| Introduction: Systemic lupus erythematosus (SLE) is a prototypic systemic autoimmune disease, characterized by a diverse array of autoantibody production, complement activation, immune complex deposition, and tissue and organ damage and influenced by both genetic and environmental factors. SLE affects predominantly in women (prevalence ratio of women to men is 9 to 1) and particularly during childbearing years. There are marked disparities in SLE incidence and prevalence worldwide, which varies in different ethnic and geographical populations. The prevalence of SLE ranges from 31 to 70 cases per 100,000 persons among Chinese and 7 to 71 in European populations, and lupus nephritis is more prevalent in Chinese than in Europeans. The ethnic and genetic heterogeneity may contribute to the complexity of its clinical manifestation.Over past two decades, numerous studies were performed and identified multiple genetic factors related to SLE by linkage and association study. In particular, recent four genome-wide association studies (GWAS) of SLE in European populations have identified more than twenty robust susceptibility genes and/or loci. Epidemiological and genetic studies the genetic heterogeneity between ethnic populations has been suggested to play an important role in the susceptibility, development and complexity of clinical manifestation of SLE. Up to today, most linkage, association studies and all GWAS for SLE were performed in European population, which called for GWAS in Chinese populations considering the genetic heterogeneity in SLE.Object: To screen SLE associated SNPs in whole genome and indetify susceptibility genes/loci for SLE in Chinese Han population by using GWAS approach. Methods: All samples in this study were recruited from the Chinese Han population through collaboration with multiple hospitals, which were matched by geographic regions. All cases and controls were separated into three independent samples, in initial stage (1,099 SLE cases and 1,254 controls) were recruited from central China, samples in replication studies were recruited from the central (Replication 1: 1,643 cases and 5,930 controls) and southern (Replication 2: 1,509 cases and 1,120 controls) China. Samples in the initial stage were genotyped by Illumina Human 610-Quard BeadChips. After quality controls, genome wide association analysis were performed to screen SLE associated SNPs, which were replicated in other two case-control samples. The results of previous SLE GWAS in European population were compared with our GWAS.Results: The genome wide association analysis revealed association at three loci: 6p21 (MHC), 2q32.3 (STAT4) and 8p23.1 (BLK) with genome-wide significance (P<5×10-8). In the MHC region, 13 SNPs, all located within the HLA class II region, showed genome-wide significant association (P<5×10-8), and the most significant association was identified at rs9271100 (P=1.42×10?12, OR=1.9). Further conditional association analysis of the 13 SNPs confirmed that there were two independent associations within the region at rs9271100 next to HLA-DRB1 and rs3997854 next to HLA-DQA2(P=2.85×10-8, OR= 0.44).We performed a replication study by genotyping 78 non-MHC SNPs (from 67 loci) in two additional cohorts of Chinese Han (Replication 1 and Replication 2). Twenty-one SNPs within 16 loci were validated with independent supporting evidence for association (P<0.03) from the two replication samples and highly significant evidence in the combined sample that surpassed genome-wide significance (Pcombined<5×10-8). The 16 confirmed susceptibility loci were located at 1q25.1, 2p22.3, 2q32.3, 5q33.1, 6q21, 6q23.3, 7p12.2, 7q11.23, 7q32.1, 8p23.1, 10q11.22, 11q23.3, 11q24.3, 12q24.32, 16p11.2 and 22q11.21 (5.17×10-42≤Pcombined≤2.77×10-8). The associations at the 16 loci were independent of the association within the MHC region, because the associations at these loci remained similar after controlling the genetic effect of rs9271100 and rs3997854 within the MHC region. The associations at 1q25.1, 2q32.3, 6q21, 6q23.3, 7q32.1, 8p23.1 and 22q11.21 were reported by previous GWAS in European populations, implicating susceptibility genes TNFSF4, STAT4, PRDM1-ATG5, TNFAIP3, IRF5,BLK and HIC2-UBE2L3 for SLE, respectively.To identify susceptibility gene underlying each of the 9 novel associations, we investigated the patterns of the recombination and LD around the risk-associated SNPs and the gene(s) located within each region harboring the association. Only one gene was implicated by each of the associations at 2p22.3 (RASGRP3), 7p12.2 (IKZF1), 11q24.3 (ETS1), 12q24.32 (SLC15A4), where a single gene was found within the LD block harboring the association. At 5q33.1, two genes, TNIP1 and GPX3, were found within this locus, but TNIP1 is more plausible as susceptibility gene, due to its important role in modulating cell activation, cytokine signaling and apoptosis. These five novel susceptibility genes provide further supporting evidence for their biological function, such as: immune complex processing (SLC15A4); Toll-like receptor function and type I interferon production (TNIP1); and immune signal transduction in lymphocytes (ETS1, RASGRP3 and IKZF1). For the association at 7q11.23, 10q11.22, 11q23.3 and 16p11.2, there were more than one gene or transcript within the each region. Further fine mapping analysis is required to determine the susceptibility genes underlying these novel association loci for SLE. Interestingly, the association at 16p11.2 located close to the susceptibility locus of ITGAM-ITGAX identified in European population. The association identified in our study with a LD pattern that was different from the one where ITGAM and ITGAX located. Furthermore, the MAFs of 5 reported SNPs within ITGAM-ITGAX locus were very low (<0.01) in Chinese Han population. Further study will be needed to confirm the susceptibility gene within this region.The association evidence for 48 SLE-associated SNPs (from 22 loci) identified by the previous GWAS in European populations was also investigated in our GWAS dataset. These SNPs were summarized into four groups. Group 1 included 13 SNPs confirmed by our GWAS. However, our study did not provide evidence for the associations at the remaining 35 SNPs, which were divided into three groups based on their allele frequencies. Group 2 included 20 SNPs are very rare in Chinese Han population (MAF<5%), especially 14 of them are almost monomorphism. However, all these 20 SNPs are common SNPs in Europeans. Group 3 included 4 SNPs with low population frequency in Chinese Han population (5% |
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