectopic Purkinje-related premature contractions (MEPPC). Most previous reports of MEPPC have implicated SCN5A variants such as R222Q that neutralize positive charges in the S4 voltage sensor helix of the channel protein NaV1.5 and generate a gating pore current. Methods and Results E171 is a highly conserved negatively-charged residue located in the S2 transmembrane helix of NaV1.5 domain I. E171 is a key component of the Gating Charge Transfer Center, a region thought to be critical for normal movement of the S4 voltage sensor helix. We used heterologous expression, CRISPR-edited induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), and molecular dynamics simulations to demonstrate that E171Q generates a gating pore current, which was suppressed by a low concentration of flecainide (IC50 = 0.71±0.07 µM). R222Q shifts voltage dependence of activation and inactivation in a negative direction but we observed positive shifts with E171Q. E171Q iPSC-CMs demonstrated abnormal spontaneous activity and prolonged action potentials. Molecular dynamics simulations revealed that both R222Q and E171Q proteins generate a water-filled permeation pathway that underlies generation of the gating pore current. Conclusion Previously identified MEPPC-associated variants that create gating pore currents are located in positively-charged residues in the S4 voltage sensor and generate negative shifts in the voltage dependence of activation and inactivation. We demonstrate that neutralizing a negatively charged S2 helix residue in the Gating Charge Transfer Center generates positive shifts but also create a gating pore pathway. These findings implicate the gating pore pathway as the primary functional and structural determinant of MEPPC and widen the spectrum of variants that are associated with gating pore-related disease in voltage-gated ion channels.
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Affiliation(s)
| | - Tao Yang
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bian Li
- Vanderbilt University Medical Center, Nashville, TN, USA
- Current address: Regeneron Pharmaceuticals Inc., Tarrytown NY, USA. Bian Li contributed to this article as an employee of Vanderbilt University Medical Center and the views expressed do not necessarily represent the views of Regeneron Pharmaceuticals Inc
| | - Dana Page
- Simon Fraser University, Burnaby, BC, Canada
| | | | - Yuko Wada
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | | | - Xiaozhi Gao
- Mayo Clinic College of Medicine and Science, Mayo Foundation, Rochester, MN, USA
| | - Michael J. Ackerman
- Mayo Clinic College of Medicine and Science, Mayo Foundation, Rochester, MN, USA
| | | | | | - Dan M. Roden
- Vanderbilt University Medical Center, Nashville, TN, USA
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12
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Davogustto G, Zhao S, Li Y, Farber-Eger E, Lowery BD, Shaffer LL, Mosley JD, Shoemaker MB, Xu Y, Roden DM, Wells QS. Unbiased characterization of atrial fibrillation phenotypic architecture provides insight to genetic liability and clinically relevant outcomes. medRxiv 2024:2024.02.13.24302788. [PMID: 38405916 PMCID: PMC10888988 DOI: 10.1101/2024.02.13.24302788] [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: 02/27/2024]
Abstract
Background Atrial Fibrillation (AF) is a common and clinically heterogeneous arrythmia. Machine learning (ML) algorithms can define data-driven disease subtypes in an unbiased fashion, but whether the AF subgroups defined in this way align with underlying mechanisms, such as high polygenic liability to AF or inflammation, and associate with clinical outcomes is unclear. Methods We identified individuals with AF in a large biobank linked to electronic health records (EHR) and genome-wide genotyping. The phenotypic architecture in the AF cohort was defined using principal component analysis of 35 expertly curated and uncorrelated clinical features. We applied an unsupervised co-clustering machine learning algorithm to the 35 features to identify distinct phenotypic AF clusters. The clinical inflammatory status of the clusters was defined using measured biomarkers (CRP, ESR, WBC, Neutrophil %, Platelet count, RDW) within 6 months of first AF mention in the EHR. Polygenic risk scores (PRS) for AF and cytokine levels were used to assess genetic liability of clusters to AF and inflammation, respectively. Clinical outcomes were collected from EHR up to the last medical contact. Results The analysis included 23,271 subjects with AF, of which 6,023 had available genome-wide genotyping. The machine learning algorithm identified 3 phenotypic clusters that were distinguished by increasing prevalence of comorbidities, particularly renal dysfunction, and coronary artery disease. Polygenic liability to AF across clusters was highest in the low comorbidity cluster. Clinically measured inflammatory biomarkers were highest in the high comorbid cluster, while there was no difference between groups in genetically predicted levels of inflammatory biomarkers. Subgroup assignment was associated with multiple clinical outcomes including mortality, stroke, bleeding, and use of cardiac implantable electronic devices after AF diagnosis. Conclusion Patient subgroups identified by unsupervised clustering were distinguished by comorbidity burden and associated with risk of clinically important outcomes. Polygenic liability to AF across clusters was greatest in the low comorbidity subgroup. Clinical inflammation, as reflected by measured biomarkers, was lowest in the subgroup with lowest comorbidities. However, there were no differences in genetically predicted levels of inflammatory biomarkers, suggesting associations between AF and inflammation is driven by acquired comorbidities rather than genetic predisposition.
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13
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O’Neill MJ, Ng CA, Aizawa T, Sala L, Bains S, Denjoy I, Winbo A, Ullah R, Shen Q, Tan CY, Kozek K, Vanags LR, Mitchell DW, Shen A, Wada Y, Kashiwa A, Crotti L, Dagradi F, Musu G, Spazzolini C, Neves R, Bos JM, Giudicessi JR, Bledsoe X, Lancaster M, Glazer AM, Roden DM, Leenhardt A, Salem JE, Earle N, Stiles R, Agee T, Johnson CN, Horie M, Skinner J, Extramiana F, Ackerman MJ, Schwartz PJ, Ohno S, Vandenberg JI, Kroncke BM. Prognostic Value of Multiplexed Assays of Variant Effect and Automated Patch-clamping for KCNH2-LQTS Risk Stratification. medRxiv 2024:2024.02.01.24301443. [PMID: 38370760 PMCID: PMC10871451 DOI: 10.1101/2024.02.01.24301443] [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] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Background Long QT syndrome (LQTS) is a lethal arrhythmia condition, frequently caused by rare loss-of-function variants in the cardiac potassium channel encoded by KCNH2. Variant-based risk stratification is complicated by heterogenous clinical data, incomplete penetrance, and low-throughput functional data. Objective To test the utility of variant-specific features, including high-throughput functional data, to predict cardiac events among KCNH2 variant heterozygotes. Methods We quantified cell-surface trafficking of 18,323 variants in KCNH2 and recorded potassium current densities for 506 KCNH2 variants. Next, we deeply phenotyped 1150 KCNH2 missense variant patients, including ECG features, cardiac event history (528 total cardiac events), and mortality. We then assessed variant functional, in silico, structural, and LQTS penetrance data to stratify event-free survival for cardiac events in the study cohort. Results Variant-specific current density (HR 0.28 [0.13-0.60]) and estimates of LQTS penetrance incorporating MAVE data (HR 3.16 [1.59-6.27]) were independently predictive of severe cardiac events when controlling for patient-specific features. Risk prediction models incorporating these data significantly improved prediction of 20 year cardiac events (AUC 0.79 [0.75-0.82]) over patient-only covariates (QTc and sex) (AUC 0.73 [0.70-0.77]). Conclusion We show that high-throughput functional data, and other variant-specific features, meaningfully contribute to both diagnosis and prognosis of a clinically actionable monogenic disease.
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Affiliation(s)
- Matthew J. O’Neill
- Vanderbilt University School of Medicine, Medical Scientist Training Program, Nashville, TN, USA
- These authors contributed equally
| | - Chai-Ann Ng
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- School of Clinical Medicine, UNSW Sydney, Darlinghurst, NSW, Australia
- These authors contributed equally
| | - Takanori Aizawa
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine Kyoto, Japan
| | - Luca Sala
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Sahej Bains
- Department of Molecular Pharmacology & Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN, USA
| | - Isabelle Denjoy
- Department of Cardiovascular Medicine, Hôpital Bichat, APHP, Université de Paris Cité, Paris, France
| | - Annika Winbo
- Department of Physiology, University of Auckland, Auckland, New Zealand
| | - Rizwan Ullah
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qianyi Shen
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Chek-Ying Tan
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Krystian Kozek
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Loren R. Vanags
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Devyn W. Mitchell
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alex Shen
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuko Wada
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Asami Kashiwa
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine Kyoto, Japan
| | - Lia Crotti
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
- Department of Medicine and Surgery, University Milano Bicocca, Milan, Italy
| | - Federica Dagradi
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Giulia Musu
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Carla Spazzolini
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Raquel Neves
- Department of Molecular Pharmacology & Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN, USA
| | - J. Martijn Bos
- Department of Molecular Pharmacology & Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN, USA
| | - John R. Giudicessi
- Department of Molecular Pharmacology & Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN, USA
| | - Xavier Bledsoe
- Vanderbilt University School of Medicine, Medical Scientist Training Program, Nashville, TN, USA
| | - Megan Lancaster
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Andrew M. Glazer
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M. Roden
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Antoine Leenhardt
- Department of Cardiovascular Medicine, Hôpital Bichat, APHP, Université de Paris Cité, Paris, France
| | - Joe-Elie Salem
- Department of Cardiovascular Medicine, Hôpital Bichat, APHP, Université de Paris Cité, Paris, France
| | - Nikki Earle
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Rachael Stiles
- Department of Cardiology, Waikato Hospital, Hamilton, New Zealand
| | - Taylor Agee
- Department of Chemistry, Mississippi State University, Starkville, MS 39759, USA
| | | | - Minoru Horie
- Department of Cardiovascular Medicine, Shiga University of Medical Science, Shiga, Japan
| | - Jonathan Skinner
- Sydney Children’s Hospital Network, University of Sydney, Sydney, Australia
| | - Fabrice Extramiana
- Department of Cardiovascular Medicine, Hôpital Bichat, APHP, Université de Paris Cité, Paris, France
| | - Michael J. Ackerman
- Department of Molecular Pharmacology & Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN, USA
| | - Peter J. Schwartz
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Seiko Ohno
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Jamie I. Vandenberg
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- School of Clinical Medicine, UNSW Sydney, Darlinghurst, NSW, Australia
| | - Brett M. Kroncke
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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14
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Lennon NJ, Kottyan LC, Kachulis C, Abul-Husn NS, Arias J, Belbin G, Below JE, Berndt SI, Chung WK, Cimino JJ, Clayton EW, Connolly JJ, Crosslin DR, Dikilitas O, Velez Edwards DR, Feng Q, Fisher M, Freimuth RR, Ge T, Glessner JT, Gordon AS, Patterson C, Hakonarson H, Harden M, Harr M, Hirschhorn JN, Hoggart C, Hsu L, Irvin MR, Jarvik GP, Karlson EW, Khan A, Khera A, Kiryluk K, Kullo I, Larkin K, Limdi N, Linder JE, Loos RJF, Luo Y, Malolepsza E, Manolio TA, Martin LJ, McCarthy L, McNally EM, Meigs JB, Mersha TB, Mosley JD, Musick A, Namjou B, Pai N, Pesce LL, Peters U, Peterson JF, Prows CA, Puckelwartz MJ, Rehm HL, Roden DM, Rosenthal EA, Rowley R, Sawicki KT, Schaid DJ, Smit RAJ, Smith JL, Smoller JW, Thomas M, Tiwari H, Toledo DM, Vaitinadin NS, Veenstra D, Walunas TL, Wang Z, Wei WQ, Weng C, Wiesner GL, Yin X, Kenny EE. Selection, optimization and validation of ten chronic disease polygenic risk scores for clinical implementation in diverse US populations. Nat Med 2024; 30:480-487. [PMID: 38374346 PMCID: PMC10878968 DOI: 10.1038/s41591-024-02796-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 05/25/2023] [Accepted: 01/02/2024] [Indexed: 02/21/2024]
Abstract
Polygenic risk scores (PRSs) have improved in predictive performance, but several challenges remain to be addressed before PRSs can be implemented in the clinic, including reduced predictive performance of PRSs in diverse populations, and the interpretation and communication of genetic results to both providers and patients. To address these challenges, the National Human Genome Research Institute-funded Electronic Medical Records and Genomics (eMERGE) Network has developed a framework and pipeline for return of a PRS-based genome-informed risk assessment to 25,000 diverse adults and children as part of a clinical study. From an initial list of 23 conditions, ten were selected for implementation based on PRS performance, medical actionability and potential clinical utility, including cardiometabolic diseases and cancer. Standardized metrics were considered in the selection process, with additional consideration given to strength of evidence in African and Hispanic populations. We then developed a pipeline for clinical PRS implementation (score transfer to a clinical laboratory, validation and verification of score performance), and used genetic ancestry to calibrate PRS mean and variance, utilizing genetically diverse data from 13,475 participants of the All of Us Research Program cohort to train and test model parameters. Finally, we created a framework for regulatory compliance and developed a PRS clinical report for return to providers and for inclusion in an additional genome-informed risk assessment. The initial experience from eMERGE can inform the approach needed to implement PRS-based testing in diverse clinical settings.
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Affiliation(s)
| | - Leah C Kottyan
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | | | | | - Josh Arias
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gillian Belbin
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Sonja I Berndt
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - James J Cimino
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | - David R Crosslin
- Tulane University, New Orleans, LA, USA
- University of Washington, Seattle, WA, USA
| | | | | | - QiPing Feng
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | - Tian Ge
- Mass General Brigham, Boston, MA, USA
| | | | | | | | | | - Maegan Harden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Margaret Harr
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joel N Hirschhorn
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | - Clive Hoggart
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Li Hsu
- Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | | | | | | | - Amit Khera
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Katie Larkin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nita Limdi
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Ruth J F Loos
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuan Luo
- Northwestern University, Evanston, IL, USA
| | | | - Teri A Manolio
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lisa J Martin
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Li McCarthy
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Tesfaye B Mersha
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | | | | | - Bahram Namjou
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Nihal Pai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | - Cynthia A Prows
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | | | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dan M Roden
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Robb Rowley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | | | | | - Hemant Tiwari
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | | | | | - Zhe Wang
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wei-Qi Wei
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | | | - Eimear E Kenny
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
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15
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Puckelwartz MJ, Pesce LL, Hernandez EJ, Webster G, Dellefave-Castillo LM, Russell MW, Geisler SS, Kearns SD, Karthik F, Etheridge SP, Monroe TO, Pottinger TD, Kannankeril PJ, Shoemaker MB, Fountain D, Roden DM, Faulkner M, MacLeod HM, Burns KM, Yandell M, Tristani-Firouzi M, George AL, McNally EM. The impact of damaging epilepsy and cardiac genetic variant burden in sudden death in the young. Genome Med 2024; 16:13. [PMID: 38229148 PMCID: PMC10792876 DOI: 10.1186/s13073-024-01284-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 02/22/2023] [Accepted: 01/03/2024] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Sudden unexpected death in children is a tragic event. Understanding the genetics of sudden death in the young (SDY) enables family counseling and cascade screening. The objective of this study was to characterize genetic variation in an SDY cohort using whole genome sequencing. METHODS The SDY Case Registry is a National Institutes of Health/Centers for Disease Control and Prevention surveillance effort to discern the prevalence, causes, and risk factors for SDY. The SDY Case Registry prospectively collected clinical data and DNA biospecimens from SDY cases < 20 years of age. SDY cases were collected from medical examiner and coroner offices spanning 13 US jurisdictions from 2015 to 2019. The cohort included 211 children (median age 0.33 year; range 0-20 years), determined to have died suddenly and unexpectedly and from whom DNA biospecimens for DNA extractions and next-of-kin consent were ascertained. A control cohort consisted of 211 randomly sampled, sex- and ancestry-matched individuals from the 1000 Genomes Project. Genetic variation was evaluated in epilepsy, cardiomyopathy, and arrhythmia genes in the SDY and control cohorts. American College of Medical Genetics/Genomics guidelines were used to classify variants as pathogenic or likely pathogenic. Additionally, pathogenic and likely pathogenic genetic variation was identified using a Bayesian-based artificial intelligence (AI) tool. RESULTS The SDY cohort was 43% European, 29% African, 3% Asian, 16% Hispanic, and 9% with mixed ancestries and 39% female. Six percent of the cohort was found to harbor a pathogenic or likely pathogenic genetic variant in an epilepsy, cardiomyopathy, or arrhythmia gene. The genomes of SDY cases, but not controls, were enriched for rare, potentially damaging variants in epilepsy, cardiomyopathy, and arrhythmia-related genes. A greater number of rare epilepsy genetic variants correlated with younger age at death. CONCLUSIONS While damaging cardiomyopathy and arrhythmia genes are recognized contributors to SDY, we also observed an enrichment in epilepsy-related genes in the SDY cohort and a correlation between rare epilepsy variation and younger age at death. These findings emphasize the importance of considering epilepsy genes when evaluating SDY.
