ARTICLE Received 28 Apr 2014 | Accepted 27 Oct 2014 | Published 6 Mar 2015 | Updated 20 May 2015 DOI: 10.1038/ncomms6681 OPEN Whole-genome sequence-based analysis of thyroid function Peter N. Taylor1,*, Eleonora Porcu2,3,4,*, Shelby Chew5,*, Purdey J. Campbell5,*, Michela Traglia6, Suzanne J. Brown5, Benjamin H. Mullin5,7,HashemA.Shihab8, Josine Min8, Klaudia Walter9,YasinMemari9, Jie Huang9, Michael R. Barnes10,JohnP.Beilby11,12, Pimphen Charoen13,14,PetrDanecek9, Frank Dudbridge13, Vincenzo Forgetta15,16, Celia Greenwood15,16,17, Elin Grundberg18,19,AndrewD.Johnson20, Jennie Hui11,12,EeM.Lim5,11,ShaneMcCarthy9, Dawn Muddyman9, Vijay Panicker5,JohnR.B.Perry21,22, Jordana T. Bell22, Wei Yuan22, Caroline Relton8, Tom Gaunt8, David Schlessinger23, Goncalo Abecasis4, Francesco Cucca2,3, Gabriela L. Surdulescu22, Wolfram Woltersdorf24, Eleftheria Zeggini9, Hou-Feng Zheng16,25, Daniela Toniolo6,26, Colin M. Dayan1, Silvia Naitza2, John P. Walsh5,7, Tim Spector22, George Davey Smith8, Richard Durbin9,J.BrentRichards15,16,22,25, Serena Sanna2,NicoleSoranzo9, Nicholas J. Timpson8,w, Scott G. Wilson5,7,22,w & the UK10K Consortiumz Normal thyroid function is essential for health, but its genetic architecture remains poorly understood. Here, for the heritable thyroid traits thyrotropin (TSH) and free thyroxine (FT4), we analyse whole-genome sequence data from the UK10K project (N ¼ 2,287). Using additional whole-genome sequence and deeply imputed data sets, we report meta-analysis results for common variants (MAFZ1%) associated with TSH and FT4 (N ¼ 16,335). For TSH, we identify a novel variant in SYN2 (MAF ¼ 23.5%, P ¼ 6.15  10 À 9) and a new independent variant in PDE8B (MAF ¼ 10.4%, P ¼ 5.94  10 À 14). For FT4, we report a low-frequency variant near B4GALT6/ SLC25A52 (MAF ¼ 3.2%, P ¼ 1.27  10 À 9)taggingarareTTR variant (MAF ¼ 0.4%, P ¼ 2.14  10 À 11). All common variants explain Z20% of the variance in TSH and FT4. Analysis of rare variants (MAFo1%) using sequence kernel association testing reveals a novel association with FT4 in NRG1. Our results demonstrate that increased coverage in whole-genome sequence association studies identifies novel variants associated with thyroid function. 1 Thyroid Research Group, Institute of Molecular & Experimental Medicine, Cardiff University School of Medicine, Cardiff University, Cardiff CF14 4XN, UK. 2 Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche, c/o Cittadella Universitaria di Monserrato, Monserrato, Cagliari CA 09042, Italy. 3 Dipartimento di Scienze Biomediche, Universita` di Sassari, Sassari 07100, Italy. 4 Center for Statistical Genetics, Biostatistics Department, University of Michigan, Ann Arbor, Michigan 48109-2029, USA. 5 Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia WA 6009, Australia. 6 Division of Genetics and Cell Biology, San Raffaele Research Institute, Milano 20132, Italy. 7 School of Medicine and Pharmacology, University of Western Australia, Crawley, Western Australia WA 6009, Australia. 8 MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Clifton, Bristol BS8 2BN, UK. 9 TheWellcomeTrust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1HH, Cambridge, UK. 10 William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK. 11 Pathwest Laboratory Medicine WA, Nedlands, Western Australia WA 6009, Australia. 12 School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, Western Australia WA 6009, Australia. 13 Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK. 14 Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok 73170, Thailand. 15 Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada H3T 1E2. 16 Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada H3T 1E2. 17 Departments of Oncology and Human Genetics, McGill University, Montreal, Que´bec, Canada H3A1A5. 18 Department of Human Genetics, McGill University, Montreal, Que´bec, Canada H3A1A5. 19 McGill University and Genome Quebec Innovation Centre, Montreal, Que´bec, Canada H3A 1A5. 20 Cardiovascular Epidemiology and Human Genomics Branch, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, USA. 21 MRC Epidemiology Unit, Institute of Metabolic Science, Box 285, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0QQ, UK. 22 The Department of Twin Research & Genetic Epidemiology, King’s College London, St Thomas’ Campus, Lambeth Palace Road, London SE1 7EH, UK. 23 Laboratory of Genetics, NIA, Baltimore, Maryland 21224, USA. 24 Facharzt fu¨r Laboratoriumsmedizin, Gescha¨ftsfu¨hrer amedes Ost, Halle/Leipzig GmbH, Leipziger Chaussee 191f, 06112 Halle (Saale), Germany. 