Hamada Daisuke, Takata Yoichiro, Osabe Dai, Nomura Kyoko, Shinohara Syuichi, Egawa Hiroshi, Nakano Syunji, Shinomiya Fumio, Scafe Charles R, Reeve Vincent M, Miyamoto Tatsuro, Moritani Maki, Kunika Kiyoshi, Inoue Hiroshi, Yasui Natsuo, Itakura Mitsuo
Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan.
Arthritis Rheum. 2005 May;52(5):1371-80. doi: 10.1002/art.21013.
To identify rheumatoid arthritis (RA) susceptibility genes in a Japanese population by conducting a large-scale case-control association analysis and linkage disequilibrium (LD) mapping on chromosome 7q31-34, a candidate susceptibility locus identified in a preliminary genome-wide scan in 53 Japanese families, using single-nucleotide polymorphisms (SNPs).
We prepared 728 dense, evenly spaced SNPs with a minor allele frequency >0.15 in each gene locus on chromosome 7q31-34. Using these SNPs, a 2-stage case-control analysis was performed on 760 RA patients (157 men and 603 women) and 806 non-RA controls (189 men and 617 women). Haplotypes and LD mapping results were assessed based on SNP genotypes in 380 controls.
Forty-eight SNPs showed allele associations (P < 0.05) in the first set of DNA samples (380 RA cases and 380 non-RA controls; first-stage analysis). For 4 of the SNPs in the SEC8L1 gene, the association was replicated (P < 0.05) in the second, independent set of DNA samples (an additional 380 RA cases and 380 non-RA controls; second-stage analysis). When data from the 2 groups were combined, the most significant allele association was observed with SNP 441, an intronic SNP of the SEC8L1 gene (P = 0.000059). The SEC8L1 SNPs with significant allele associations were all located in a single conserved LD block (block 4). Haplotype analysis revealed the disease-risk (P = 0.0015) and disease-protective (P = 0.0000062) haplotypes. Resequencing of coding exons within block 4 did not identify any nonsynonymous SNPs. Real-time quantitative polymerase chain reaction revealed that SEC8L1 was expressed ubiquitously in human tissues, including fibroblast-like synoviocytes from RA patients.
Our locus-wide association and LD analyses identified intronic SNPs and haplotypes in the SEC8L1 gene that are strongly associated with RA. We propose that SEC8L1, which encodes a component of the exocyst complex, is a candidate susceptibility gene for RA in the Japanese population.
通过对53个日本家庭进行初步全基因组扫描确定的候选易感位点7q31 - 34染色体上进行大规模病例对照关联分析和连锁不平衡（LD）图谱分析，利用单核苷酸多态性（SNP）来鉴定日本人群中的类风湿关节炎（RA）易感基因。
我们在7q31 - 34染色体上的每个基因座制备了728个密度高、间隔均匀且次要等位基因频率>0.15的SNP。使用这些SNP，对760例RA患者（157名男性和603名女性）和806名非RA对照（189名男性和617名女性）进行了两阶段病例对照分析。基于380名对照的SNP基因型评估单倍型和LD图谱结果。
在第一组DNA样本（380例RA病例和380例非RA对照；第一阶段分析）中，48个SNP显示出等位基因关联（P < 0.05）。对于SEC8L1基因中的4个SNP，该关联在第二组独立的DNA样本（另外380例RA病例和380例非RA对照；第二阶段分析）中得到重复（P < 0.05）。当两组数据合并时，观察到与SEC8L1基因内含子SNP 441的等位基因关联最为显著（P = 0.000059）。具有显著等位基因关联的SEC8L1 SNP均位于单个保守的LD块（块4）中。单倍型分析揭示了疾病风险（P = 0.0015）和疾病保护（P = 0.0000062）单倍型。对块4内的编码外显子进行重测序未发现任何非同义SNP。实时定量聚合酶链反应显示SEC8L1在包括RA患者的成纤维样滑膜细胞在内的人体组织中普遍表达。
我们的全基因座关联和LD分析确定了SEC8L1基因中的内含子SNP和单倍型与RA密切相关。我们提出，编码外囊复合体成分的SEC8L1是日本人群中RA的候选易感基因。
