Association analyses based on false discovery rate implicate new loci for coronary artery disease

Christopher P. Nelson, Anuj Goel, Adam S. Butterworth, Stavroula Kanoni, Tom R. Webb, Eirini Marouli, Lingyao Zeng, Ioanna Ntalla, Florence Y. Lai, Jemma C. Hopewell, Olga Giannakopoulou, Tao Jiang, Stephen E. Hamby, Emanuele Di Angelantonio, Themistocles L. Assimes, Erwin P. Bottinger, John C. Chambers, Robert Clarke, Colin N.A. Palmer, Richard M. CubbonPatrick Ellinor, Raili Ermel, Evangelos Evangelou, Paul W. Franks, Christopher Grace, Dongfeng Gu, Aroon D. Hingorani, Joanna M.M. Howson, Erik Ingelsson, Adnan Kastrati, Thorsten Kessler, Theodosios Kyriakou, Terho Lehtimäki, Xiangfeng Lu, Yingchang Lu, Winfried März, Ruth McPherson, Andres Metspalu, Mar Pujades-Rodriguez, Arno Ruusalepp, Eric E. Schadt, Amand F. Schmidt, Michael J. Sweeting, Pierre A. Zalloua, Kamal Alghalayini, Bernard D. Keavney, Jaspal S. Kooner, Ruth J.F. Loos, Riyaz S. Patel, Martin K. Rutter, Maciej Tomaszewski, Ioanna Tzoulaki, Eleftheria Zeggini, Jeanette Erdmann, George Dedoussis, Johan L.M. Björkegren, Heribert Schunkert, Martin Farrall, John Danesh, Nilesh J. Samani, Hugh Watkins*, Panos Deloukas

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

264 Citations (Scopus)


Genome-wide association studies (GWAS) in coronary artery disease (CAD) had identified 66 loci at 'genome-wide significance' (P < 5 × 10 '8) at the time of this analysis, but a much larger number of putative loci at a false discovery rate (FDR) of 5% (refs. 1,2,3,4). Here we leverage an interim release of UK Biobank (UKBB) data to evaluate the validity of the FDR approach. We tested a CAD phenotype inclusive of angina (SOFT; n cases = 10,801) as well as a stricter definition without angina (HARD; n cases = 6,482) and selected cases with the former phenotype to conduct a meta-analysis using the two most recent CAD GWAS. This approach identified 13 new loci at genome-wide significance, 12 of which were on our previous list of loci meeting the 5% FDR threshold, thus providing strong support that the remaining loci identified by FDR represent genuine signals. The 304 independent variants associated at 5% FDR in this study explain 21.2% of CAD heritability and identify 243 loci that implicate pathways in blood vessel morphogenesis as well as lipid metabolism, nitric oxide signaling and inflammation.

Original languageEnglish
Pages (from-to)1385-1391
Number of pages7
JournalNature Genetics
Issue number9
Publication statusPublished - 1 Sep 2017
Externally publishedYes

