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Hartwell EE, Jinwala Z, Milone J, Ramirez S, Gelernter J, Kranzler HR, Kember RL. Application of polygenic scores to a deeply phenotyped sample enriched for substance use disorders reveals extensive pleiotropy with psychiatric and somatic traits. Neuropsychopharmacology 2024; 49:1958-1967. [PMID: 39043921 PMCID: PMC11480112 DOI: 10.1038/s41386-024-01922-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 06/07/2024] [Accepted: 06/28/2024] [Indexed: 07/25/2024]
Abstract
Co-occurring psychiatric, medical, and substance use disorders (SUDs) are common, but the complex pathways leading to such comorbidities are poorly understood. A greater understanding of genetic influences on this phenomenon could inform precision medicine efforts. We used the Yale-Penn dataset, a cross-sectional sample enriched for individuals with SUDs, to examine pleiotropic effects of genetic liability for psychiatric and somatic traits. Participants completed an in-depth interview that provides information on demographics, environment, medical illnesses, and psychiatric and SUDs. Polygenic scores (PGS) for psychiatric disorders and somatic traits were calculated in European-ancestry (EUR; n = 5691) participants and, when discovery datasets were available, for African-ancestry (AFR; n = 4918) participants. Phenome-wide association studies (PheWAS) were then conducted. In AFR participants, the only PGS with significant associations was bipolar disorder (BD), all of which were with substance use phenotypes. In EUR participants, PGS for major depressive disorder (MDD), generalized anxiety disorder (GAD), post-traumatic stress disorder (PTSD), schizophrenia (SCZ), body mass index (BMI), coronary artery disease (CAD), and type 2 diabetes (T2D) all showed significant associations, the majority of which were with phenotypes in the substance use categories. For instance, PGSMDD was associated with over 200 phenotypes, 15 of which were depression-related (e.g., depression criterion count), 55 of which were other psychiatric phenotypes, and 126 of which were substance use phenotypes; and PGSBMI was associated with 138 phenotypes, 105 of which were substance related. Genetic liability for psychiatric and somatic traits is associated with numerous phenotypes across multiple categories, indicative of the broad genetic liability of these traits.
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Affiliation(s)
- Emily E Hartwell
- Crescenz VA Medical Center, Philadelphia, PA, USA
- University of Pennsylvania, Philadelphia, PA, USA
| | - Zeal Jinwala
- Crescenz VA Medical Center, Philadelphia, PA, USA
- University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Joel Gelernter
- West Haven VA Medical Center, West Haven, CT, USA
- Yale University, New Haven, CT, USA
| | - Henry R Kranzler
- Crescenz VA Medical Center, Philadelphia, PA, USA
- University of Pennsylvania, Philadelphia, PA, USA
| | - Rachel L Kember
- Crescenz VA Medical Center, Philadelphia, PA, USA.
- University of Pennsylvania, Philadelphia, PA, USA.
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Mekhael M, Bidaoui G, Falloon A, Pandey AC. Personalization of primary prevention: Exploring the role of coronary artery calcium and polygenic risk score in cardiovascular diseases. Trends Cardiovasc Med 2024:S1050-1738(24)00094-X. [PMID: 39442739 DOI: 10.1016/j.tcm.2024.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 10/14/2024] [Accepted: 10/18/2024] [Indexed: 10/25/2024]
Abstract
Personalized healthcare is becoming increasingly popular given the vast heterogeneity in disease manifestation between individuals. Many commonly encountered diseases within cardiology are multifactorial in nature and disease progression and response is often variable due to environmental and genetic factors influencing disease states. This makes accurate early identification and primary prevention difficult in certain populations, especially young patients with limited Atherosclerotic Cardiovascular Disease (ASCVD) risk factors. Newer strategies, such as coronary artery calcium (CAC) scans and polygenic risk scores (PRS), are being implemented to aid in the detection of subclinical disease and heritable risk, respectively. Data surrounding CAC scans have shown promising results in their ability to detect subclinical atherosclerosis and predict the risk of future coronary events, especially at the extremes; however, predictive variability exists among different patient populations, limiting the test's specificity. Furthermore, relying only on CAC scores and ASCVD risk scores may fail to identify a large group of patients needing primary prevention who lack subclinical disease and traditional risk factors, but harbor genetic variabilities strongly associated with certain cardiovascular diseases. PRS can overcome these limitations. These scores can be measured in individuals as early as birth to identify genetic variants placing them at elevated risk for developing cardiovascular disease, irrespective of their current cardiovascular health status. By applying PRS alongside CAC scores, previously overlooked patient populations can be identified and begin primary prevention strategies early to achieve optimal outcomes. In this review, we expand on the current knowledge surrounding CAC scores and PRS and highlight the future possibilities of these technologies for preventive cardiology.
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Affiliation(s)
- Mario Mekhael
- Section of Cardiology, Deming Dept of Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Ghassan Bidaoui
- Section of Cardiology, Deming Dept of Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Austin Falloon
- Section of Cardiology, Deming Dept of Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Amitabh C Pandey
- Section of Cardiology, Deming Dept of Medicine, Tulane University School of Medicine, New Orleans, LA, United States; Southeast Louisiana Veterans Health Care System, New Orleans, LA, United States.