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Affiliation(s)
- Megan J Puckelwartz
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Lorenzo L Pesce
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Gregory Webster
- Division of Cardiology, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | | | - Mark W Russell
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Sarah S Geisler
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Samuel D Kearns
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Felix Karthik
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Susan P Etheridge
- Division of Pediatric Cardiology, University of Utah, Salt Lake City, UT, USA
| | - Tanner O Monroe
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Tess D Pottinger
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Prince J Kannankeril
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M Benjamin Shoemaker
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Darlene Fountain
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | - Kristin M Burns
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | | | - Alfred L George
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Elizabeth M McNally
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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16
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Stollings JL, Boncyk CS, Birdrow CI, Chen W, Raman R, Gupta DK, Roden DM, Rivera EL, Maiga AW, Rakhit S, Pandharipande PP, Ely EW, Girard TD, Patel MB. Antipsychotics and the QTc Interval During Delirium in the Intensive Care Unit: A Secondary Analysis of a Randomized Clinical Trial. JAMA Netw Open 2024; 7:e2352034. [PMID: 38252439 PMCID: PMC10804270 DOI: 10.1001/jamanetworkopen.2023.52034] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/28/2023] [Indexed: 01/23/2024] Open
Abstract
Importance Antipsychotic medications, often prescribed for delirium in intensive care units (ICUs), may contribute to QTc interval prolongation. Objective To determine whether antipsychotics increase the QTc interval in patients with delirium in the ICU. Design, Setting, and Participants An a priori analysis of a randomized clinical trial in medical/surgical ICUs within 16 centers across the US was conducted. Participants included adults with delirium in the ICU with baseline QTc interval less than 550 ms. The study was conducted from December 2011 to August 2017. Data analysis was performed from April 25 to August 18, 2021. Interventions Patients were randomized 1:1:1 to intravenous haloperidol, ziprasidone, or saline placebo administered twice daily until resolution of delirium, ICU discharge, or 14 days. Main Outcomes and Measures Twelve-lead electrocardiograms were used to measure baseline QTc before study drug initiation and telemetry was used to measure QTc before each subsequent dose of study drug. Unadjusted day-to-day changes in QTc were calculated and multivariable proportional odds regression was used to estimate the effects of antipsychotics vs placebo on next-day maximum QTc interval, adjusting for prespecified baseline covariates and potential interactions with sex. Safety end points, including the occurrence of torsade de pointes, were evaluated. All analyses were conducted based on the intention to treat principle. Results A total of 566 patients were randomized to haloperidol (n = 192), ziprasidone (n = 190), or placebo (n = 184). Median age was 60.1 (IQR, 51.4-68.7) years; 323 were men (57%). Baseline median QTc intervals across the groups were similar: haloperidol, 458.0 (IQR, 432.0-479.0) ms; ziprasidone, 451.0 (IQR, 424.0-472.0) ms; and placebo, 452.0 (IQR, 432.0-472.0) ms. From day 1 to day 2, median QTc changed minimally: haloperidol, -1.0 (IQR, -28.0 to 15.0) ms; ziprasidone, 0 (IQR, -23.0 to 20.0) ms; and placebo, -3.5 (IQR, -24.8 to 17.0) ms. Compared with placebo, neither haloperidol (odds ratio [OR], 0.95; 95% CI, 0.66-1.37; P = .78) nor ziprasidone (OR, 1.09; 95% CI, 0.75-1.57; P = .78) was associated with next-day QTc intervals. Effects were not significantly modified by sex (P = .41 for interaction). There were 2 occurrences of nonfatal torsade de pointes, both in the haloperidol group. Neither was associated with study drug administration. Conclusions and Relevance The findings of this trial suggest that daily QTc interval monitoring during antipsychotic use may have limited value in patients in the ICU with normal baseline QTc and few risk factors for QTc prolongation. Trial Registration ClinicalTrials.gov Identifier: NCT01211522.
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Affiliation(s)
- Joanna L. Stollings
- Critical Illness, Brain Dysfunction, and Survivorship Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Pharmaceutical Services, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Christina S. Boncyk
- Critical Illness, Brain Dysfunction, and Survivorship Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Caroline I. Birdrow
- Critical Illness, Brain Dysfunction, and Survivorship Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Wencong Chen
- Critical Illness, Brain Dysfunction, and Survivorship Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Rameela Raman
- Critical Illness, Brain Dysfunction, and Survivorship Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Deepak K. Gupta
- Center for Health Services Research, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt Heart Imaging Core Lab, Vanderbilt Translational and Clinical Cardiovascular Research Center, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Dan M. Roden
- Department of Medicine, Departments of Pharmacology and Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Erika L. Rivera
- Section of Surgical Sciences, Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
- Surgical Service, Department of Veterans Affairs Medical Center, Tennessee Valley Healthcare System, Nashville, Tennessee
| | - Amelia W. Maiga
- Critical Illness, Brain Dysfunction, and Survivorship Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Section of Surgical Sciences, Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Shayan Rakhit
- Critical Illness, Brain Dysfunction, and Survivorship Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Section of Surgical Sciences, Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Pratik P. Pandharipande
- Critical Illness, Brain Dysfunction, and Survivorship Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, Tennessee
- Center for Health Services Research, Vanderbilt University Medical Center, Nashville, Tennessee
- Anesthesia Service, Veterans Affairs Medical Center, Tennessee Valley Healthcare System, Nashville
- Geriatric Research Education and Clinical Center, Veterans Affairs Medical Center, Tennessee Valley Healthcare System, Nashville
| | - E. Wesley Ely
- Critical Illness, Brain Dysfunction, and Survivorship Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Center for Health Services Research, Vanderbilt University Medical Center, Nashville, Tennessee
- Geriatric Research Education and Clinical Center, Veterans Affairs Medical Center, Tennessee Valley Healthcare System, Nashville
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Timothy D. Girard
- Critical Illness, Brain Dysfunction, and Survivorship Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Center for Research, Investigation, and Systems Modeling of Acute Illness in the Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Mayur B. Patel
- Critical Illness, Brain Dysfunction, and Survivorship Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Center for Health Services Research, Vanderbilt University Medical Center, Nashville, Tennessee
- Section of Surgical Sciences, Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
- Surgical Service, Department of Veterans Affairs Medical Center, Tennessee Valley Healthcare System, Nashville, Tennessee
- Geriatric Research Education and Clinical Center, Veterans Affairs Medical Center, Tennessee Valley Healthcare System, Nashville
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17
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Cutler MJ, Eckhardt LL, Kaufman ES, Arbelo E, Behr ER, Brugada P, Cerrone M, Crotti L, deAsmundis C, Gollob MH, Horie M, Huang DT, Krahn AD, London B, Lubitz SA, Mackall JA, Nademanee K, Perez MV, Probst V, Roden DM, Sacher F, Sarquella-Brugada G, Scheinman MM, Shimizu W, Shoemaker B, Sy RW, Watanabe A, Wilde AAM. Clinical Management of Brugada Syndrome: Commentary From the Experts. Circ Arrhythm Electrophysiol 2024; 17:e012072. [PMID: 38099441 PMCID: PMC10824563 DOI: 10.1161/circep.123.012072] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Although there is consensus on the management of patients with Brugada Syndrome with high risk for sudden cardiac arrest, asymptomatic or intermediate-risk patients present clinical management challenges. This document explores the management opinions of experts throughout the world for patients with Brugada Syndrome who do not fit guideline recommendations. Four real-world clinical scenarios were presented with commentary from small expert groups for each case. All authors voted on case-specific questions to evaluate the level of consensus among the entire group in nuanced diagnostic and management decisions relevant to each case. Points of agreement, points of controversy, and gaps in knowledge are highlighted.
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Affiliation(s)
- Michael J Cutler
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT (M.J.C.)
| | - Lee L Eckhardt
- Cellular and Molecular Arrhythmia Research Program, Division of CVM, Department of Medicine, University of Wisconsin-Madison (L.L.E.)
| | - Elizabeth S Kaufman
- Heart and Vascular Center, MetroHealth Campus, Case Western Reserve University, Cleveland, OH (E.S.K.)
| | - Elena Arbelo
- Arrhythmia Section, Cardiology Department, Hospital Clínic, Universitat de Barcelona (E.A.)
- Centro de Investigacion Biomedica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid (E.A.)
- IDIBAPS, Institut d'Investigacio August Pi I Sunyer, Barcelona, Spain (E.A.)
| | - Elijah R Behr
- Cardiovascular Clinical Academic Group, Cardiology Section, St. George's, University of London and St. George's University Hospitals NHS Foundation Trust (E.R.B.)
- Mayo Clinic Healthcare, London, United Kingdom (E.R.B.)
| | - Pedro Brugada
- Cardiovascular Division, UZ Brussel-VUB, Belgium (P.B.)
- Arrhythmia Unit, Helicopteros Sanitarios Hospital (HSH), Puerto Banús, Marbella, Malaga, Spain (P.B.)
| | - Marina Cerrone
- New York Univ Grossman School of Medicine, Leon H. Charney Division of Cardiology (M.C.)
| | - Lia Crotti
- Department of Medicine and Surgery, University of Milano-Bicocca (L.C.)
- Istituto Auxologico Italiano IRCCS, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milan, Italy (L.C.)
| | - Carlo deAsmundis
- Heart Rhythm Management Center, Postgraduate Program in Cardiac Electrophysiology and Pacing, Universitair Ziekenhuis Brussel-Vrije Universiteit Brussel, European Reference Networks Guard-Heart, Belgium (C.D.)
| | - Michael H Gollob
- Peter Munk Cardiac Center, Division of Cardiology, Toronto General Hospital, University Health Network, Canada (M.H.G.)
| | - Minoru Horie
- Department of Cardiovascular Medicine, Shiga University of Medical Science, Ohtsu, Japan (M.H.)
| | | | - Andrew D Krahn
- Center for Cardiovascular Innovation, Division of Cardiology, University of British Columbia, Vancouver, Canada (A.D.K.)
| | - Barry London
- Division of Cardiovascular Medicine, Department of Internal Medicine and Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City (B.L.)
| | - Steven A Lubitz
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston (S.A.L.)
| | - Judith A Mackall
- Department of Medicine, Division of Cardiology, University Hospitals Harrington Heart and Vascular Institute, Case Western Reserve University School of Medicine, Cleveland, OH (J.A.M.)
| | - Koonlawee Nademanee
- Center of Excellence in Arrhythmia Research, Department of Medicine, Faculty of Medicine, Chulalongkorn University (K.N.)
- Pacific Rim Electrophysiology Research Institute at Bumrungrad Hospital, Bangkok, Thailand (K.N.)
| | - Marco V Perez
- Stanford Center for Inherited Cardiovascular Diseases, Stanford University, CA (M.V.P.)
| | - Vincent Probst
- Université Nantes, CHU Nantes, CNRS, INSERM, Service de Cardiologie, l'institut du thorax, Nantes, France (V.P.)
| | - Dan M Roden
- Departments of Medicine, Pharmacology and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN (D.M.R.)
| | - Frederic Sacher
- Arrhythmia Department, Bordeaux University Hospital, IHU LIRYC, Pessac, France (F.S.)
| | - Georgia Sarquella-Brugada
- Pediatric Arrhythmias, Inherited Cardiac Diseases and Sudden Death Unit, Hospital Sant Joan de Déu, Universitat de Barcelona (G.S.-B.)
- Arrítmies Pediàtriques, Cardiologia Genètica i Mort sobtada, Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain (G.S.-B.)
| | - Melvin M Scheinman
- Section of Cardiac Electrophysiology, Division of Cardiology, University of California-San Francisco (M.M.S.)
| | - Wataru Shimizu
- Department of Cardiovascular Medicine, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan (W.S.)
| | - Benjamin Shoemaker
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN (B.S.)
| | - Raymond W Sy
- Faculty of Medicine and Heath, The University of Sydney (R.W.S.)
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia (R.W.S.)
| | - Atsuyuki Watanabe
- Department of Cardiology, National Hospital Organization Okayama Medical Center, Japan (A.W.)
| | - Arthur A M Wilde
- Department of Cardiology, University of Amsterdam (A.A.M.W.)
- Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, Amsterdam, the Netherlands (A.A.M.W.)
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18
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Seagle HM, Hellwege JN, Mautz BS, Li C, Xu Y, Zhang S, Roden DM, McGregor TL, Velez Edwards DR, Edwards TL. Evidence of recent and ongoing admixture in the U.S. and influences on health and disparities. Pac Symp Biocomput 2024; 29:374-388. [PMID: 38160293] [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] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Many researchers in genetics and social science incorporate information about race in their work. However, migrations (historical and forced) and social mobility have brought formerly separated populations of humans together, creating younger generations of individuals who have more complex and diverse ancestry and race profiles than older age groups. Here, we sought to better understand how temporal changes in genetic admixture influence levels of heterozygosity and impact health outcomes. We evaluated variation in genetic ancestry over 100 birth years in a cohort of 35,842 individuals with electronic health record (EHR) information in the Southeastern United States. Using the software STRUCTURE, we analyzed 2,678 ancestrally informative markers relative to three ancestral clusters (African, East Asian, and European) and observed rising levels of admixture for all clinically-defined race groups since 1990. Most race groups also exhibited increases in heterozygosity and long-range linkage disequilibrium over time, further supporting the finding of increasing admixture in young individuals in our cohort. These data are consistent with United States Census information from broader geographic areas and highlight the changing demography of the population. This increased diversity challenges classic approaches to studies of genotype-phenotype relationships which motivated us to explore the relationship between heterozygosity and disease diagnosis. Using a phenome-wide association study approach, we explored the relationship between admixture and disease risk and found that increased admixture resulted in protective associations with female reproductive disorders and increased risk for diseases with links to autoimmune dysfunction. These data suggest that tendencies in the United States population are increasing ancestral complexity over time. Further, these observations imply that, because both prevalence and severity of many diseases vary by race groups, complexity of ancestral origins influences health and disparities.
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Affiliation(s)
- Hannah M Seagle
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
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19
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Ma JG, O’Neill MJ, Richardson E, Thomson KL, Ingles J, Muhammad A, Solus JF, Davogustto G, Anderson KC, Benjamin Shoemaker M, Stergachis AB, Floyd BJ, Dunn K, Parikh VN, Chubb H, Perrin MJ, Roden DM, Vandenberg JI, Ng CA, Glazer AM. Multi-site validation of a functional assay to adjudicate SCN5A Brugada Syndrome-associated variants. medRxiv 2023:2023.12.19.23299592. [PMID: 38196587 PMCID: PMC10775332 DOI: 10.1101/2023.12.19.23299592] [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] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Brugada Syndrome (BrS) is an inheritable arrhythmia condition that is associated with rare, loss-of-function variants in the cardiac sodium channel gene, SCN5A. Interpreting the pathogenicity of SCN5A missense variants is challenging and ~79% of SCN5A missense variants in ClinVar are currently classified as Variants of Uncertain Significance (VUS). An in vitro SCN5A-BrS automated patch clamp assay was generated for high-throughput functional studies of NaV1.5. The assay was independently studied at two separate research sites - Vanderbilt University Medical Center and Victor Chang Cardiac Research Institute - revealing strong correlations, including peak INa density (R2=0.86). The assay was calibrated according to ClinGen Sequence Variant Interpretation recommendations using high-confidence variant controls (n=49). Normal and abnormal ranges of function were established based on the distribution of benign variant assay results. The assay accurately distinguished benign controls (24/25) from pathogenic controls (23/24). Odds of Pathogenicity values derived from the experimental results yielded 0.042 for normal function (BS3 criterion) and 24.0 for abnormal function (PS3 criterion), resulting in up to strong evidence for both ACMG criteria. The calibrated assay was then used to study SCN5A VUS observed in four families with BrS and other arrhythmia phenotypes associated with SCN5A loss-of-function. The assay revealed loss-of-function for three of four variants, enabling reclassification to likely pathogenic. This validated APC assay provides clinical-grade functional evidence for the reclassification of current VUS and will aid future SCN5A-BrS variant classification.
