Multistage genome-wide association meta-analyses identified two new loci for bone mineral density

Abstract

Aiming to identify novel genetic variants and to confirm previously identified genetic variants associated with bone mineral density (BMD), we conducted a three-stage genome-wide association (GWA) meta-analysis in 27 061 study subjects. Stage 1 meta-analyzed seven GWA samples and 11 140 subjects for BMDs at the lumbar spine, hip and femoral neck, followed by a Stage 2 in silico replication of 33 SNPs in 9258 subjects, and by a Stage 3 de novo validation of three SNPs in 6663 subjects. Combining evidence from all the stages, we have identified two novel loci that have not been reported previously at the genome-wide significance (GWS; 5.0 × 10(-8)) level: 14q24.2 (rs227425, P-value 3.98 × 10(-13), SMOC1) in the combined sample of males and females and 21q22.13 (rs170183, P-value 4.15 × 10(-9), CLDN14) in the female-specific sample. The two newly identified SNPs were also significant in the GEnetic Factors for OSteoporosis consortium (GEFOS, n = 32 960) summary results. We have also independently confirmed 13 previously reported loci at the GWS level: 1p36.12 (ZBTB40), 1p31.3 (GPR177), 4p16.3 (FGFRL1), 4q22.1 (MEPE), 5q14.3 (MEF2C), 6q25.1 (C6orf97, ESR1), 7q21.3 (FLJ42280, SHFM1), 7q31.31 (FAM3C, WNT16), 8q24.12 (TNFRSF11B), 11p15.3 (SOX6), 11q13.4 (LRP5), 13q14.11 (AKAP11) and 16q24 (FOXL1). Gene expression analysis in osteogenic cells implied potential functional association of the two candidate genes (SMOC1 and CLDN14) in bone metabolism. Our findings independently confirm previously identified biological pathways underlying bone metabolism and contribute to the discovery of novel pathways, thus providing valuable insights into the intervention and treatment of osteoporosis.

Figure 1.

Diagram workflow of the study design. This study of meta-analysis comprises three stages. In the first stage, seven genome-wide association study (GWAS) samples were analyzed for a meta-analysis. In the second stage, a set of significant SNPs were selected from Stage 1 and subjected to in silico analysis in three additional samples. Novel SNPs significant (or nearly significant) at the GWS level from joint analysis of the above stages were followed up by Stage 3 de novo genotyping in two additional samples. BMD: bone mineral density.

Figure 2.

Stage 1 logarithmic quantile–quantile (QQ) plot of GWAS results. A logarithmic QQ plots for BMDs in the combined sample (left) and in the female-specific sample (right). For each sample, results were plotted for the hip (red), femoral neck (blue) and spine (green) BMDs.

Figure 3.

Forest plots for the two newly identified SNPs. Regression coefficient (beta) and its 95% confidence interval (CI) were presented as un-transformed estimates from individual studies.