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Capalbo A, de Wert G, Mertes H, Klausner L, Coonen E, Spinella F, Van de Velde H, Viville S, Sermon K, Vermeulen N, Lencz T, Carmi S. Screening embryos for polygenic disease risk: a review of epidemiological, clinical, and ethical considerations. Hum Reprod Update 2024:dmae012. [PMID: 38805697 DOI: 10.1093/humupd/dmae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/25/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND The genetic composition of embryos generated by in vitro fertilization (IVF) can be examined with preimplantation genetic testing (PGT). Until recently, PGT was limited to detecting single-gene, high-risk pathogenic variants, large structural variants, and aneuploidy. Recent advances have made genome-wide genotyping of IVF embryos feasible and affordable, raising the possibility of screening embryos for their risk of polygenic diseases such as breast cancer, hypertension, diabetes, or schizophrenia. Despite a heated debate around this new technology, called polygenic embryo screening (PES; also PGT-P), it is already available to IVF patients in some countries. Several articles have studied epidemiological, clinical, and ethical perspectives on PES; however, a comprehensive, principled review of this emerging field is missing. OBJECTIVE AND RATIONALE This review has four main goals. First, given the interdisciplinary nature of PES studies, we aim to provide a self-contained educational background about PES to reproductive specialists interested in the subject. Second, we provide a comprehensive and critical review of arguments for and against the introduction of PES, crystallizing and prioritizing the key issues. We also cover the attitudes of IVF patients, clinicians, and the public towards PES. Third, we distinguish between possible future groups of PES patients, highlighting the benefits and harms pertaining to each group. Finally, our review, which is supported by ESHRE, is intended to aid healthcare professionals and policymakers in decision-making regarding whether to introduce PES in the clinic, and if so, how, and to whom. SEARCH METHODS We searched for PubMed-indexed articles published between 1/1/2003 and 1/3/2024 using the terms 'polygenic embryo screening', 'polygenic preimplantation', and 'PGT-P'. We limited the review to primary research papers in English whose main focus was PES for medical conditions. We also included papers that did not appear in the search but were deemed relevant. OUTCOMES The main theoretical benefit of PES is a reduction in lifetime polygenic disease risk for children born after screening. The magnitude of the risk reduction has been predicted based on statistical modelling, simulations, and sibling pair analyses. Results based on all methods suggest that under the best-case scenario, large relative risk reductions are possible for one or more diseases. However, as these models abstract several practical limitations, the realized benefits may be smaller, particularly due to a limited number of embryos and unclear future accuracy of the risk estimates. PES may negatively impact patients and their future children, as well as society. The main personal harms are an unindicated IVF treatment, a possible reduction in IVF success rates, and patient confusion, incomplete counselling, and choice overload. The main possible societal harms include discarded embryos, an increasing demand for 'designer babies', overemphasis of the genetic determinants of disease, unequal access, and lower utility in people of non-European ancestries. Benefits and harms will vary across the main potential patient groups, comprising patients already requiring IVF, fertile people with a history of a severe polygenic disease, and fertile healthy people. In the United States, the attitudes of IVF patients and the public towards PES seem positive, while healthcare professionals are cautious, sceptical about clinical utility, and concerned about patient counselling. WIDER IMPLICATIONS The theoretical potential of PES to reduce risk across multiple polygenic diseases requires further research into its benefits and harms. Given the large number of practical limitations and possible harms, particularly unnecessary IVF treatments and discarded viable embryos, PES should be offered only within a research context before further clarity is achieved regarding its balance of benefits and harms. The gap in attitudes between healthcare professionals and the public needs to be narrowed by expanding public and patient education and providing resources for informative and unbiased genetic counselling.
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Affiliation(s)
- Antonio Capalbo
- Juno Genetics, Department of Reproductive Genetics, Rome, Italy
- Center for Advanced Studies and Technology (CAST), Department of Medical Genetics, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Guido de Wert
- Department of Health, Ethics & Society, CAPHRI-School for Public Health and Primary Care and GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Heidi Mertes
- Department of Philosophy and Moral Sciences, Ghent University, Ghent, Belgium
- Department of Public Health and Primary Care, Ghent University, Ghent, Belgium
| | - Liraz Klausner
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Edith Coonen
- Departments of Clinical Genetics and Reproductive Medicine, Maastricht University Medical Centre, Maastricht, The Netherlands
- School for Oncology and Developmental Biology, GROW, Maastricht University, Maastricht, The Netherlands
| | - Francesca Spinella
- Eurofins GENOMA Group Srl, Molecular Genetics Laboratories, Department of Scientific Communication, Rome, Italy
| | - Hilde Van de Velde
- Research Group Genetics Reproduction and Development (GRAD), Vrije Universiteit Brussel, Brussel, Belgium
- Brussels IVF, UZ Brussel, Brussel, Belgium
| | - Stephane Viville
- Laboratoire de Génétique Médicale LGM, Institut de Génétique Médicale d'Alsace IGMA, INSERM UMR 1112, Université de Strasbourg, France
- Laboratoire de Diagnostic Génétique, Unité de Génétique de l'infertilité (UF3472), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Karen Sermon
- Research Group Genetics Reproduction and Development (GRAD), Vrije Universiteit Brussel, Brussel, Belgium
| | | | - Todd Lencz
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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Andreoli L, Peeters H, Van Steen K, Dierickx K. Taking the risk. A systematic review of ethical reasons and moral arguments in the clinical use of polygenic risk scores. Am J Med Genet A 2024:e63584. [PMID: 38450933 DOI: 10.1002/ajmg.a.63584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/08/2024] [Accepted: 02/24/2024] [Indexed: 03/08/2024]
Abstract
Debates about the prospective clinical use of polygenic risk scores (PRS) have grown considerably in the last years. The potential benefits of PRS to improve patient care at individual and population levels have been extensively underlined. Nonetheless, the use of PRS in clinical contexts presents a number of unresolved ethical challenges and consequent normative gaps that hinder their optimal implementation. Here, we conducted a systematic review of reasons of the normative literature discussing ethical issues and moral arguments related to the use of PRS for the prevention and treatment of common complex diseases. In total, we have included and analyzed 34 records, spanning from 2013 to 2023. The findings have been organized in three major themes: in the first theme, we consider the potential harms of PRS to individuals and their kin. In the theme "Threats to health equity," we consider ethical concerns of social relevance, with a focus on justice issues. Finally, the theme "Towards best practices" collects a series of research priorities and provisional recommendations to be considered for an optimal clinical translation of PRS. We conclude that the use of PRS in clinical care reinvigorates old debates in matters of health justice; however, open questions, regarding best practices in clinical counseling, suggest that the ethical considerations applicable in monogenic settings will not be sufficient to face PRS emerging challenges.
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Affiliation(s)
- Lara Andreoli
- Department of Public Health and Primary Care, Centre for Biomedical Ethics and Law, KU Leuven, Leuven, Belgium
| | - Hilde Peeters
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Kris Dierickx
- Department of Public Health and Primary Care, Centre for Biomedical Ethics and Law, KU Leuven, Leuven, Belgium
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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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Qin M, Wu Y, Fang X, Pan C, Zhong S. Polygenic risk score predicts all-cause death in East Asian patients with prior coronary artery disease. Front Cardiovasc Med 2024; 11:1296415. [PMID: 38414927 PMCID: PMC10896892 DOI: 10.3389/fcvm.2024.1296415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/31/2024] [Indexed: 02/29/2024] Open
Abstract
Introduction Coronary artery disease (CAD) is a highly heritable and multifactorial disease. Numerous genome-wide association studies (GWAS) facilitated the construction of polygenic risk scores (PRS) for predicting future incidence of CAD, however, exclusively in European populations. Furthermore, identifying CAD patients with elevated risks of all-cause death presents a critical challenge in secondary prevention, which will contribute largely to reducing the burden for public healthcare. Methods We recruited a cohort of 1,776 Chinese CAD patients and performed medical follow-up for up to 11 years. A pruning and thresholding method was used to calculate PRS of CAD and its 14 risk factors. Their correlations with all-cause death were computed via Cox regression. Results and discussion We found that the PRS for CAD and its seven risk factors, namely myocardial infarction, ischemic stroke, angina, heart failure, low-density lipoprotein cholesterol, total cholesterol and C-reaction protein, were significantly associated with death (P ≤ 0.05), whereas the PRS of body mass index displayed moderate association (P < 0.1). Elastic-net Cox regression with 5-fold cross-validation was used to integrate these nine PRS models into a meta score, metaPRS, which performed well in stratifying patients at different risks for death (P < 0.0001). Combining metaPRS with clinical risk factors further increased the discerning power and a 4% increase in sensitivity. The metaPRS generated from the genetic susceptibility to CAD and its risk factors can well stratify CAD patients by their risks of death. Integrating metaPRS and clinical risk factors may contribute to identifying patients at higher risk of poor prognosis.