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Affiliation(s)
- Joanne G. Ma
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- School of Clinical Medicine, UNSW Sydney, Darlinghurst, NSW, Australia
| | | | - Ebony Richardson
- Clinical Genomics Laboratory, Centre for Population Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia and Murdoch Children Research Institute, Melbourne, Australia
| | - Kate L. Thomson
- Oxford Genetics Laboratories, Churchill Hospital, Oxford, UK
| | - Jodie Ingles
- Clinical Genomics Laboratory, Centre for Population Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia and Murdoch Children Research Institute, Melbourne, Australia
| | - Ayesha Muhammad
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Joseph F. Solus
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Giovanni Davogustto
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Katherine C. Anderson
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M. Benjamin Shoemaker
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Andrew B. Stergachis
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Brendan J. Floyd
- Stanford Center for Inherited Cardiovascular Disease, Stanford University School of Medicine, Stanford, CA, USA
| | - Kyla Dunn
- Stanford Center for Inherited Cardiovascular Disease, Stanford University School of Medicine, Stanford, CA, USA
| | - Victoria N. Parikh
- Stanford Center for Inherited Cardiovascular Disease, Stanford University School of Medicine, Stanford, CA, USA
| | - Henry Chubb
- Stanford Center for Inherited Cardiovascular Disease, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark J. Perrin
- Department of Genomic Medicine, Royal Melbourne Hospital, Victoria, Australia
| | - Dan M. Roden
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jamie I. Vandenberg
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- School of Clinical Medicine, UNSW Sydney, Darlinghurst, NSW, Australia
| | - Chai-Ann Ng
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- School of Clinical Medicine, UNSW Sydney, Darlinghurst, NSW, Australia
| | - Andrew M. Glazer
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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20
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Manolio TA, Narula J, Bult CJ, Chisholm RL, Deverka PA, Ginsburg GS, Green ED, Hooker G, Jarvik GP, Mensah GA, Ramos EM, Roden DM, Rowley R, Williams MS. Genomic medicine year in review: 2023. Am J Hum Genet 2023; 110:1992-1995. [PMID: 38065071 PMCID: PMC10716532 DOI: 10.1016/j.ajhg.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023] Open
Affiliation(s)
- Teri A Manolio
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Jahnavi Narula
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carol J Bult
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME 04609, USA
| | - Rex L Chisholm
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | | | - Geoffrey S Ginsburg
- All of Us Research Program, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eric D Green
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - George A Mensah
- Center for Translation Research and Implementation Science, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erin M Ramos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dan M Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robb Rowley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marc S Williams
- Department of Genomic Health, Geisinger, Danville, PA 17822, USA
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21
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Master H, Annis J, Huang S, Beckman JA, Ratsimbazafy F, Marginean K, Carroll R, Natarajan K, Harrell FE, Roden DM, Harris P, Brittain EL. Author Correction: Association of step counts over time with the risk of chronic disease in the All of Us Research Program. Nat Med 2023; 29:3270. [PMID: 37046000 PMCID: PMC10719085 DOI: 10.1038/s41591-023-02313-8] [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: 04/14/2023]
Affiliation(s)
- Hiral Master
- Vanderbilt Institute of Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeffrey Annis
- Vanderbilt Institute of Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shi Huang
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Joshua A Beckman
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Francis Ratsimbazafy
- Vanderbilt Institute of Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kayla Marginean
- Vanderbilt Institute of Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Robert Carroll
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Karthik Natarajan
- Department Biomedical Informatics, Columbia University, New York, NY, USA
| | - Frank E Harrell
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Dan M Roden
- Department of Medicine and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Paul Harris
- Department of Biomedical Informatics, Biomedical Engineering and Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Evan L Brittain
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
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22
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Shuey MM, Stead WW, Aka I, Barnado AL, Bastarache JA, Brokamp E, Campbell M, Carroll RJ, Goldstein JA, Lewis A, Malow BA, Mosley JD, Osterman T, Padovani-Claudio DA, Ramirez A, Roden DM, Schuler BA, Siew E, Sucre J, Thomsen I, Tinker RJ, Van Driest S, Walsh C, Warner JL, Wells QS, Wheless L, Bastarache L. Next-generation phenotyping: introducing phecodeX for enhanced discovery research in medical phenomics. Bioinformatics 2023; 39:btad655. [PMID: 37930895 PMCID: PMC10627409 DOI: 10.1093/bioinformatics/btad655] [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: 06/09/2023] [Revised: 09/13/2023] [Indexed: 11/08/2023] Open
Abstract
MOTIVATION Phecodes are widely used and easily adapted phenotypes based on International Classification of Diseases codes. The current version of phecodes (v1.2) was designed primarily to study common/complex diseases diagnosed in adults; however, there are numerous limitations in the codes and their structure. RESULTS Here, we present phecodeX, an expanded version of phecodes with a revised structure and 1,761 new codes. PhecodeX adds granularity to phenotypes in key disease domains that are under-represented in the current phecode structure-including infectious disease, pregnancy, congenital anomalies, and neonatology-and is a more robust representation of the medical phenome for global use in discovery research. AVAILABILITY AND IMPLEMENTATION phecodeX is available at https://github.com/PheWAS/phecodeX.
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Affiliation(s)
- Megan M Shuey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, United States
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - William W Stead
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Ida Aka
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - April L Barnado
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Julie A Bastarache
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Elly Brokamp
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Meredith Campbell
- Department of Pediatrics, Virginia Commonwealth University, Richmond, VA 23219, United States
| | - Robert J Carroll
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Jeffrey A Goldstein
- Department of Pathology, Northwestern Feinberg School of Medicine, Chicago, IL 60611, United States
| | - Adam Lewis
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Beth A Malow
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Jonathan D Mosley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, United States
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Travis Osterman
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Dolly A Padovani-Claudio
- Department of Ophthalmology, Vanderbilt University Medical Center, Nashville, TN 37232, United States
| | - Andrea Ramirez
- All of Us Research Program, National Institutes of Health, Bethesda, MD 20892, United States
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, United States
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Bryce A Schuler
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Edward Siew
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Jennifer Sucre
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Isaac Thomsen
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Rory J Tinker
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Sara Van Driest
- All of Us Research Program, National Institutes of Health, Bethesda, MD 20892, United States
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Colin Walsh
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Jeremy L Warner
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Quinn S Wells
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Lee Wheless
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
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23
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Affiliation(s)
- William G Stevenson
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Harikrishna Tandri
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Dan M Roden
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN
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24
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Krogager ML, Skals RK, Appel EVR, Schnurr TM, Engelbrechtsen L, Have CT, Pedersen O, Engstrøm T, Roden DM, Gislason G, Poulsen HE, Køber L, Stender S, Hansen T, Grarup N, Andersson C, Torp-Pedersen C, Weeke PE. Correction: Hypertension genetic risk score is associated with burden of coronary heart disease among patients referred for coronary angiography. PLoS One 2023; 18:e0293765. [PMID: 37883362 PMCID: PMC10602353 DOI: 10.1371/journal.pone.0293765] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0208645.].
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25
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Pershad Y, Mack T, Poisner H, Jakubek YA, Stilp AM, Mitchell BD, Lewis JP, Boerwinkle E, Loos RJ, Chami N, Wang Z, Barnes K, Pankratz N, Fornage M, Redline S, Psaty BM, Bis JC, Shojaie A, Silverman EK, Cho MH, Yun J, DeMeo D, Levy D, Johnson A, Mathias R, Taub M, Arnett D, North K, Raffield LM, Carson A, Doyle MF, Rich SS, Rotter JI, Guo X, Cox N, Roden DM, Franceschini N, Desai P, Reiner A, Auer PL, Scheet P, Jaiswal S, Weinstock JS, Bick AG. Determinants of mosaic chromosomal alteration fitness. medRxiv 2023:2023.10.20.23297280. [PMID: 37905118 PMCID: PMC10615010 DOI: 10.1101/2023.10.20.23297280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Clonal hematopoiesis (CH) is characterized by the acquisition of a somatic mutation in a hematopoietic stem cell that results in a clonal expansion. These driver mutations can be single nucleotide variants in cancer driver genes or larger structural rearrangements called mosaic chromosomal alterations (mCAs). The factors that influence the variations in mCA fitness and ultimately result in different clonal expansion rates are not well-understood. We used the Passenger-Approximated Clonal Expansion Rate (PACER) method to estimate clonal expansion rate for 6,381 individuals in the NHLBI TOPMed cohort with gain, loss, and copy-neutral loss of heterozygosity mCAs. Our estimates of mCA fitness were correlated (R 2 = 0.49) with an alternative approach that estimated fitness of mCAs in the UK Biobank using a theoretical probability distribution. Individuals with lymphoid-associated mCAs had a significantly higher white blood cell count and faster clonal expansion rate. In a cross-sectional analysis, genome-wide association study of estimates of mCA expansion rate identified TCL1A , NRIP1 , and TERT locus variants as modulators of mCA clonal expansion rate.
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26
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Haas KM, McGregor MJ, Bouhaddou M, Polacco BJ, Kim EY, Nguyen TT, Newton BW, Urbanowski M, Kim H, Williams MAP, Rezelj VV, Hardy A, Fossati A, Stevenson EJ, Sukerman E, Kim T, Penugonda S, Moreno E, Braberg H, Zhou Y, Metreveli G, Harjai B, Tummino TA, Melnyk JE, Soucheray M, Batra J, Pache L, Martin-Sancho L, Carlson-Stevermer J, Jureka AS, Basler CF, Shokat KM, Shoichet BK, Shriver LP, Johnson JR, Shaw ML, Chanda SK, Roden DM, Carter TC, Kottyan LC, Chisholm RL, Pacheco JA, Smith ME, Schrodi SJ, Albrecht RA, Vignuzzi M, Zuliani-Alvarez L, Swaney DL, Eckhardt M, Wolinsky SM, White KM, Hultquist JF, Kaake RM, García-Sastre A, Krogan NJ. Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets. Nat Commun 2023; 14:6030. [PMID: 37758692 PMCID: PMC10533562 DOI: 10.1038/s41467-023-41442-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 09/28/2022] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
Influenza A Virus (IAV) is a recurring respiratory virus with limited availability of antiviral therapies. Understanding host proteins essential for IAV infection can identify targets for alternative host-directed therapies (HDTs). Using affinity purification-mass spectrometry and global phosphoproteomic and protein abundance analyses using three IAV strains (pH1N1, H3N2, H5N1) in three human cell types (A549, NHBE, THP-1), we map 332 IAV-human protein-protein interactions and identify 13 IAV-modulated kinases. Whole exome sequencing of patients who experienced severe influenza reveals several genes, including scaffold protein AHNAK, with predicted loss-of-function variants that are also identified in our proteomic analyses. Of our identified host factors, 54 significantly alter IAV infection upon siRNA knockdown, and two factors, AHNAK and coatomer subunit COPB1, are also essential for productive infection by SARS-CoV-2. Finally, 16 compounds targeting our identified host factors suppress IAV replication, with two targeting CDK2 and FLT3 showing pan-antiviral activity across influenza and coronavirus families. This study provides a comprehensive network model of IAV infection in human cells, identifying functional host targets for pan-viral HDT.
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Affiliation(s)
- Kelsey M Haas
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Michael J McGregor
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Mehdi Bouhaddou
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Benjamin J Polacco
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Eun-Young Kim
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Thong T Nguyen
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Billy W Newton
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
| | - Matthew Urbanowski
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Heejin Kim
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Michael A P Williams
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Veronica V Rezelj
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Alexandra Hardy
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Andrea Fossati
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Erica J Stevenson
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Ellie Sukerman
- Division of Infectious Diseases, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Tiffany Kim
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Sudhir Penugonda
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal and IRYCIS, Madrid, Spain
- Centro de Investigación en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Hannes Braberg
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Yuan Zhou
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Giorgi Metreveli
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bhavya Harjai
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Tia A Tummino
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
- Graduate Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - James E Melnyk
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Margaret Soucheray
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Jyoti Batra
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Lars Pache
- Infectious and Inflammatory Disease Center, Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Laura Martin-Sancho
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Infectious Disease, Imperial College London, London, SW7 2BX, UK
| | - Jared Carlson-Stevermer
- Synthego Corporation, Redwood City, CA, 94063, USA
- Serotiny Inc., South San Francisco, CA, 94080, USA
| | - Alexander S Jureka
- Molecular Virology and Vaccine Team, Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunization & Respiratory Diseases, Centers for Disease Control & Prevention, Atlanta, GA, 30333, USA
- General Dynamics Information Technology, Federal Civilian Division, Atlanta, GA, 30329, USA
| | - Christopher F Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Brian K Shoichet
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Leah P Shriver
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63105, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, 63105, USA
| | - Jeffrey R Johnson
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Megan L Shaw
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Medical Biosciences, University of the Western Cape, Bellville, 7535, Western Cape, South Africa
| | - Sumit K Chanda
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Tonia C Carter
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, 54449, USA
| | - Leah C Kottyan
- Center of Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Rex L Chisholm
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Jennifer A Pacheco
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Maureen E Smith
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Steven J Schrodi
- Laboratory of Genetics, School of Medicine and Public Health, University of Wisconsin Madison, Madison, WI, 53706, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Marco Vignuzzi
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Lorena Zuliani-Alvarez
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Danielle L Swaney
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Manon Eckhardt
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Steven M Wolinsky
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Kris M White
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Judd F Hultquist
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA.
| | - Robyn M Kaake
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
| | - Adolfo García-Sastre
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Nevan J Krogan
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
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27
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Lancaster MC, Chen HH, Shoemaker MB, Fleming MR, Baker JT, Evans G, Polikowsky HG, Samuels DC, Huff CD, Roden DM, Below JE. Detection of distant relatedness in biobanks for identification of undiagnosed carriers of a Mendelian disease variant: application to Long QT Syndrome. Res Sq 2023:rs.3.rs-3314860. [PMID: 37790303 PMCID: PMC10543295 DOI: 10.21203/rs.3.rs-3314860/v1] [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] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Rare genetic diseases are typically studied in referral populations, resulting in underdiagnosis and biased assessment of penetrance and phenotype. To address this, we developed a generalizable method of genotype inference based on distant relatedness and deployed this to identify undiagnosed Type 5 Long QT Syndrome (LQT5) rare variant carriers in a non-referral population. We identified 9 LQT5 families referred to a single specialty clinic, each carrying p.Asp76Asn, the most common LQT5 variant. We uncovered recent common ancestry and a single shared haplotype among probands. Application to a non-referral population of 69,819 BioVU biobank subjects identified 22 additional subjects sharing this haplotype, subsequently confirmed to carry p.Asp76Asn. Referral and non-referral carriers had prolonged QTc compared to controls, and, among carriers, QTc polygenic score additively associated with QTc prolongation. Thus, our novel analysis of shared chromosomal segments identified undiagnosed cases of genetic disease and refined the understanding of LQT5 penetrance and phenotype.
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Affiliation(s)
- Megan C Lancaster
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A
| | - Hung-Hsin Chen
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A
| | - M Benjamin Shoemaker
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A
| | - Matthew R Fleming
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A
| | - James T Baker
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A
| | - Grahame Evans
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A
| | - Hannah G Polikowsky
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A
| | - David C Samuels
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, 37232, U.S.A
| | - Chad D Huff
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, U.S.A
| | - Dan M Roden
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A
| | - Jennifer E Below
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A
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28
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O'Neill MJ, Yang T, Laudeman J, Calandranis M, Solus J, Roden DM, Glazer AM. ParSE-seq: A Calibrated Multiplexed Assay to Facilitate the Clinical Classification of Putative Splice-altering Variants. medRxiv 2023:2023.09.04.23295019. [PMID: 37732247 PMCID: PMC10508793 DOI: 10.1101/2023.09.04.23295019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Background Interpreting the clinical significance of putative splice-altering variants outside 2-base pair canonical splice sites remains difficult without functional studies. Methods We developed Parallel Splice Effect Sequencing (ParSE-seq), a multiplexed minigene-based assay, to test variant effects on RNA splicing quantified by high-throughput sequencing. We studied variants in SCN5A, an arrhythmia-associated gene which encodes the major cardiac voltage-gated sodium channel. We used the computational tool SpliceAI to prioritize exonic and intronic candidate splice variants, and ClinVar to select benign and pathogenic control variants. We generated a pool of 284 barcoded minigene plasmids, transfected them into Human Embryonic Kidney (HEK293) cells and induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), sequenced the resulting pools of splicing products, and calibrated the assay to the American College of Medical Genetics and Genomics scheme. Variants were interpreted using the calibrated functional data, and experimental data were compared to SpliceAI predictions. We further studied some splice-altering missense variants by cDNA-based automated patch clamping (APC) in HEK cells and assessed splicing and sodium channel function in CRISPR-edited iPSC-CMs. Results ParSE-seq revealed the splicing effect of 224 SCN5A variants in iPSC-CMs and 244 variants in HEK293 cells. The scores between the cell types were highly correlated (R2=0.84). In iPSCs, the assay had concordant scores for 21/22 benign/likely benign and 24/25 pathogenic/likely pathogenic control variants from ClinVar. 43/112 exonic variants and 35/70 intronic variants with determinate scores disrupted splicing. 11 of 42 variants of uncertain significance were reclassified, and 29 of 34 variants with conflicting interpretations were reclassified using the functional data. SpliceAI computational predictions correlated well with experimental data (AUC = 0.96). We identified 20 unique SCN5A missense variants that disrupted splicing, and 2 clinically observed splice-altering missense variants of uncertain significance had normal function when tested with the cDNA-based APC assay. A splice-altering intronic variant detected by ParSE-seq, c.1891-5C>G, also disrupted splicing and sodium current when introduced into iPSC-CMs at the endogenous locus by CRISPR editing. Conclusions ParSE-seq is a calibrated, multiplexed, high-throughput assay to facilitate the classification of candidate splice-altering variants.
