六个新的寻常型银屑病易感基因的鉴定
发布时间：2018-08-02 18:58
【摘要】： 研究背景 银屑病是一种临床常见的以红斑鳞屑为基本表现的慢性炎症性皮肤疾病。该病发病原因不清,可能和遗传、免疫以及各种环境因素共同作用有关。家系研究及人群流行病学研究证实了银屑病的遗传学发病基础,早期的连锁分析、候选基因研究及全基因组关联分析研究(Genome-Wide Association Study ,GWAS)发现银屑病的多个易感基因位点,其中多数未能被证实。目前发现的遗传信号不能完全解释银屑病的发病机制,提示可能尚有其他遗传因素的存在。此外,中国和高加索人群GWAS结果的差异提示该病在不同人群中的易感等位基因或位点存在异质性。 人类基因组计划(Human Genome Project,HGP)和国际单体型图计划(International HapMap Project ,Hap2Map)的完成,为复杂疾病的易感基因研究提供了重要的生物信息和分析工具。GWAS是近几年兴起的一种搜寻复杂疾病易感基因的强效有力的方法,被科学界认为是目前最为有效的搜寻重大疾病易感基因的研究方法之一。 本研究小组前期首次对中国人群银屑病易感基因进行了大规模GWAS研究。除证实高加索人群两个已知的易感位点:MHC和IL12B,还发现了位于染色体1q21上一个新的银屑病易感位点LCE基因簇。通过银屑病、系统性红斑狼疮、白癜风等多个皮肤复杂疾病易感基因的GWAS研究,目前已建立了较完整的复杂疾病易感基因研究的GWAS操作平台和统计分析方法,并通过建立的遗传资源库收集了大量的银屑病和对照样本。 本研究是在前期银屑病易感基因GWAS研究的基础上,采取六阶段验证方法,对来自中国的8,312个病例和12,919个对照进行验证试验,同时对来自欧洲的3,293个病例和4,188个正常对照以及254个核心家系进行验证,以进一步搜寻汉族人银屑病其他可能的易感基因位点。 目的 进一步搜寻中国汉族人银屑病相关的易感基因位点;确定汉族人相关的银屑病遗传危险因素;比较中国人群与高加索人群的银屑病遗传学异质性。 方法 (一)样本来源: 验证1(4,610个病例和5,373名对照)和验证2(2,024例患者和5,495名对照)的样本来源于全国多家合作医院收集的汉族人群。验证3(539名病例和824名健康对照)的样本,来自新疆维吾尔自治区的维吾尔族人群。验证4(823个病例和1,840名对照)的样本来自德国。验证5(2,470名患者和2,348名对照)的样本及验证6的254个同胞对核心家系来自美国。每一阶段的验证样本中,病例和对照均来源于同一地区和同一种族。 (二)验证阶段SNP的选取: 本研究采用了两种挑选SNP的方法。第一种方法,在1,139病例和1,227对照的关联分析结果中挑选了21个P10-5的SNP。第二种方法:将3496例其他自身免疫性相关疾病作为拟对照,同1,227例正常对照一起共5173例,作为共同的对照标本,统计分析,参与选点,从中选取P10-5的40个SNP参与进一步验证。最终选取61个SNP参与验证实验。 验证2共有35个SNP被选取分型,其中包括:1)从验证1中挑选的20个P 0.05的SNP; 2)从高加索人群中报道银屑病相关的8个位点中选取的15个SNP。 (三)GWAS中基因分型和质量控制: 基于前期GWAS(包括1,139银屑病患者和1,132对照的620,901 SNP和CNV探针)的分型数据,加入95例新的正常对照基因分型数据以解释数据质控。采用Cochran-Armitage trend检验法计算基因型-表型的关联性。 (四)验证阶段的基因分型和质量控制: 验证1-3采用Sequenom MassArray系统(San Diego, USA)和Biosystems TaqMan assays (USA)进行基因分型。MALDI-TOF MS检测等位基因。MassARRAY TYPER软件(Sequenom公司)完成质谱图分析。 验证4和5的基因分型采用TaqMan assays (Applied Biosystems)完成。数据的质量控制通过PLINK 1.05完成。 验证6的标本运用Sequenom MassArray system完成。 (五)统计分析: 采用统计分析软件R绘制染色体图和Q-Q图。PCA分析法评估有异常偏离样本及人群分层存在。病例和对照进行PCA分析,经过质量控制后,SNPs分型数据在GWAS阶段进行分析。 在验证1-5中,分别采用Cochran-Armitage trend检验计算其关联性。在多阶段验证研究的合并分析中,采用固定效应模型或随机效应模型分析进行分析。家系的关联研究采用半似然函数进行病例对照关联分析。 多重logistic回归分析用于检测区域内的信号的独立性。 在病例中采用将临床亚型作为输出变量的logistic回归分析检测与临床亚型有关的SNP。 采用异质性检验方法检测不同组间的遗传异质性。 结果 一、第一阶段验证中,在汉族人群的4,610例患者和5,373例对照中对61个SNP进行基因分型。