| Background:Atopic dermatitis (AD) is a chronic, relapsing form of inflammatory skin disorder, characterized by a skin itching, skin pantomorphous lesions with exudative tendencies and often accompanied by asthma, allergic rhinitis and elevated serum IgE. Atopic dermatitis is a common skin disease in children and adolescents. The prevalence of atopic dermatitis has doubled or tripled during the past three decades; 15% to 30% of children and 2% to 10% of adults are affected. The etiology and pathogenesis of atopic dermatitis is not clear. The results of a large number of people, family and twin studies show that the genetic factors are the main susceptibility factors to AD, and AD is a polygenic disease.In the past years, researches mainly used genome-wide linkage studies, candidate genes studies or other research strategies to search AD susceptibility genes and some progress was made. However, there are limitations in these studies. For example, there are few microsatellite markers in genome-wide linkage studies and the targeted region is large, which is why it is often difficult to identify the real susceptibility genes. Meanwhile, the genome linkage method is a family-based approach, which identified the diseases susceptibility locus. Whether it can represent the sporadic cases is unknown. Similar to candidate genes studies, researchers often selected candidate genes based on available data which suggest an implication of this gene in the disease. So, there are some limitations in candidate genes study, which could not uncover susceptibility genes of AD with a genome wide coverage.After 2005, completion of the Human Genome Project (HGP) and the Human Genome Haplotype Mapping Project (HapMap) facilitated the rapid development of high-throughput gene genotyping technologies and the reduction of genotyping costs, which made genome-wide association study become possible in large-scale approaches. The method of genome wide SNP analysis is highly effective to uncover disease susceptibility genes. GWAS is one of the most effective ways currently described to identify susceptibility genes of complex diseases. The success of a large number of GWAS shows a strong efficiency to uncover susceptibility genes of complex diseases, which provide new ideas and methods to search susceptibility genes of AD. In 2009, Esparza-Gordillo et. al. performed a large-scale GWAS study in German population and found that 11q13.5 (C11orf30) is a AD susceptibility locus.AD is genetically heterogeneous among different ethnic populations, which is mainly showed by differences in clinical manifestations, the incidence and prevalence rates. However, Many studies were performed in the Caucasian population. It is not clear whether these susceptibility genes/loci have the same function in the Chinese population. Therefore, AD susceptibility genes studies are necessary in the Chinese population. This is the first GWAS realized in the Chinese Han population which identified susceptibility genes of AD in the whole genome.Objective:To screen for AD associated SNPs with genome-wide coverage and identify susceptibility genes/loci for AD, using the GWAS approach in Chinese Han population.Methods:(1) Initial GWAS stage: Samples were genotyped by Illumina Human 610-Quard BeadChips in 1,012 cases and 1,362 controls of Chinese Han.(2) Replication stage:①Replication in the first stage: After quality control and statistical analysis, we selected 67 SNPs for replication in two independent samples of Chinese Han (Northern population: 1,119 cases and 1,203 controls; Southern population: 2,505 cases and 6,762 controls) by using the Sequenom(?) MassARRAY platform.②Replication in the second stage: we further genotyped the most promising 19 (of the 67 selected) SNPs that showed supportive association evidence in the initial validation study in additional 276 controls for the northern Chinese population and 3,956 controls for the southern Chinese population by using Sequenom(?) MassARRAY platform. Then, for statistical analysis we combined GWAS, replication of the first stage and replication of the second stage together and found several SNPs reached genome-wide significance.③Replication in the third stage: the most significant SNPs of the 67 SNPs were further genotyped in German population (1,806 cases and 3,256 controls) by using TaqMan assays.Results:(1) In the first stage replication, we genotyped 67 SNPs in 3624 cases and 7965 controls of Chinese Han population. Then, a joint analysis was carried out in the combined GWAS and replication samples of Chinese Han. The replication analysis revealed 3 SNPs within 2 loci showing association with AD at genome-wide significance (Pcombined<5×10?8): rs3126085/rs11204971 at 1q21.3 (Pcombined=5.75×10-12, OR=0.83; Pcombined=5.02×10-9, OR=0.86, respectively); and rs7701890 at 5q22.1 (Pcombined=4.33×10-8, OR=1.23).(2) In the second stage replication, we selected 19 SNPs from the first stage replication and genotyped in additional 4232 controls. Then a joint analysis was carried out in the combined GWAS and two stage replications samples of Chinese Han. The associations at 7 SNPs located in 3 loci (1q21.3, 5q22.1 and 20q13.33) reached genome-wide significance: rs3126085/rs11204971 at 1q21.3 (Pcombined=5.90×10-12, OR=0.82; Pcombined=1.20×10-10, OR=0.85, respectively); rs7701890/rs10067777/rs13360927/ rs13361382 at 5q22.1 (Pcombined=3.15×10-9, OR=1.24; Pcombined=1.20×10-8, OR=1.24; Pcombined=2.45×10-8, OR=1.22; Pcombined=4.02×10-8, OR=1.22, respectively); rs6010620 at 20q13.33. In addition, one promising SNP (rs2393903 at 10q21.2) showed a genome-wide association barely below significance (Pcombined=1.05×10-7, OR=1.15). (3) In the third replication stage, the 20q13.33 locus also showed evidence for association in the Germany sample (rs6010620, P=2.87×10-5, OR=1.25).Conclusion:This study was the first large scale GWAS of AD to uncover susceptibility genes in the Chinese Han population and successfully constructed the first AD cases-controls database of GWAS. Two new susceptibility genes/loci: 5q22.1(TMEM232 /SLC25A46),20q13.33(TNFRSF6B/ZGPAT) were identified in this study. Furthermore, this study identified a susceptibility locus 1q21.3(FLG) which had been reported previously in European population and Asian population. We also found a suggestive susceptibility locus 10q21.2(ZNF365).In addition, the 20q13.33(TNFRSF6B/ZGPAT) locus also showed evidence for association in the German sample. |
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