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Affiliation(s)
| | - Tao Yang
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Julie Laudeman
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Maria Calandranis
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Joseph Solus
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Dan M Roden
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Andrew M Glazer
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
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29
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Deflaux N, Selvaraj MS, Condon HR, Mayo K, Haidermota S, Basford MA, Lunt C, Philippakis AA, Roden DM, Denny JC, Musick A, Collins R, Allen N, Effingham M, Glazer D, Natarajan P, Bick AG. Demonstrating paths for unlocking the value of cloud genomics through cross cohort analysis. Nat Commun 2023; 14:5419. [PMID: 37669985 PMCID: PMC10480504 DOI: 10.1038/s41467-023-41185-x] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 08/24/2023] [Indexed: 09/07/2023] Open
Abstract
Recently, large scale genomic projects such as All of Us and the UK Biobank have introduced a new research paradigm where data are stored centrally in cloud-based Trusted Research Environments (TREs). To characterize the advantages and drawbacks of different TRE attributes in facilitating cross-cohort analysis, we conduct a Genome-Wide Association Study of standard lipid measures using two approaches: meta-analysis and pooled analysis. Comparison of full summary data from both approaches with an external study shows strong correlation of known loci with lipid levels (R2 ~ 83-97%). Importantly, 90 variants meet the significance threshold only in the meta-analysis and 64 variants are significant only in pooled analysis, with approximately 20% of variants in each of those groups being most prevalent in non-European, non-Asian ancestry individuals. These findings have important implications, as technical and policy choices lead to cross-cohort analyses generating similar, but not identical results, particularly for non-European ancestral populations.
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Affiliation(s)
| | - Margaret Sunitha Selvaraj
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Henry Robert Condon
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kelsey Mayo
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sara Haidermota
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Division of Cardiology, Massachusetts General Hospital, Boston, MA, USA
| | - Melissa A Basford
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Chris Lunt
- All of Us Research Program, National Institutes of Health, Bethesda, MD, USA
| | | | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joshua C Denny
- All of Us Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Anjene Musick
- All of Us Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Rory Collins
- Nuffield Department of Population Health, University of Oxford, Oxford, Oxfordshire, UK
- UK Biobank, Cheadle, Stockport, UK
| | - Naomi Allen
- Nuffield Department of Population Health, University of Oxford, Oxford, Oxfordshire, UK
- UK Biobank, Cheadle, Stockport, UK
| | | | | | - Pradeep Natarajan
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Division of Cardiology, Massachusetts General Hospital, Boston, MA, USA
| | - Alexander G Bick
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
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30
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Giles JB, Rollin J, Martinez KL, Selleng K, Thiele T, Pouplard C, Sheppard JAI, Heddle NM, Phillips EJ, Roden DM, Gruel Y, Warkentin TE, Greinacher A, Karnes JH. Laboratory and demographic predictors of functional assay positive status in suspected heparin-induced thrombocytopenia: A multicenter retrospective cohort study. Thromb Res 2023; 229:198-208. [PMID: 37541168 PMCID: PMC10528503 DOI: 10.1016/j.thromres.2023.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 03/01/2023] [Revised: 06/16/2023] [Accepted: 07/18/2023] [Indexed: 08/06/2023]
Abstract
Heparin-induced thrombocytopenia (HIT) is an antibody-mediated immune response against platelet factor 4 (PF4) bound to heparin anticoagulants. A priori identification of patients at-risk for HIT remains elusive and a number of risk factors have been identified, but these associations and their effect sizes have limited validation in large cohorts of suspected HIT patients. The aim of this study was to investigate existing anti-PF4/heparin antibody thresholds and model the relationship of demographic variables and anti-PF4/heparin antibody levels with functional assay positivity across multiple institutions in the absence of detailed clinical data. In a large collection of suspected HIT patients (n = 8904), we tested for associations between laboratory and demographic variables and functional assay positive status as well as anti-PF4/heparin antibody levels. We also tested for correlation between IgG-specific and polyspecific (IgG/IgA/IgM) anti-PF4/heparin antibody values and their ability to predict functional assay positive status using area under the receiver operating characteristic (AUROC). Logistic regression identified increasing anti-PF4/heparin antibody OD levels (OR = 51.84 [37.27-74.34], p < 2.0 × 10-16) and female sex (OR = 1.47 [1.19-1.82], p = 3.5 × 10-4) as risk factors for positive functional assay in the largest cohort with consistent effect sizes in two other cohorts. In a subset of 1175 patients, polyspecific and IgG-specific anti-PF4/heparin antibody values were heterogeneous (mean coefficient of variation = 31.9 %), but strongly correlated (rho = 0.878; p < 2 × 10-16) with similar prediction of functional assay positivity (polyspecific AUROC = 0.976 and IgG-specific AUROC = 0.980). Thus, we recapitulate previously identified risk factors of functional assay positivity, providing precise effect sizes in a large observational population of suspected HIT patients. Our data reinforce the necessity of functional assay confirmation and suggest that, despite heterogeneity, polyspecific and IgG-specific anti-PF4/heparin antibody assays predict functional assay positive status similarly, even in the absence of 4Ts scores and detailed clinical data.
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Affiliation(s)
- Jason B Giles
- Department of Pharmacy Practice and Science, University of Arizona R. Ken Coit College of Pharmacy, Tucson, AZ, USA
| | - Jerome Rollin
- Regional University Hospital Centre Tours, Department of Hemostasis, Tours, France; University of Tours, EA4245, T2i, Tours, France
| | - Kiana L Martinez
- Department of Pharmacy Practice and Science, University of Arizona R. Ken Coit College of Pharmacy, Tucson, AZ, USA
| | - Kathleen Selleng
- Institute of Immunology and Transfusion Medicine, University of Greifswald, Greifswald, Germany
| | - Thomas Thiele
- Institute of Immunology and Transfusion Medicine, University of Greifswald, Greifswald, Germany
| | - Claire Pouplard
- Regional University Hospital Centre Tours, Department of Hemostasis, Tours, France; University of Tours, EA4245, T2i, Tours, France
| | - Jo-Ann I Sheppard
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Nancy M Heddle
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Elizabeth J Phillips
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yves Gruel
- Regional University Hospital Centre Tours, Department of Hemostasis, Tours, France; University of Tours, EA4245, T2i, Tours, France
| | - Theodore E Warkentin
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Andreas Greinacher
- Institute of Immunology and Transfusion Medicine, University of Greifswald, Greifswald, Germany
| | - Jason H Karnes
- Department of Pharmacy Practice and Science, University of Arizona R. Ken Coit College of Pharmacy, Tucson, AZ, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.
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31
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Zhang X, Brody JA, Graff M, Highland HM, Chami N, Xu H, Wang Z, Ferrier K, Chittoor G, Josyula NS, Li X, Li Z, Allison MA, Becker DM, Bielak LF, Bis JC, Boorgula MP, Bowden DW, Broome JG, Buth EJ, Carlson CS, Chang KM, Chavan S, Chiu YF, Chuang LM, Conomos MP, DeMeo DL, Du M, Duggirala R, Eng C, Fohner AE, Freedman BI, Garrett ME, Guo X, Haiman C, Heavner BD, Hidalgo B, Hixson JE, Ho YL, Hobbs BD, Hu D, Hui Q, Hwu CM, Jackson RD, Jain D, Kalyani RR, Kardia SL, Kelly TN, Lange EM, LeNoir M, Li C, Marchand LL, McDonald MLN, McHugh CP, Morrison AC, Naseri T, O’Connell J, O’Donnell CJ, Palmer ND, Pankow JS, Perry JA, Peters U, Preuss MH, Rao D, Regan EA, Reupena SM, Roden DM, Rodriguez-Santana J, Sitlani CM, Smith JA, Tiwari HK, Vasan RS, Wang Z, Weeks DE, Wessel J, Wiggins KL, Wilkens LR, Wilson PW, Yanek LR, Yoneda ZT, Zhao W, Zöllner S, Arnett DK, Ashley-Koch AE, Barnes KC, Blangero J, Boerwinkle E, Burchard EG, Carson AP, Chasman DI, Chen YDI, Curran JE, Fornage M, Gordeuk VR, He J, Heckbert SR, Hou L, Irvin MR, Kooperberg C, Minster RL, Mitchell BD, Nouraie M, Psaty BM, Raffield LM, Reiner AP, Rich SS, Rotter JI, Shoemaker MB, Smith NL, Taylor KD, Telen MJ, Weiss ST, Zhang Y, Heard-Costa N, Sun YV, Lin X, Adrienne Cupples L, Lange LA, Liu CT, Loos RJ, North KE, Justice AE. WHOLE GENOME SEQUENCING ANALYSIS OF BODY MASS INDEX IDENTIFIES NOVEL AFRICAN ANCESTRY-SPECIFIC RISK ALLELE. medRxiv 2023:2023.08.21.23293271. [PMID: 37662265 PMCID: PMC10473809 DOI: 10.1101/2023.08.21.23293271] [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] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Obesity is a major public health crisis associated with high mortality rates. Previous genome-wide association studies (GWAS) investigating body mass index (BMI) have largely relied on imputed data from European individuals. This study leveraged whole-genome sequencing (WGS) data from 88,873 participants from the Trans-Omics for Precision Medicine (TOPMed) Program, of which 51% were of non-European population groups. We discovered 18 BMI-associated signals (P < 5 × 10-9). Notably, we identified and replicated a novel low frequency single nucleotide polymorphism (SNP) in MTMR3 that was common in individuals of African descent. Using a diverse study population, we further identified two novel secondary signals in known BMI loci and pinpointed two likely causal variants in the POC5 and DMD loci. Our work demonstrates the benefits of combining WGS and diverse cohorts in expanding current catalog of variants and genes confer risk for obesity, bringing us one step closer to personalized medicine.
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Affiliation(s)
- Xinruo Zhang
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Heather M. Highland
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hanfei Xu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kendra Ferrier
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | | | | | - Xihao Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Zilin Li
- Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Matthew A. Allison
- Department of Family Medicine, Division of Preventive Medicine, The University of California San Diego, La Jolla, CA, USA
| | - Diane M. Becker
- Department of Medicine, General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lawrence F. Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Donald W. Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jai G. Broome
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Erin J. Buth
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Christopher S. Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kyong-Mi Chang
- The Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sameer Chavan
- Department of Medicine, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Yen-Feng Chiu
- Institute of Population Health Sciences, National Health Research Institutes, Taipei, Taiwan
| | - Lee-Ming Chuang
- Department of Internal Medicine, Division of Metabolism/Endocrinology, National Taiwan University Hospital, Taipei, Taiwan
| | - Matthew P. Conomos
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Dawn L. DeMeo
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Margaret Du
- Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ravindranath Duggirala
- Life Sciences, College of Arts and Sciences, Texas A&M University-San Antonio, San Antonio, TX, USA
| | - Celeste Eng
- Department of Medicine, Lung Biology Center, University of California, San Francisco, San Francisco, CA, USA
| | - Alison E. Fohner
- Epidemiology, Institute of Public Health Genetics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Barry I. Freedman
- Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Melanie E. Garrett
- Department of Medicine, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Xiuqing Guo
- Department of Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Chris Haiman
- Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Benjamin D. Heavner
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Bertha Hidalgo
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham School of Public Health, Birmingham, AL, USA
| | - James E. Hixson
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Yuk-Lam Ho
- Veterans Affairs Boston Healthcare System, Boston, MA, USA
| | - Brian D. Hobbs
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Donglei Hu
- Department of Medicine, Lung Biology Center, University of California, San Francisco, San Francisco, CA, USA
| | - Qin Hui
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
- Atlanta VA Health Care System, Decatur, GA, USA
| | - Chii-Min Hwu
- Department of Medicine, Division of Endocrinology and Metabolism, Taipei Veterans General Hospital, Taipei, Taiwan, Taiwan
| | | | - Deepti Jain
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Rita R. Kalyani
- Department of Medicine, Endocrinology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sharon L.R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Tanika N. Kelly
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Ethan M. Lange
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Michael LeNoir
- Department of Pediatrics, Bay Area Pediatrics, Oakland, CA, USA
| | - Changwei Li
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Loic Le. Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Merry-Lynn N. McDonald
- Department of Medicine, Pulmonary, Allergy and Critical Care, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Caitlin P. McHugh
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Alanna C. Morrison
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | | | - Jeffrey O’Connell
- Department of Medicine, Program for Personalized and Genomic Medicine, University of Maryland, Baltimore, MD, USA
| | - Christopher J. O’Donnell
- Veterans Affairs Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicholette D. Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - James S. Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - James A. Perry
- Department of Medicine, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Michael H. Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - D.C. Rao
- Division of Biostatistics, Washington University in St. Louis, St. Louis, MO, USA
| | - Elizabeth A. Regan
- Department of Medicine, Rheumatology, National Jewish Health, Denver, CO, USA
| | | | - Dan M. Roden
- Medicine, Pharmacology, and Biomedical Informatics, Clinical Pharmacology and Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Colleen M. Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Hemant K. Tiwari
- Department of Biostatistics, University of Alabama at Birmingham School of Public Health, Birmingham, AL, USA
| | | | - Zeyuan Wang
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Daniel E. Weeks
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jennifer Wessel
- Department of Epidemiology, Indiana University, Indianapolis, IN, USA
- Department of Medicine, Indiana University, Indianapolis, IN, USA
- Diabaetes Translational Research Center, Indiana University, Indianapolis, IN, USA
| | - Kerri L. Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Lynne R. Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Peter W.F. Wilson
- Atlanta VA Health Care System, Decatur, GA, USA
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Lisa R. Yanek
- Department of Medicine, General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zachary T. Yoneda
- Department of Medicine, Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Sebastian Zöllner
- Department of Biostatistics, Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Donna K. Arnett
- Department of Epidemiology, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Allison E. Ashley-Koch
- Department of Medicine, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Kathleen C. Barnes
- Department of Medicine, School of Medicine, University of Colorado, Aurora, CO, USA
| | - John Blangero
- Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Esteban G. Burchard
- Bioengineering and Therapeutic Sciences and Medicine, Lung Biology Center, University of California, San Francisco, San Francisco, CA, USA
| | - April P. Carson
- Department of Medicine, University of Mississippi, Jackson, MI, USA
| | - Daniel I. Chasman
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Yii-Der Ida Chen
- Department of Medical Genetics, Genomic Outcomes, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Joanne E. Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Myriam Fornage
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Victor R. Gordeuk
- Department of Medicine, School of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Jiang He
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Susan R. Heckbert
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Lifang Hou
- Northwestern University, Chicago, IL, USA
| | - Marguerite R. Irvin
- Department of Epidemiology, University of Alabama at Birmingham School of Public Health, Birmingham, AL, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ryan L. Minster
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Braxton D. Mitchell
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland, Baltimore, MD, USA
| | - Mehdi Nouraie
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Stephen S. Rich
- Public Health Science, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I. Rotter
- Department of Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - M. Benjamin Shoemaker
- Department of Medicine, Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nicholas L. Smith
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
- Seattle Epidemiologic Research and Information Center, Office of Research and Development, Department of Veterans Affairs, Seattle, WA, USA
| | - Kent D. Taylor
- Department of Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Marilyn J. Telen
- Department of Medicine, Hematology, Duke University Medical Center, Durham, NC, USA
| | - Scott T. Weiss
- Department of Medicine, Channing Division of Network Medicine, Harvard Medical School, Boston, MA, USA
| | - Yingze Zhang
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nancy Heard-Costa
- Framingham Heart Study, School of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Yan V. Sun
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
- Atlanta VA Health Care System, Decatur, GA, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Statistics, Harvard University, Boston, MA, USA
| | - L. Adrienne Cupples
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Leslie A. Lange
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Ching-Ti Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Mosley JD, Shelley JP, Dickson AL, Zanussi J, Daniel LL, Zheng NS, Bastarache L, Wei WQ, Shi M, Jarvik GP, Rosenthal EA, Khan A, Sherafati A, Kullo IJ, Walunas TL, Glessner J, Hakonarson H, Cox NJ, Roden DM, Frangakis SG, Vanderwerff B, Stein CM, Van Driest SL, Borinstein SC, Shu XO, Zawistowski M, Chung CP, Kawai VK. Clinical consequences of a polygenic predisposition to benign lower white blood cell counts: Consequences of benign WBC count genetics. medRxiv 2023:2023.08.20.23294331. [PMID: 37662324 PMCID: PMC10473820 DOI: 10.1101/2023.08.20.23294331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Polygenic variation unrelated to disease contributes to interindividual variation in baseline white blood cell (WBC) counts, but its clinical significance is undefined. We investigated the clinical consequences of a genetic predisposition toward lower WBC counts among 89,559 biobank participants from tertiary care centers using a polygenic score for WBC count (PGSWBC) comprising single nucleotide polymorphisms not associated with disease. A predisposition to lower WBC counts was associated with a decreased risk of identifying pathology on a bone marrow biopsy performed for a low WBC count (odds-ratio=0.55 per standard deviation increase in PGSWBC [95%CI, 0.30 - 0.94], p=0.04), an increased risk of leukopenia (a low WBC count) when treated with a chemotherapeutic (n=1,724, hazard ratio [HR]=0.78 [0.69 - 0.88], p=4.0×10-5) or immunosuppressant (n=354, HR=0.61 [0.38 - 0.99], p=0.04). A predisposition to benign lower WBC counts was associated with an increased risk of discontinuing azathioprine treatment (n=1,466, HR=0.62 [0.44 - 0.87], p=0.006). Collectively, these findings suggest that a WBC count polygenic score identifies individuals who are susceptible to escalations or alterations in clinical care that may be harmful or of little benefit.