综合GWAS和验证1的结果显示其中的4个SNP达到了全基因组显著性标准(P5.0×10-8),这四个SNP分别是位于5q33.1(TNIP1/ANXA6)区域的rs3762999和rs999556(P=1.1×10-12,OR=1.24;P=4.3×10-13,OR=1.24);位于5q33.3(PTTG1)区域的rs2431697(P=1.1×10-8,OR=1.20)和位于13q12.11(GJB2)区域的rs3751385(P=1.7×10-10,OR=1.18)。 二、对GWAS,验证1和验证2的综合分析结果中发现7个区域的9个SNP达到了全基因组显著性水平,它们分别是:位于5q15 (ERAP1)的rs151823,PCombined=9.3×10-9;位于5q33.1(TNIP1/ANXA6)的rs999556和rs3762999, PCombined分别是3.8×10-21和4.6×10-18;位于5q33.3 (PTTG1)的rs2431697,PCombined=1.1×10-8;位于8p23.2 (CSMD1)的rs10088247和rs7007032,PCombined分别是4.5×10-9和3.8×10-8;位于13q12.11 (GJB2)的rs3751385,PCombined=8.6×10-8(PGWAS+Replication1=1.7×10-10);位于18q22.1 (SERPINB8)的rs514315,PCombined=5.9×10-9;以及位于19q13.41 (ZNF816A)的rs9304742,PCombined=2.1×10-9。 三、对维吾尔人群(验证3)、德国人群(验证4)、美国人群(验证5)及254个核心家系(验证6)的分型数据进行统计分析,结果显示位于13q12.11 (GJB2)的rs3751385以及位于5q15 (ERAP1)的rs151823分别在德国人群及中国维吾尔人群中与银屑病相关(P=3.6×10-3,OR=1.26;P=2.9×10-5,OR=1.45)。ZNF816A在汉族人群(P=2.1×10-9,OR=0.88)、中国维吾尔人群(P=1.7×10-3,OR=0.77)和德国人群中(P=7.9×10-3,OR=0.84)均显示一致的关联性,在美国人群(验证5)中提示关联性证据(P=1.6×10-2,OR=0.90)。对高加索人群(验证4和5)的合并分析,显示新发现的SNP位点在高加索人群中均与银屑病不相关。 四、汉族人合并分型数据提示ZNF816A(rs9304742)和ERAP1(rs151823)可能与早发型银屑病有关联性(P=1.5×10-3,OR=0.85;P=6.5×10-3,OR=0.88)。 结论 在中国汉族人群中发现了六个新的银屑病易感位点,同时证实了高加索人群报道的易感位点5q33.1也在汉族人群中发挥作用。ZNF816A和GJB2在德国人群中与银屑病相关联。ERAP1和ZNF816A与汉族人I型银屑病的发生有显著的相关性。研究结果丰富了银屑病的遗传危险因素,提示遗传因素可能导致该病发病年龄的差异,并发现银屑病遗传易感因素在中国人与欧洲人群中存在异质性,为银屑病的发病机制提供了新的潜在的生物学证据。
[Abstract]:Research background
Psoriasis is a common chronic inflammatory skin disease characterized by erythema scales. The cause of the disease is not clear and may be associated with the combination of genetic, immune and various environmental factors. Family studies and population epidemiological studies have confirmed the genetic basis of psoriasis, early linkage analysis, candidate bases. Genome-Wide Association Study (GWAS) has found multiple susceptibility loci of psoriasis, most of which have not been confirmed. The present genetic signals can not fully explain the pathogenesis of psoriasis, suggesting the presence of other genetic factors. In addition, GW in China and the Caucasus population. The difference of AS results suggests that there are heterogeneity in susceptible alleles or loci in different populations.