25 Departments of Medicine & Human Genetics, McGill University, Montreal, Que´bec, Canada H3A1A5. 26 Institute of Molecular Genetics–CNR, Pavia 27100, Italy. * These authors contributed equally to this work. w These authors jointly supervised this work. z Members of the UK10K Consortium are listed at the end of the paper. Correspondence and requests for materials should be addressed to P.N.T. (email: [email protected]) or to S.G.W. (email: [email protected]). NATURE COMMUNICATIONS | 6:5681 | DOI: 10.1038/ncomms6681 | www.nature.com/naturecommunications 1 & 2015 Macmillan Publishers Limited. All rights reserved. ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms6681 hyroid hormones have fundamental but diverse (N ¼ 2,287) analysing up to 8,816,734 markers (Supplementary physiological roles in vertebrate physiology, ranging from Tables 1 and 2; Supplementary Methods), we find associations Tinduction of metamorphosis in amphibians to photo- at two previously described loci for TSH. These are periodic regulation of seasonal breeding in birds1. In humans, NR3C2 (rs11728154; MAF ¼ 21.0%, B ¼ 0.21, s.e. ¼ 0.037, they are essential for adult health and childhood development2,3 P ¼ 8.21  10 À 9; r2 ¼ 0.99 with the previously reported and levothyroxine is one of the commonest drugs prescribed rs10028213) and FOXE1 (rs1877431; MAF ¼ 39.5%, B ¼À0.19, worldwide. Clinically, thyroid function is assessed by measuring s.e. ¼ 0.030, P ¼ 2.29  10 À 10; r2 ¼ 0.99 with the previously circulating concentrations of free thyroxine (FT4) and the reported rs965513). We find one borderline signal (between pituitary hormone thyrotropin (TSH); the complex inverse P ¼ 5.0  10 À 08 and P ¼ 1.17  10 À 08) at a novel locus relationship between them renders TSH the more sensitive FAM222A (rs11067829; MAF ¼ 18.3%, B ¼ 0.210, s.e. ¼ 0.038, marker of thyroid status4. Even small differences in TSH and FT4, P ¼ 3.73  10 À 8; Supplementary Figs 1a and 2; Supplementary within the normal population reference range, are associated with Table 3). No variants show genome-wide significant association a wide range of clinical parameters, including blood pressure, for FT4 (Supplementary Figs 1a and 3). lipids and cardiovascular mortality, as well as obesity, bone In a meta-analysis of the discovery cohorts and five additional mineral density and lifetime cancer risk5. cohorts, we find associations for 13 SNPs at 11 loci for TSH Twin and family studies estimate the heritability of TSH and (N ¼ 16,335) of which 11 loci have been identified previously FT4 as up to 65%6. Genome-wide association studies (GWAS) and 4 SNPs at 4 loci for FT4 (N ¼ 13,651) of which 3 identified common variants associated with TSH and FT47–9;ina have been identified previously (Table 1; Figs 1a–c,2a,b and 3; recent HapMap-based meta-analysis10, we identified 19 loci Supplementary Figs 1b and 3–6). associated with TSH and 4 with FT4. However, these accounted To determine whether our identified associations at established for only 5.6% of the variance in TSH and 2.3% in FT4. Therefore, loci represented previous association signals, we analysed most of the heritability of these important traits remains the linkage disequilibrium (LD) between the strongest unexplained. associated variants from this study and those from our The unidentified genetic component of variance might be previous study10 (Supplementary Table 4). The top variants explained by common variants poorly tagged by markers assessed from loci in both studies were in strong LD (r240.6), apart in previous studies, or those with small effects. However, rarer from MBIP and FOXE1, although these were in strong variants within the minor allele frequency (MAF) spectrum might LD with variants previously associated with TSH by others8. also account for a substantial proportion of the missing Two SNPs associated with TSH in our study are novel, one at heritability as has been proposed for many polygenic traits11. SYN2 (rs310763; MAF ¼ 23.5%, B ¼ 0.082, s.e. ¼ 0.014, These variants, although individually rare (MAFo1%), are P ¼ 6.15  10 À 9; Fig. 1a–c). SYN2 is a member of a family of collectively frequent, and while their effects may be insufficient neuron-specific phosphoproteins involved in the regulation of to produce clear familial aggregation, effect sizes for individual neurotransmitter release with expression in the pituitary and variants are potentially much greater than those observed for hypothalamus (http://biogps.org/#goto=genereport&id=6854). common variants. In addition, a greater understanding