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Affiliation(s)
- Min Qin
- School of Medicine, South China University of Technology, Guangzhou, China
- Department of Pharmacy, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Yonglin Wu
- Department of Pharmacy, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, Guangzhou, China
| | - Xianhong Fang
- Department of Cardiology, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Guangzhou, China
| | - Cuiping Pan
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, Guangzhou, China
- Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Shilong Zhong
- School of Medicine, South China University of Technology, Guangzhou, China
- Department of Pharmacy, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Coronary Heart Disease Prevention, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Guangzhou, China
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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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Torkamani A, Chen SF, Lee SE, Sadaei H, Park JB, Khattab A, Henegar C, Wineinger N, Muse E. Meta-Prediction of Coronary Artery Disease Risk. RESEARCH SQUARE 2023:rs.3.rs-3694374. [PMID: 38196609 PMCID: PMC10775391 DOI: 10.21203/rs.3.rs-3694374/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Coronary artery disease (CAD) remains the leading cause of mortality and morbidity worldwide. Recent advances in large-scale genome-wide association studies have highlighted the potential of genetic risk, captured as polygenic risk scores (PRS), in clinical prevention. However, the current clinical utility of PRS models is limited to identifying high-risk populations based on the top percentiles of genetic susceptibility. While some studies have attempted integrative prediction using genetic and non-genetic factors, many of these studies have been cross-sectional and focused solely on risk stratification. Our primary objective in this study was to integrate unmodifiable (age / genetics) and modifiable (clinical / biometric) risk factors into a prospective prediction framework which also produces actionable and personalized risk estimates for the purpose of CAD prevention in a heterogenous adult population. Thus, we present an integrative, omnigenic, meta-prediction framework that effectively captures CAD risk subgroups, primarily distinguished by degree and nature of genetic risk, with distinct risk reduction profiles predicted from standard clinical interventions. Initial model development considered ~ 2,000 predictive features, including demographic data, lifestyle factors, physical measurements, laboratory tests, medication usage, diagnoses, and genetics. To power our meta-prediction approach, we stratified the UK Biobank into two primary cohorts: 1) a prevalent CAD cohort used to train baseline and prospective predictive models for contributing risk factors and diagnoses, and 2) an incident CAD cohort used to train the final CAD incident risk prediction model. The resultant 10-year incident CAD risk model is composed of 35 derived meta-features from models trained on the prevalent risk cohort, most of which are predicted baseline diagnoses with multiple embedded PRSs. This model achieved an AUC of 0.81 and macro-averaged F1-score of 0.65, outperforming standard clinical scores and prior integrative models. We further demonstrate that individualized risk reduction profiles can be derived from this model, with genetic risk mediating the degree of risk reduction achieved by standard clinical interventions.
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Affiliation(s)
- Ali Torkamani
- Scripps Research & Scripps Research Translational Institute
| | - Shang-Fu Chen
- Scripps Research & Scripps Research Translational Institute
| | - Sang Eun Lee
- Asan Medical Center, University of Ulsan College of Medicine
| | - Hossein Sadaei
- Scripps Research & Scripps Research Translational Institute
| | | | - Ahmed Khattab
- Scripps Research & Scripps Research Translational Institute
| | | | | | - Evan Muse
- Scripps Translational Science Institute, The Scripps Research Institute, Scripps Health
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7
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Zhang X, Luo X, Tian L, Yue P, Li M, Liu K, Zhu D, Huang C, Shi Q, Yang L, Xia Z, Zhao J, Ma Z, Li J, Leung JW, Lin Y, Yuan J, Meng W, Li X, Chen Y. The gut microbiome dysbiosis and regulation by fecal microbiota transplantation: umbrella review. Front Microbiol 2023; 14:1286429. [PMID: 38029189 PMCID: PMC10655098 DOI: 10.3389/fmicb.2023.1286429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Background Gut microbiome dysbiosis has been implicated in various gastrointestinal and extra-gastrointestinal diseases, but evidence on the efficacy and safety of fecal microbiota transplantation (FMT) for therapeutic indications remains unclear. Methods The gutMDisorder database was used to summarize the associations between gut microbiome dysbiosis and diseases. We performed an umbrella review of published meta-analyses to determine the evidence synthesis on the efficacy and safety of FMT in treating various diseases. Our study was registered in PROSPERO (CRD42022301226). Results Gut microbiome dysbiosis was associated with 117 gastrointestinal and extra-gastrointestinal. Colorectal cancer was associated with 92 dysbiosis. Dysbiosis involving Firmicutes (phylum) was associated with 34 diseases. We identified 62 published meta-analyses of FMT. FMT was found to be effective for 13 diseases, with a 95.56% cure rate (95% CI: 93.88-97.05%) for recurrent Chloridoids difficile infection (rCDI). Evidence was high quality for rCDI and moderate to high quality for ulcerative colitis and Crohn's disease but low to very low quality for other diseases. Conclusion Gut microbiome dysbiosis may be implicated in numerous diseases. Substantial evidence suggests FMT improves clinical outcomes for certain indications, but evidence quality varies greatly depending on the specific indication, route of administration, frequency of instillation, fecal preparation, and donor type. This variability should inform clinical, policy, and implementation decisions regarding FMT.
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Affiliation(s)
- Xianzhuo Zhang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Xufei Luo
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Liang Tian
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Ping Yue
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou, China
| | - Mengyao Li
- The Second Clinical Medical College, Lanzhou University, Lanzhou, China
| | - Kefeng Liu
- Department of Pharmacy, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Daoming Zhu
- Department of Radiology, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, China
| | - Chongfei Huang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Qianling Shi
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Liping Yang
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou, China
| | - Zhili Xia
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Jinyu Zhao
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Zelong Ma
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Jianlong Li
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Joseph W. Leung
- Division of Gastroenterology and Hepatology, UC Davis Medical Center and Sacramento VA Medical Center, Sacramento, CA, United States
| | - Yanyan Lin
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou, China
| | - Jinqiu Yuan
- Clinical Research Center, Big Data Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Wenbo Meng
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou, China
| | - Xun Li
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yaolong Chen
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
- Research Unit of Evidence-Based Evaluation and Guidelines, Chinese Academy of Medical Sciences, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
- Institute of Health Data Science, Lanzhou University, Lanzhou, China
- WHO Collaborating Centre for Guideline Implementation and Knowledge Translation, Lanzhou, China
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8
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Tabassum R, Widén E, Ripatti S. Effect of biological sex on human circulating lipidome: An overview of the literature. Atherosclerosis 2023; 384:117274. [PMID: 37743161 DOI: 10.1016/j.atherosclerosis.2023.117274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/28/2023] [Accepted: 09/01/2023] [Indexed: 09/26/2023]
Abstract
Cardiovascular diseases (CVD) are the leading cause of death worldwide for both men and women, but their prevalence and burden show marked sex differences. The existing knowledge gaps in research, prevention, and treatment for women emphasize the need for understanding the biological mechanisms contributing to the sex differences in CVD. Sex differences in the plasma lipids that are well-known risk factors and predictors of CVD events have been recognized and are believed to contribute to the known disparities in CVD manifestations in men and women. However, the current understanding of sex differences in lipids has mainly come from the studies on routinely measured standard lipids- low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), total triglycerides, and total cholesterol, which have been the mainstay of the lipid profiling. Sex differences in individual lipid species, collectively called the lipidome, have until recently been less explored due to the technological challenges and analytic costs. With the technological advancements in the last decade and growing interest in understanding mechanisms of sexual dimorphism in metabolic disorders, many investigators utilized metabolomics and lipidomics based platforms to examine the effect of biological sex on detailed lipidomic profiles and individual lipid species. This review presents an overview of the research on sex differences in the concentrations of circulating lipid species, focusing on findings from the metabolome- and lipidome-wide studies. We also discuss the potential contribution of genetic factors including sex chromosomes and sex-specific physiological factors such as menopause and sex hormones to the sex differences in lipidomic profiles.