The completion of the Human Genome Project (HGP) and the international mono plograph plan (International HapMap Project, Hap2Map) provides an important biological information and analysis tool for the study of the susceptible genes of complex diseases..GWAS is a powerful and powerful method to search for the susceptible genes of complex diseases in recent years. The academic community believes that it is currently one of the most effective methods to search for susceptible genes of major diseases.
A large GWAS study of psoriatic susceptibility genes in Chinese people was conducted for the first time. In addition to two known predisposing sites in the Caucasus, MHC and IL12B, a new LCE gene cluster of psoriatic susceptibility loci on chromosome 1q21 was found. The GWAS study of the susceptible genes for complex diseases has now established a complete GWAS operating platform and statistical analysis method for the study of susceptible genes for complex diseases, and a large number of psoriasis and control samples have been collected through the establishment of a genetic resource pool.
This study was based on the preliminary study of the predisposing gene GWAS of psoriasis. The six stage validation method was used to test 8312 cases and 12919 controls from China, and 3293 cases from Europe, 4188 normal controls and 254 core families were tested to further search for psoriasis in Han people. His possible locus of susceptibility.
objective
To further search for the susceptibility loci related to psoriasis in Chinese Han people, to determine the genetic risk factors associated with psoriasis in Han people, and to compare the genetic heterogeneity of psoriasis between Chinese and Caucasus.
Method
(I) sample sources:
Samples of 1 (4610 cases and 5373 controls) and 2 (2024 patients and 5495 controls) were collected from the Han population collected from multiple cooperative hospitals throughout the country. A sample of 3 (539 cases and 824 healthy controls) from the Uygur population from the Xinjiang Uygur Autonomous Region. A sample of 4 (823 cases and 1840 controls) was tested. From Germany. A sample of 5 (2470 patients and 2348 controls) and 6 of 254 siblings from the core family were from the United States. In each stage of the validation sample, both the case and the control were derived from the same area and the same race.
(two) the selection of SNP in the verification phase:
Two methods of selecting SNP were used in this study. The first method selected 21 P10-5 SNP. second methods in the correlation analysis of 1139 cases and 1227 controls: 3496 cases of other autoimmune related diseases as comparison, and 5173 cases with 1227 normal controls as a common control specimen, statistical analysis, and participation. The 40 SNP of P10-5 was selected for further verification. Finally, 61 SNP were selected to participate in the verification test.
A total of 35 SNP types were selected for validation 2, including: 1) 20 P 0.05 SNP selected from verification 1; 2) from the Caucasus, 15 SNP. of the 8 loci related to psoriasis were selected.
(three) genotyping and quality control in GWAS:
Based on the typing data of early GWAS (including 1139 psoriasis patients and 1132 controls 620901 SNP and CNV probes), 95 new normal control genotyping data were added to explain the data quality control. The genotype phenotype correlation was calculated by Cochran-Armitage trend test.
(four) genotyping and quality control at the stage of verification:
Verification 1-3 uses the Sequenom MassArray system (San Diego, USA) and Biosystems TaqMan assays (USA) to carry out the alleles of the genotyping.MALDI-TOF MS detection allele and perform the mass spectrogram analysis.
The genotypes of 4 and 5 were verified by TaqMan assays (Applied Biosystems). Data quality control was completed by PLINK 1.05.
6 of the specimens were verified by Sequenom MassArray system.
(five) statistical analysis:
The statistical analysis software R was used to draw the chromosome map and Q-Q map.PCA analysis to evaluate the abnormal deviation samples and the population stratification. The cases and the controls were analyzed by PCA. After quality control, the SNPs typing data were analyzed in the GWAS stage.
In the verification 1-5, Cochran-Armitage trend test was used to calculate its relevance respectively. In the combined analysis of multi stage validation study, the fixed effect model or random effect model was used to analyze. The family association study was analyzed by semi likelihood function for case control correlation.
Multiple logistic regression analysis is used to detect the independence of signals in the region.
In the case, SNP. was used to detect the clinical subtype of logistic by using the clinical subtype as the output variable.
Heterogenous test was used to detect genetic heterogeneity among different groups.
