Sequence variants in the PTCH1 gene associate with spine bone mineral density and osteoporotic fractures

Abstract

Bone mineral density (BMD) is a measure of osteoporosis and is useful in evaluating the risk of fracture. In a genome-wide association study of BMD among 20,100 Icelanders, with follow-up in 10,091 subjects of European and East-Asian descent, we found a new BMD locus that harbours the PTCH1 gene, represented by rs28377268 (freq. 11.4-22.6%) that associates with reduced spine BMD (P=1.0 × 10(-11), β=-0.09). We also identified a new spine BMD signal in RSPO3, rs577721086 (freq. 6.8%), that associates with increased spine BMD (P=6.6 × 10(-10), β=0.14). Importantly, both variants associate with osteoporotic fractures and affect expression of the PTCH1 and RSPO3 genes that is in line with their influence on BMD and known biological function of these genes. Additional new BMD signals were also found at the AXIN1 and SOST loci and a new lead SNP at the EN1 locus.

Figure 1. Manhattan plot of discovery genome-wide association study.

The P values (−log₁₀) are plotted against their respective positions on each chromosome. P=5 × 10⁻⁸ is indicated by the horizontal pink line. The plots were created using qqman: an R package for visualizing GWAS results using Q-Q and Manhattan plots. (a) Results for spine BMD. The P values of the associations are given within brackets at each locus: 1p36.12 (P=1.08 × 10⁻⁸), 1p31.3 (P=1.11 × 10⁻¹⁷), 2q14.2 (P=2.28 × 10⁻¹⁰), 3p22.1 (P=1.28 × 10⁻⁹), 4q22.1 (P=1.41 × 10⁻¹²), 6q25.1 (P=1.03 × 10⁻¹⁶), 7q21.3 (P=1.08 × 10⁻⁹), 8q24.12 (P=3.08 × 10⁻¹¹), 9q22.23 (P=2.68 × 10⁻⁹) new locus, 10q22.3 (P=2.12 × 10⁻⁸), 12q13.13 (P=3.47 × 10⁻⁸) and 13q14 (P=1.94 × 10⁻²⁶). (b) Results for hip BMD. The P values of the associations are given within brackets at each locus: 1p36.12 (P=8.93 × 10⁻¹⁰), 1p31.3 (P=8.38 × 10⁻¹¹), 2q14.2 (P=9.36 × 10⁻¹⁴), 3p22.1 (P=3.62 × 10⁻⁸), 5q14.3 (P=2.23 × 10⁻⁹), 6q25.1 (P=7.14 × 10⁻¹²), 7q21.3 (P=1.48 × 10⁻⁹), 8q24.12 (P=2.52 × 10⁻¹⁰), 13q14 (P=3.54 × 10⁻¹⁵), and 17q21.31 (P=3.56 × 10⁻⁸).

Figure 2. Regional association plot for the 9q22.23 PTCH1 locus, potential functional elements and genotype-dependent expression.

(a) Regional association plot for the 9q22.23 PTCH1 locus. P values (−log10) of SNP association with spine BMD in the Icelandic discovery samples are plotted against their positions at the 9q22.23 locus. SNPs are coloured to reflect their linkage disequilibrium (LD) with rs28377268 in the data set. The red line indicates recombination rates, based on the Icelandic recombination map for males and females combined, with the peaks indicating recombination hotspots defining LD blocks in Icelanders. Known genes in the region are shown underneath the plot, taken from the UCSC genes track in the UCSC Genome Browser. All positions are in NCBI Build 36 coordinates. The plot was created using a stand-alone version of LocusZoom software. (b) Functional annotation of potential functional elements in the region. Transcription factor binding sites and DNase hypersensitive areas from the ENCODE data is shown and enhancer and promoter states from the Roadmap consortium. Location of rs28377268 is indicated by a green vertical line. (c) Genotype-dependent gene expression or the PTCH1 gene in blood samples. The P value is derived from regression of the MLR on the carrier status of rs28377268, adjusting for age and sex, and differential cell counts.

Figure 3. Regional association plot for the 6q22.33 RSPO3 locus, potential functional elements and genotype-dependent expression.

(a) Regional association plot for the 6q22.33 RSPO3 locus. P values (−log10) of SNP association with spine BMD in the Icelandic discovery samples are plotted against their positions at the 6q22.33 locus. SNPs are coloured to reflect their linkage disequilibrium (LD) with rs577721086 in the data set. The red line indicates recombination rates, based on the Icelandic recombination map for males and females combined, with the peaks indicating recombination hotspots defining LD blocks in Icelanders. Known genes in the region are shown underneath the plot, taken from the UCSC genes track in the UCSC Genome Browser. All positions are in NCBI Build 36 coordinates. The plot was created using a stand-alone version of LocusZoom software. (b) Functional annotation of potential functional elements in the region. Transcription factor binding sites and DNase hypersensitive areas from the ENCODE data is shown and enhancer and promoter states from the Roadmap consortium. Location of rs577721086 is indicated by a green vertical line. (c) Genotype-dependent gene expression of the RSPO3 gene. P value is derived from regression of the MLR on the carrier status of rs577721086, adjusting for age and sex.