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Affiliation(s)
- Rubina Tabassum
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland.
| | - Elisabeth Widén
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland; Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
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9
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Krittanawong C, Khawaja M, Tamis‐Holland JE, Girotra S, Rao SV. Acute Myocardial Infarction: Etiologies and Mimickers in Young Patients. J Am Heart Assoc 2023; 12:e029971. [PMID: 37724944 PMCID: PMC10547302 DOI: 10.1161/jaha.123.029971] [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] [Indexed: 09/21/2023]
Abstract
Acute myocardial infarction is an important cause of death worldwide. While it often affects patients of older age, acute myocardial infarction is garnering more attention as a significant cause of morbidity and mortality among young patients (<45 years of age). More specifically, there is a focus on recognizing the unique etiologies for myocardial infarction in these younger patients as nonatherosclerotic etiologies occur more frequently in this population. As such, there is a potential for delayed and inaccurate diagnoses and treatments that can carry serious clinical implications. The understanding of acute myocardial infarction manifestations in young patients is evolving, but there remains a significant need for better strategies to rapidly diagnose, risk stratify, and manage such patients. This comprehensive review explores the various etiologies for acute myocardial infarction in young adults and outlines the approach to efficient diagnosis and management for these unique patient phenotypes.
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Affiliation(s)
| | - Muzamil Khawaja
- Cardiology DivisionEmory University School of MedicineAtlantaGAUSA
| | | | - Saket Girotra
- Division of Cardiovascular MedicineUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Sunil V. Rao
- New York University Langone Health SystemNew YorkNYUSA
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10
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Lo Faro V, Johansson T, Höglund J, Hadizadeh F, Johansson Å. Polygenic risk scores and risk stratification in deep vein thrombosis. Thromb Res 2023; 228:151-162. [PMID: 37331118 DOI: 10.1016/j.thromres.2023.06.011] [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: 01/03/2023] [Revised: 05/18/2023] [Accepted: 06/09/2023] [Indexed: 06/20/2023]
Abstract
INTRODUCTION Deep vein thrombosis (DVT) is a complex disease, where 60 % of risk is due to genetic factors, such as the Factor V Leiden (FVL) variant. DVT is either asymptomatic or manifests with unspecific symptoms and, if left untreated, DVT leads to severe complications. The impact is dramatic and currently, there is still a research gap in DVT prevention. We characterized the genetic contribution and stratified individuals based on genetic makeup to evaluate if it favorably impacts risk prediction. METHODS In the UK Biobank (UKB), we performed gene-based association tests using exome sequencing data, as well as a genome-wide association study. We also constructed polygenic risk scores (PRS) in a subset of the cohort (Number of cases = 8231; Number of controls = 276,360) and calculated the impact on the prediction capacity of the PRS in a non-overlapping part of the cohort (Number of cases = 4342; Number of controls = 142,822). We generated additional PRSs that excluded the known causative variants. RESULTS We discovered and replicated a novel common variant (rs11604583) near the region where are located the TRIM51 and LRRC55 genes and identified a novel rare variant (rs187725533) located near the CREB3L1 gene, associated with 2.5-fold higher risk of DVT. In one of the PRS models constructed, the top decile of risk is associated with 3.4-fold increased risk, an effect that is 2.3-fold when excluding FVL carriers. In the top PRS decile, the cumulative risk of DVT at the age of 80 years is 10 % for FVL carriers, contraposed to 5 % for non-carriers. The population attributable fractions of having a high polygenic risk on the rate of DVT was estimated to be around 20 % in our cohort. CONCLUSION Individuals with a high polygenic risk of DVT, and not only carriers of well-studied variants such as FVL, may benefit from prevention strategies.
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Affiliation(s)
- Valeria Lo Faro
- Department of Immunology, Genetics and Pathology, Genomics and Neurobiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Therese Johansson
- Department of Immunology, Genetics and Pathology, Genomics and Neurobiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Centre for Women's Mental Health during the Reproductive Lifespan - Womher, Uppsala University, Uppsala, Sweden
| | - Julia Höglund
- Department of Immunology, Genetics and Pathology, Genomics and Neurobiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Fatemeh Hadizadeh
- Department of Immunology, Genetics and Pathology, Genomics and Neurobiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Åsa Johansson
- Department of Immunology, Genetics and Pathology, Genomics and Neurobiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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11
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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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12
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Smith JL, Schaid DJ, Kullo IJ. Implementing Reporting Standards for Polygenic Risk Scores for Atherosclerotic Cardiovascular Disease. Curr Atheroscler Rep 2023; 25:323-330. [PMID: 37223852 PMCID: PMC10495216 DOI: 10.1007/s11883-023-01104-3] [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] [Accepted: 04/13/2023] [Indexed: 05/25/2023]
Abstract
PURPOSE OF REVIEW There is considerable interest in using polygenic risk scores (PRSs) for assessing risk of atherosclerotic cardiovascular disease (ASCVD). A barrier to the clinical use of PRSs is heterogeneity in how PRS studies are reported. In this review, we summarize approaches to establish a uniform reporting framework for PRSs for coronary heart disease (CHD), the most common form of ASCVD. RECENT FINDINGS Reporting standards for PRSs need to be contextualized for disease specific applications. In addition to metrics of predictive performance, reporting standards for PRSs for CHD should include how cases/control were ascertained, degree of adjustment for conventional CHD risk factors, portability to diverse genetic ancestry groups and admixed individuals, and quality control measures for clinical deployment. Such a framework will enable PRSs to be optimized and benchmarked for clinical use.
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Affiliation(s)
- Johanna L Smith
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Daniel J Schaid
- Department of Quantitative Health Sciences, Rochester, MN, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA.
- Gonda Vascular Center, Rochester, MN, USA.
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13
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Zucker R, Kovalerchik M, Linial M. Gene-based association study reveals a distinct female genetic signal in primary hypertension. Hum Genet 2023:10.1007/s00439-023-02567-9. [PMID: 37133573 DOI: 10.1007/s00439-023-02567-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/25/2023] [Indexed: 05/04/2023]
Abstract
Hypertension is a polygenic disease that affects over 1.2 billion adults aged 30-79 worldwide. It is a major risk factor for renal, cerebrovascular, and cardiovascular diseases. The heritability of hypertension is estimated to be high; nevertheless, our understanding of its underlying mechanisms remains scarce and incomplete. This study covered the entries from European ancestry from the UK-Biobank (UKB), with 74,090 cases diagnosed with essential (primary) hypertension and 200,734 controls. We compared the findings from large-scale genome-wide association studies (GWAS) to the gene-based method of proteome-wide association studies (PWAS). We focused on 70 statistically significant associated genes, most of which failed to reach significance in variant-based GWAS. A total of 30% of the PWAS-associated genes were validated against independent cohorts, including the Finnish Biobank. Furthermore, gene-based analyses that were performed on both sexes revealed sex-dependent genetics with a stronger genetic component associated with females. Analysis of systolic and diastolic blood pressure measurements confirms a strong genetic effect associated with females. We demonstrated that gene-based approaches provide insight into the underlying biology of hypertension. Specifically, the expression profiles of the identified genes exposed the enrichment of endothelial cells from multiple organs. Furthermore, females' top-ranked significant genes are involved in cellular immunity. We conclude that studying hypertension and blood pressure via gene-based association methods improves interpretability and exposes sex-dependent genetic effects, which enhances clinical utility.