Result
First, in the first stage, 4610 patients and 5373 controls of the Han population were genotyping. The results of integrated GWAS and verifying 1 showed that 4 SNP reached the whole genomic significance standard (P5.0 x 10-8), and these four SNP were rs3762999 and rs999556 (P=1.1 * 10-12, OR) located in the 5q33.1 (TNIP1/ANXA6) region. (P = 1.24; P = 4.3 x 10-13, OR = 1.24); rs2431697 (P = 1.1 x 10-8, OR = 1.20) in 5q33.3 (PTTG1) and rs3751385 (P = 1.7 x 10-10, OR = 1.18) in 13q12.11 (GJB2).
Two, the comprehensive analysis of GWAS, verification 1 and verification 2 found that 9 SNP in the 7 regions reached the level of the whole genome, they were rs151823, PCombined=9.3 x 10-9 in 5q15 (ERAP1), rs999556 and rs3762999 in 5q33.1 (TNIP1/ANXA6), PCombined 3.8 * 10-21 and 4.6 x 10-18, respectively. 2431697, PCombined=1.1 x 10-8; rs10088247 and rs7007032 in 8p23.2 (CSMD1), PCombined 4.5 * 10-9 and 3.8 x 10-8, rs3751385, PCombined=8.6 * 10-8 (PGWAS+Replication1=1.7 * 10-10) in 13q12.11 (GJB2); Combined=2.1 x 10-9.
Three, the Uygur population (verification 3), German population (verification 4), American population (verification 5) and 254 core families (verification 6) were analyzed statistically. The results showed that rs3751385 in 13q12.11 (GJB2) and rs151823 in 5q15 (ERAP1) were associated with psoriasis in German and Chinese Uygur populations (P=3.6 x 10-3, O). R=1.26; P=2.9 * 10-5, OR=1.45).ZNF816A showed a consistent association in the Han population (P=2.1 * 10-9, OR=0.88), Chinese Uygur population (P=1.7 x 10-3, OR=0.77) and German population (P=7.9 x 10-3, OR=0.84). The associated evidence (P=1.6 * 10-2, OR=0.90) was suggested in the United States population (5). Combined analysis of the Caucasus population (verification 4 and 5), The newly discovered SNP locus is not associated with psoriasis in Caucasian populations.
Four, the Han population combined with typing data suggested that ZNF816A (rs9304742) and ERAP1 (rs151823) may be associated with early onset psoriasis (P=1.5 * 10-3, OR=0.85; P=6.5 x 10-3, OR=0.88).
conclusion
Six new susceptibility loci of psoriasis were found in the Chinese Han population, and it was confirmed that the susceptible locus 5q33.1 reported by the Caucasus also played a role in the Han population..ZNF816A and GJB2 were associated with psoriasis in the German population..ERAP1 and ZNF816A were significantly related to the occurrence of I psoriasis in the Han people. The results were abundant. The genetic risk factors of psoriasis suggest that the genetic factors may lead to the difference in the age of the disease, and that the genetic susceptibility to psoriasis is heterogeneous in the Chinese and European population, and provides new potential biological evidence for the pathogenesis of psoriasis.
【学位授予单位】：安徽医科大学
【学位级别】：博士
【学位授予年份】：2010
【分类号】：R758.63
本文编号：2160412
[Abstract]:Research background
Psoriasis is a common chronic inflammatory skin disease characterized by erythema scales. The cause of the disease is not clear and may be associated with the combination of genetic, immune and various environmental factors. Family studies and population epidemiological studies have confirmed the genetic basis of psoriasis, early linkage analysis, candidate bases. Genome-Wide Association Study (GWAS) has found multiple susceptibility loci of psoriasis, most of which have not been confirmed. The present genetic signals can not fully explain the pathogenesis of psoriasis, suggesting the presence of other genetic factors. In addition, GW in China and the Caucasus population. The difference of AS results suggests that there are heterogeneity in susceptible alleles or loci in different populations.
The completion of the Human Genome Project (HGP) and the international mono plograph plan (International HapMap Project, Hap2Map) provides an important biological information and analysis tool for the study of the susceptible genes of complex diseases..GWAS is a powerful and powerful method to search for the susceptible genes of complex diseases in recent years. The academic community believes that it is currently one of the most effective methods to search for susceptible genes of major diseases.
A large GWAS study of psoriatic susceptibility genes in Chinese people was conducted for the first time. In addition to two known predisposing sites in the Caucasus, MHC and IL12B, a new LCE gene cluster of psoriatic susceptibility loci on chromosome 1q21 was found. The GWAS study of the susceptible genes for complex diseases has now established a complete GWAS operating platform and statistical analysis method for the study of susceptible genes for complex diseases, and a large number of psoriasis and control samples have been collected through the establishment of a genetic resource pool.