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Wu J, Yang D, Zhang Y, Xian H, Weng Z, Ji L, Yang F. Non-invasive imaging innovation: FFR-CT combined with plaque characterization, safeguarding your cardiac health. J Cardiovasc Comput Tomogr 2024:S1934-5925(24)00433-7. [PMID: 39299900 DOI: 10.1016/j.jcct.2024.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 08/27/2024] [Accepted: 08/29/2024] [Indexed: 09/22/2024]
Abstract
Studies have shown that high-risk plaque features (including thin fibrous caps, lipid-rich cores, large plaque volumes, and intraplaque microcalcifications) are closely associated with the occurrence of acute coronary events. CT-derived fractional flow reserve (CT-FFR) is a non-invasive imaging post-processing technique that utilizes artificial intelligence to analyze data obtained from conventional coronary CT angiography (CCTA). FFR-CT technology offers the hemodynamic assessment of coronary lesions, aiding in the prediction of potential cardiovascular risks. This review summarizes the latest research progress on the complex relationship between FFR-CT, plaque characteristics, and hemodynamics, closely linking plaque volume, composition, and distribution with the clinical significance of coronary artery stenosis. It is hoped that these research findings will provide valuable guidance for clinicians, promoting the application of CT in the non-invasive detection of vulnerable plaques, thereby more effectively preventing and managing coronary artery disease. In the future, further optimization of FFR-CT technology and expansion of its clinical application are expected to significantly reduce the incidence and mortality of coronary artery disease, offering new hope for the prevention and treatment of cardiovascular diseases.
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Affiliation(s)
- Jianjun Wu
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin, 150001, China
| | - Dawei Yang
- Department of Orthopedics, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Youqi Zhang
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin, 150001, China
| | - Huimin Xian
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Ziqian Weng
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Liu Ji
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin, 150001, China
| | - Fan Yang
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, China; Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin, 150001, China.
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Elmore AR, Adhikari N, Hartley AE, Aparicio HJ, Posner DC, Hemani G, Tilling K, Gaunt TR, Wilson PW, Casas JP, Gaziano JM, Davey Smith G, Paternoster L, Cho K, Peloso GM. Protein Identification for Stroke Progression via Mendelian Randomization in Million Veteran Program and UK Biobank. Stroke 2024; 55:2045-2054. [PMID: 39038097 PMCID: PMC11259242 DOI: 10.1161/strokeaha.124.047103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 06/07/2024] [Indexed: 07/24/2024]
Abstract
BACKGROUND Individuals who have experienced a stroke, or transient ischemic attack, face a heightened risk of future cardiovascular events. Identification of genetic and molecular risk factors for subsequent cardiovascular outcomes may identify effective therapeutic targets to improve prognosis after an incident stroke. METHODS We performed genome-wide association studies for subsequent major adverse cardiovascular events (MACE; ncases=51 929; ncontrols=39 980) and subsequent arterial ischemic stroke (AIS; ncases=45 120; ncontrols=46 789) after the first incident stroke within the Million Veteran Program and UK Biobank. We then used genetic variants associated with proteins (protein quantitative trait loci) to determine the effect of 1463 plasma protein abundances on subsequent MACE using Mendelian randomization. RESULTS Two variants were significantly associated with subsequent cardiovascular events: rs76472767 near gene RNF220 (odds ratio, 0.75 [95% CI, 0.64-0.85]; P=3.69×10-8) with subsequent AIS and rs13294166 near gene LINC01492 (odds ratio, 1.52 [95% CI, 1.37-1.67]; P=3.77×10-8) with subsequent MACE. Using Mendelian randomization, we identified 2 proteins with an effect on subsequent MACE after a stroke: CCL27 ([C-C motif chemokine 27], effect odds ratio, 0.77 [95% CI, 0.66-0.88]; adjusted P=0.05) and TNFRSF14 ([tumor necrosis factor receptor superfamily member 14], effect odds ratio, 1.42 [95% CI, 1.24-1.60]; adjusted P=0.006). These proteins are not associated with incident AIS and are implicated to have a role in inflammation. CONCLUSIONS We found evidence that 2 proteins with little effect on incident stroke appear to influence subsequent MACE after incident AIS. These associations suggest that inflammation is a contributing factor to subsequent MACE outcomes after incident AIS and highlights potential novel targets.
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Affiliation(s)
- Andrew R. Elmore
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and University of Bristol, United Kingdom (A.R.E., A.E.H., G.H., K.T., T.R.G., G.D.S., L.P.)
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, United Kingdom (A.R.E., A.E.H., G.H., K.T., T.R.G., G.D.S., L.P.)
| | - Nimish Adhikari
- Veteran’s Affairs Healthcare System, Boston, MA (N.A., D.C.P., J.P.C., J.M.G., K.C., G.M.P.)
- Department of Biostatistics, Boston University School of Public Health, MA (N.A., G.M.P.)
| | - April E. Hartley
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and University of Bristol, United Kingdom (A.R.E., A.E.H., G.H., K.T., T.R.G., G.D.S., L.P.)
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, United Kingdom (A.R.E., A.E.H., G.H., K.T., T.R.G., G.D.S., L.P.)
| | - Hugo Javier Aparicio
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, MA (H.J.A.)
- Boston Medical Center, MA (H.J.A.)
| | - Daniel C. Posner
- Veteran’s Affairs Healthcare System, Boston, MA (N.A., D.C.P., J.P.C., J.M.G., K.C., G.M.P.)
| | - Gibran Hemani
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and University of Bristol, United Kingdom (A.R.E., A.E.H., G.H., K.T., T.R.G., G.D.S., L.P.)
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, United Kingdom (A.R.E., A.E.H., G.H., K.T., T.R.G., G.D.S., L.P.)
| | - Kate Tilling
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and University of Bristol, United Kingdom (A.R.E., A.E.H., G.H., K.T., T.R.G., G.D.S., L.P.)
