Identification of 153 new loci associated with heel bone mineral density and functional involvement of GPC6 in osteoporosis

John P Kemp, Carolina Medina-Gomez, Vincenzo Forgetta, Nicole M Warrington, Scott E Youlten, Jie Zheng, Celia L Gregson, Elin Grundberg, Katerina Trajanoska, John G Logan, Andrea S Pollard, Penny C Sparkes, Elena J Ghirardello, Victoria D Leitch, Natalie C Butterfield, Davide Komla-Ebri, Anne-Tounsia Adoum, Katharine F Curry, Jacqueline K White, Fiona KussyKeelin M Greenlaw, Changjiang Xu, Nicholas C Harvey, Cyrus Cooper, Celia M T Greenwood, Matthew T Maurano, Stephen Kaptoge, Fernando Rivadeneira, Jonathan H Tobias, Peter I Croucher, Cheryl L Ackert-Bicknell, J H Duncan Bassett, J Brent Richards, David M Evans

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Abstract

Osteoporosis is a common disease diagnosed primarily by measurement of bone mineral density (BMD). We undertook a genome-wide association study (GWAS) in 142,487 individuals from the UK Biobank to identify loci associated with BMD as estimated by quantitative ultrasound of the heel. We identified 307 conditionally independent single-nucleotide polymorphisms (SNPs) that attained genome-wide significance at 203 loci, explaining approximately 12% of the phenotypic variance. These included 153 previously unreported loci, and several rare variants with large effect sizes. To investigate the underlying mechanisms, we undertook (1) bioinformatic, functional genomic annotation and human osteoblast expression studies; (2) gene-function prediction; (3) skeletal phenotyping of 120 knockout mice with deletions of genes adjacent to lead independent SNPs; and (4) analysis of gene expression in mouse osteoblasts, osteocytes and osteoclasts. The results implicate GPC6 as a novel determinant of BMD, and also identify abnormal skeletal phenotypes in knockout mice associated with a further 100 prioritized genes.

Original languageEnglish
Pages (from-to)1468–1475
Number of pages15
JournalNature Genetics
Volume49
Early online date4 Sep 2017
DOIs
Publication statusPublished - 1 Oct 2017

Keywords

  • Bone mineral density
  • Genome-wide association
  • GPC6
  • Osteoporosis
  • UK Biobank
  • Ultrasound

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    MRC UoB UNITE Unit - programme 4

    Davey Smith, G. & Evans, D.

    1/06/131/04/18

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    Cite this

    Kemp, J. P., Medina-Gomez, C., Forgetta, V., Warrington, N. M., Youlten, S. E., Zheng, J., Gregson, C. L., Grundberg, E., Trajanoska, K., Logan, J. G., Pollard, A. S., Sparkes, P. C., Ghirardello, E. J., Leitch, V. D., Butterfield, N. C., Komla-Ebri, D., Adoum, A-T., Curry, K. F., White, J. K., ... Evans, D. M. (2017). Identification of 153 new loci associated with heel bone mineral density and functional involvement of GPC6 in osteoporosis. Nature Genetics, 49, 1468–1475. https://doi.org/10.1038/ng.3949