Genome-Wide Association Study in a Lebanese Cohort Confirms PHACTR1 as a Major Determinant of Coronary Artery Stenosis The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Hager, Jörg, Yoichiro Kamatani, Jean-Baptiste Cazier, Sonia Youhanna, Michella Ghassibe-Sabbagh, Daniel E. Platt, Antoine B. Abchee,et al. 2012. Genome-wide association study in a lebanese cohort confirms phactr1 as a major determinant of coronary artery stenosis. PLoS ONE 7(6): e38663. Published Version doi:10.1371/journal.pone.0038663 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:10497276 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Genome-Wide Association Study in a Lebanese Cohort Confirms PHACTR1 as a Major Determinant of Coronary Artery Stenosis Jo¨ rg Hager1, Yoichiro Kamatani2., Jean-Baptiste Cazier3., Sonia Youhanna4, Michella Ghassibe- Sabbagh4, Daniel E. Platt5, Antoine B. Abchee6, Jihane Romanos4, Georges Khazen4, Raed Othman7, Danielle A. Badro4, Marc Haber4, Angelique K. Salloum4, Bouchra Douaihy4, Nabil Shasha7, Samer Kabbani7, Hana Sbeite4, Elie Chammas4, Hamid el Bayeh4, Francis Rousseau8, Diana Zelenika1, Ivo Gut1, Mark Lathrop1, Martin Farrall3, Dominique Gauguier3,9, Pierre A. Zalloua4,10*, the FGENTCARD Consortium" 1 CEA-Genomics Institute, Centre National de Ge´notypage, Evry, France, 2 Centre d’Etude du Polymorphisme Humain, Paris, France, 3 The Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford, United Kingdom, 4 Lebanese American University, School of Medicine, Beirut, Lebanon, 5 Bioinformatics and Pattern Discovery, IBM T. J. Watson Research Centre, New York, New York, United States of America, 6 Department of Internal Medicine, American University of Beirut, Beirut, Lebanon, 7 Division of Cardiology, Rafic Hariri University Hospital, Beirut, Lebanon, 8 IntegraGen SA, Genopole Campus 1 - Genavenir 8, Evry, France, 9 INSERM, UMRS872, Centre de Recherche des Cordeliers, Paris, France, 10 Harvard School of Public Health, Boston, Massachusetts, United States of America Abstract The manifestation of coronary artery disease (CAD) follows a well-choreographed series of events that includes damage of arterial endothelial cells and deposition of lipids in the sub-endothelial layers. Genome-wide association studies (GWAS) of multiple populations with distinctive genetic and lifestyle backgrounds are a crucial step in understanding global CAD pathophysiology. In this study, we report a GWAS on the genetic basis of arterial stenosis as measured by cardiac catheterization in a Lebanese population. The locus of the phosphatase and actin regulator 1 gene (PHACTR1) showed association with coronary stenosis in a discovery experiment with genome wide data in 1,949 individuals (rs9349379, OR = 1.37, p = 1.5761025). The association was replicated in an additional 2,547 individuals (OR = 1.31, p = 8.8561026), leading to genome-wide significant association in a combined analysis (OR = 1.34, p = 8.02610210). Results from this GWAS support a central role of PHACTR1 in CAD susceptibility irrespective of lifestyle and ethnic divergences. This association provides a plausible component for understanding molecular mechanisms involved in the formation of stenosis in cardiac vessels and a potential drug target against CAD. Citation: Hager J, Kamatani Y, Cazier J-B, Youhanna S, Ghassibe-Sabbagh M, et al. (2012) Genome-Wide Association Study in a Lebanese Cohort Confirms PHACTR1 as a Major Determinant of Coronary Artery Stenosis. PLoS ONE 7(6): e38663. doi:10.1371/journal.pone.0038663 Editor: Dan Nebert, University of Cincinnati, United States of America Received November 24, 2011; Accepted May 9, 2012; Published June 20, 2012 Copyright: ß 2012 Hager et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by a grant from the European Commission (FGENTCARD, LSHG-CT-2006-037683). JBC is supported by the Wellcome Trust core award grant number 075491/Z/04. DG held a Wellcome Trust senior fellowship in basic biomedical science (057733). MF is supported by a BHF Clinical Research Excellence award. MGS and PAZ are partly funded by Qatar National Research Fund (QNRF, NPRP 09-215-3-049), JR is partly funded by QNRF (NPRP 4- 230-1-047). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: DEP is an employee of Bioinformatics and Pattern Discovery, IBM, FR is an employee of IntegraGenSA, Ulla Grove Sidelmann is an employee of Novo Nordisk and Frank Bonner is an employee of Metabometrix Ltd. There are no patents, products in development or marketed products to declare. This does not alter the authors’ adherence to all the PLoS ONE policies on sharing data and materials, as detailed online in the guide for authors. * E-mail: [email protected] . These authors contributed equally to this work. "Members of the FGENTCARD Consortium are listed in the Acknowledgments. Introduction [5–7]. A small proportion of CAD cases can be attributed to rare, highly penetrant monogenic effects [8,9], whereas most cases Heart disease is a leading cause of illness, disability and death in result from the cumulative effect of multiple susceptibility alleles industrialized countries, particularly in older people [1,2]. The and environmental factors [5,10–13]. Indeed, recent GWAS have manifestation of CAD follows a well-choreographed series of identified common variants in several novel candidate genes for events that includes the damaging of endothelial cells of the cardiovascular disease, such as the CDKN2A/2B/ANRIL gene arteries and the gradual deposition of lipids in the sub-endothelial cluster on 9p21.3, and PHACTR1 on chromosome 6p24.1 [14– layers [3,4]. CAD is a multifactorial disease, with both acquired 16]. However, differences in lifestyle can have major impact on and inherited components implicated in its etiology [4]. While CAD risk and how these may influence the genetic association is most CAD risk factors can be ameliorated through lifestyle largely unknown. changes, such as diet and exercise, inherited causes, i.e. genetic make-up and family history of the disease, are not modifiable PLoS ONE | www.plosone.org 1 June 2012 | Volume 7 | Issue 6 | e38663 PHACTR1 Is Associated with Coronary Artery Disease Table 1. Association of CAD stenosis categories with conventional risk factors. GWA phase p value1) Replication phase p value1) Total p value1) Stenosis level no mild severe no mild severe p value2) no mild severe Total sample size n = 426 n = 216 n = 1307 n = 458 n = 414 n = 1675 n = 1076 n = 630 n = 2982 Gender (%) ,0.001 ,0.001 ,0.001 ,0.001 Female 184 (43.2) 76 (35.2) 273 (20.9) 232 (50.7) 173 (41.8) 444 (26.5) 416 (38.7) 249 (39.5) 717 (24.0) Male 242 (56.8) 140 (64.8) 1034 (79.1) 226 (49.3) 240 (58.0) 1230 (73.4) 468 (43.5) 380 (60.3) 2264 (75.9) Age (SD) 56.3 (11.7) 62.6 (11.4) 63.6 (10.8) ,0.001 56.1 (10.9 ) 60.2 (11.1 ) 63.2 (10.7 ) ,0.001 0.11 56.2 (11.3) 61.0 (11.3) 63.4 ,0.001 (10.7) History of type 2 70 (16.4) 45 (20.8) 458 (35.0) ,0.001 84 (18.3) 101 (24.4) 610 (36.4) ,0.001 0.2 154 (14.3) 146 (23.2) 1068 ,0.001 Diabetes (%) (35.8) History of 183 (43.0) 117 (54.2) 763 (58.4) ,0.001 250 (54.6) 261 (63.0) 1129 (67.4) ,0.001 ,0.001 433 (40.2) 378 (60.0) 1892 ,0.001 Hypertension (%) (63.4) History of 155 (36.4) 94 (43.5) 685 (52.4) ,0.001 178 (38.9) 190 (45.9) 882 (52.7) ,0.001 0.52 333 (30.9) 284 (45.1) 1567 ,0.001 Hyperlipidemia (52.5) (%) Family history 273 (64.1) 130 (60.2) 928 (71.0) ,0.001 187 (40.8) 166 (40.1) 711 (42.4) 0.626 ,0.001 460 (42.8) 296 (47.0) 1639 ,0.001 of CAD (%) (55.0) Analysis was done in GWA (discovery) and replication phases separately and combined (total). No, mild, and severe correspond to CAD severity categories 1, 2 and 3. 1) p value indicating association of risk factors with CAD categories. 2) p value indicating association of risk factors with different phases. See Methods section for details. doi:10.1371/journal.pone.0038663.t001 Replication of the GWAS results for the most significantly Materials and Methods associated polymorphisms in multiple populations with distinctive genetic and lifestyle backgrounds may provide deeper understanding 1. Study Subjects of the pathophysiology of a multifactorial disease like CAD. The The study subjects consisted of 4,741 individuals who under- current trend in GWA studies relies on genetic analyses of ever went cardiac catheterization following a single consistent and increasingly large numbers of individuals, with meta-analysis of stringent recruitment protocol between August, 2007 and June, cohorts that often are from different phenotypic, genetic and 2009 at several hospitals in Lebanon [21]. Catheterization was environmental backgrounds as well as with diverse ascertainment prompted for myocardial infarction (MI) (13.1%) as diagnosed by schemes [17–19]. A complementary approach lies in the use of smaller electrocardiogram and high troponin levels, unstable angina but phenotypically well-characterized populations to probe genetic (30.3%), or other reasons, such as stable angina, or heart failure, determinants of CAD intermediary phenotypes.