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, United Kingdom (A.R.E., A.E.H., G.H., K.T., T.R.G., G.D.S., L.P.)
| | - Tom R. Gaunt
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and University of Bristol, United Kingdom (A.R.E., A.E.H., G.H., K.T., T.R.G., G.D.S., L.P.)
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, United Kingdom (A.R.E., A.E.H., G.H., K.T., T.R.G., G.D.S., L.P.)
| | | | - Juan P. Casas
- Veteran’s Affairs Healthcare System, Boston, MA (N.A., D.C.P., J.P.C., J.M.G., K.C., G.M.P.)
- Division of Aging, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA (J.P.C., J.M.G., K.C.)
| | - John Michael Gaziano
- Veteran’s Affairs Healthcare System, Boston, MA (N.A., D.C.P., J.P.C., J.M.G., K.C., G.M.P.)
- Division of Aging, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA (J.P.C., J.M.G., K.C.)
| | - George Davey Smith
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and University of Bristol, United Kingdom (A.R.E., A.E.H., G.H., K.T., T.R.G., G.D.S., L.P.)
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, United Kingdom (A.R.E., A.E.H., G.H., K.T., T.R.G., G.D.S., L.P.)
| | - Lavinia Paternoster
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and University of Bristol, United Kingdom (A.R.E., A.E.H., G.H., K.T., T.R.G., G.D.S., L.P.)
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, United Kingdom (A.R.E., A.E.H., G.H., K.T., T.R.G., G.D.S., L.P.)
| | - Kelly Cho
- Veteran’s Affairs Healthcare System, Boston, MA (N.A., D.C.P., J.P.C., J.M.G., K.C., G.M.P.)
- Division of Aging, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA (J.P.C., J.M.G., K.C.)
| | - Gina M. Peloso
- Veteran’s Affairs Healthcare System, Boston, MA (N.A., D.C.P., J.P.C., J.M.G., K.C., G.M.P.)
- Department of Biostatistics, Boston University School of Public Health, MA (N.A., G.M.P.)
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Wei A, Border R, Fu B, Cullina S, Brandes N, Jang SK, Sankararaman S, Kenny E, Udler MS, Ntranos V, Zaitlen N, Arboleda V. Investigating the sources of variable impact of pathogenic variants in monogenic metabolic conditions. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.09.14.23295564. [PMID: 37745486 PMCID: PMC10516069 DOI: 10.1101/2023.09.14.23295564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Over three percent of people carry a dominant pathogenic variant, yet only a fraction of carriers develop disease. Disease phenotypes from carriers of variants in the same gene range from mild to severe. Here, we investigate underlying mechanisms for this heterogeneity: variable variant effect sizes, carrier polygenic backgrounds, and modulation of carrier effect by genetic background (marginal epistasis). We leveraged exomes and clinical phenotypes from the UK Biobank and the Mt. Sinai BioMe Biobank to identify carriers of pathogenic variants affecting cardiometabolic traits. We employed recently developed methods to study these cohorts, observing strong statistical support and clinical translational potential for all three mechanisms of variable carrier penetrance and disease severity. For example, scores from our recent model of variant pathogenicity were tightly correlated with phenotype amongst clinical variant carriers, they predicted effects of variants of unknown significance, and they distinguished gain- from loss-of-function variants. We also found that polygenic scores predicted phenotypes amongst pathogenic carriers and that epistatic effects can exceed main carrier effects by an order of magnitude.
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Fuat A, Adlen E, Monane M, Coll R, Groves S, Little E, Wild J, Kamali FJ, Soni Y, Haining S, Riding H, Riveros-Mckay F, Peneva I, Lachapelle A, Giner-Delgado C, Weale ME, Plagnol V, Harrison S, Donnelly P. A polygenic risk score added to a QRISK®2 cardiovascular disease risk calculator demonstrated robust clinical acceptance and clinical utility in the primary care setting. Eur J Prev Cardiol 2024; 31:716-722. [PMID: 38243727 DOI: 10.1093/eurjpc/zwae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 01/21/2024]
Abstract
AIMS The aim of the study was to assess the real-world feasibility, acceptability, and impact of an integrated risk tool for cardiovascular disease (CVD IRT, combining the standard QRISK®2 risk algorithm with a polygenic risk score), implemented within routine primary practice in the UK National Health Service. METHODS AND RESULTS The Healthcare Evaluation of Absolute Risk Testing Study (NCT05294419) evaluated participants undergoing primary care health checks. Both QRISK2 and CVD IRT scores were returned to the healthcare providers (HCPs), who then communicated the results to participants. The primary outcome of the study was feasibility of CVD IRT implementation. Secondary outcomes included changes in CVD risk (QRISK2 vs. CVD IRT) and impact of the CVD IRT on clinical decision-making. A total of 832 eligible participants (median age 55 years, 62% females, 97.5% White ethnicity) were enrolled across 12 UK primary care practices. Cardiovascular disease IRT scores were obtained on 100% of the blood samples. Healthcare providers stated that the CVD IRT could be incorporated into routine primary care in a straightforward manner in 90.7% of reports. Participants stated they were 'likely' or 'very likely' to recommend the use of this test to their family or friends in 86.9% of reports. Participants stated that the test was personally useful (98.8%) and that the results were easy to understand (94.6%). When CVD IRT exceeded QRISK2, HCPs planned changes in management for 108/388 (27.8%) of participants and 47% (62/132) of participants with absolute risk score changes of >2%. CONCLUSION Amongst HCPs and participants who agreed to the trial of genetic data for refinement of clinical risk prediction in primary care, we observed that CVD IRT implementation was feasible and well accepted. The CVD IRT results were associated with planned changes in prevention strategies.
