Systematic analysis of polymorphisms and linkage dsequilibrium in the osteoporosis susceptibility genes

为了明确骨质疏松易感基因候选基因位点多态性的基因组连锁，我们通过对数千个人群进行大规模单核苷酸多态性（SNP）关联研究的原始调查，选择了12个候选基因位点。通过提取分布在某些位点上的多个有用的snp，我们分析了这些位点的连锁不平衡（LD）。分析的基因座为维生素D结合蛋白基因（DBP）、白介素-1受体相关激酶1基因（IRAK1）、肿瘤坏死因子受体相关因子相互作用蛋白基因（I-TRAF）、促性腺激素释放激素基因（GnRH）、谷氨酰胺肽环转移酶（QPCT）、低密度脂蛋白受体相关蛋白5基因（LRP5）、黑素原基因（POMC）、白血病抑制因子受体基因（LIFR）、内缩素1基因（ADD1）、骨形态发生蛋白8基因（BMP8）、热休克蛋白1A基因（HSPAIA）和破骨细胞相关受体基因（OSCAR）。由于存在邻近的重复基因（如BMP8），对某些区域的分析比较困难，而长距离PCR通常可以解决这个问题。通过对LD、D′、r2等指标的分析，我们一般在每个基因中检测到单个LD块覆盖整个基因座，但在LRP5等基因座中观察到多个LD块。通过澄清这些位点中LD的范围和程度，并在每个LD块中选择具有代表性的标签snp，我们继续使用更大的受试者群体进行关联研究，以了解这些候选基因多态性对骨量测定的遗传贡献。

To clarify the genomic linkage of polymorphisms in the candidate gene loci of osteoporosis susceptibility genes, 12 candidate gene loci were selected through our original investigation of large scale single nucleotide polymorphism (SNP) association study using thousands of population subjects. By extracting multiple useful SNPs distributing throughout and beyond the loci in some cases, we analyzed linkage disequilibrium (LD) of those loci. Analyzed loci were the vitamin D binding protein gene (DBP), interleukin-1 receptor associated kinase 1 gene (IRAK1), tumor necrosis factor receptor-associated factor interacting protein gene (I-TRAF), gonadotropin releasing hormone gene (GnRH), glutaminyl-peptide cyclotransferase (QPCT), low density lipoprotein receptor-related protein 5 gene (LRP5), proopiomelanocortin gene (POMC), leukemia inhibitory factor receptor gene (LIFR), adducin 1 gene (ADD1), bone morphogenetic protein 8 gene (BMP8), heat shock protein 1A gene (HSPAIA), and the osteoclast-associated receptor gene (OSCAR). Analyses on some regions was difficult because of the existence of neighboring duplicated genes, like BMP8, however long range PCR usually solved the problem. By analyzing the indices of LD, D' and r2, we generally detected a single LD block covering the entire locus in each gene, however in several gene loci like LRP5 locus multiple block was observed. By clarifying the extent and the degree of LD in those loci, and selecting representative tag-SNPs in each LD blocks, we continued the association study using larger subject groups, to understand the genetic contribution of these candidate gene polymorphisms for bone mass determination.