| BackgroundPsoriasis is a common chronic inflammatory skin disorder,with the basic clinical manifestation of scaly erythema. Its etiology is unclear; the genetic, immunological and environmental components are probably related to the role. Family-based analyses and population-based epidemiological studies have confirmed the genetic basis of psoriasis and suggested a genetic influence upon its age at onset. Earlier linkage analyses, candidate gene study and genome-wide association studies have implicated many genomic regions in the pathogenesis of psoriasis, most of which have not been confirmed. However, these genetic signals identified so far can not fully account for the pathogenesis of psoriasis, suggesting that additional genetic factors may exist. Furthermore, differences in the results of similarly-powered GWAS of psoriasis in Chinese and Caucasian populations suggest the existence of allelic and/or locus heterogeneity between different populations.The completion of Human Genome Project (HGP) and the International HapMap Project (Hap2Map) provides important biological information and analytical tools for susceptibility genes study of complex diseases. GWAS is a powerful and effective method of searching susceptibility genes for complex diseases rising in recent years, and it is considered to be one of the most effective methods of searching susceptibility genes for major diseases by the scientific community.In our initial study, we reported the first large genome-wide association study(GWAS) in a Chinese population to identify susceptibility variants for psoriasis using a two-stage case-control design. In addition to the strong replication for two known susceptibility loci MHC and IL12B in Caucasian population, we identified a new susceptibility locus within the LCE gene cluster(rs4085613) on 1q21.According to our GWAS of psoriasis, systemic lupus erythematosus, vitiligo and other complex diseases, we have set up a complete GWAS platform and statistical method, and have collected a large number of psoriasis and control samples through the established genetic resource bank.Based on our previous GWAS of psoriasis, we performed a six-stage replication study involving 8,312 cases and 12,919 controls from China as well as 3,293 cases, 4,188 controls and 254 nuclear families of European origin to identify additional susceptibility loci for psoriasis in Chinese Han population.ObjectiveTo identify susceptibility loci for psoriasis in Chinese Han population; to determinate the genetic risk factor of psoriasis of Chinese Han; to compare the genetic heterogeneity between Chinese and Caucasian populations.MethodsSamples: Replication 1 (4,610 cases and 5,373 controls) and Replication 2 (2,024 cases and 5,495 controls) samples were recruited from the Chinese Han population through collaboration with multiple hospitals in China. Replication 3 (539 cases and 824 matched controls of Chinese Uygur consisted) obtained from Xinjiang Uygur Autonomous Region in China. Replication 4 (823 cases and 1,840 controls) samples from Germany were provided by Prof Andre Franke. Replication 5 (2,470 cases, 2,348 controls) from the U.S. was provided by Prof. James T. Elder and Replication 6 (254 nuclear families with two siblings with psoriasis) from the U.S. was provided by Prof Anne Bowcock7-9. All the controls and cases for each replication cohort were sampled from the same locality and the same population.SNP selection for replication: We adopted two approaches to select SNPs for replication study. As the first approach, we selected the 21 top SNPs with P<10-5 in the association analysis of 1,139 cases and 1,227 healthy controls. As the second approach, we took advantage of the genotype data from additional 3,496 cases with other immune related diseases by using them as"pseudo-controls", and then selected additional 40 SNPs whose p values of association were less than 10-5 in the genome-wide analysis of 5,173 controls. Genotyping and quality control in GWAS: Our GWAS dataset comprised of 620,901 SNPs and CNV probes genotyped in 1,139 psoriasis cases and 1,132 controls, we added additional genotype data of 95 healthy controls in the current study. The Cochran-Armitage trend test was conducted to calculate the genotype-phenotype association.Genotyping and quality control in the replication study: Genotyping analyses in Replication 1-3 were conducted by using Sequenom MassArray system (San Diego, USA) and Biosystems TaqMan assays (USA). Allele detection was performed using MALDI-TOF MS. The mass