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Affiliation(s)
| | - Ella Adlen
- Genomics plc, King Charles House, Park End Street, Oxford OX1 1JD, UK
| | - Mark Monane
- Genomics plc, King Charles House, Park End Street, Oxford OX1 1JD, UK
| | - Ruth Coll
- Genomics plc, King Charles House, Park End Street, Oxford OX1 1JD, UK
| | - Sarah Groves
- Genomics plc, King Charles House, Park End Street, Oxford OX1 1JD, UK
| | | | | | | | - Yusuf Soni
- Riverside General Practice, Stockton-on-Tees, UK
| | - Shona Haining
- Research and Evidence, NHS North of England Commissioning Support, Durham, UK
| | - Helen Riding
- Research and Evidence, NHS North of England Commissioning Support, Durham, UK
| | | | - Iliana Peneva
- Genomics plc, King Charles House, Park End Street, Oxford OX1 1JD, UK
| | | | | | - Michael E Weale
- Genomics plc, King Charles House, Park End Street, Oxford OX1 1JD, UK
| | - Vincent Plagnol
- Genomics plc, King Charles House, Park End Street, Oxford OX1 1JD, UK
| | - Seamus Harrison
- Genomics plc, King Charles House, Park End Street, Oxford OX1 1JD, UK
| | - Peter Donnelly
- Genomics plc, King Charles House, Park End Street, Oxford OX1 1JD, UK
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Almuwaqqat Z, Hui Q, Liu C, Zhou JJ, Voight BF, Ho YL, Posner DC, Vassy JL, Gaziano JM, Cho K, Wilson PWF, Sun YV. Long-Term Body Mass Index Variability and Adverse Cardiovascular Outcomes. JAMA Netw Open 2024; 7:e243062. [PMID: 38512255 PMCID: PMC10958234 DOI: 10.1001/jamanetworkopen.2024.3062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/23/2024] [Indexed: 03/22/2024] Open
Abstract
Importance Body mass index (BMI; calculated as weight in kilograms divided by height in meters squared) is a commonly used estimate of obesity, which is a complex trait affected by genetic and lifestyle factors. Marked weight gain and loss could be associated with adverse biological processes. Objective To evaluate the association between BMI variability and incident cardiovascular disease (CVD) events in 2 distinct cohorts. Design, Setting, and Participants This cohort study used data from the Million Veteran Program (MVP) between 2011 and 2018 and participants in the UK Biobank (UKB) enrolled between 2006 and 2010. Participants were followed up for a median of 3.8 (5th-95th percentile, 3.5) years. Participants with baseline CVD or cancer were excluded. Data were analyzed from September 2022 and September 2023. Exposure BMI variability was calculated by the retrospective SD and coefficient of variation (CV) using multiple clinical BMI measurements up to the baseline. Main Outcomes and Measures The main outcome was incident composite CVD events (incident nonfatal myocardial infarction, acute ischemic stroke, and cardiovascular death), assessed using Cox proportional hazards modeling after adjustment for CVD risk factors, including age, sex, mean BMI, systolic blood pressure, total cholesterol, high-density lipoprotein cholesterol, smoking status, diabetes status, and statin use. Secondary analysis assessed whether associations were dependent on the polygenic score of BMI. Results Among 92 363 US veterans in the MVP cohort (81 675 [88%] male; mean [SD] age, 56.7 [14.1] years), there were 9695 Hispanic participants, 22 488 non-Hispanic Black participants, and 60 180 non-Hispanic White participants. A total of 4811 composite CVD events were observed from 2011 to 2018. The CV of BMI was associated with 16% higher risk for composite CVD across all groups (hazard ratio [HR], 1.16; 95% CI, 1.13-1.19). These associations were unchanged among subgroups and after adjustment for the polygenic score of BMI. The UKB cohort included 65 047 individuals (mean [SD] age, 57.30 (7.77) years; 38 065 [59%] female) and had 6934 composite CVD events. Each 1-SD increase in BMI variability in the UKB cohort was associated with 8% increased risk of cardiovascular death (HR, 1.08; 95% CI, 1.04-1.11). Conclusions and Relevance This cohort study found that among US veterans, higher BMI variability was a significant risk marker associated with adverse cardiovascular events independent of mean BMI across major racial and ethnic groups. Results were consistent in the UKB for the cardiovascular death end point. Further studies should investigate the phenotype of high BMI variability.