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Affiliation(s)
- Jonathan D. Mosley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John P. Shelley
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alyson L. Dickson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jacy Zanussi
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Laura L. Daniel
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Neil S. Zheng
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Yale School of Medicine, New Haven, CT, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mingjian Shi
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gail P. Jarvik
- Department of Genome Sciences, University of Washington Medical Center, Seattle WA, USA
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle WA, USA
| | - Elisabeth A. Rosenthal
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle WA, USA
| | - Atlas Khan
- Division of Nephrology, Dept of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Alborz Sherafati
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester MN USA
| | - Iftikhar J. Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester MN USA
| | - Theresa L. Walunas
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Joe Glessner
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nancy J. Cox
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M. Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Stephan G. Frangakis
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Brett Vanderwerff
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - C. Michael Stein
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sara L. Van Driest
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Scott C. Borinstein
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiao-Ou Shu
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Matthew Zawistowski
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Cecilia P. Chung
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Vivian K. Kawai
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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Mayo KR, Basford MA, Carroll RJ, Dillon M, Fullen H, Leung J, Master H, Rura S, Sulieman L, Kennedy N, Banks E, Bernick D, Gauchan A, Lichtenstein L, Mapes BM, Marginean K, Nyemba SL, Ramirez A, Rotundo C, Wolfe K, Xia W, Azuine RE, Cronin RM, Denny JC, Kho A, Lunt C, Malin B, Natarajan K, Wilkins CH, Xu H, Hripcsak G, Roden DM, Philippakis AA, Glazer D, Harris PA. The All of Us Data and Research Center: Creating a Secure, Scalable, and Sustainable Ecosystem for Biomedical Research. Annu Rev Biomed Data Sci 2023; 6:443-464. [PMID: 37561600 DOI: 10.1146/annurev-biodatasci-122120-104825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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] [Indexed: 08/12/2023]
Abstract
The All of Us Research Program's Data and Research Center (DRC) was established to help acquire, curate, and provide access to one of the world's largest and most diverse datasets for precision medicine research. Already, over 500,000 participants are enrolled in All of Us, 80% of whom are underrepresented in biomedical research, and data are being analyzed by a community of over 2,300 researchers. The DRC created this thriving data ecosystem by collaborating with engaged participants, innovative program partners, and empowered researchers. In this review, we first describe how the DRC is organized to meet the needs of this broad group of stakeholders. We then outline guiding principles, common challenges, and innovative approaches used to build the All of Us data ecosystem. Finally, we share lessons learned to help others navigate important decisions and trade-offs in building a modern biomedical data platform.
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Affiliation(s)
- Kelsey R Mayo
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Melissa A Basford
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Robert J Carroll
- Deparment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
| | - Moira Dillon
- Verily Life Sciences, South San Francisco, California, USA
| | - Heather Fullen
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jesse Leung
- Verily Life Sciences, South San Francisco, California, USA
| | - Hiral Master
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Shimon Rura
- Verily Life Sciences, South San Francisco, California, USA
| | - Lina Sulieman
- Deparment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
| | - Nan Kennedy
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Eric Banks
- Data Sciences Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - David Bernick
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Asmita Gauchan
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Lee Lichtenstein
- Data Sciences Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Brandy M Mapes
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kayla Marginean
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Steve L Nyemba
- Deparment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
| | - Andrea Ramirez
- The All of Us Research Program, National Institutes of Health, Bethesda, Maryland, USA
| | - Charissa Rotundo
- Vanderbilt University Medical Center Enterprise Cybersecurity, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Keri Wolfe
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Weiyi Xia
- Deparment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
| | - Romuladus E Azuine
- The All of Us Research Program, National Institutes of Health, Bethesda, Maryland, USA
| | - Robert M Cronin
- Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Joshua C Denny
- The All of Us Research Program, National Institutes of Health, Bethesda, Maryland, USA
| | - Abel Kho
- Department of Medicine and Institute for Augmented Intelligence in Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Christopher Lunt
- The All of Us Research Program, National Institutes of Health, Bethesda, Maryland, USA
| | - Bradley Malin
- Deparment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
| | - Karthik Natarajan
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Consuelo H Wilkins
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Hua Xu
- Section of Biomedical Informatics and Data Science, School of Medicine, Yale University, New Haven, Connecticut, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Dan M Roden
- Deparment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - David Glazer
- Verily Life Sciences, South San Francisco, California, USA
| | - Paul A Harris
- Deparment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
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O'Neill MJ, Chen SN, Rumping L, Johnson R, van Slegtenhorst M, Glazer AM, Yang T, Solus JF, Laudeman J, Mitchell DW, Vanags LR, Kroncke BM, Anderson K, Gao S, Verdonschot JAJ, Brunner H, Hellebrekers D, Taylor MRG, Roden DM, Wessels MW, Lekanne Dit Deprez RH, Fatkin D, Mestroni L, Shoemaker MB. Multicenter clinical and functional evidence reclassifies a recurrent noncanonical filamin C splice-altering variant. Heart Rhythm 2023; 20:1158-1166. [PMID: 37164047 PMCID: PMC10530503 DOI: 10.1016/j.hrthm.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 04/25/2023] [Accepted: 05/03/2023] [Indexed: 05/12/2023]
Abstract
BACKGROUND Truncating variants in filamin C (FLNC) can cause arrhythmogenic cardiomyopathy (ACM) through haploinsufficiency. Noncanonical splice-altering variants may contribute to this phenotype. OBJECTIVE The purpose of this study was to investigate the clinical and functional consequences of a recurrent FLNC intronic variant of uncertain significance (VUS), c.970-4A>G. METHODS Clinical data in 9 variant heterozygotes from 4 kindreds were obtained from 5 tertiary health care centers. We used in silico predictors and functional studies with peripheral blood and patient-specific induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). Isolated RNA was studied by reverse transcription polymerase chain reaction. iPSC-CMs were further characterized at baseline and after nonsense-mediated decay (NMD) inhibition, using quantitative polymerase chain reaction (qPCR), RNA-sequencing, and cellular electrophysiology. American College of Medical Genetics and Genomics (ACMG) criteria were used to adjudicate variant pathogenicity. RESULTS Variant heterozygotes displayed a spectrum of disease phenotypes, spanning from mild ventricular dysfunction with palpitations to severe ventricular arrhythmias requiring device shocks or progressive cardiomyopathy requiring heart transplantation. Consistent with in silico predictors, the c.970-4A>G FLNC variant activated a cryptic splice acceptor site, introducing a 3-bp insertion containing a premature termination codon. NMD inhibition upregulated aberrantly spliced transcripts by qPCR and RNA-sequencing. Patch clamp studies revealed irregular spontaneous action potentials, increased action potential duration, and increased sodium late current in proband-derived iPSC-CMs. These findings fulfilled multiple ACMG criteria for pathogenicity. CONCLUSION Clinical, in silico, and functional evidence support the prediction that the intronic c.970-4A>G VUS disrupts splicing and drives ACM, enabling reclassification from VUS to pathogenic.
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Affiliation(s)
- Matthew J O'Neill
- Vanderbilt University School of Medicine, Medical Scientist Training Program, Vanderbilt University, Nashville, Tennessee
| | - Suet Nee Chen
- Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Lynne Rumping
- Department of Human Genetics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Renee Johnson
- Molecular Cardiology Division, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia; School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | | | - Andrew M Glazer
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Tao Yang
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Joseph F Solus
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Julie Laudeman
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Devyn W Mitchell
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Loren R Vanags
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Brett M Kroncke
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Katherine Anderson
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Shanshan Gao
- Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Job A J Verdonschot
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Han Brunner
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Debby Hellebrekers
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | | | - Dan M Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Marja W Wessels
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Diane Fatkin
- Molecular Cardiology Division, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia; School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia; Cardiology Department, St. Vincent's Hospital, Sydney, NSW, Australia
| | - Luisa Mestroni
- Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - M Benjamin Shoemaker
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.
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35
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Zhang S, Strayer N, Vessels T, Choi K, Wang GW, Li Y, Bejan CA, Hsi RS, Bick AG, Velez Edwards DR, Savona MR, Philips EJ, Pulley J, Self WH, Hopkins WC, Roden DM, Smoller JW, Ruderfer DM, Xu Y. PheMIME: An Interactive Web App and Knowledge Base for Phenome-Wide, Multi-Institutional Multimorbidity Analysis. medRxiv 2023:2023.07.23.23293047. [PMID: 37547012 PMCID: PMC10402210 DOI: 10.1101/2023.07.23.23293047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Motivation Multimorbidity, characterized by the simultaneous occurrence of multiple diseases in an individual, is an increasing global health concern, posing substantial challenges to healthcare systems. Comprehensive understanding of disease-disease interactions and intrinsic mechanisms behind multimorbidity can offer opportunities for innovative prevention strategies, targeted interventions, and personalized treatments. Yet, there exist limited tools and datasets that characterize multimorbidity patterns across different populations. To bridge this gap, we used large-scale electronic health record (EHR) systems to develop the Phenome-wide Multi-Institutional Multimorbidity Explorer (PheMIME), which facilitates research in exploring and comparing multimorbidity patterns among multiple institutions, potentially leading to the discovery of novel and robust disease associations and patterns that are interoperable across different systems and organizations. Results PheMIME integrates summary statistics from phenome-wide analyses of disease multimorbidities. These are currently derived from three major institutions: Vanderbilt University Medical Center, Mass General Brigham, and the UK Biobank. PheMIME offers interactive exploration of multimorbidity through multi-faceted visualization. Incorporating an enhanced version of associationSubgraphs, PheMIME enables dynamic analysis and inference of disease clusters, promoting the discovery of multimorbidity patterns. Once a disease of interest is selected, the tool generates interactive visualizations and tables that users can delve into multimorbidities or multimorbidity networks within a single system or compare across multiple systems. The utility of PheMIME is demonstrated through a case study on schizophrenia. Availability and implementation The PheMIME knowledge base and web application are accessible at https://prod.tbilab.org/PheMIME/. A comprehensive tutorial, including a use-case example, is available at https://prod.tbilab.org/PheMIME_supplementary_materials/. Furthermore, the source code for PheMIME can be freely downloaded from https://github.com/tbilab/PheMIME. Data availability statement The data underlying this article are available in the article and in its online web application or supplementary material.
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Affiliation(s)
- Siwei Zhang
- Department of Biostatistics, Vanderbilt University, Nashville, TN, USA
| | | | - Tess Vessels
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Karmel Choi
- Psychiatric & Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston MA
- Center for Precision Psychiatry, Department of Psychiatry, Massachusetts General Hospital, Boston MA
| | | | - Yajing Li
- Department of Biostatistics, Vanderbilt University, Nashville, TN, USA
| | - Cosmin A Bejan
- Department of Biomedical informatics, Vanderbilt University, Nashville, TN, USA
| | - Ryan S Hsi
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alexander G Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Digna R Velez Edwards
- Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Michael R Savona
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Elizabeth J Philips
- Center for Drug Safety and Immunology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - Jill Pulley
- Vanderbilt Institute for Clinical and Translational Science, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wesley H Self
- Vanderbilt Institute for Clinical and Translational Science, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wilkins Consuelo Hopkins
- Vanderbilt Institute for Clinical and Translational Science, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M Roden
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jordan W Smoller
- Psychiatric & Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston MA
- Center for Precision Psychiatry, Department of Psychiatry, Massachusetts General Hospital, Boston MA
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA
| | - Douglas M Ruderfer
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical informatics, Vanderbilt University, Nashville, TN, USA
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University, Nashville, TN, USA
- Department of Biomedical informatics, Vanderbilt University, Nashville, TN, USA
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36
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Yan C, Grabowska ME, Dickson AL, Li B, Wen Z, Roden DM, Stein CM, Embí PJ, Peterson JF, Feng Q, Malin BA, Wei WQ. Leveraging Generative AI to Prioritize Drug Repurposing Candidates: Validating Identified Candidates for Alzheimer's Disease in Real-World Clinical Datasets. medRxiv 2023:2023.07.07.23292388. [PMID: 37461512 PMCID: PMC10350158 DOI: 10.1101/2023.07.07.23292388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Drug repurposing represents an attractive alternative to the costly and time-consuming process of new drug development, particularly for serious, widespread conditions with limited effective treatments, such as Alzheimer's disease (AD). Emerging generative artificial intelligence (GAI) technologies like ChatGPT offer the promise of expediting the review and summary of scientific knowledge. To examine the feasibility of using GAI for identifying drug repurposing candidates, we iteratively tasked ChatGPT with proposing the twenty most promising drugs for repurposing in AD, and tested the top ten for risk of incident AD in exposed and unexposed individuals over age 65 in two large clinical datasets: 1) Vanderbilt University Medical Center and 2) the All of Us Research Program. Among the candidates suggested by ChatGPT, metformin, simvastatin, and losartan were associated with lower AD risk in meta-analysis. These findings suggest GAI technologies can assimilate scientific insights from an extensive Internet-based search space, helping to prioritize drug repurposing candidates and facilitate the treatment of diseases.
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El-Harasis MA, Yoneda ZT, Davogustto GE, Crawford DM, Laws JL, Frye B, Herrmann T, Patel B, Touchton SA, Roden DM, Richardson TD, Saavedra P, Shen ST, Estrada JC, Kanagasundram AN, Montgomery JA, Michaud GF, Crossley GH, Ellis CR, Shoemaker MB. Pulmonary Vein Myocardial Sleeve Length and its Association With Sex and 4q25/PITX2 Genotype. JACC Clin Electrophysiol 2023; 9:1147-1157. [PMID: 37495323 DOI: 10.1016/j.jacep.2022.12.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 09/29/2022] [Revised: 11/10/2022] [Accepted: 12/15/2022] [Indexed: 07/28/2023]
Abstract
BACKGROUND Experimental evidence suggests genetic variation in 4q25/PITX2 modulates pulmonary vein (PV) myocardial sleeve length. Although PV sleeves are the main target of atrial fibrillation (AF) ablation, little is known about the association between different PV sleeve characteristics with ablation outcomes. OBJECTIVES This study sought to evaluate the association between clinical and genetic (4q25) risk factors with PV sleeve length in humans, and to evaluate the association between PV sleeve length and recurrence after AF ablation. METHODS In a prospective, observational study of patients undergoing de novo AF ablation, PV sleeve length was measured using electroanatomic voltage mapping before ablation. The sentinel 4q25 AF susceptibility single nucleotide polymorphism, rs2200733, was genotyped. The primary analysis tested the association between clinical and genetic (4q25) risk factors with PV sleeve length using a multivariable linear regression model. Covariates included age, sex, body mass index, height, and persistent AF. The association between PV sleeve length and atrial arrhythmia recurrence (>30 seconds) was tested using a multivariable Cox proportional hazards model. RESULTS Between 2014 and 2019, 197 participants were enrolled (median age 63 years [IQR: 55 to 70 years], 133 male [67.5%]). In multivariable modeling, men were found to have PV sleeves 2.94 mm longer than women (95% CI: 0.99-4.90 mm; P < 0.001). Sixty participants (30.5%) had one 4q25 risk allele and 6 (3.1%) had 2 alleles. There was no association between 4q25 genotype and PV sleeve length. Forty-six participants (23.4%) experienced arrhythmia recurrence within 3 to 12 months, but there was no association between recurrence and PV sleeve length. CONCLUSIONS Common genetic variation at 4q25 was not associated with PV sleeve length and PV sleeve length was not associated with ablation outcomes. Men did have longer PV sleeves than women, but more research is needed to define the potential clinical significance of this observation.
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Affiliation(s)
- Majd A El-Harasis
- Department of Medicine, Division of Cardiovascular Medicine. Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Zachary T Yoneda
- Department of Medicine, Division of Cardiovascular Medicine. Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Giovanni E Davogustto
- Department of Medicine, Division of Cardiovascular Medicine. Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Diane M Crawford
- Department of Medicine, Division of Cardiovascular Medicine. Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - James L Laws
- Department of Medicine, Division of Cardiovascular Medicine. Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | | | | | | | - Dan M Roden
- Department of Medicine, Division of Cardiovascular Medicine. Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Travis D Richardson
- Department of Medicine, Division of Cardiovascular Medicine. Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Pablo Saavedra
- Department of Medicine, Division of Cardiovascular Medicine. Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Sharon T Shen
- Department of Medicine, Division of Cardiovascular Medicine. Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Juan C Estrada
- Department of Medicine, Division of Cardiovascular Medicine. Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Arvindh N Kanagasundram
- Department of Medicine, Division of Cardiovascular Medicine. Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jay A Montgomery
- Department of Medicine, Division of Cardiovascular Medicine. Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Gregory F Michaud
- Department of Medicine, Division of Cardiovascular Medicine. Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - George H Crossley
- Department of Medicine, Division of Cardiovascular Medicine. Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Christopher R Ellis
- Department of Medicine, Division of Cardiovascular Medicine. Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - M Benjamin Shoemaker
- Department of Medicine, Division of Cardiovascular Medicine. Vanderbilt University Medical Center, Nashville, Tennessee, USA.