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Affiliation(s)
- Roei Zucker
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Michael Kovalerchik
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Michal Linial
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
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Marston NA, Pirruccello JP, Melloni GEM, Koyama S, Kamanu FK, Weng LC, Roselli C, Kamatani Y, Komuro I, Aragam KG, Butterworth AS, Ito K, Lubitz SA, Ellinor PT, Sabatine MS, Ruff CT. Predictive Utility of a Coronary Artery Disease Polygenic Risk Score in Primary Prevention. JAMA Cardiol 2023; 8:130-137. [PMID: 36576811 PMCID: PMC9857431 DOI: 10.1001/jamacardio.2022.4466] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/13/2022] [Indexed: 12/29/2022]
Abstract
Importance The clinical utility of polygenic risk scores (PRS) for coronary artery disease (CAD) has not yet been established. Objective To investigate the ability of a CAD PRS to potentially guide statin initiation in primary prevention after accounting for age and clinical risk. Design, Setting, and Participants This was a longitudinal cohort study with enrollment starting on January 1, 2006, and ending on December 31, 2010, with data updated to mid-2021, using data from the UK Biobank, a long-term population study of UK citizens. A replication analysis was performed in Biobank Japan. The analysis included all patients without a history of CAD and who were not taking lipid-lowering therapy. Data were analyzed from January 1 to June 30, 2022. Exposures Polygenic risk for CAD was defined as low (bottom 20%), intermediate, and high (top 20%) using a CAD PRS including 241 genome-wide significant single-nucleotide variations (SNVs). The pooled cohort equations were used to estimate 10-year atherosclerotic cardiovascular disease (ASCVD) risk and classify individuals as low (<5%), borderline (5-<7.5%), intermediate (7.5-<20%), or high risk (≥20%). Main Outcomes and Measures Myocardial infarction (MI) and ASCVD events (defined as incident clinical CAD [including MI], stroke, or CV death). Results A total of 330 201 patients (median [IQR] age, 57 [40-74] years; 189 107 female individuals [57%]) were included from the UK Biobank. Over the 10-year follow-up, 4454 individuals had an MI. The CAD PRS was significantly associated with the risk of MI in all age groups but had significantly stronger risk prediction at younger ages (age <50 years: hazard ratio [HR] per 1 SD of PRS, 1.72; 95% CI, 1.56-1.89; age 50-60 years: HR, 1.46; 95% CI, 1.38-1.53; age >60 years: HR, 1.42; 95% CI, 1.37-1.48; P for interaction <.001). In patients younger than 50 years, those with high PRS had a 3- to 4-fold increased associated risk of MI compared with those in the low PRS category. A significant interaction between CAD PRS and age was replicated in Biobank Japan. When CAD PRS testing was added to the clinical ASCVD risk score in individuals younger than 50 years, 591 of 4373 patients (20%) with borderline risk were risk stratified into intermediate risk, warranting initiation of statin therapy and 3198 of 7477 patients (20%) with both borderline or intermediate risk were stratified as low risk, thus not warranting therapy. Conclusions and Relevance Results of this cohort study suggest that the predictive ability of a CAD PRS was greater in younger individuals and can be used to better identify patients with borderline and intermediate clinical risk who should initiate statin therapy.
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Affiliation(s)
- Nicholas A. Marston
- TIMI Study Group, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - James P. Pirruccello
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Division of Cardiology, University of California San Francisco, San Francisco
| | - Giorgio E. M. Melloni
- TIMI Study Group, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Satoshi Koyama
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Frederick K. Kamanu
- TIMI Study Group, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lu-Chen Weng
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Carolina Roselli
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Yoichiro Kamatani
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Issei Komuro
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Krishna G. Aragam
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Adam S. Butterworth
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, United Kingdom
- The National Institute for Health and Care at the University of Cambridge, Cambridge, United Kingdom
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care University of Cambridge, Cambridge, United Kingdom
- BHF Centre of Research Excellence University of Cambridge, Cambridge, United Kingdom
| | - Kaoru Ito
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Steve A. Lubitz
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Patrick T. Ellinor
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Marc S. Sabatine
- TIMI Study Group, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Christian T. Ruff
- TIMI Study Group, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
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15
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Sutton NR, Malhotra R, Hilaire C, Aikawa E, Blumenthal RS, Gackenbach G, Goyal P, Johnson A, Nigwekar SU, Shanahan CM, Towler DA, Wolford BN, Chen Y. Molecular Mechanisms of Vascular Health: Insights From Vascular Aging and Calcification. Arterioscler Thromb Vasc Biol 2023; 43:15-29. [PMID: 36412195 PMCID: PMC9793888 DOI: 10.1161/atvbaha.122.317332] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/11/2022] [Indexed: 11/23/2022]
Abstract
Cardiovascular disease is the most common cause of death worldwide, especially beyond the age of 65 years, with the vast majority of morbidity and mortality due to myocardial infarction and stroke. Vascular pathology stems from a combination of genetic risk, environmental factors, and the biologic changes associated with aging. The pathogenesis underlying the development of vascular aging, and vascular calcification with aging, in particular, is still not fully understood. Accumulating data suggests that genetic risk, likely compounded by epigenetic modifications, environmental factors, including diabetes and chronic kidney disease, and the plasticity of vascular smooth muscle cells to acquire an osteogenic phenotype are major determinants of age-associated vascular calcification. Understanding the molecular mechanisms underlying genetic and modifiable risk factors in regulating age-associated vascular pathology may inspire strategies to promote healthy vascular aging. This article summarizes current knowledge of concepts and mechanisms of age-associated vascular disease, with an emphasis on vascular calcification.
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Affiliation(s)
- Nadia R. Sutton
- Division of Cardiovascular Medicine, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Rajeev Malhotra
- Cardiology Division, Massachusetts General Hospital and Harvard Medical School, Boston, MA USA
| | - Cynthia Hilaire
- Division of Cardiology, Departments of Medicine and Bioengineering, Pittsburgh Heart, Lung, and Blood Vascular Medicine Institute, University of Pittsburgh, 1744 BSTWR, 200 Lothrop St, Pittsburgh, PA, 15260 USA
| | - Elena Aikawa
- Cardiovascular Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Roger S. Blumenthal
- Johns Hopkins Ciccarone Center for the Prevention of Cardiovascular Disease; Baltimore, MD
| | - Grace Gackenbach
- Division of Cardiovascular Medicine, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Parag Goyal
- Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Adam Johnson
- Cardiology Division, Massachusetts General Hospital and Harvard Medical School, Boston, MA USA
| | - Sagar U. Nigwekar
- Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA USA
| | - Catherine M. Shanahan
- School of Cardiovascular and Metabolic Medicine and Sciences, King’s College London, London, UK
| | - Dwight A. Towler
- Department of Medicine | Endocrine Division and Pak Center for Mineral Metabolism Research, UT Southwestern Medical Center, Dallas, TX USA
| | - Brooke N. Wolford
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - Yabing Chen
- Department of Pathology, University of Alabama at Birmingham and Research Department, Veterans Affairs Birmingham Medical Center, Birmingham, AL, USA
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16
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Mars N, Lindbohm JV, Della Briotta Parolo P, Widén E, Kaprio J, Palotie A, Ripatti S. Systematic comparison of family history and polygenic risk across 24 common diseases. Am J Hum Genet 2022; 109:2152-2162. [PMID: 36347255 PMCID: PMC9748261 DOI: 10.1016/j.ajhg.2022.10.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022] Open
Abstract
Family history is the standard indirect measure of inherited susceptibility in clinical care, whereas polygenic risk scores (PRSs) have more recently demonstrated potential for more directly capturing genetic risk in many diseases. Few studies have systematically compared how these overlap and complement each other across common diseases. Within FinnGen (N = 306,418), we leverage family relationships, up to 50 years of nationwide registries, and genome-wide genotyping to examine the interplay of family history and genome-wide PRSs. We explore the dynamic for three types of family history across 24 common diseases: first- and second-degree family history and parental causes of death. Covering a large proportion of the burden of non-communicable diseases in adults, we show that family history and PRS are independent and not interchangeable measures, but instead provide complementary information on inherited disease susceptibility. The PRSs explained on average 10% of the effect of first-degree family history, and first-degree family history 3% of PRSs, and PRS effects were independent of both early- and late-onset family history. The PRS stratified the risk similarly in individuals with and without family history. In most diseases, including coronary artery disease, glaucoma, and type 2 diabetes, a positive family history with a high PRS was associated with a considerably elevated risk, whereas a low PRS compensated completely for the risk implied by positive family history. This study provides a catalogue of risk estimates for both family history of disease and PRSs and highlights opportunities for a more comprehensive way of assessing inherited disease risk across common diseases.