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Affiliation(s)
- Zakaria Almuwaqqat
- Veterans Affairs Atlanta Healthcare System, Decatur, Georgia
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Qin Hui
- Veterans Affairs Atlanta Healthcare System, Decatur, Georgia
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, Georgia
| | - Chang Liu
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, Georgia
| | - Jin J. Zhou
- Department of Medicine and Biostatistics, University of California, Los Angeles
- Veterans Affairs Phoenix Healthcare System, Phoenix, Arizona
| | - Benjamin F. Voight
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, Pennsylvania
- Department of Systems Pharmacology and Translational Therapeutics, Department of Genetics, University of Pennsylvania, Philadelphia\
| | - Yuk-Lam Ho
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston
| | - Daniel C. Posner
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston
| | - Jason L. Vassy
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - J. Michael Gaziano
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston
- Division of Aging, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Kelly Cho
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Peter W. F. Wilson
- Veterans Affairs Atlanta Healthcare System, Decatur, Georgia
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Yan V. Sun
- Veterans Affairs Atlanta Healthcare System, Decatur, Georgia
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, Georgia
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8
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Xiang R, Kelemen M, Xu Y, Harris LW, Parkinson H, Inouye M, Lambert SA. Recent advances in polygenic scores: translation, equitability, methods and FAIR tools. Genome Med 2024; 16:33. [PMID: 38373998 PMCID: PMC10875792 DOI: 10.1186/s13073-024-01304-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
Polygenic scores (PGS) can be used for risk stratification by quantifying individuals' genetic predisposition to disease, and many potentially clinically useful applications have been proposed. Here, we review the latest potential benefits of PGS in the clinic and challenges to implementation. PGS could augment risk stratification through combined use with traditional risk factors (demographics, disease-specific risk factors, family history, etc.), to support diagnostic pathways, to predict groups with therapeutic benefits, and to increase the efficiency of clinical trials. However, there exist challenges to maximizing the clinical utility of PGS, including FAIR (Findable, Accessible, Interoperable, and Reusable) use and standardized sharing of the genomic data needed to develop and recalculate PGS, the equitable performance of PGS across populations and ancestries, the generation of robust and reproducible PGS calculations, and the responsible communication and interpretation of results. We outline how these challenges may be overcome analytically and with more diverse data as well as highlight sustained community efforts to achieve equitable, impactful, and responsible use of PGS in healthcare.
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Affiliation(s)
- Ruidong Xiang
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Martin Kelemen
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Yu Xu
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Laura W Harris
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK.
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK.
| | - Samuel A Lambert
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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9
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Elmore A, Adhikari N, Hartley AE, Javier Aparicio H, Posner DC, Hemani G, Tilling K, Gaunt TR, Wilson P, Casas JP, Michael Gaziano J, Smith GD, Paternoster L, Cho K, Peloso GM. Protein identification for stroke progression via Mendelian Randomization in Million Veteran Program and UK Biobank. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.31.24302111. [PMID: 38352469 PMCID: PMC10863017 DOI: 10.1101/2024.01.31.24302111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Background Individuals who have experienced a stroke, or transient ischemic attack, face a heightened risk of future cardiovascular events. Identification of genetic and molecular risk factors for subsequent cardiovascular outcomes may identify effective therapeutic targets to improve prognosis after an incident stroke. Methods We performed genome-wide association studies (GWAS) for subsequent major adverse cardiovascular events (MACE) (Ncases=51,929, Ncntrl=39,980) and subsequent arterial ischemic stroke (AIS) Ncases=45,120, Ncntrl=46,789) after first incident stroke within the Million Veteran Program and UK Biobank. We then used genetic variants associated with proteins (pQTLs) to determine the effect of 1,463 plasma protein abundances on subsequent MACE using Mendelian randomization (MR). Results Two variants were significantly associated with subsequent cardiovascular events: rs76472767 (OR=0.75, 95% CI = 0.64-0.85, p= 3.69×10-08) with subsequent AIS and rs13294166 (OR=1.52, 95% CI = 1.37-1.67, p=3.77×10-08) with subsequent MACE. Using MR, we identified 2 proteins with an effect on subsequent MACE after a stroke: CCL27 (effect OR= 0.77, 95% CI = 0.66-0.88, adj. p=0.05), and TNFRSF14 (effect OR=1.42, 95% CI = 1.24-1.60, adj. p=0.006). These proteins are not associated with incident AIS and are implicated to have a role in inflammation. Conclusions We found evidence that two proteins with little effect on incident stroke appear to influence subsequent MACE after incident AIS. These associations suggest that inflammation is a contributing factor to subsequent MACE outcomes after incident AIS and highlights potential novel targets.
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Affiliation(s)
- Andrew Elmore
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and University of Bristol
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol
| | - Nimish Adhikari
- Veteran’s Affairs Healthcare System, Boston, MA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - April E Hartley
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and University of Bristol
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol
| | - Hugo Javier Aparicio
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
- Boston Medical Center, Boston, MA
| | | | - Gibran Hemani
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and University of Bristol
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol
| | - Kate Tilling
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and University of Bristol
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol
| | - Tom R Gaunt
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and University of Bristol
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol
| | | | - JP Casas
- Veteran’s Affairs Healthcare System, Boston, MA
- Division of Aging, Brigham and Women’s Hospital, Harvard Medical School
| | - John Michael Gaziano
- Veteran’s Affairs Healthcare System, Boston, MA
- Division of Aging, Brigham and Women’s Hospital, Harvard Medical School
| | - George Davey Smith
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and University of Bristol
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol
| | - Lavinia Paternoster
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and University of Bristol
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol
| | - Kelly Cho
- Veteran’s Affairs Healthcare System, Boston, MA
- Division of Aging, Brigham and Women’s Hospital, Harvard Medical School
| | - Gina M Peloso
- Veteran’s Affairs Healthcare System, Boston, MA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
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10
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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: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [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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11
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Hartwell EE, Jinwala Z, Milone J, Ramirez S, Gelernter J, Kranzler HR, Kember RL. Application of polygenic scores to a deeply phenotyped sample enriched for substance use disorders reveals extensive pleiotropy with psychiatric and medical traits. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.22.24301615. [PMID: 38343859 PMCID: PMC10854354 DOI: 10.1101/2024.01.22.24301615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Co-occurring psychiatric, medical, and substance use disorders (SUDs) are common, but the complex pathways leading to such comorbidities are poorly understood. A greater understanding of genetic influences on this phenomenon could inform precision medicine efforts. We used the Yale-Penn dataset, a cross-sectional sample enriched for individuals with SUDs, to examine pleiotropic effects of genetic liability for psychiatric and medical traits. Participants completed an in-depth interview that provides information on demographics, environment, medical illnesses, and psychiatric and SUDs. Polygenic scores (PGS) for psychiatric disorders and medical traits were calculated in European-ancestry (EUR; n=5,691) participants and, when discovery datasets were available, for African-ancestry (AFR; n=4,918) participants. Phenome-wide association studies (PheWAS) were then conducted. In AFR participants, the only PGS with significant associations was bipolar disorder (BD), all of which were with substance use phenotypes. In EUR participants, PGS for major depressive disorder (MDD), generalized anxiety disorder (GAD), post-traumatic stress disorder (PTSD), schizophrenia (SCZ), body mass index (BMI), coronary artery disease (CAD), and type 2 diabetes (T2D) all showed significant associations, the majority of which were with phenotypes in the substance use categories. For instance, PGS MDD was associated with over 200 phenotypes, 15 of which were depression-related (e.g., depression criterion count), 55 of which were other psychiatric phenotypes, and 126 of which were substance use phenotypes; and PGS BMI was associated with 138 phenotypes, 105 of which were substance related. Genetic liability for psychiatric and medical traits is associated with numerous phenotypes across multiple categories, indicative of the broad genetic liability of these traits.
