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Study Report - GWAS of bone mineral density in Caucasian subjects (HGVST362)| HGVbaseG2P identifier | HGVST362 | ||||||||||||||||||||
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| Study name | GWAS of bone mineral density in Caucasian subjects | ||||||||||||||||||||
| Phenotype(s) tested | Bone mineral density |
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| Study design | Quantitative trait analysis with replication | ||||||||||||||||||||
| Genotype Platforms |
Affymetrix 342,854 | ||||||||||||||||||||
| Abstract | Abstract Bone mineral density (BMD) measured at femoral neck (FN) is the most important risk phenotype for osteoporosis and has been used as a reference standard for describing osteoporosis. The specific genes influencing FN BMD remain largely unknown. To identify such genes, we first performed a genome-wide association (GWA) analysis for FN BMD in a discovery sample comprising 983 unrelated Caucasian subjects. We then tested those top significant SNPs (175 SNPs with P < 5x10(-4)) for replication in a family-based sample of 2,557 Caucasian subjects. Combing results from these two samples, we found that two genes, parathyroid hormone (PTH) and interleukin 21 receptor (IL21R), achieved consistent association results in both the discovery and replication samples. The PTH gene SNPs, rs9630182, rs2036417 and rs7125774, achieved P values of 1.10x10(-4), 3.24x10(-4), and 3.06x10(-4), respectively, in the discovery sample, P values of 6.50x10(-4), 5.08x10(-3), and 5.68x10(-3), respectively, in the replication sample, and combined P values of 3.98x10(-7), 9.52x10(-6), and 1.05x10(-5), respectively, in the total sample. The IL21R gene SNPs, rs8057551, rs8061992, and rs7199138, achieved P values of 1.51x10(-4), 1.53x10(-4), and 3.88x10(-4), respectively, in the discovery sample, P values of 2.36x10(-3), 6.74x10(-3), and 6.41x10(-3), respectively, in the replication sample, and combined P values of 2.31x10(-6), 8.62x10(-6), and 1.41x10(-5), respectively, in the total sample. The effect size of each SNP was approximately 0.11 SD estimated in the discovery sample. PTH and IL21R both have potential biological functions important to bone metabolism. Overall, our findings provide some new clues to the understanding of the genetic architecture of osteoporosis. | ||||||||||||||||||||
| Submission information |
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| Cross-references |
NHGRI GWAS catalog study annotation for HGVST362 |
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| Background | Not supplied | ||||||||||||||||||||
| Objectives | Not supplied | ||||||||||||||||||||
| Key results | Not supplied | ||||||||||||||||||||
| Conclusions | Not supplied | ||||||||||||||||||||
| Reason for study size | Not supplied | ||||||||||||||||||||
| Study power | Not supplied | ||||||||||||||||||||
| Sources of bias | Not supplied | ||||||||||||||||||||
| Limitations | Not supplied | ||||||||||||||||||||
| Acknowledgements | Not supplied | ||||||||||||||||||||
| Other citations |
Hindorff LA, Sethupathy P, Junkins HA et al.
Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proceedings of the National Academy of Sciences U S A. 2009 May 27
Guo Y, Zhang LS, Yang TL et al.
PTH and IL21R May Underlie Variation of Femoral Neck Bone Mineral Density as Revealed by a Genome-Wide Association Study. Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2009 |