Bibliographical note

Funding Information:
This work was funded by British Heart Foundation (BHF) grants RG/14/5/30893 to P.D. and FS/14/66/31293 to O.G. The work of P.D. forms part of the research themes contributing to the translational research portfolios of the Barts Biomedical Research Centre and Leicester Biomedical Research Centre funded by the UK National Institute for Health Research (NIHR). F.Y.L. and S.E.H. are funded by NIHR. C.P.N., T.R.W. and N.J.S. are funded from BHF, the Transatlantic Networks of Excellence Award (12CVD02) from the Leducq Foundation and EU-FP7/2007-2013 grant HEALTH-F2-2013-601456. N.J.S. is an NIHR Senior Investigator. PROCARDIS was supported by EU-FP6 (LSHM-CT-2007-037273), AstraZeneca, BHF, the Swedish Research Council, the Knut and Alice Wallenberg Foundation, the Swedish Heart-Lung Foundation, the Torsten and Ragnar Söderberg Foundation, Karolinska Institutet, Foundation Strategic Research and the Stockholm County Council (560283). M.F. and H.W. are supported by Wellcome Trust award 090532/Z/09/Z, and M.F., H.W. and T.K. are supported by the BHF Centre of Research Excellence. A.G., H.W. and T.K. are supported by FP7/2007-2013 (HEALTH-F2-2013-601456 (CVGenes@Target)), and A.G. is supported by the Wellcome Trust and the TriPartite Immunometabolism Consortium-Novo Nordisk Foundation (NNF15CC0018486). HPS (ISRCTN48489393) was supported by the Medical Research Council (MRC), BHF, Merck and Co, and Roche Vitamins, Ltd. HPS acknowledges National Blood Service donor and UK-Twin Study controls (Wellcome Trust 07611, FP7/2007-2013). J.C.H. is funded by BHF (FS/14/55/30806). The Mount Sinai BioMe Biobank is supported by the Andrea and Charles Bronfman Philanthropies. The GLACIER Study and P.W.F. are funded by the European Commission (CoG-2015_681742_NASCENT), the Swedish Research Council (Distinguished Young Researchers Award), the Heart-Lung Foundation and the Novo Nordisk Foundation. OHGS studies were funded by the Canadian Institutes of Health Research, the Canada Foundation for Innovation and the Heart & Stroke Foundation of Canada. LURIC was funded from the EU-FP7 (Atheroremo (201668), RiskyCAD (305739), INTERREG IV Oberrhein Program), the European Regional Development Fund (ERDF), Wissenschaftsoffensive TMO and from the German Ministry for Education and Research, project e: AtheroSysMed (01ZX1313A-K). LOLIPOP is supported by the NIHR-BRC Imperial College Healthcare NHS Trust, BHF (SP/04/002), MRC (G0601966, G0700931), the Wellcome Trust (084723/Z/08/Z), NIHR (RP-PG-0407-10371), EU-FP7 (EpiMigrant, 279143) and Action on Hearing Loss (G51). The Helsinki Sudden Death Study was funded by EU-FP7 (201668, AtheroRemo), the Tampere University Foundation, Tampere University Hospital Medical Funds (grants 9M048 and 9N035 for T.L.), the Emil Aaltonen Foundation (T.L.), the Finnish Foundation of Cardiovascular Research (T.L., P.K.), the Pirkanmaa Regional Fund of the Finnish Cultural Foundation, the Yrjö Jahnsson Foundation, the Tampere Tuberculosis Foundation (T.L.), the Signe and Ane Gyllenberg Foundation (T.L.) and the Diabetes Research Foundation of the Finnish Diabetes Association (T.L.).

Funding Information:
M.T. (PG/16/49/32176) and R.C. (FS/12/80/29821) are supported by BHF. E.Z. acknowledges Wellcome Trust funding (098051). H.S. was supported by Deutsche Forschungsgemeinschaft (Sonderforschungsbereich CRC 1123 (B02)). The MRC/BHF Cardiovascular Epidemiology Unit was funded by MRC (G0800270), BHF (SP/09/002), NIHR-BRC Cambridge, the European Research Council (ERC; 268834), EU-FP7 (HEALTH-F2-2012-279233), Pfizer, Merck and Biogen. EPIC-CVD was supported by the University of Cambridge, EU-FP7 (HEALTH-F2-2012-279233), MRC (G0800270), BHF (SP/09/002) and ERC (268834). We thank all EPIC participants and staff and S. Spackman. EGCUT was funded by the Estonian Research Council grant for data management and the EPIC-CVD Coordinating Centre team. (IUT20-60), the Centre of Excellence in Genomics and Translational Medicine (GENTRANSMED), EU structural fund (Archimedes Foundation; 3.2.1001.11-0033), PerMed I and EU2020 (692145 ePerMed). This research was supported by BHF (SP/13/2/30111) and conducted using the UK Biobank Resource (application number 9922).

Publisher Copyright:
© 2017 Nature America, Inc., part of Springer Nature. All rights reserved.


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