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Virk ZM, Richardson TL, Nowatzke JF, Ullah A, Pedrotty DM, Shoemaker MB, Kanagasundram A, Roden DM, Stevenson WG. Cardiac Sarcoidosis and a Likely Pathogenic TTN Variant in a Patient Presenting With Ventricular Tachycardia. JACC Case Rep 2023; 16:101878. [PMID: 37396334 PMCID: PMC10313492 DOI: 10.1016/j.jaccas.2023.101878] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 02/05/2023] [Revised: 04/12/2023] [Accepted: 04/20/2023] [Indexed: 07/04/2023]
Abstract
Rare variants in TTN are the most common monogenic cause of early-onset atrial fibrillation and dilated cardiomyopathy. Whereas cardiac sarcoidosis is very underdiagnosed, a common presentation can be ventricular arrhythmias. This report presents a patient with a likely pathogenic TTN variant and cardiac sarcoidosis. (Level of Difficulty: Intermediate.).
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Affiliation(s)
- Zain M. Virk
- Vanderbilt University Medical Center, Department of Medicine Division of Cardiology, Nashville, Tennessee, USA
| | - T. Lee Richardson
- Vanderbilt University Medical Center, Department of Medicine Division of Cardiology, Nashville, Tennessee, USA
| | - Joseph F. Nowatzke
- Vanderbilt University Medical Center, Department of Medicine Division of Cardiology, Nashville, Tennessee, USA
| | - Asad Ullah
- Vanderbilt University Medical Center, Department of Pathology, Nashville, Tennessee, USA
| | - Dawn M. Pedrotty
- Vanderbilt University Medical Center, Department of Medicine Division of Cardiology, Nashville, Tennessee, USA
| | - M. Benjamin Shoemaker
- Vanderbilt University Medical Center, Department of Medicine Division of Cardiology, Nashville, Tennessee, USA
| | - Arvindh Kanagasundram
- Vanderbilt University Medical Center, Department of Medicine Division of Cardiology, Nashville, Tennessee, USA
| | - Dan M. Roden
- Vanderbilt University Medical Center, Department of Medicine Division of Cardiology, Nashville, Tennessee, USA
| | - William G. Stevenson
- Vanderbilt University Medical Center, Department of Medicine Division of Cardiology, Nashville, Tennessee, USA
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Muhammad A, Calandranis ME, Li B, Yang T, Blackwell DJ, Harvey ML, Smith JE, Chew AE, Capra JA, Matreyek KA, Fowler DM, Roden DM, Glazer AM. High-throughput functional mapping of variants in an arrhythmia gene, KCNE1, reveals novel biology. bioRxiv 2023:2023.04.28.538612. [PMID: 37162834 PMCID: PMC10168370 DOI: 10.1101/2023.04.28.538612] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Background KCNE1 encodes a 129-residue cardiac potassium channel (IKs) subunit. KCNE1 variants are associated with long QT syndrome and atrial fibrillation. However, most variants have insufficient evidence of clinical consequences and thus limited clinical utility. Results Here, we demonstrate the power of variant effect mapping, which couples saturation mutagenesis with high-throughput sequencing, to ascertain the function of thousands of protein coding KCNE1 variants. We comprehensively assayed KCNE1 variant cell surface expression (2,554/2,709 possible single amino acid variants) and function (2,539 variants). We identified 470 loss-of-surface expression and 588 loss-of-function variants. Out of the 588 loss-of-function variants, only 155 had low cell surface expression. The latter half of the protein is dispensable for protein trafficking but essential for channel function. 22 of the 30 KCNE1 residues (73%) highly intolerant of variation were in predicted close contact with binding partners KCNQ1 or calmodulin. Our data were highly concordant with gold standard electrophysiological data (ρ = -0.65), population and patient cohorts (32/38 concordant variants), and computational metrics (ρ = -0.55). Our data provide moderate-strength evidence for the ACMG/AMP functional criteria for benign and pathogenic variants. Conclusions Comprehensive variant effect maps of KCNE1 can both provide insight into IKs channel biology and help reclassify variants of uncertain significance.
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Affiliation(s)
- Ayesha Muhammad
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN 37232, USA
| | - Maria E. Calandranis
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Bian Li
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Tao Yang
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Daniel J. Blackwell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - M. Lorena Harvey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jeremy E. Smith
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ashli E. Chew
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - John A. Capra
- Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94143, USA
| | - Kenneth A. Matreyek
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Douglas M. Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Dan M. Roden
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Andrew M. Glazer
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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Lancaster MC, Chen HH, Shoemaker MB, Fleming MR, Baker JT, Polikowsky HG, Samuels DC, Huff CD, Roden DM, Below JE. Detection of distant familial relatedness in biobanks for identification of undiagnosed carriers of a Mendelian disease variant: application to Long QT syndrome. medRxiv 2023:2023.04.19.23288831. [PMID: 37163006 PMCID: PMC10168417 DOI: 10.1101/2023.04.19.23288831] [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] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Importance The diagnosis and study of rare genetic disease is often limited to referral populations, leading to underdiagnosis and a biased assessment of penetrance and phenotype. Objective To develop a generalizable method of genotype inference based on distant relatedness and to deploy this to identify undiagnosed Type 5 Long QT Syndrome (LQT5) rare variant carriers in a non-referral population. Participants We identified 9 LQT5 probands and 3 first-degree relatives referred to a single Genetic Arrhythmia clinic, each carrying D76N (p.Asp76Asn), the most common variant implicated in LQT5. The non-referral population consisted of 69,879 ancestry-matched subjects in BioVU, a large biobank that links electronic health records to dense array data. Participants were enrolled from 2007-2022. Data analysis was performed in 2022. Exposures We developed and applied a novel approach to genotype inference (Distant Relatedness for Identification and Variant Evaluation, or DRIVE) to identify shared, identical-by-descent (IBD) large chromosomal segments in array data. Main Outcomes and Measures We sought to establish genetic relatedness among the probands and to use genomic segments underlying D76N to identify other potential carriers in BioVU. We then further studied the role of D76N in LQT5 pathogenesis. Results Genetic reconstruction of pedigrees and distant relatedness detection among clinic probands using DRIVE revealed shared recent common ancestry and identified a single long shared haplotype. Interrogation of the non-referral population in BioVU identified a further 23 subjects sharing this haplotype, and sequencing confirmed D76N carrier status in 22, all previously undiagnosed with LQT5. The QTc was prolonged in D76N carriers compared to BioVU controls, with 40% penetrance of QTc ≥ 480 msec. Among D76N carriers, a QTc polygenic score was additively associated with QTc prolongation. Conclusions and Relevance Detection of IBD shared chromosomal segments around D76N enabled identification of distantly related and previously undiagnosed rare-variant carriers, demonstrated the contribution of polygenic risk to monogenic disease penetrance, and further established LQT5 as a primary arrhythmia disorder. Analysis of shared chromosomal regions spanning disease-causing mutations can identify undiagnosed cases of genetic diseases.
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Affiliation(s)
| | - Hung-Hsin Chen
- Vanderbilt University Medical Center, Nashville, Tennessee
| | | | | | - James T Baker
- Vanderbilt University Medical Center, Nashville, Tennessee
| | | | | | - Chad D Huff
- University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dan M Roden
- Vanderbilt University Medical Center, Nashville, Tennessee
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Perry AS, Annis JS, Master H, Nayor M, Hughes A, Kouame A, Natarajan K, Marginean K, Murthy V, Roden DM, Harris PA, Shah R, Brittain EL. Association of Longitudinal Activity Measures and Diabetes Risk: An Analysis From the National Institutes of Health All of Us Research Program. J Clin Endocrinol Metab 2023; 108:1101-1109. [PMID: 36458881 PMCID: PMC10306083 DOI: 10.1210/clinem/dgac695] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/18/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022]
Abstract
CONTEXT Prior studies of the relationship between physical activity and incident type 2 diabetes mellitus (T2DM) relied primarily on questionnaires at a single time point. OBJECTIVE We sought to investigate the relationship between physical activity and incident T2DM with an innovative approach using data from commercial wearable devices linked to electronic health records in a real-world population. METHODS Using All of Us participants' accelerometer data from their personal Fitbit devices, we used a time-varying Cox proportional hazards models with repeated measures of physical activity for the outcome of incident T2DM. We evaluated for effect modification with age, sex, body mass index (BMI), and sedentary time using multiplicative interaction terms. RESULTS From 5677 participants in the All of Us Research Program (median age 51 years; 74% female; 89% White), there were 97 (2%) cases of incident T2DM over a median follow-up period of 3.8 years between 2010 to 2021. In models adjusted for age, sex, and race, the hazard of incident diabetes was reduced by 44% (95% CI, 15%-63%; P = 0.01) when comparing those with an average daily step count of 10 700 to those with 6000. Similar benefits were seen comparing groups based on average duration of various intensities of activity (eg, lightly active, fairly active, very active). There was no evidence for effect modification by age, sex, BMI, or sedentary time. CONCLUSION Greater time in any type of physical activity intensity was associated with lower risk of T2DM irrespective of age, sex, BMI, or sedentary time.
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Affiliation(s)
- Andrew S Perry
- Vanderbilt Translational and Clinical Cardiovascular Research Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Jeffrey S Annis
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Hiral Master
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Matthew Nayor
- Sections of Cardiovascular Medicine and Preventive Medicine and Epidemiology, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Andrew Hughes
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Aymone Kouame
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Karthik Natarajan
- Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
| | - Kayla Marginean
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Venkatesh Murthy
- Department of Medicine and Radiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37203, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Paul A Harris
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
- Department of Biomedical Engineering, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Ravi Shah
- Vanderbilt Translational and Clinical Cardiovascular Research Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Evan L Brittain
- Vanderbilt Translational and Clinical Cardiovascular Research Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
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42
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Linder JE, Allworth A, Bland HT, Caraballo PJ, Chisholm RL, Clayton EW, Crosslin DR, Dikilitas O, DiVietro A, Esplin ED, Forman S, Freimuth RR, Gordon AS, Green R, Harden MV, Holm IA, Jarvik GP, Karlson EW, Labrecque S, Lennon NJ, Limdi NA, Mittendorf KF, Murphy SN, Orlando L, Prows CA, Rasmussen LV, Rasmussen-Torvik L, Rowley R, Sawicki KT, Schmidlen T, Terek S, Veenstra D, Velez Edwards DR, Absher D, Abul-Husn NS, Alsip J, Bangash H, Beasley M, Below JE, Berner ES, Booth J, Chung WK, Cimino JJ, Connolly J, Davis P, Devine B, Fullerton SM, Guiducci C, Habrat ML, Hain H, Hakonarson H, Harr M, Haverfield E, Hernandez V, Hoell C, Horike-Pyne M, Hripcsak G, Irvin MR, Kachulis C, Karavite D, Kenny EE, Khan A, Kiryluk K, Korf B, Kottyan L, Kullo IJ, Larkin K, Liu C, Malolepsza E, Manolio TA, May T, McNally EM, Mentch F, Miller A, Mooney SD, Murali P, Mutai B, Muthu N, Namjou B, Perez EF, Puckelwartz MJ, Rakhra-Burris T, Roden DM, Rosenthal EA, Saadatagah S, Sabatello M, Schaid DJ, Schultz B, Seabolt L, Shaibi GQ, Sharp RR, Shirts B, Smith ME, Smoller JW, Sterling R, Suckiel SA, Thayer J, Tiwari HK, Trinidad SB, Walunas T, Wei WQ, Wells QS, Weng C, Wiesner GL, Wiley K, Peterson JF. Returning integrated genomic risk and clinical recommendations: The eMERGE study. Genet Med 2023; 25:100006. [PMID: 36621880 PMCID: PMC10085845 DOI: 10.1016/j.gim.2023.100006] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [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: 07/26/2022] [Revised: 12/16/2022] [Accepted: 12/21/2022] [Indexed: 01/09/2023] Open
Abstract
PURPOSE Assessing the risk of common, complex diseases requires consideration of clinical risk factors as well as monogenic and polygenic risks, which in turn may be reflected in family history. Returning risks to individuals and providers may influence preventive care or use of prophylactic therapies for those individuals at high genetic risk. METHODS To enable integrated genetic risk assessment, the eMERGE (electronic MEdical Records and GEnomics) network is enrolling 25,000 diverse individuals in a prospective cohort study across 10 sites. The network developed methods to return cross-ancestry polygenic risk scores, monogenic risks, family history, and clinical risk assessments via a genome-informed risk assessment (GIRA) report and will assess uptake of care recommendations after return of results. RESULTS GIRAs include summary care recommendations for 11 conditions, education pages, and clinical laboratory reports. The return of high-risk GIRA to individuals and providers includes guidelines for care and lifestyle recommendations. Assembling the GIRA required infrastructure and workflows for ingesting and presenting content from multiple sources. Recruitment began in February 2022. CONCLUSION Return of a novel report for communicating monogenic, polygenic, and family history-based risk factors will inform the benefits of integrated genetic risk assessment for routine health care.
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Affiliation(s)
- Jodell E Linder
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | - Aimee Allworth
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Harris T Bland
- Department of Biomedical Informatics and Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Pedro J Caraballo
- Department of Internal Medicine and Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Rex L Chisholm
- Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Ellen Wright Clayton
- Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, Nashville, TN
| | - David R Crosslin
- Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA
| | - Ozan Dikilitas
- Mayo Clinician Investigator Training Program, Department of Internal Medicine and Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Alanna DiVietro
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | | | - Sophie Forman
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | - Robert R Freimuth
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN
| | - Adam S Gordon
- Department of Pharmacology, Feinberg School of Medicine, and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Richard Green
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | | | - Ingrid A Holm
- Division of Genetics and Genomics and Manton Center for Orphan Diseases Research, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine and Department of Genome Science, University of Washington Medical Center, Seattle, WA
| | - Elizabeth W Karlson
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Sofia Labrecque
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | | | - Nita A Limdi
- Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Kathleen F Mittendorf
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Shawn N Murphy
- Department of Neurology, Massachusetts General Hospital, Boston, MA
| | - Lori Orlando
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
| | - Cynthia A Prows
- Divisions of Human Genetics and Patient Services, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Luke V Rasmussen
- Department of Preventive Medicine, Northwestern University, Chicago, IL
| | | | - Robb Rowley
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Konrad Teodor Sawicki
- Department of Cardiology and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | | | - Shannon Terek
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - David Veenstra
- School of Pharmacy, University of Washington, Seattle, WA
| | - Digna R Velez Edwards
- Division of Quantitative Science, Department of Obstetrics and Gynecology, Department of Biomedical Sciences, Vanderbilt University Medical Center, Nashville, TN
| | | | - Noura S Abul-Husn
- Institute for Genomic Health, Department of Medicine, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Hana Bangash
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Mark Beasley
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | - Jennifer E Below
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Eta S Berner
- Department of Health Services Administration, University of Alabama at Birmingham, Birmingham, AL
| | - James Booth
- Department of Emergency Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - James J Cimino
- Division of General Internal Medicine and the Informatics Institute, Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - John Connolly
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Patrick Davis
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | - Beth Devine
- School of Pharmacy, University of Washington, Seattle, WA
| | - Stephanie M Fullerton
- Department of Bioethics and Humanities, University of Washington School of Medicine, Seattle, WA
| | | | - Melissa L Habrat
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | - Heather Hain
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Margaret Harr
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | - Christin Hoell
- Department of Obstetrics & Gynecology and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Martha Horike-Pyne
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | | | - Dean Karavite
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Eimear E Kenny
- Institute for Genomic Health, Department of Medicine, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Bruce Korf
- Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Leah Kottyan
- The Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Katie Larkin
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Cong Liu
- Department of Biomedical Informatics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | | | - Teri A Manolio
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Thomas May
- Elson S. Floyd College of Medicine, Washington State University, Vancouver, WA
| | | | - Frank Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Alexandra Miller
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Sean D Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | - Priyanka Murali
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Brenda Mutai
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Naveen Muthu
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Bahram Namjou
- The Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Emma F Perez
- Department of Medicine, Brigham and Women's Hospital, Mass General Brigham Personalized Medicine, Boston, MA
| | - Megan J Puckelwartz
- Department of Pharmacology, Feinberg School of Medicine, and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | | | - Dan M Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Elisabeth A Rosenthal
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | | | - Maya Sabatello
- Division of Nephrology, Department of Medicine & Division of Ethics, Department of Medical Humanities and Ethics, Columbia University Irving Medical Center, New York, NY
| | - Dan J Schaid
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Baergen Schultz
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Lynn Seabolt
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | - Gabriel Q Shaibi
- Center for Health Promotion and Disease Prevention, Arizona State University, Phoenix, AZ
| | - Richard R Sharp
- Biomedical Ethics Program, Department of Quantitative Health Science, Mayo Clinic, Rochester, MN
| | - Brian Shirts
- Department of Laboratory Medicine & Pathology, University of Washington Medical Center, Seattle, WA
| | - Maureen E Smith
- Department of Cardiology and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Jordan W Smoller
- Department of Psychiatry and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Rene Sterling
- Division of Genomics and Society, National Human Genome Research Institute, Bethesda, MD
| | - Sabrina A Suckiel
- The Institute for Genomic Health, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jeritt Thayer
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hemant K Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | - Susan B Trinidad
- Department of Bioethics and Humanities, University of Washington School of Medicine, Seattle, WA
| | - Theresa Walunas
- Department of Medicine and Center for Health Information Partnerships, Northwestern University, Chicago, IL
| | - Wei-Qi Wei
- Department of Biomedical Informatics and Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Quinn S Wells
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - Georgia L Wiesner
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Ken Wiley
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Josh F Peterson
- Center for Precision Medicine, Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN.