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12
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Haldar SM. Keeping translational research grounded in human biology. J Clin Invest 2024; 134:e178332. [PMID: 38226617 PMCID: PMC10763720 DOI: 10.1172/jci178332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024] Open
Affiliation(s)
- Saptarsi M. Haldar
- Amgen Research, South San Francisco, California, USA
- UCSF, San Francisco, California, USA
- Gladstone Institutes, San Francisco, California, USA
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13
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Cornelissen A, Gadhoke NV, Ryan K, Hodonsky CJ, Mitchell R, Bihlmeyer NA, Duong T, Chen Z, Dikongue A, Sakamoto A, Sato Y, Kawakami R, Mori M, Kawai K, Fernandez R, Ghosh SKB, Braumann R, Abebe B, Kutys R, Kutyna M, Romero ME, Kolodgie FD, Miller CL, Hong CC, Grove ML, Brody JA, Sotoodehnia N, Arking DE, Schunkert H, Mitchell BD, Guo L, Virmani R, Finn AV. Polygenic Risk Score Associates With Atherosclerotic Plaque Characteristics at Autopsy. Arterioscler Thromb Vasc Biol 2024; 44:300-313. [PMID: 37916415 DOI: 10.1161/atvbaha.123.319818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/19/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND Polygenic risk scores (PRSs) for coronary artery disease (CAD) potentially improve cardiovascular risk prediction. However, their relationship with histopathologic features of CAD has never been examined systematically. METHODS From 4327 subjects referred to CVPath by the State of Maryland Office Chief Medical Examiner for sudden death between 1994 and 2015, 2455 cases were randomly selected for genotyping. We generated PRS from 291 known CAD risk loci. Detailed histopathologic examination of the coronary arteries was performed in all subjects. The primary study outcome measurements were histopathologic plaque features determining severity of atherosclerosis, including %stenosis, calcification, thin-cap fibroatheromas, and thrombotic CAD. RESULTS After exclusion of cases with insufficient DNA sample quality or with missing data, 954 cases (mean age, 48.8±14.7 years; 75.7% men) remained in the final study cohort. Subjects in the highest PRS quintile exhibited more severe atherosclerosis compared with subjects in the lowest quintile, with greater %stenosis (80.3%±27.0% versus 50.4%±38.7%; adjusted P<0.001) and a higher frequency of calcification (69.6% versus 35.8%; adjusted P=0.004) and thin-cap fibroatheroma (26.7% versus 9.5%; adjusted P=0.007). Even after adjustment for traditional CAD risk factors, subjects within the highest PRS quintile had higher odds of severe atherosclerosis (ie, ≥75% stenosis; adjusted odds ratio, 3.77 [95% CI, 2.10-6.78]; P<0.001) and plaque rupture (adjusted odds ratio, 4.05 [95% CI, 2.26-7.24]; P<0.001). Moreover, subjects within the highest quintile had higher odds of CAD-associated cause of death, especially among those aged ≤50 years (adjusted odds ratio, 4.08 [95% CI, 2.01-8.30]; P<0.001). No statistically significant associations were observed with plaque erosion after adjusting for covariates. CONCLUSIONS This is the first autopsy study investigating associations between PRS and atherosclerosis severity at the histopathologic level in subjects with sudden death. Our pathological analysis suggests PRS correlates with plaque burden and features of advanced atherosclerosis and may be useful as a method for CAD risk stratification, especially in younger subjects.
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Affiliation(s)
- Anne Cornelissen
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
- Department of Cardiology, University Hospital RWTH Aachen, Germany (A.C.)
| | - Neel V Gadhoke
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Kathleen Ryan
- Department of Medicine, University of Maryland School of Medicine, Baltimore (K.R., C.C.H., B.D.M., A.V.F.)
| | - Chani J Hodonsky
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville (C.J.H., C.L.M.)
| | - Rebecca Mitchell
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (R.M., N.A.B., T.D., M.L.G., N.S., D.E.A.)
| | - Nathan A Bihlmeyer
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (R.M., N.A.B., T.D., M.L.G., N.S., D.E.A.)
| | - ThuyVy Duong
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (R.M., N.A.B., T.D., M.L.G., N.S., D.E.A.)
| | - Zhifen Chen
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany (Z.C., H.S.)