spectrograms were analyzed by the MassARRAY TYPER software (Sequenom). Genotyping of Replication 4 and 5 was done using TaqMan assays (Applied Biosystems). Quality control was performed in each dataset separately using PLINK version 1.0534. Genotyping of Replication 6 conducted was performed with the Sequenom MassArray system.Statistical analysis: The quantile-quantile plot and genomic control were calculated using the statistical analysis program R. Case and control samples were subsequently assessed for population outlier and stratification using a principal component analysis (PCA) based approach. After quality control, we analyzed genotype data of SNPs in cases and controls of GWAS stage.We conducted Cochran-Armitage trend test in five replication samples (Replication 1-5) respectively. In combined analysis for multiple studies, the fixed effects model (Mantel–Haenszel) or the random effects model (DerSimonian-Laird) was used. Multiple logistic regression analyses were used to test association patterns. Recombination plots of discovered susceptibility loci were generated using the information from the HapMap project. To test sub-phenotypes specific related SNPs, we used the logistic regression analyses restricted to cases with subclinical phenotypes as the outcome variable. Heterogeneity test (I2 and p-values of Q statistic) between different groups was performed.Results(1) In Replication 1, 61 SNPs were selected in the GWAS dataset, and genotyped in an independent sample of 4,610 cases and 5,373 controls from Chinese Han population. Combined analysis (GWAS and Replication 1) showed that 4 SNPs satisfied the genome-wide significant threshold (P<5.0×10-8): rs3762999 at 5q33.1 (TNIP1/ANXA6), PCombined=1.1×10-12, OR=1.24; rs999556 at 5q33.1 (TNIP1/ANXA6), PCombined=4.3×10-13, OR=1.24; rs2431697 at 5q33.3 (PTTG1), PCombined=1.1×10-8, OR=1.20; rs3751385 at 13q12.11 (GJB2), PCombined=1.7×10-10, OR=0.85.(2)In the joint association analysis using samples from GWAS, Replication 1 and Replication 2, 9 SNPs annotated in 7 loci reached genome-wide significance: rs151823 at 5q15 (ERAP1), PCombined=9.3×10-9; rs999556/rs3762999 at 5q33.1 (TNIP1/ANXA6), PCombined=3.8×10-21 and PCombined=4.6×10-18; rs2431697 at 5q33.3 (PTTG1), PCombined=1.1×10-8; rs10088247/rs7007032 at 8p23.2 (CSMD1), PCombined=4.5×10-9 and PCombined=3.8×10-8; rs3751385 at 13q12.11 (GJB2), PCombined=8.6×10-8 (PGWAS+Replication1=1.7×10-10); rs514315 at 18q22.1 (SERPINB8), PCombined=5.9×10-9; and rs9304742 at 19q13.41 (ZNF816A), PCombined=2.1×10-9.(3)To further assess the impact of the 6 new loci on genetic risk for psoriasis in diverse populations We analyzed genotyping data from four additional cohorts: Chinese Uygur (Replication 3: 539 cases, 824 controls), Germany (Replication 4: 823 cases, 1,840 controls) and the U.S. (Replication 5: 2,470 cases, 2,348 controls and Replication 6: 254 nuclear families described elsewhere7-9). The results revealed that rs3751385 at 13q12.11 (GJB2) and rs151823 at 5q15 (ERAP1) were associated with psoriasis (P=3.6×10-3, OR=0.79 and P=2.9×10-5, OR=0.69, respectively) in the cohorts of German and Chinese Uygur, respectively. Interestingly, ZNF816A showed consistent association among Chinese Han (P=2.1×10-9, OR=0.88), Chinese Uygur (P=1.7×10-3, OR=0.77), and Germans (P=7.9×10-3, OR=0.84), as well a suggestive evidence of association in the U.S. cohort from Replication 5 (P=1.6×10-2, OR=0.90). In the combined analyses of Caucasian population, none of these newly-discovered SNPs conferred significant risk for psoriasis. (4)ZNF816A(rs9304742)and ERAP1(rs151823)gene were preferentially associated with Type I psoriasis in the combined Chinese Han datasets (P=1.5×10-3,OR=0.85;P=6.5×10-3,OR=0.88).ConclusionIn this study, we identified six novel susceptibility loci for psoriasis, and confirmed the loci 5q33.1 previously reported in Chinese Han population. ZNF816A and GJB2 were shown suggestive association with psoriasis in German cohorts. ZNF816A(rs9304742)and ERAP1(rs151823)were preferentially associated with Type I psoriasis in Chinese Han population. Our findings increase the number of genetic risk factors of psoriasis, suggest additional genetic factors that may contribute to its age at onset, and provide insight into genetic heterogeneity of psoriasis across different ethnic populations, which will highlight novel and plausible biological pathways in psoriasis, and thus advance our understanding of the genetic basis of psoriasis... |
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