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43
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Dikilitas O, Sherafati A, Saadatagah S, Satterfield BA, Kochan DC, Anderson KC, Chung WK, Hebbring SJ, Salvati ZM, Sharp RR, Sturm AC, Gibbs RA, Rowley R, Venner E, Linder JE, Jones LK, Perez EF, Peterson JF, Jarvik GP, Rehm HL, Zouk H, Roden DM, Williams MS, Manolio TA, Kullo IJ. Familial Hypercholesterolemia in the Electronic Medical Records and Genomics Network: Prevalence, Penetrance, Cardiovascular Risk, and Outcomes After Return of Results. Circ Genom Precis Med 2023; 16:e003816. [PMID: 37071725 PMCID: PMC10113961 DOI: 10.1161/circgen.122.003816] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 01/03/2023] [Indexed: 02/24/2023]
Abstract
BACKGROUND The implications of secondary findings detected in large-scale sequencing projects remain uncertain. We assessed prevalence and penetrance of pathogenic familial hypercholesterolemia (FH) variants, their association with coronary heart disease (CHD), and 1-year outcomes following return of results in phase III of the electronic medical records and genomics network. METHODS Adult participants (n=18 544) at 7 sites were enrolled in a prospective cohort study to assess the clinical impact of returning results from targeted sequencing of 68 actionable genes, including LDLR, APOB, and PCSK9. FH variant prevalence and penetrance (defined as low-density lipoprotein cholesterol >155 mg/dL) were estimated after excluding participants enrolled on the basis of hypercholesterolemia. Multivariable logistic regression was used to estimate the odds of CHD compared to age- and sex-matched controls without FH-associated variants. Process (eg, referral to a specialist or ordering new tests), intermediate (eg, new diagnosis of FH), and clinical (eg, treatment modification) outcomes within 1 year after return of results were ascertained by electronic health record review. RESULTS The prevalence of FH-associated pathogenic variants was 1 in 188 (69 of 13,019 unselected participants). Penetrance was 87.5%. The presence of an FH variant was associated with CHD (odds ratio, 3.02 [2.00-4.53]) and premature CHD (odds ratio, 3.68 [2.34-5.78]). At least 1 outcome occurred in 92% of participants; 44% received a new diagnosis of FH and 26% had treatment modified following return of results. CONCLUSIONS In a multisite cohort of electronic health record-linked biobanks, monogenic FH was prevalent, penetrant, and associated with presence of CHD. Nearly half of participants with an FH-associated variant received a new diagnosis of FH and a quarter had treatment modified after return of results. These results highlight the potential utility of sequencing electronic health record-linked biobanks to detect FH.
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Affiliation(s)
- Ozan Dikilitas
- Department of Internal Medicine (O.D.), Mayo Clinic, Rochester, MN
- Department of Cardiovascular Medicine (O.D., A.S., S.S., B.A.S., D.C.K., I.J.K.), Mayo Clinic, Rochester, MN
| | - Alborz Sherafati
- Department of Cardiovascular Medicine (O.D., A.S., S.S., B.A.S., D.C.K., I.J.K.), Mayo Clinic, Rochester, MN
| | - Seyedmohammad Saadatagah
- Department of Cardiovascular Medicine (O.D., A.S., S.S., B.A.S., D.C.K., I.J.K.), Mayo Clinic, Rochester, MN
| | - Benjamin A Satterfield
- Department of Cardiovascular Medicine (O.D., A.S., S.S., B.A.S., D.C.K., I.J.K.), Mayo Clinic, Rochester, MN
| | - David C Kochan
- Department of Cardiovascular Medicine (O.D., A.S., S.S., B.A.S., D.C.K., I.J.K.), Mayo Clinic, Rochester, MN
| | - Katherine C Anderson
- Department of Medicine (K.C.A., J.E.L., J.F.P.), Vanderbilt University Medical Center, Nashville, TN
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York (W.K.C.)
| | | | - Zachary M Salvati
- Genomic Medicine Institute, Geisinger, Danville, PA (Z.M.S., A.C.S., L.K.J., M.S.W.)
| | - Richard R Sharp
- Biomedical Ethics Research Program (R.R.S.), Mayo Clinic, Rochester, MN
| | - Amy C Sturm
- Genomic Medicine Institute, Geisinger, Danville, PA (Z.M.S., A.C.S., L.K.J., M.S.W.)
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX (R.A.G., E.V.)
| | - Robb Rowley
- National Human Genome Research Institute, Bethesda, MD (R.R., T.A.M.)
| | - Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX (R.A.G., E.V.)
| | - Jodell E Linder
- Department of Medicine (K.C.A., J.E.L., J.F.P.), Vanderbilt University Medical Center, Nashville, TN
| | - Laney K Jones
- Genomic Medicine Institute, Geisinger, Danville, PA (Z.M.S., A.C.S., L.K.J., M.S.W.)
| | - Emma F Perez
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA (E.F.P.)
| | - Josh F Peterson
- Department of Medicine (K.C.A., J.E.L., J.F.P.), Vanderbilt University Medical Center, Nashville, TN
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington Medical Center, Seattle (G.P.J.)
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge (H.L.R., H.Z.)
| | - Hana Zouk
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge (H.L.R., H.Z.)
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston (H.Z.)
| | - Dan M Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics (D.M.R.), Vanderbilt University Medical Center, Nashville, TN
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger, Danville, PA (Z.M.S., A.C.S., L.K.J., M.S.W.)
| | - Teri A Manolio
- National Human Genome Research Institute, Bethesda, MD (R.R., T.A.M.)
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine (O.D., A.S., S.S., B.A.S., D.C.K., I.J.K.), Mayo Clinic, Rochester, MN
- Gonda Vascular Ctr (I.J.K.), Mayo Clinic, Rochester, MN
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44
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Weinstock JS, Gopakumar J, Burugula BB, Uddin MM, Jahn N, Belk JA, Bouzid H, Daniel B, Miao Z, Ly N, Mack TM, Luna SE, Prothro KP, Mitchell SR, Laurie CA, Broome JG, Taylor KD, Guo X, Sinner MF, von Falkenhausen AS, Kääb S, Shuldiner AR, O'Connell JR, Lewis JP, Boerwinkle E, Barnes KC, Chami N, Kenny EE, Loos RJF, Fornage M, Hou L, Lloyd-Jones DM, Redline S, Cade BE, Psaty BM, Bis JC, Brody JA, Silverman EK, Yun JH, Qiao D, Palmer ND, Freedman BI, Bowden DW, Cho MH, DeMeo DL, Vasan RS, Yanek LR, Becker LC, Kardia SLR, Peyser PA, He J, Rienstra M, Van der Harst P, Kaplan R, Heckbert SR, Smith NL, Wiggins KL, Arnett DK, Irvin MR, Tiwari H, Cutler MJ, Knight S, Muhlestein JB, Correa A, Raffield LM, Gao Y, de Andrade M, Rotter JI, Rich SS, Tracy RP, Konkle BA, Johnsen JM, Wheeler MM, Smith JG, Melander O, Nilsson PM, Custer BS, Duggirala R, Curran JE, Blangero J, McGarvey S, Williams LK, Xiao S, Yang M, Gu CC, Chen YDI, Lee WJ, Marcus GM, Kane JP, Pullinger CR, Shoemaker MB, Darbar D, Roden DM, Albert C, Kooperberg C, Zhou Y, Manson JE, Desai P, Johnson AD, Mathias RA, Blackwell TW, Abecasis GR, Smith AV, Kang HM, Satpathy AT, Natarajan P, Kitzman JO, Whitsel EA, Reiner AP, Bick AG, Jaiswal S. Aberrant activation of TCL1A promotes stem cell expansion in clonal haematopoiesis. Nature 2023; 616:755-763. [PMID: 37046083 PMCID: PMC10360040 DOI: 10.1038/s41586-023-05806-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/08/2023] [Indexed: 04/14/2023]
Abstract
Mutations in a diverse set of driver genes increase the fitness of haematopoietic stem cells (HSCs), leading to clonal haematopoiesis1. These lesions are precursors for blood cancers2-6, but the basis of their fitness advantage remains largely unknown, partly owing to a paucity of large cohorts in which the clonal expansion rate has been assessed by longitudinal sampling. Here, to circumvent this limitation, we developed a method to infer the expansion rate from data from a single time point. We applied this method to 5,071 people with clonal haematopoiesis. A genome-wide association study revealed that a common inherited polymorphism in the TCL1A promoter was associated with a slower expansion rate in clonal haematopoiesis overall, but the effect varied by driver gene. Those carrying this protective allele exhibited markedly reduced growth rates or prevalence of clones with driver mutations in TET2, ASXL1, SF3B1 and SRSF2, but this effect was not seen in clones with driver mutations in DNMT3A. TCL1A was not expressed in normal or DNMT3A-mutated HSCs, but the introduction of mutations in TET2 or ASXL1 led to the expression of TCL1A protein and the expansion of HSCs in vitro. The protective allele restricted TCL1A expression and expansion of mutant HSCs, as did experimental knockdown of TCL1A expression. Forced expression of TCL1A promoted the expansion of human HSCs in vitro and mouse HSCs in vivo. Our results indicate that the fitness advantage of several commonly mutated driver genes in clonal haematopoiesis may be mediated by TCL1A activation.
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Affiliation(s)
- Joshua S Weinstock
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | | | | | - Md Mesbah Uddin
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Nikolaus Jahn
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia A Belk
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hind Bouzid
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bence Daniel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Zhuang Miao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Nghi Ly
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Taralynn M Mack
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Sofia E Luna
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Katherine P Prothro
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Shaneice R Mitchell
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | - Jai G Broome
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Kent D Taylor
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
- Institute for Translational Genomics and Populations Sciences, Lundquist Institute, Torrance, CA, USA
| | - Xiuqing Guo
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
- Lundquist Institute, Torrance, CA, USA
| | - Moritz F Sinner
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
| | - Aenne S von Falkenhausen
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
| | - Stefan Kääb
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
| | - Alan R Shuldiner
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Jeffrey R O'Connell
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Joshua P Lewis
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD, USA
- University of Maryland, Baltimore, MD, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- University of Texas Health at Houston, Houston, TX, USA
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Nathalie Chami
- The Charles Bronfman Institute of Personalized Medicine, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eimear E Kenny
- Institute for Genomic Health, New York, NY, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute of Personalized Medicine, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Myriam Fornage
- University of Texas Health at Houston, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northeastern University, Chicago, IL, USA
| | | | - Susan Redline
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Brian E Cade
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Bruce M Psaty
- University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer A Brody
- University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Edwin K Silverman
- Brigham and Women's Hospital, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jeong H Yun
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dandi Qiao
- Brigham and Women's Hospital, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest Baptist Health, Winston-Salem, NC, USA
| | - Barry I Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest Baptist Health, Winston-Salem, NC, USA
| | - Michael H Cho
- Brigham and Women's Hospital, Boston, MA, USA
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dawn L DeMeo
- Brigham and Women's Hospital, Boston, MA, USA
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ramachandran S Vasan
- National Heart Lung and Blood Institute's, Boston University's Framingham Heart Study, Framingham, MA, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Johns Hopkins University, Baltimore, MD, USA
| | - Lewis C Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Johns Hopkins University, Baltimore, MD, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- University of Michigan, Ann Arbor, MI, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- University of Michigan, Ann Arbor, MI, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
- Tulane University, New Orleans, LA, USA
| | - Michiel Rienstra
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Pim Van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Albert Einstein College of Medicine, New York, NY, USA
| | - Susan R Heckbert
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA, USA
- Broad Institute, Cambridge, MA, USA
| | - Kerri L Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Donna K Arnett
- College of Public Health, University of Kentucky, Lexington, KY, USA
- University of Kentucky, Lexington, KY, USA
| | | | - Hemant Tiwari
- Department of Biostatistics, University of Alabama, Birmingham, AL, USA
| | - Michael J Cutler
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, USA
| | - Stacey Knight
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, USA
| | - J Brent Muhlestein
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, USA
| | - Adolfo Correa
- Department of Medicine, Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS, USA
- Department of Population Health Science, University of Mississippi, Jackson, MS, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yan Gao
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
- University of Mississippi, Jackson, MS, USA
| | - Mariza de Andrade
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Jerome I Rotter
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics, Lundquist Institute, Torrance, CA, USA
| | - Stephen S Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- University of Virginia, Charlottesville, VA, USA
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine and Biochemistry, Larner College of Medicine at the University of Vermont, Colchester, VT, USA
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, VT, USA
| | - Barbara A Konkle
- Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
- Blood Works Northwest, Seattle, WA, USA
| | - Jill M Johnsen
- Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
- Research Institute, Bloodworks Northwest, Seattle, WA, USA
| | | | - J Gustav Smith
- Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Gothenburg University, Gothenburg, Sweden
- Wallenberg Center for Molecular Medicine and Lund University Diabetes Center, Lund University, Lund, Sweden
- Department of Cardiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Olle Melander
- Department of Internal Medicine, Clinical Sciences, Lund University and Skane University Hospital, Malmo, Sweden
| | - Peter M Nilsson
- Department of Internal Medicine, Clinical Sciences, Lund University and Skane University Hospital, Malmo, Sweden
| | | | - Ravindranath Duggirala
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Joanne E Curran
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - John Blangero
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Stephen McGarvey
- Department of Epidemiology and International Health Institute, Brown University School of Public Health, Providence, RI, USA
- Department of Epidemiology, Brown University, Providence, RI, USA
| | - L Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
- Henry Ford Health System, Detroit, MI, USA
| | - Shujie Xiao
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Mao Yang
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - C Charles Gu
- Division of Biostatistics, Washington University School of Medicine, St Louis, MO, USA
- Washington University in St Louis, St Louis, MO, USA
| | - Yii-Der Ida Chen
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
- Lundquist Institute, Torrance, CA, USA
| | - Wen-Jane Lee
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Taichung Veterans General Hospital Taiwan, Taichung City, Taiwan
| | - Gregory M Marcus
- Division of Cardiology, University of California, San Francisco, San Francisco, CA, USA
| | - John P Kane
- Department of Medicine, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Clive R Pullinger
- Cardiovascular Research Institute, University of California, San Francisco, USA
| | - M Benjamin Shoemaker
- Division of Cardiology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine and Cardiology, Vanderbilt University, Nashville, TN, USA
| | - Dawood Darbar
- Division of Cardiology, University of Illinois at Chicago, Chicago, IL, USA
- University of Illinois at Chicago, Chicago, IL, USA
| | - Dan M Roden
- Departments of Medicine, Pharmacology and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christine Albert
- Department of Cardiology, Cedars-Sinai, Los Angeles, CA, USA
- Cedars-Sinai, Boston, MA, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ying Zhou
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - JoAnn E Manson
- Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Pinkal Desai
- Division of Hematology and Oncology, Weill Cornell Medicine, New York, NY, USA
- Englander Institute of Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andrew D Johnson
- National Heart, Lung and Blood Institute, Population Sciences Branch, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Johns Hopkins University, Baltimore, MD, USA
| | - Thomas W Blackwell
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Goncalo R Abecasis
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Albert V Smith
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Hyun M Kang
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Pradeep Natarajan
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Jacob O Kitzman
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Alexander P Reiner
- Broad Institute, Cambridge, MA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA, USA
| | - Alexander G Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA.
| | - Siddhartha Jaiswal
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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Puckelwartz MJ, Pesce LL, Hernandez EJ, Webster G, Dellefave-Castillo LM, Russell MW, Geisler SS, Kearns SD, Etheridge FK, Etheridge SP, Monroe TO, Pottinger TD, Kannankeril PJ, Shoemaker MB, Fountain D, Roden DM, MacLeod H, Burns KM, Yandell M, Tristani-Firouzi M, George AL, McNally EM. The impact of damaging epilepsy and cardiac genetic variant burden in sudden death in the young. medRxiv 2023:2023.03.27.23287711. [PMID: 37034657 PMCID: PMC10081419 DOI: 10.1101/2023.03.27.23287711] [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: 06/19/2023]
Abstract
Background Sudden unexpected death in children is a tragic event. Understanding the genetics of sudden death in the young (SDY) enables family counseling and cascade screening. The objective of this study was to characterize genetic variation in an SDY cohort using whole genome sequencing. Methods The SDY Case Registry is a National Institutes of Health/Centers for Disease Control surveillance effort to discern the prevalence, causes, and risk factors for SDY. The SDY Case Registry prospectively collected clinical data and DNA biospecimens from SDY cases <20 years of age. SDY cases were collected from medical examiner and coroner offices spanning 13 US jurisdictions from 2015-2019. The cohort included 211 children (mean age 1 year; range 0-20 years), determined to have died suddenly and unexpectedly and in whom DNA biospecimens and next-of-kin consent were ascertained. A control cohort consisted of 211 randomly sampled, sex-and ancestry-matched individuals from the 1000 Genomes Project. Genetic variation was evaluated in epilepsy, cardiomyopathy and arrhythmia genes in the SDY and control cohorts. American College of Medical Genetics/Genomics guidelines were used to classify variants as pathogenic or likely pathogenic. Additionally, genetic variation predicted to be damaging was identified using a Bayesian-based artificial intelligence (AI) tool. Results The SDY cohort was 42% European, 30% African, 17% Hispanic, and 11% with mixed ancestries, and 39% female. Six percent of the cohort was found to harbor a pathogenic or likely pathogenic genetic variant in an epilepsy, cardiomyopathy or arrhythmia gene. The genomes of SDY cases, but not controls, were enriched for rare, damaging variants in epilepsy, cardiomyopathy and arrhythmia-related genes. A greater number of rare epilepsy genetic variants correlated with younger age at death. Conclusions While damaging cardiomyopathy and arrhythmia genes are recognized contributors to SDY, we also observed an enrichment in epilepsy-related genes in the SDY cohort, and a correlation between rare epilepsy variation and younger age at death. These findings emphasize the importance of considering epilepsy genes when evaluating SDY.