- Deutsches Zentrum für Herz-und Kreislauferkrankungen (DZHK), Partner Site Munich Heart Alliance, Germany (Z.C., H.S.)
| | - Armelle Dikongue
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Atsushi Sakamoto
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Yu Sato
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Rika Kawakami
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Masayuki Mori
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Kenji Kawai
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Raquel Fernandez
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Saikat Kumar B Ghosh
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Ryan Braumann
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Biniyam Abebe
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Robert Kutys
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Matthew Kutyna
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Maria E Romero
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Frank D Kolodgie
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Clint L Miller
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville (C.J.H., C.L.M.)
| | - Charles C Hong
- Department of Medicine, University of Maryland School of Medicine, Baltimore (K.R., C.C.H., B.D.M., A.V.F.)
| | - Megan L Grove
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (R.M., N.A.B., T.D., M.L.G., N.S., D.E.A.)
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle (J.A.B.)
| | - Nona Sotoodehnia
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (R.M., N.A.B., T.D., M.L.G., N.S., D.E.A.)
| | - Dan E Arking
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (R.M., N.A.B., T.D., M.L.G., N.S., D.E.A.)
| | - Heribert Schunkert
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany (Z.C., H.S.)
- Deutsches Zentrum für Herz-und Kreislauferkrankungen (DZHK), Partner Site Munich Heart Alliance, Germany (Z.C., H.S.)
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore (K.R., C.C.H., B.D.M., A.V.F.)
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, MD (B.D.M.)
| | - Liang Guo
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Renu Virmani
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
| | - Aloke V Finn
- CVPath Institute, Gaithersburg, MD (A.C., N.V.G., A.D., A.S., Y.S., R. Kawakami, M.M., K.K., R.F., S.K.B.G., R.B., B.A., R. Kutys, M.K., M.E.R., F.D.K., L.G., R.V., A.V.F.)
- Department of Medicine, University of Maryland School of Medicine, Baltimore (K.R., C.C.H., B.D.M., A.V.F.)
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14
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Morley TJ, Willimitis D, Ripperger M, Lee H, Han L, Zhou Y, Kang J, Davis LK, Smoller JW, Choi KW, Walsh CG, Ruderfer DM. Evaluating the impact of modeling choices on the performance of integrated genetic and clinical models. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.01.23297927. [PMID: 37961557 PMCID: PMC10635256 DOI: 10.1101/2023.11.01.23297927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The value of genetic information for improving the performance of clinical risk prediction models has yielded variable conclusions. Many methodological decisions have the potential to contribute to differential results across studies. Here, we performed multiple modeling experiments integrating clinical and demographic data from electronic health records (EHR) and genetic data to understand which decision points may affect performance. Clinical data in the form of structured diagnostic codes, medications, procedural codes, and demographics were extracted from two large independent health systems and polygenic risk scores (PRS) were generated across all patients with genetic data in the corresponding biobanks. Crohn's disease was used as the model phenotype based on its substantial genetic component, established EHR-based definition, and sufficient prevalence for model training and testing. We investigated the impact of PRS integration method, as well as choices regarding training sample, model complexity, and performance metrics. Overall, our results show that including PRS resulted in higher performance by some metrics but the gain in performance was only robust when combined with demographic data alone. Improvements were inconsistent or negligible after including additional clinical information. The impact of genetic information on performance also varied by PRS integration method, with a small improvement in some cases from combining PRS with the output of a clinical model (late-fusion) compared to its inclusion an additional feature (early-fusion). The effects of other modeling decisions varied between institutions though performance increased with more compute-intensive models such as random forest. This work highlights the importance of considering methodological decision points in interpreting the impact on prediction performance when including PRS information in clinical models.
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Affiliation(s)
- Theodore J. Morley
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville TN
- Center for Digital Genomic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville TN
| | - Drew Willimitis
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville TN
| | - Michael Ripperger
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville TN
| | - Hyunjoon Lee
- 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
| | - Lide Han
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville TN
- Center for Digital Genomic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville TN
| | - Yu Zhou
- 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
| | - Jooeun Kang
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville TN
| | - Lea K. Davis
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville TN
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville TN
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN
| | - 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
| | - Karmel W. 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
| | - Colin G. Walsh
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville TN
- Center for Digital Genomic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville TN
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville TN
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN
| | - Douglas M. Ruderfer
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville TN
- Center for Digital Genomic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville TN
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville TN
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN
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15