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Affiliation(s)
- Nina Mars
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joni V Lindbohm
- Clinicum, Department of Public Health, University of Helsinki, Helsinki, Finland; Department of Epidemiology and Public Health, University College London, London, UK; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Elisabeth Widén
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland; Clinicum, Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland; Clinicum, Department of Public Health, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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17
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Ramírez J, van Duijvenboden S, Young WJ, Tinker A, Lambiase PD, Orini M, Munroe PB. Prediction of Coronary Artery Disease and Major Adverse Cardiovascular Events Using Clinical and Genetic Risk Scores for Cardiovascular Risk Factors. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2022; 15:e003441. [PMID: 35861959 PMCID: PMC9584057 DOI: 10.1161/circgen.121.003441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Coronary artery disease (CAD) and major adverse cardiovascular events (MACE) are the leading causes of death in the general population, but risk stratification remains suboptimal. CAD genetic risk scores (GRSs) predict risk independently from clinical tools, like QRISK3. We assessed the added value of GRSs for a variety of cardiovascular traits (CV GRSs) for predicting CAD and MACE and tested their early-life screening potential by comparing against the CAD GRS only. METHODS We used data from 379 581 participants in the UK Biobank without known cardiovascular conditions (follow-up, 11.3 years; 3.3% CAD cases and 5.2% MACE cases). In a training subset (50%) we built 3 scores: QRISK3; QRISK3 and an established CAD GRS; and QRISK3, the CAD GRS and the CV GRSs. In an independent subset (50%), we evaluated each score's performance using the concordance index, odds ratio and net reclassification index. We then repeated the analyses without considering QRISK3. RESULTS For CAD, the combination of QRISK3 and the CAD GRS had a better performance than QRISK3 alone (concordance index, 0.766 versus 0.753; odds ratio, 5.47 versus 4.82; net reclassification index, 7.7%). Adding the CV GRSs did not significantly improve risk stratification. When only looking at genetic information, the combination of CV GRSs and the CAD GRS had a better performance than the CAD GRS alone (concordance index, 0.637 versus 0.625; odds ratio, 2.17 versus 2.07; net reclassification index, 3.3%). Similar results were obtained for MACE. CONCLUSIONS In individuals without known cardiovascular disease, the inclusion of CV GRSs to a clinical tool and an established CAD GRS does not improve CAD or MACE risk stratification. However, their combination only with the CAD GRS increases prediction performance indicating potential use in early-life screening before the advanced development of conventional cardiovascular risk factors.
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Affiliation(s)
- Julia Ramírez
- Clinical Pharmacology and Precision Medicine Deparment, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom (J.R., S.v.D., W.J.Y., A.T., P.B.M.).,Electronic Engineering and Communications Department, Aragon Institute of Engineering Research, University of Zaragoza, Spain and CIBER's Bioengineering, Biomaterials and Nanomedicine, Spain. (J.R.)
| | - Stefan van Duijvenboden
- Clinical Pharmacology and Precision Medicine Deparment, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom (J.R., S.v.D., W.J.Y., A.T., P.B.M.).,Institute of Cardiovascular Science, University College London, London, United Kingdom (S.v.D., P.D.L., M.O.)
| | - William J Young
- Clinical Pharmacology and Precision Medicine Deparment, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom (J.R., S.v.D., W.J.Y., A.T., P.B.M.).,Barts Heart Centre, St Bartholomew's Hospital, London, United Kingdom (W.J.Y., P.D.L., M.O.)
| | - Andrew Tinker
- Clinical Pharmacology and Precision Medicine Deparment, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom (J.R., S.v.D., W.J.Y., A.T., P.B.M.).,NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom (A.T., P.B.M.)
| | - Pier D Lambiase
- Institute of Cardiovascular Science, University College London, London, United Kingdom (S.v.D., P.D.L., M.O.).,Barts Heart Centre, St Bartholomew's Hospital, London, United Kingdom (W.J.Y., P.D.L., M.O.)
| | - Michele Orini
- Institute of Cardiovascular Science, University College London, London, United Kingdom (S.v.D., P.D.L., M.O.).,Barts Heart Centre, St Bartholomew's Hospital, London, United Kingdom (W.J.Y., P.D.L., M.O.)
| | - Patricia B Munroe
- Clinical Pharmacology and Precision Medicine Deparment, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom (J.R., S.v.D., W.J.Y., A.T., P.B.M.).,NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom (A.T., P.B.M.)
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18
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Polygenic risk scores: improving the prediction of future disease or added complexity? Br J Gen Pract 2022; 72:396-398. [PMID: 35902257 PMCID: PMC9343049 DOI: 10.3399/bjgp22x720437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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19
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Schaid DJ, Sinnwell JP, Batzler A, McDonnell SK. Polygenic risk for prostate cancer: Decreasing relative risk with age but little impact on absolute risk. Am J Hum Genet 2022; 109:900-908. [PMID: 35353984 PMCID: PMC9118111 DOI: 10.1016/j.ajhg.2022.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/09/2022] [Indexed: 12/14/2022] Open
Abstract
Polygenic risk scores (PRSs) for a variety of diseases have recently been shown to have relative risks that depend on age, and genetic relative risks decrease with increasing age. A refined understanding of the age dependency of PRSs for a disease is important for personalized risk predictions and risk stratification. To further evaluate how the PRS relative risk for prostate cancer depends on age, we refined analyses for a validated PRS for prostate cancer by using 64,274 prostate cancer cases and 46,432 controls of diverse ancestry (82.8% European, 9.8% African American, 3.8% Latino, 2.8% Asian, and 0.8% Ghanaian). Our strategy applied a novel weighted proportional hazards model to case-control data to fully utilize age to refine how the relative risk decreased with age. We found significantly greater relative risks for younger men (age 30-55 years) compared with older men (70-88 years) for both relative risk per standard deviation of the PRS and dichotomized according to the upper 90th percentile of the PRS distribution. For the largest European ancestral group that could provide reliable resolution, the log-relative risk decreased approximately linearly from age 50 to age 75. Despite strong evidence of age-dependent genetic relative risk, our results suggest that absolute risk predictions differed little from predictions that assumed a constant relative risk over ages, from short-term to long-term predictions, simplifying implementation of risk discussions into clinical practice.
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Affiliation(s)
- Daniel J. Schaid
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA,Corresponding author
| | - Jason P. Sinnwell
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Anthony Batzler
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
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20
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Nagpal S, Tandon R, Gibson G. Canalization of the Polygenic Risk for Common Diseases and Traits in the UK Biobank Cohort. Mol Biol Evol 2022; 39:6547257. [PMID: 35275999 PMCID: PMC9004416 DOI: 10.1093/molbev/msac053] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Since organisms develop and thrive in the face of constant perturbations due to environmental and genetic variation, species may evolve resilient genetic architectures. We sought evidence for this process, known as canalization, through a comparison of the prevalence of phenotypes as a function of the polygenic score (PGS) across environments in the UK Biobank cohort study. Contrasting seven diseases and three categorical phenotypes with respect to 151 exposures in 408,925 people, the deviation between the prevalence-risk curves was observed to increase monotonically with the PGS percentile in one-fifth of the comparisons, suggesting extensive PGS-by-Environment (PGS×E) interaction. After adjustment for the dependency of allelic effect sizes on increased prevalence in the perturbing environment, cases where polygenic influences are greater or lesser than expected are seen to be particularly pervasive for educational attainment, obesity, and metabolic condition type-2 diabetes. Inflammatory bowel disease analysis shows fewer interactions but confirms that smoking and some aspects of diet influence risk. Notably, body mass index has more evidence for decanalization (increased genetic influence at the extremes of polygenic risk), whereas the waist-to-hip ratio shows canalization, reflecting different evolutionary pressures on the architectures of these weight-related traits. An additional 10 % of comparisons showed evidence for an additive shift of prevalence independent of PGS between exposures. These results provide the first widespread evidence for canalization protecting against disease in humans and have implications for personalized medicine as well as understanding the evolution of complex traits. The findings can be explored through an R shiny app at https://canalization-gibsonlab.shinyapps.io/rshiny/.
