Robust and comprehensive analysis of 20 osteoporosis candidate genes by very high-density single-nucleotide polymorphism screen among 405 white nuclear families identified significant association and gene-gene interaction

Abstract

Many "novel" osteoporosis candidate genes have been proposed in recent years. To advance our knowledge of their roles in osteoporosis, we screened 20 such genes using a set of high-density SNPs in a large family-based study. Our efforts led to the prioritization of those osteoporosis genes and the detection of gene-gene interactions.

Introduction: We performed large-scale family-based association analyses of 20 novel osteoporosis candidate genes using 277 single nucleotide polymorphisms (SNPs) for the quantitative trait BMD variation and the qualitative trait osteoporosis (OP) at three clinically important skeletal sites: spine, hip, and ultradistal radius (UD).

Materials and methods: One thousand eight hundred seventy-three subjects from 405 white nuclear families were genotyped and analyzed with an average density of one SNP per 4 kb across the 20 genes. We conducted association analyses by SNP- and haplotype-based family-based association test (FBAT) and performed gene-gene interaction analyses using multianalytic approaches such as multifactor-dimensionality reduction (MDR) and conditional logistic regression.

Results and conclusions: We detected four genes (DBP, LRP5, CYP17, and RANK) that showed highly suggestive associations (10,000-permutation derived empirical global p < or = 0.01) with spine BMD/OP; four genes (CYP19, RANK, RANKL, and CYP17) highly suggestive for hip BMD/OP; and four genes (CYP19, BMP2, RANK, and TNFR2) highly suggestive for UD BMD/OP. The associations between BMP2 with UD BMD and those between RANK with OP at the spine, hip, and UD also met the experiment-wide stringent criterion (empirical global p < or = 0.0007). Sex-stratified analyses further showed that some of the significant associations in the total sample were driven by either male or female subjects. In addition, we identified and validated a two-locus gene-gene interaction model involving GCR and ESR2, for which prior biological evidence exists. Our results suggested the prioritization of osteoporosis candidate genes from among the many proposed in recent years and revealed the significant gene-gene interaction effects influencing osteoporosis risk.

FIG. 1

Association results for spine BMD using single SNP markers and haplotype windows. Empirical global p values from HBAT analyses are calculated after 10,000 permutations. Triangles, SNP results; bold lines, 4-SNP haplotype sliding window results. Any suggestive significant results (p ≤ 0.05) were marked with associated genes.

FIG. 2

Association results for hip BMD using single SNP markers and haplotype windows. Empirical global p values from HBAT analyses are calculated after 10,000 permutations. Triangles, SNP results; bold lines, 4-SNP haplotype sliding window results. Any suggestive significant results (p ≤ 0.05) were marked with associated genes.

FIG. 3

Association results for UD BMD using single SNP markers and haplotype windows. Empirical global p values from HBAT analyses are calculated after 10,000 permutations. Triangles, SNP results; bold lines, 4-SNP haplotype sliding window results. Any suggestive significant results (p ≤ 0.05) were marked with associated genes.

FIG. 4

Gene-specific results for BMD variation. Empirical global p values are plotted. For spine BMD: SNP, diamond; haplotype window, dotted line; haplotype, dotted line with arrow. For hip BMD: SNP, triangle; haplotype window, solid line; haplotype, solid line with arrow. For UD BMD: SNP, circle; haplotype window, long-dashed line; haplotype, long-dashed line with arrow. Only haplotypes with suggestive evidence (−log p ≥ 1.3, i.e., p ≤ 0.05) or haplotypes showing best signals (if no significant haplotypes exist) were plotted. x-axes were in the unit of megabases; vertical bars represent exons.

FIG. 4

Gene-specific results for BMD variation. Empirical global p values are plotted. For spine BMD: SNP, diamond; haplotype window, dotted line; haplotype, dotted line with arrow. For hip BMD: SNP, triangle; haplotype window, solid line; haplotype, solid line with arrow. For UD BMD: SNP, circle; haplotype window, long-dashed line; haplotype, long-dashed line with arrow. Only haplotypes with suggestive evidence (−log p ≥ 1.3, i.e., p ≤ 0.05) or haplotypes showing best signals (if no significant haplotypes exist) were plotted. x-axes were in the unit of megabases; vertical bars represent exons.

FIG. 4

Gene-specific results for BMD variation. Empirical global p values are plotted. For spine BMD: SNP, diamond; haplotype window, dotted line; haplotype, dotted line with arrow. For hip BMD: SNP, triangle; haplotype window, solid line; haplotype, solid line with arrow. For UD BMD: SNP, circle; haplotype window, long-dashed line; haplotype, long-dashed line with arrow. Only haplotypes with suggestive evidence (−log p ≥ 1.3, i.e., p ≤ 0.05) or haplotypes showing best signals (if no significant haplotypes exist) were plotted. x-axes were in the unit of megabases; vertical bars represent exons.

FIG. 4

Gene-specific results for BMD variation. Empirical global p values are plotted. For spine BMD: SNP, diamond; haplotype window, dotted line; haplotype, dotted line with arrow. For hip BMD: SNP, triangle; haplotype window, solid line; haplotype, solid line with arrow. For UD BMD: SNP, circle; haplotype window, long-dashed line; haplotype, long-dashed line with arrow. Only haplotypes with suggestive evidence (−log p ≥ 1.3, i.e., p ≤ 0.05) or haplotypes showing best signals (if no significant haplotypes exist) were plotted. x-axes were in the unit of megabases; vertical bars represent exons.