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Cornelissen A, Gadhoke NV, Ryan K, Hodonsky CJ, Mitchell R, Bihlmeyer N, Duong T, Chen Z, Dikongue A, Sakamoto A, Sato Y, Kawakami R, Mori M, Kawai K, Fernandez R, Ghosh SKB, Braumann R, Abebe B, Kutys R, Kutyna M, Romero ME, Kolodgie FD, Miller CL, Hong CC, Grove ML, Brody JA, Sotoodehnia N, Arking DE, Schunkert H, Mitchell BD, Guo L, Virmani R, Finn AV. Polygenic Risk Score Associates with Atherosclerotic Plaque Characteristics at Autopsy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.05.547891. [PMID: 37461703 PMCID: PMC10350003 DOI: 10.1101/2023.07.05.547891] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Background Polygenic risk scores (PRS) for coronary artery disease (CAD) potentially improve cardiovascular risk prediction. However, their relationship with histopathologic features of CAD has never been examined systematically. Methods From 4,327 subjects referred to CVPath by the State of Maryland Office Chief Medical Examiner (OCME) for sudden death between 1994 and 2015, 2,455 cases were randomly selected for genotyping. We generated PRS from 291 known CAD risk loci. Detailed histopathologic examination of the coronary arteries was performed in all subjects. The primary study outcome measurements were histopathologic plaque features determining severity of atherosclerosis, including %stenosis, calcification, thin-cap fibroatheromas (TCFA), and thrombotic CAD. Results After exclusion of cases with insufficient DNA sample quality or with missing data, 954 cases (mean age 48.8±14.7; 75.7% men) remained in the final study cohort. Subjects in the highest PRS quintile exhibited more severe atherosclerosis compared to subjects in the lowest quintile, with greater %stenosis (80.3%±27.0% vs. 50.4%±38.7%; adjusted p<0.001) and a higher frequency of calcification (69.6% vs. 35.8%; adjusted p=0.004) and TCFAs (26.7% vs. 9.5%; adjusted p=0.007). Even after adjustment for traditional CAD risk factors subjects within the highest PRS quintile had higher odds of severe atherosclerosis (i.e., ≥75% stenosis; adjusted OR 3.77; 95%CI 2.10-6.78; p<0.001) and plaque rupture (adjusted OR 4.05; 95%CI 2.26-7.24; p<0.001). Moreover, subjects within the highest quintile had higher odds of CAD-associated cause of death, especially among those aged 50 years and younger (adjusted OR 4.08; 95%CI 2.01-8.30; p<0.001). No associations were observed with plaque erosion. Conclusions This is the first autopsy study investigating associations between PRS and atherosclerosis severity at the histopathologic level in subjects with sudden death. Our pathological analysis suggests PRS correlates with plaque burden and features of advanced atherosclerosis and may be useful as a method for CAD risk stratification, especially in younger subjects. Highlights In this autopsy study including 954 subjects within the CVPath Sudden Death Registry, high PRS correlated with plaque burden and atherosclerosis severity.The PRS showed differential associations with plaque rupture and plaque erosion, suggesting different etiologies to these two causes of thrombotic CAD.PRS may be useful for risk stratification, particularly in the young. Further examination of individual risk loci and their association with plaque morphology may help understand molecular mechanisms of atherosclerosis, potentially revealing new therapy targets of CAD. Graphic Abstract A polygenic risk score, generated from 291 known CAD risk loci, was assessed in 954 subjects within the CVPath Sudden Death Registry. Histopathologic examination of the coronary arteries was performed in all subjects. Subjects in the highest PRS quintile exhibited more severe atherosclerosis as compared to subjects in the lowest quintile, with a greater plaque burden, more calcification, and a higher frequency of plaque rupture.
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16
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Li C, Pan Y, Zhang R, Huang Z, Li D, Han Y, Larkin C, Rao V, Sun X, Kelly TN. Genomic Innovation in Early Life Cardiovascular Disease Prevention and Treatment. Circ Res 2023; 132:1628-1647. [PMID: 37289909 PMCID: PMC10328558 DOI: 10.1161/circresaha.123.321999] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cardiovascular disease (CVD) is a leading cause of morbidity and mortality globally. Although CVD events do not typically manifest until older adulthood, CVD develops gradually across the life-course, beginning with the elevation of risk factors observed as early as childhood or adolescence and the emergence of subclinical disease that can occur in young adulthood or midlife. Genomic background, which is determined at zygote formation, is among the earliest risk factors for CVD. With major advances in molecular technology, including the emergence of gene-editing techniques, along with deep whole-genome sequencing and high-throughput array-based genotyping, scientists now have the opportunity to not only discover genomic mechanisms underlying CVD but use this knowledge for the life-course prevention and treatment of these conditions. The current review focuses on innovations in the field of genomics and their applications to monogenic and polygenic CVD prevention and treatment. With respect to monogenic CVD, we discuss how the emergence of whole-genome sequencing technology has accelerated the discovery of disease-causing variants, allowing comprehensive screening and early, aggressive CVD mitigation strategies in patients and their families. We further describe advances in gene editing technology, which might soon make possible cures for CVD conditions once thought untreatable. In relation to polygenic CVD, we focus on recent innovations that leverage findings of genome-wide association studies to identify druggable gene targets and develop predictive genomic models of disease, which are already facilitating breakthroughs in the life-course treatment and prevention of CVD. Gaps in current research and future directions of genomics studies are also discussed. In aggregate, we hope to underline the value of leveraging genomics and broader multiomics information for characterizing CVD conditions, work which promises to expand precision approaches for the life-course prevention and treatment of CVD.
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Affiliation(s)
- Changwei Li
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA (C. Li, R.Z., Z.H., X.S.)
| | - Yang Pan
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois Chicago (Y.P., D.L., Y.H., C.L., V.R., T.N.K.)
| | - Ruiyuan Zhang
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA (C. Li, R.Z., Z.H., X.S.)
| | - Zhijie Huang
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA (C. Li, R.Z., Z.H., X.S.)
| | - Davey Li
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois Chicago (Y.P., D.L., Y.H., C.L., V.R., T.N.K.)
| | - Yunan Han
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois Chicago (Y.P., D.L., Y.H., C.L., V.R., T.N.K.)
| | - Claire Larkin
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois Chicago (Y.P., D.L., Y.H., C.L., V.R., T.N.K.)
| | - Varun Rao
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois Chicago (Y.P., D.L., Y.H., C.L., V.R., T.N.K.)
| | - Xiao Sun
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA (C. Li, R.Z., Z.H., X.S.)
| | - Tanika N Kelly
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois Chicago (Y.P., D.L., Y.H., C.L., V.R., T.N.K.)
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