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Affiliation(s)
- Sini Nagpal
- School of Biological Sciences, and Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Raghav Tandon
- Wallace H. Coulter Department of Biomedical Engineering, and Center for Machine Learning, Georgia Institute of Technology, Atlanta, GA, USA
| | - Greg Gibson
- School of Biological Sciences, and Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA, USA
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21
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Muse ED, Chen SF, Liu S, Fernandez B, Schrader B, Molparia B, León AN, Lee R, Pubbi N, Mejia N, Ren C, El-Kalliny A, Montes de Oca EP, Aguilar H, Ghoshal A, Dias R, Evans D, Chen KY, Zhang Y, Wineinger NE, Spencer EG, Topol EJ, Torkamani A. Impact of polygenic risk communication: an observational mobile application-based coronary artery disease study. NPJ Digit Med 2022; 5:30. [PMID: 35277577 PMCID: PMC8917120 DOI: 10.1038/s41746-022-00578-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/11/2022] [Indexed: 12/12/2022] Open
Abstract
We developed a smartphone application, MyGeneRank, to conduct a prospective observational cohort study (NCT03277365) involving the automated generation, communication, and electronic capture of response to a polygenic risk score (PRS) for coronary artery disease (CAD). Adults with a smartphone and an existing 23andMe genetic profiling self-referred to the study. We evaluated self-reported actions taken in response to personal CAD PRS information, with special interest in the initiation of lipid-lowering therapy. 19% (721/3,800) of participants provided complete responses for baseline and follow-up use of lipid-lowering therapy. 20% (n = 19/95) of high CAD PRS vs 7.9% (n = 8/101) of low CAD PRS participants initiated lipid-lowering therapy at follow-up (p-value = 0.002). Both the initiation of statin and non-statin lipid-lowering therapy was associated with degree of CAD PRS: 15.2% (n = 14/92) vs 6.0% (n = 6/100) for statins (p-value = 0.018) and 6.8% (n = 8/118) vs 1.6% (n = 2/123) for non-statins (p-value = 0.022) in high vs low CAD PRS, respectively. High CAD PRS was also associated with earlier initiation of lipid lowering therapy (average age of 52 vs 65 years in high vs low CAD PRS respectively, p-value = 0.007). Overall, degree of CAD PRS was associated with use of any lipid-lowering therapy at follow-up: 42.4% (n = 56/132) vs 28.5% (n = 37/130) (p-value = 0.009). We find that digital communication of personal CAD PRS information is associated with increased and earlier lipid-lowering initiation in individuals of high CAD PRS. Loss to follow-up is the primary limitation of this study. Alternative communication routes, and long-term studies with EHR-based outcomes are needed to understand the generalizability and durability of this finding.
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Affiliation(s)
- Evan D Muse
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA.,Scripps Clinic, La Jolla, CA, 92037, USA
| | - Shang-Fu Chen
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA.,Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, 92037, USA
| | - Shuchen Liu
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA.,Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, 92037, USA
| | - Brianna Fernandez
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA.,Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, 92037, USA
| | - Brian Schrader
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA
| | - Bhuvan Molparia
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA
| | - André Nicolás León
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA.,Scripps Clinic, La Jolla, CA, 92037, USA
| | - Raymond Lee
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA
| | - Neha Pubbi
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA
| | - Nolan Mejia
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA
| | | | | | - Ernesto Prado Montes de Oca
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA.,Personalized Medicine National Laboratory, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C, Guadalajara, Jalisco, 44270, México
| | - Hector Aguilar
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA
| | - Arjun Ghoshal
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA
| | - Raquel Dias
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA.,Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, 92037, USA
| | - Doug Evans
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA.,Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, 92037, USA
| | - Kai-Yu Chen
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA.,Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, 92037, USA
| | - Yunyue Zhang
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA
| | - Nathan E Wineinger
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA.,Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, 92037, USA
| | - Emily G Spencer
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA
| | - Eric J Topol
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA.,Scripps Clinic, La Jolla, CA, 92037, USA
| | - Ali Torkamani
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA. .,Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, 92037, USA.
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22
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Ho WK, Tai MC, Dennis J, Shu X, Li J, Ho PJ, Millwood IY, Lin K, Jee YH, Lee SH, Mavaddat N, Bolla MK, Wang Q, Michailidou K, Long J, Wijaya EA, Hassan T, Rahmat K, Tan VKM, Tan BKT, Tan SM, Tan EY, Lim SH, Gao YT, Zheng Y, Kang D, Choi JY, Han W, Lee HB, Kubo M, Okada Y, Namba S, Park SK, Kim SW, Shen CY, Wu PE, Park B, Muir KR, Lophatananon A, Wu AH, Tseng CC, Matsuo K, Ito H, Kwong A, Chan TL, John EM, Kurian AW, Iwasaki M, Yamaji T, Kweon SS, Aronson KJ, Murphy RA, Koh WP, Khor CC, Yuan JM, Dorajoo R, Walters RG, Chen Z, Li L, Lv J, Jung KJ, Kraft P, Pharoah PDB, Dunning AM, Simard J, Shu XO, Yip CH, Taib NAM, Antoniou AC, Zheng W, Hartman M, Easton DF, Teo SH. Polygenic risk scores for prediction of breast cancer risk in Asian populations. Genet Med 2022; 24:586-600. [PMID: 34906514 PMCID: PMC7612481 DOI: 10.1016/j.gim.2021.11.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 08/03/2021] [Accepted: 11/09/2021] [Indexed: 02/08/2023] Open
Abstract
PURPOSE Non-European populations are under-represented in genetics studies, hindering clinical implementation of breast cancer polygenic risk scores (PRSs). We aimed to develop PRSs using the largest available studies of Asian ancestry and to assess the transferability of PRS across ethnic subgroups. METHODS The development data set comprised 138,309 women from 17 case-control studies. PRSs were generated using a clumping and thresholding method, lasso penalized regression, an Empirical Bayes approach, a Bayesian polygenic prediction approach, or linear combinations of multiple PRSs. These PRSs were evaluated in 89,898 women from 3 prospective studies (1592 incident cases). RESULTS The best performing PRS (genome-wide set of single-nucleotide variations [formerly single-nucleotide polymorphism]) had a hazard ratio per unit SD of 1.62 (95% CI = 1.46-1.80) and an area under the receiver operating curve of 0.635 (95% CI = 0.622-0.649). Combined Asian and European PRSs (333 single-nucleotide variations) had a hazard ratio per SD of 1.53 (95% CI = 1.37-1.71) and an area under the receiver operating curve of 0.621 (95% CI = 0.608-0.635). The distribution of the latter PRS was different across ethnic subgroups, confirming the importance of population-specific calibration for valid estimation of breast cancer risk. CONCLUSION PRSs developed in this study, from association data from multiple ancestries, can enhance risk stratification for women of Asian ancestry.