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Bersell KR, Yang T, Mosley JD, Glazer AM, Hale AT, Kryshtal DO, Kim K, Steimle JD, Brown JD, Salem JE, Campbell CC, Hong CC, Wells QS, Johnson AN, Short L, Blair MA, Behr ER, Petropoulou E, Jamshidi Y, Benson MD, Keyes MJ, Ngo D, Vasan RS, Yang Q, Gerszten RE, Shaffer C, Parikh S, Sheng Q, Kannankeril PJ, Moskowitz IP, York JD, Wang TJ, Knollmann BC, Roden DM. Transcriptional Dysregulation Underlies Both Monogenic Arrhythmia Syndrome and Common Modifiers of Cardiac Repolarization. Circulation 2023; 147:824-840. [PMID: 36524479 PMCID: PMC9992308 DOI: 10.1161/circulationaha.122.062193] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/03/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND Brugada syndrome (BrS) is an inherited arrhythmia syndrome caused by loss-of-function variants in the cardiac sodium channel gene SCN5A (sodium voltage-gated channel alpha subunit 5) in ≈20% of subjects. We identified a family with 4 individuals diagnosed with BrS harboring the rare G145R missense variant in the cardiac transcription factor TBX5 (T-box transcription factor 5) and no SCN5A variant. METHODS We generated induced pluripotent stem cells (iPSCs) from 2 members of a family carrying TBX5-G145R and diagnosed with Brugada syndrome. After differentiation to iPSC-derived cardiomyocytes (iPSC-CMs), electrophysiologic characteristics were assessed by voltage- and current-clamp experiments (n=9 to 21 cells per group) and transcriptional differences by RNA sequencing (n=3 samples per group), and compared with iPSC-CMs in which G145R was corrected by CRISPR/Cas9 approaches. The role of platelet-derived growth factor (PDGF)/phosphoinositide 3-kinase (PI3K) pathway was elucidated by small molecule perturbation. The rate-corrected QT (QTc) interval association with serum PDGF was tested in the Framingham Heart Study cohort (n=1893 individuals). RESULTS TBX5-G145R reduced transcriptional activity and caused multiple electrophysiologic abnormalities, including decreased peak and enhanced "late" cardiac sodium current (INa), which were entirely corrected by editing G145R to wild-type. Transcriptional profiling and functional assays in genome-unedited and -edited iPSC-CMs showed direct SCN5A down-regulation caused decreased peak INa, and that reduced PDGF receptor (PDGFRA [platelet-derived growth factor receptor α]) expression and blunted signal transduction to PI3K was implicated in enhanced late INa. Tbx5 regulation of the PDGF axis increased arrhythmia risk due to disruption of PDGF signaling and was conserved in murine model systems. PDGF receptor blockade markedly prolonged normal iPSC-CM action potentials and plasma levels of PDGF in the Framingham Heart Study were inversely correlated with the QTc interval (P<0.001). CONCLUSIONS These results not only establish decreased SCN5A transcription by the TBX5 variant as a cause of BrS, but also reveal a new general transcriptional mechanism of arrhythmogenesis of enhanced late sodium current caused by reduced PDGF receptor-mediated PI3K signaling.
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Affiliation(s)
- Kevin R Bersell
- Departments of Pharmacology (K.R.B., A.M.G., D.O.K., K.K., J-E.S., C.C.C., Q.S.W., S.P., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Tao Yang
- Medicine (T.Y., J.D.M., J.D.B., J-E.S., Q.S.W., L.S., M.A.B., C.S., T.J.W., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Jonathan D Mosley
- Departments of Pharmacology (K.R.B., A.M.G., D.O.K., K.K., J-E.S., C.C.C., Q.S.W., S.P., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Andrew M Glazer
- Departments of Pharmacology (K.R.B., A.M.G., D.O.K., K.K., J-E.S., C.C.C., Q.S.W., S.P., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Andrew T Hale
- Biochemistry (A.T.H., J.D.Y.), Vanderbilt University, Nashville, TN
| | - Dmytro O Kryshtal
- Departments of Pharmacology (K.R.B., A.M.G., D.O.K., K.K., J-E.S., C.C.C., Q.S.W., S.P., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Kyungsoo Kim
- Departments of Pharmacology (K.R.B., A.M.G., D.O.K., K.K., J-E.S., C.C.C., Q.S.W., S.P., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Jeffrey D Steimle
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, IL (J.D.S., I.P.M.)
| | - Jonathan D Brown
- Medicine (T.Y., J.D.M., J.D.B., J-E.S., Q.S.W., L.S., M.A.B., C.S., T.J.W., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Joe-Elie Salem
- Departments of Pharmacology (K.R.B., A.M.G., D.O.K., K.K., J-E.S., C.C.C., Q.S.W., S.P., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
- Medicine (T.Y., J.D.M., J.D.B., J-E.S., Q.S.W., L.S., M.A.B., C.S., T.J.W., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
- Assistance Publique - Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Department of Pharmacology, CIC-1901, Sorbonne University, Paris, France (J-E.S.)
- Sorbonne Universités, UPMC Univ Paris 06, Faculty of Medicine, France (J-E.S.)
| | - Courtney C Campbell
- Departments of Pharmacology (K.R.B., A.M.G., D.O.K., K.K., J-E.S., C.C.C., Q.S.W., S.P., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Charles C Hong
- Department of Medicine, University of Maryland School of Medicine, Baltimore (C.C.H.)
| | - Quinn S Wells
- Departments of Pharmacology (K.R.B., A.M.G., D.O.K., K.K., J-E.S., C.C.C., Q.S.W., S.P., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
- Medicine (T.Y., J.D.M., J.D.B., J-E.S., Q.S.W., L.S., M.A.B., C.S., T.J.W., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
- Biomedical Informatics (Q.S.W., D.M.R.), Vanderbilt University, Nashville, TN
| | - Amanda N Johnson
- Molecular Physiology and Biophysics (A.N.J.), Vanderbilt University, Nashville, TN
| | - Laura Short
- Medicine (T.Y., J.D.M., J.D.B., J-E.S., Q.S.W., L.S., M.A.B., C.S., T.J.W., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Marcia A Blair
- Medicine (T.Y., J.D.M., J.D.B., J-E.S., Q.S.W., L.S., M.A.B., C.S., T.J.W., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | | | - Evmorfia Petropoulou
- Cardiology Clinical Academic Group, Molecular and Clinical Sciences Institute, St George's, University of London and St George's University Hospitals National Health Service Foundation Trust, London, UK (E.P., Y.J.)
| | - Yalda Jamshidi
- Cardiology Clinical Academic Group, Molecular and Clinical Sciences Institute, St George's, University of London and St George's University Hospitals National Health Service Foundation Trust, London, UK (E.P., Y.J.)
| | - Mark D Benson
- Cardiovascular Research Center (E.J.B., M.D.B., M.J.K., R.E.G.), Beth Israel Deaconess Hospital, Boston, MA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA (M.D.B.)
| | - Michelle J Keyes
- Cardiovascular Research Center (E.J.B., M.D.B., M.J.K., R.E.G.), Beth Israel Deaconess Hospital, Boston, MA
| | - Debby Ngo
- Division of Pulmonary and Cardiovascular Medicine (D.N., R.E.G.), Beth Israel Deaconess Hospital, Boston, MA
| | | | - Qiong Yang
- Boston University School of Medicine, MA (R.S.V., Q.Y.)
| | - Robert E Gerszten
- Cardiovascular Research Center (E.J.B., M.D.B., M.J.K., R.E.G.), Beth Israel Deaconess Hospital, Boston, MA
- Division of Pulmonary and Cardiovascular Medicine (D.N., R.E.G.), Beth Israel Deaconess Hospital, Boston, MA
| | - Christian Shaffer
- Medicine (T.Y., J.D.M., J.D.B., J-E.S., Q.S.W., L.S., M.A.B., C.S., T.J.W., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Shan Parikh
- Departments of Pharmacology (K.R.B., A.M.G., D.O.K., K.K., J-E.S., C.C.C., Q.S.W., S.P., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | | | | | - Ivan P Moskowitz
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, IL (J.D.S., I.P.M.)
| | - John D York
- Biochemistry (A.T.H., J.D.Y.), Vanderbilt University, Nashville, TN
| | - Thomas J Wang
- Medicine (T.Y., J.D.M., J.D.B., J-E.S., Q.S.W., L.S., M.A.B., C.S., T.J.W., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Bjorn C Knollmann
- Departments of Pharmacology (K.R.B., A.M.G., D.O.K., K.K., J-E.S., C.C.C., Q.S.W., S.P., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
- Medicine (T.Y., J.D.M., J.D.B., J-E.S., Q.S.W., L.S., M.A.B., C.S., T.J.W., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Dan M Roden
- Departments of Pharmacology (K.R.B., A.M.G., D.O.K., K.K., J-E.S., C.C.C., Q.S.W., S.P., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
- Medicine (T.Y., J.D.M., J.D.B., J-E.S., Q.S.W., L.S., M.A.B., C.S., T.J.W., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
- Biomedical Informatics (Q.S.W., D.M.R.), Vanderbilt University, Nashville, TN
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Saldivar B, El-Harasis M, Laws L, Wright A, Williams HL, Davogustto G, Anderson K, Wells QS, Kannankeril PJ, Stevenson WG, Stevenson LW, Roden DM, Shoemaker MB. SURVEY OF PROVIDER OPINIONS ON GENETIC EVALUATION OF EARLY ONSET ATRIAL FIBRILLATION. J Am Coll Cardiol 2023. [DOI: 10.1016/s0735-1097(23)00598-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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O'Neill MJ, Sala L, Denjoy I, Wada Y, Kozek K, Crotti L, Dagradi F, Kotta MC, Spazzolini C, Leenhardt A, Salem JE, Kashiwa A, Ohno S, Tao R, Roden DM, Horie M, Extramiana F, Schwartz PJ, Kroncke BM. Continuous Bayesian variant interpretation accounts for incomplete penetrance among Mendelian cardiac channelopathies. Genet Med 2023; 25:100355. [PMID: 36496179 PMCID: PMC9992222 DOI: 10.1016/j.gim.2022.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 08/11/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
PURPOSE The congenital Long QT Syndrome (LQTS) and Brugada Syndrome (BrS) are Mendelian autosomal dominant diseases that frequently precipitate fatal cardiac arrhythmias. Incomplete penetrance is a barrier to clinical management of heterozygotes harboring variants in the major implicated disease genes KCNQ1, KCNH2, and SCN5A. We apply and evaluate a Bayesian penetrance estimation strategy that accounts for this phenomenon. METHODS We generated Bayesian penetrance models for KCNQ1-LQT1 and SCN5A-LQT3 using variant-specific features and clinical data from the literature, international arrhythmia genetic centers, and population controls. We analyzed the distribution of posterior penetrance estimates across 4 genotype-phenotype relationships and compared continuous estimates with ClinVar annotations. Posterior estimates were mapped onto protein structure. RESULTS Bayesian penetrance estimates of KCNQ1-LQT1 and SCN5A-LQT3 are empirically equivalent to 10 and 5 clinically phenotype heterozygotes, respectively. Posterior penetrance estimates were bimodal for KCNQ1-LQT1 and KCNH2-LQT2, with a higher fraction of missense variants with high penetrance among KCNQ1 variants. There was a wide distribution of variant penetrance estimates among identical ClinVar categories. Structural mapping revealed heterogeneity among "hot spot" regions and featured high penetrance estimates for KCNQ1 variants in contact with calmodulin and the S6 domain. CONCLUSIONS Bayesian penetrance estimates provide a continuous framework for variant interpretation.
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Affiliation(s)
- Matthew J O'Neill
- Vanderbilt University School of Medicine, Medical Scientist Training Program, Vanderbilt University, Nashville, TN
| | - Luca Sala
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Isabelle Denjoy
- Department of Cardiovascular Medicine, Hôpital Bichat, APHP, Université de Paris Cité, Paris, France
| | - Yuko Wada
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Krystian Kozek
- Vanderbilt University School of Medicine, Medical Scientist Training Program, Vanderbilt University, Nashville, TN
| | - Lia Crotti
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Federica Dagradi
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Maria-Christina Kotta
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Carla Spazzolini
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Antoine Leenhardt
- Department of Cardiovascular Medicine, Hôpital Bichat, APHP, Université de Paris Cité, Paris, France
| | - Joe-Elie Salem
- Department of Cardiovascular Medicine, Hôpital Bichat, APHP, Université de Paris Cité, Paris, France
| | - Asami Kashiwa
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine Kyoto, Japan
| | - Seiko Ohno
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN
| | - Dan M Roden
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Minoru Horie
- Department of Cardiovascular Medicine, Shiga University of Medical Science, Shiga, Japan
| | - Fabrice Extramiana
- Department of Cardiovascular Medicine, Hôpital Bichat, APHP, Université de Paris Cité, Paris, France
| | - Peter J Schwartz
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Brett M Kroncke
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN.
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49
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Desine S, Master H, Annis J, Hughes A, Roden DM, Harris PA, Brittain EL. Daily Step Counts Before and After the COVID-19 Pandemic Among All of Us Research Participants. JAMA Netw Open 2023; 6:e233526. [PMID: 36939705 PMCID: PMC10028484 DOI: 10.1001/jamanetworkopen.2023.3526] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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] [Received: 11/21/2022] [Accepted: 01/31/2023] [Indexed: 03/21/2023] Open
Abstract
This cohort study of US adults examines changes in physical activity following the onset of the COVID-19 pandemic.
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Affiliation(s)
- Stacy Desine
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Hiral Master
- Vanderbilt Institute of Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jeffrey Annis
- Vanderbilt Institute of Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Andrew Hughes
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Dan M. Roden
- Department of Medicine and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Paul A. Harris
- Departments of Biomedical Informatics, Biomedical Engineering and Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Evan L. Brittain
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
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50
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Fouda M, Glazer AM, Yang T, Page DA, Wada Y, Sanatani S, Roden DM, Ruben PC. A de novo arrhythmogenic Nav1.5 variant, E171Q, causes multiple biophysical defects. Biophys J 2023; 122:99a. [PMID: 36785119 DOI: 10.1016/j.bpj.2022.11.725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Mohamed Fouda
- Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Andrew M Glazer
- Clinical Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Tao Yang
- Clinical Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Dana A Page
- Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Yuko Wada
- Clinical Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Shubhayan Sanatani
- Cardiology, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Dan M Roden
- Clinical Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Peter C Ruben
- Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
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