Phenotypic Dissection of Bone Mineral Density Reveals Skeletal Site Specificity and Facilitates the Identification of Novel Loci in the Genetic Regulation of Bone Mass Attainment John P. Kemp 1,2. *, Carolina Medina-Gomez 3,4,5,6. , Karol Estrada 7 , Beate St Pourcain 1,8,9 , Denise H. M. Heppe 4,5,10 , Nicole M. Warrington 2 , Ling Oei 3,5,6 , Susan M. Ring 1 , Claudia J. Kruithof 4,5 , Nicholas J. Timpson 1 , Lisa E. Wolber 11 , Sjur Reppe 12 , Kaare Gautvik 12,13 , Elin Grundberg 14,15 , Bing Ge 15 , Bram van der Eerden 3 , Jeroen van de Peppel 3 , Matthew A. Hibbs 16,17 , Cheryl L. Ackert-Bicknell 17 , Kwangbom Choi 17 , Daniel L. Koller 18 , Michael J. Econs 18,19 , Frances M. K. Williams 11 , Tatiana Foroud 18 , M. Carola Zillikens 3,6 , Claes Ohlsson 20 , Albert Hofman 4,5,6 , Andre ´ G. Uitterlinden 3,4,5,6 , George Davey Smith 1 , Vincent W. V. Jaddoe 4,5,10 , Jonathan H. Tobias 21" , Fernando Rivadeneira 3,4,5,6" , David M. Evans 1,2" 1 MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom, 2 University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia, 3 Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands, 4 The Generation R Study Group, Erasmus University Medical Center, Rotterdam, The Netherlands, 5 Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands, 6 Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), The Netherlands, 7 Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America, 8 School of Oral and Dental Sciences, University of Bristol, Bristol, United Kingdom, 9 School of Experimental Psychology, University of Bristol, Bristol, United Kingdom, 10 Department of Paediatrics, Erasmus University Medical Center, Rotterdam, The Netherlands, 11 Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom, 12 Department of Medical Biochemistry, Oslo University Hospital, Ullevaal, Oslo, Norway, 13 Department of Medical Biochemistry, Oslo Deacon Hospital, Oslo, Norway, 14 Department of Human Genetics, McGill University, Montre ´al, Canada, 15 McGill University and Genome Que ´ bec Innovation Centre, Montre ´ al, Canada, 16 Department of Computer Science, Trinity University, San Antonio, Texas, United States of America, 17 The Jackson Laboratory, Bar Harbor, Maine, United States of America, 18 Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America, 19 Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America, 20 Center for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden, 21 School of Clinical Sciences, University of Bristol, Bristol, United Kingdom Abstract Heritability of bone mineral density (BMD) varies across skeletal sites, reflecting different relative contributions of genetic and environmental influences. To quantify the degree to which common genetic variants tag and environmental factors influence BMD, at different sites, we estimated the genetic (r g ) and residual (r e ) correlations between BMD measured at the upper limbs (UL-BMD), lower limbs (LL-BMD) and skull (SK-BMD), using total-body DXA scans of ,4,890 participants recruited by the Avon Longitudinal Study of Parents and their Children (ALSPAC). Point estimates of r g indicated that appendicular sites have a greater proportion of shared genetic architecture (LL-/UL-BMD r g = 0.78) between them, than with the skull (UL-/SK-BMD r g = 0.58 and LL-/SK-BMD r g = 0.43). Likewise, the residual correlation between BMD at appendicular sites (r e = 0.55) was higher than the residual correlation between SK-BMD and BMD at appendicular sites (r e = 0.20–0.24). To explore the basis for the observed differences in r g and r e , genome-wide association meta-analyses were performed (n,9,395), combining data from ALSPAC and the Generation R Study identifying 15 independent signals from 13 loci associated at genome-wide significant level across different skeletal regions. Results suggested that previously identified BMD-associated variants may exert site-specific effects (i.e. differ in the strength of their association and magnitude of effect across different skeletal sites). In particular, variants at CPED1 exerted a larger influence on SK-BMD and UL-BMD when compared to LL-BMD (P = 2.01 6 10 237 ), whilst variants at WNT16 influenced UL-BMD to a greater degree when compared to SK- and LL-BMD (P = 2.31 6 10 214 ). In addition, we report a novel association between RIN3 (previously associated with Paget’s disease) and LL-BMD (rs754388: b = 0.13, SE = 0.02, P = 1.4 6 10 210 ). Our results suggest that BMD at different skeletal sites is under a mixture of shared and specific genetic and environmental influences. Allowing for these differences by performing genome-wide association at different skeletal sites may help uncover new genetic influences on BMD. Citation: Kemp JP, Medina-Gomez C, Estrada K, St Pourcain B, Heppe DHM, et al. (2014) Phenotypic Dissection of Bone Mineral Density Reveals Skeletal Site Specificity and Facilitates the Identification of Novel Loci in the Genetic Regulation of Bone Mass Attainment. PLoS Genet 10(6): e1004423. doi:10.1371/journal. pgen.1004423 Editor: Scott M. Williams, Dartmouth College, United States of America Received October 22, 2013; Accepted April 14, 2014; Published June 19, 2014 Copyright: ß 2014 Kemp 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. PLOS Genetics | www.plosgenetics.org 1 June 2014 | Volume 10 | Issue 6 | e1004423