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Affiliation(s)
- Weang-Kee Ho
- School of Mathematical Sciences, Faculty of Science and Engineering, University of Nottingham Malaysia, Selangor, Malaysia; Cancer Research Malaysia, Selangor, Malaysia.
| | | | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Xiang Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN; Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jingmei Li
- Department of Surgery, University Surgical Cluster, National University Hospital, Singapore, Singapore; Genome Institute of Singapore, Laboratory of Women's Health and Genetics, Singapore, Singapore
| | - Peh Joo Ho
- Genome Institute of Singapore, Laboratory of Women's Health and Genetics, Singapore, Singapore
| | - Iona Y Millwood
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, University of Oxford, Oxford, United Kingdom
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Yon-Ho Jee
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Su-Hyun Lee
- Graduate School of Public Health, Yonsei University, Seoul, Korea
| | - Nasim Mavaddat
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom; Biostatistics Unit, The Cyprus Institute of Neurology & Genetics, Ayios Dometios, Cyprus; Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology & Genetics, Ayios Dometios, Cyprus
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN
| | | | | | - Kartini Rahmat
- Biomedical Imaging Department, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Veronique Kiak Mien Tan
- Department of Breast Surgery, Singapore General Hospital, Singapore, Singapore; Division of Surgery and Surgical Oncology, National Cancer Center Singapore, Singapore, Singapore
| | - Benita Kiat Tee Tan
- Department of Breast Surgery, Singapore General Hospital, Singapore, Singapore; Division of Surgery and Surgical Oncology, National Cancer Center Singapore, Singapore, Singapore; Department of General Surgery, Sengkang General Hospital, Singapore, Singapore
| | - Su Ming Tan
- Division of Breast Surgery, Changi General Hospital, Singapore, Singapore
| | - Ern Yu Tan
- Department of General Surgery, Tan Tock Seng Hospital, Singapore, Singapore
| | - Swee Ho Lim
- KK Breast Department, KK Women's and Children's Hospital, Singapore, Singapore
| | - Yu-Tang Gao
- State Key Laboratory of Oncogene and Related Genes & Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ying Zheng
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Daehee Kang
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea; Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Ji-Yeob Choi
- Cancer Research Institute, Seoul National University, Seoul, Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea; Institute of Health Policy and Management, Medical Research Center, Seoul National University, Seoul, Korea
| | - Wonshik Han
- Cancer Research Institute, Seoul National University, Seoul, Korea; Department of Surgery, Seoul National University College of Medicine, Seoul, South Korea
| | - Han-Byoel Lee
- Cancer Research Institute, Seoul National University, Seoul, Korea; Department of Surgery, Seoul National University College of Medicine, Seoul, South Korea
| | - Michiki Kubo
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Graduate School of Medicine, Faculty of Medicine, Osaka University, Suita, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan; Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Shinichi Namba
- Department of Statistical Genetics, Graduate School of Medicine, Faculty of Medicine, Osaka University, Suita, Japan
| | - Sue K Park
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea; Cancer Research Institute, Seoul National University, Seoul, Korea; Integrated Major in Innovative Medical Science, Seoul National University College of Medicine, Seoul, Korea
| | - Sung-Won Kim
- Department of Surgery, Daerim Saint Mary's Hospital, Seoul, Korea
| | - Chen-Yang Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Pei-Ei Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Boyoung Park
- Department of Medicine, Hanyang University College of Medicine, Seoul, Korea
| | - Kenneth R Muir
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, The University of Manchester, Manchester, United Kingdom
| | - Artitaya Lophatananon
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, The University of Manchester, Manchester, United Kingdom
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Chiu-Chen Tseng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan; Division of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hidemi Ito
- Division of Cancer Information and Control, Aichi Cancer Center Research Institute, Nagoya, Japan; Division of Descriptive Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Ava Kwong
- Hong Kong Hereditary Breast Cancer Family Registry, Cancer Genetics Centre, Happy Valley, Hong Kong; Department of Surgery, The University of Hong Kong, Pok Fu Lam, Hong Kong; Department of Surgery, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong
| | - Tsun L Chan
- Hong Kong Hereditary Breast Cancer Family Registry, Cancer Genetics Centre, Happy Valley, Hong Kong; Department of Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong
| | - Esther M John
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA; Department of Epidemiology & Population Health, Stanford University School of Medicine, Stanford, CA
| | - Allison W Kurian
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA; Department of Epidemiology & Population Health, Stanford University School of Medicine, Stanford, CA
| | - Motoki Iwasaki
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Taiki Yamaji
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Hwasun, Korea; Jeonnam Regional Cancer Center, Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Kristan J Aronson
- Department of Public Health Sciences, and Cancer Research Institute, School of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Rachel A Murphy
- Cancer Control Research, BC Cancer, Vancouver, British Columbia, Canada; School of Population and Public Health, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Woon-Puay Koh
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chiea-Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jian-Min Yuan
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA; Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Rajkumar Dorajoo
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore; Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, University of Oxford, Oxford, United Kingdom
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, University of Oxford, Oxford, United Kingdom
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Keum-Ji Jung
- Institute for Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, Korea
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Paul D B Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom; Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Jacques Simard
- Genomics Center, CHU de Québec-Université Laval Research Center, Quebec City, Quebec, Canada
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN
| | | | - Nur Aishah Mohd Taib
- Department of Surgery, Faculty of Medicine, University of Malaya Centre, UM Cancer Research Institute, Kuala Lumpur, Malaysia
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN
| | - Mikael Hartman
- Department of Surgery, University Surgical Cluster, National University Hospital, Singapore, Singapore; Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore; Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom; Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Soo-Hwang Teo
- Cancer Research Malaysia, Selangor, Malaysia; Department of Surgery, Faculty of Medicine, University of Malaya Centre, UM Cancer Research Institute, Kuala Lumpur, Malaysia.
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23
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Huang K, Xiao C, Glass LM, Critchlow CW, Gibson G, Sun J. Machine learning applications for therapeutic tasks with genomics data. PATTERNS (NEW YORK, N.Y.) 2021; 2:100328. [PMID: 34693370 PMCID: PMC8515011 DOI: 10.1016/j.patter.2021.100328] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Thanks to the increasing availability of genomics and other biomedical data, many machine learning algorithms have been proposed for a wide range of therapeutic discovery and development tasks. In this survey, we review the literature on machine learning applications for genomics through the lens of therapeutic development. We investigate the interplay among genomics, compounds, proteins, electronic health records, cellular images, and clinical texts. We identify 22 machine learning in genomics applications that span the whole therapeutics pipeline, from discovering novel targets, personalizing medicine, developing gene-editing tools, all the way to facilitating clinical trials and post-market studies. We also pinpoint seven key challenges in this field with potentials for expansion and impact. This survey examines recent research at the intersection of machine learning, genomics, and therapeutic development.
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Affiliation(s)
- Kexin Huang
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Cao Xiao
- Amplitude, San Francisco, CA 94105, USA
| | - Lucas M. Glass
- Analytics Center of Excellence, IQVIA, Cambridge, MA 02139, USA
| | | | - Greg Gibson
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jimeng Sun
- Computer Science Department and Carle's Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
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24
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Wells QS, Bagheri M, Aday AW, Gupta DK, Shaffer CM, Wei WQ, Vaitinadin NS, Khan SS, Greenland P, Wang TJ, Stein CM, Roden DM, Mosley JD. Polygenic Risk Score to Identify Subclinical Coronary Heart Disease Risk in Young Adults. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2021; 14:e003341. [PMID: 34463132 PMCID: PMC8530876 DOI: 10.1161/circgen.121.003341] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Polygenic risk scores (PRS) may enhance risk stratification for coronary heart disease among young adults. Whether a coronary heart disease PRS improves prediction beyond modifiable risk factors in this population is not known. METHODS Genotyped adults aged 18 to 35 years were selected from the CARDIA study (Coronary Artery Risk Development in Young Adults; n=1132) and FOS (Framingham Offspring Study; n=663). Systolic blood pressure, total and HDL (high-density lipoprotein) cholesterol, triglycerides, smoking, and waist circumference or body mass index were measured at the visit 1 exam of each study, and coronary artery calcium, a measure of coronary atherosclerosis, was assessed at year 15 (CARDIA) or year 30 (FOS). A previously validated PRS for coronary heart disease was computed for each subject. The C statistic and integrated discrimination improvement were used to compare improvements in prediction of elevated coronary artery calcium between models containing the PRS, risk factors, or both. RESULTS There were 62 (5%) and 93 (14%) participants with a coronary artery calcium score >20 (CARDIA) and >300 (FOS), respectively. At these thresholds, the C statistic changes of adding the PRS to a risk factor-based model were 0.015 (0.004-0.028) and 0.020 (0.001-0.039) in CARDIA and FOS, respectively. When adding risk factors to a PRS-based model, the respective changes were 0.070 (0.033-0.109) and 0.051 (0.017-0.079). The integrated discrimination improvement, when adding the PRS to a risk factor model, was 0.027 (-0.006 to 0.054) in CARDIA and 0.039 (0.0005-0.072) in FOS. CONCLUSIONS Among young adults, a PRS improved model discrimination for coronary atherosclerosis, but improvements were smaller than those associated with modifiable risk factors.
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Affiliation(s)
- Quinn S. Wells
- Department of Medicine, Vanderbilt University Medical Center,Department of Pharmacology, Vanderbilt University, Nashville, TN,Department of Biomedical Informatics, Vanderbilt University Medical Center
| | - Minoo Bagheri
- Department of Medicine, Vanderbilt University Medical Center
| | - Aaron W. Aday
- Department of Medicine, Vanderbilt University Medical Center
| | - Deepak K. Gupta
- Department of Medicine, Vanderbilt University Medical Center
| | | | - Wei-Qi Wei
- Department of Medicine, Vanderbilt University Medical Center,Department of Biomedical Informatics, Vanderbilt University Medical Center
| | | | - Sadiya S. Khan
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL,Division of Cardiology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Philip Greenland
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Thomas J. Wang
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX
| | - C. Michael Stein
- Department of Medicine, Vanderbilt University Medical Center,Department of Pharmacology, Vanderbilt University, Nashville, TN
| | - Dan M. Roden
- Department of Medicine, Vanderbilt University Medical Center,Department of Pharmacology, Vanderbilt University, Nashville, TN,Department of Biomedical Informatics, Vanderbilt University Medical Center
| | - Jonathan D. Mosley
- Department of Medicine, Vanderbilt University Medical Center,Department of Biomedical Informatics, Vanderbilt University Medical Center
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25
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Liou L, Kaptoge S, Dennis J, Shah M, Tyrer J, Inouye M, Easton DF, Pharoah PDP. Genomic risk prediction of coronary artery disease in women with breast cancer: a prospective cohort study. Breast Cancer Res 2021; 23:94. [PMID: 34593009 PMCID: PMC8482562 DOI: 10.1186/s13058-021-01465-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/24/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Advancements in cancer therapeutics have resulted in increases in cancer-related survival; however, there is a growing clinical dilemma. The current balancing of survival benefits and future cardiotoxic harms of oncotherapies has resulted in an increased burden of cardiovascular disease in breast cancer survivors. Risk stratification may help address this clinical dilemma. This study is the first to assess the association between a coronary artery disease-specific polygenic risk score and incident coronary artery events in female breast cancer survivors. METHODS We utilized the Studies in Epidemiology and Research in Cancer Heredity prospective cohort involving 12,413 women with breast cancer with genotype information and without a baseline history of cardiovascular disease. Cause-specific hazard ratios for association of the polygenic risk score and incident coronary artery disease (CAD) were obtained using left-truncated Cox regression adjusting for age, genotype array, conventional risk factors such as smoking and body mass index, as well as other sociodemographic, lifestyle, and medical variables. RESULTS Over a median follow-up of 10.3 years (IQR: 16.8) years, 750 incident fatal or non-fatal coronary artery events were recorded. A 1 standard deviation higher polygenic risk score was associated with an adjusted hazard ratio of 1.33 (95% CI 1.20, 1.47) for incident CAD. CONCLUSIONS This study provides evidence that a coronary artery disease-specific polygenic risk score can risk-stratify breast cancer survivors independently of other established cardiovascular risk factors.
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Affiliation(s)
- Lathan Liou
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
| | - Stephen Kaptoge
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Mitul Shah
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Jonathan Tyrer
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Michael Inouye
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Douglas F Easton
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
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26
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Jiang X, Holmes C, McVean G. The impact of age on genetic risk for common diseases. PLoS Genet 2021; 17:e1009723. [PMID: 34437535 PMCID: PMC8389405 DOI: 10.1371/journal.pgen.1009723] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 07/16/2021] [Indexed: 11/19/2022] Open
Abstract
Inherited genetic variation contributes to individual risk for many complex diseases and is increasingly being used for predictive patient stratification. Previous work has shown that genetic factors are not equally relevant to human traits across age and other contexts, though the reasons for such variation are not clear. Here, we introduce methods to infer the form of the longitudinal relationship between genetic relative risk for disease and age and to test whether all genetic risk factors behave similarly. We use a proportional hazards model within an interval-based censoring methodology to estimate age-varying individual variant contributions to genetic relative risk for 24 common diseases within the British ancestry subset of UK Biobank, applying a Bayesian clustering approach to group variants by their relative risk profile over age and permutation tests for age dependency and multiplicity of profiles. We find evidence for age-varying relative risk profiles in nine diseases, including hypertension, skin cancer, atherosclerotic heart disease, hypothyroidism and calculus of gallbladder, several of which show evidence, albeit weak, for multiple distinct profiles of genetic relative risk. The predominant pattern shows genetic risk factors having the greatest relative impact on risk of early disease, with a monotonic decrease over time, at least for the majority of variants, although the magnitude and form of the decrease varies among diseases. As a consequence, for diseases where genetic relative risk decreases over age, genetic risk factors have stronger explanatory power among younger populations, compared to older ones. We show that these patterns cannot be explained by a simple model involving the presence of unobserved covariates such as environmental factors. We discuss possible models that can explain our observations and the implications for genetic risk prediction. The genes we inherit from our parents influence our risk for almost all diseases, from cancer to severe infections. With the explosion of genomic technologies, we are now able to use an individual’s genome to make useful predictions about future disease risk. However, recent work has shown that the predictive value of genetic information varies by context, including age, sex and ethnicity. In this paper we introduce, validate and apply new statistical methods for investigating the relationship between age and the contributions of genetic risk. These methods allow us to ask questions such as whether relative risk is constant over time, precisely how relative risk changes over time and whether all genetic risk factors have similar age profiles. By applying the methods to data from the UK Biobank, a prospective study of 500,000 people, we show that there is a tendency for genetic relative risk to decline with increasing age. We consider a series of possible explanations for the observation and conclude that there must be processes acting that we are currently unaware of, such as distinct phases of life in which genetic risk manifests itself, or interactions between genes and the environment.
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Affiliation(s)
- Xilin Jiang
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
- Department of Statistics, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Chris Holmes
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
- Department of Statistics, University of Oxford, Oxford, United Kingdom
- The Alan Turing Institute, London, United Kingdom
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
- * E-mail:
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27
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Affiliation(s)
- Muin J Khoury
- Office of Genomics and Precision Public Health, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Kathryn E Holt
- Monash University, Melbourne, Australia. .,London School of Hygiene and Tropical Medicine, London, UK.
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28
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Lewis ACF, Green RC. Polygenic risk scores in the clinic: new perspectives needed on familiar ethical issues. Genome Med 2021; 13:14. [PMID: 33509269 PMCID: PMC7844961 DOI: 10.1186/s13073-021-00829-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 01/07/2021] [Indexed: 12/12/2022] Open
Abstract
Clinical use of polygenic risk scores (PRS) will look very different to the more familiar monogenic testing. Here we argue that despite these differences, most of the ethical, legal, and social issues (ELSI) raised in the monogenic setting, such as the relevance of results to family members, the approach to secondary and incidental findings, and the role of expert mediators, continue to be relevant in the polygenic context, albeit in modified form. In addition, PRS will reanimate other old debates. Their use has been proposed both in the practice of clinical medicine and of public health, two contexts with differing norms. In each of these domains, it is unclear what endpoints clinical use of PRS should aim to maximize and under what constraints. Reducing health disparities is a key value for public health, but clinical use of PRS could exacerbate race-based health disparities owing to differences in predictive power across ancestry groups. Finally, PRS will force a reckoning with pre-existing questions concerning biomarkers, namely the relevance of self-reported race, ethnicity and ancestry, and the relationship of risk factors to disease diagnoses. In this Opinion, we argue that despite the parallels to the monogenic setting, new work is urgently needed to gather data, consider normative implications, and develop best practices around this emerging branch of genomics.
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Affiliation(s)
- Anna C F Lewis
- E J Safra Center for Ethics, Harvard University, 124 Mount Auburn, Street, Cambridge, 02138, USA.
| | - Robert C Green
- Brigham and Women's Hospital, 75 Francis St, Boston, MA 02115, USA
- Ariadne Labs, 401 Park Dr 3rd Floor, Boston, MA 02215, USA
- Broad Institute of Harvard and MIT, 415 Main St, Cambridge, MA 02142, USA
- Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA
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