This study was based on the preliminary study of the predisposing gene GWAS of psoriasis. The six stage validation method was used to test 8312 cases and 12919 controls from China, and 3293 cases from Europe, 4188 normal controls and 254 core families were tested to further search for psoriasis in Han people. His possible locus of susceptibility.
objective
To further search for the susceptibility loci related to psoriasis in Chinese Han people, to determine the genetic risk factors associated with psoriasis in Han people, and to compare the genetic heterogeneity of psoriasis between Chinese and Caucasus.
Method
(I) sample sources:
Samples of 1 (4610 cases and 5373 controls) and 2 (2024 patients and 5495 controls) were collected from the Han population collected from multiple cooperative hospitals throughout the country. A sample of 3 (539 cases and 824 healthy controls) from the Uygur population from the Xinjiang Uygur Autonomous Region. A sample of 4 (823 cases and 1840 controls) was tested. From Germany. A sample of 5 (2470 patients and 2348 controls) and 6 of 254 siblings from the core family were from the United States. In each stage of the validation sample, both the case and the control were derived from the same area and the same race.
(two) the selection of SNP in the verification phase:
Two methods of selecting SNP were used in this study. The first method selected 21 P10-5 SNP. second methods in the correlation analysis of 1139 cases and 1227 controls: 3496 cases of other autoimmune related diseases as comparison, and 5173 cases with 1227 normal controls as a common control specimen, statistical analysis, and participation. The 40 SNP of P10-5 was selected for further verification. Finally, 61 SNP were selected to participate in the verification test.
A total of 35 SNP types were selected for validation 2, including: 1) 20 P 0.05 SNP selected from verification 1; 2) from the Caucasus, 15 SNP. of the 8 loci related to psoriasis were selected.
(three) genotyping and quality control in GWAS:
Based on the typing data of early GWAS (including 1139 psoriasis patients and 1132 controls 620901 SNP and CNV probes), 95 new normal control genotyping data were added to explain the data quality control. The genotype phenotype correlation was calculated by Cochran-Armitage trend test.
(four) genotyping and quality control at the stage of verification:
Verification 1-3 uses the Sequenom MassArray system (San Diego, USA) and Biosystems TaqMan assays (USA) to carry out the alleles of the genotyping.MALDI-TOF MS detection allele and perform the mass spectrogram analysis.
The genotypes of 4 and 5 were verified by TaqMan assays (Applied Biosystems). Data quality control was completed by PLINK 1.05.
6 of the specimens were verified by Sequenom MassArray system.
(five) statistical analysis:
The statistical analysis software R was used to draw the chromosome map and Q-Q map.PCA analysis to evaluate the abnormal deviation samples and the population stratification. The cases and the controls were analyzed by PCA. After quality control, the SNPs typing data were analyzed in the GWAS stage.
In the verification 1-5, Cochran-Armitage trend test was used to calculate its relevance respectively. In the combined analysis of multi stage validation study, the fixed effect model or random effect model was used to analyze. The family association study was analyzed by semi likelihood function for case control correlation.
Multiple logistic regression analysis is used to detect the independence of signals in the region.
In the case, SNP. was used to detect the clinical subtype of logistic by using the clinical subtype as the output variable.
Heterogenous test was used to detect genetic heterogeneity among different groups.
Result
First, in the first stage, 4610 patients and 5373 controls of the Han population were genotyping. The results of integrated GWAS and verifying 1 showed that 4 SNP reached the whole genomic significance standard (P5.0 x 10-8), and these four SNP were rs3762999 and rs999556 (P=1.1 * 10-12, OR) located in the 5q33.1 (TNIP1/ANXA6) region. (P = 1.24; P = 4.3 x 10-13, OR = 1.24); rs2431697 (P = 1.1 x 10-8, OR = 1.20) in 5q33.3 (PTTG1) and rs3751385 (P = 1.7 x 10-10, OR = 1.18) in 13q12.11 (GJB2).
Two, the comprehensive analysis of GWAS, verification 1 and verification 2 found that 9 SNP in the 7 regions reached the level of the whole genome, they were rs151823, PCombined=9.3 x 10-9 in 5q15 (ERAP1), rs999556 and rs3762999 in 5q33.1 (TNIP1/ANXA6), PCombined 3.8 * 10-21 and 4.6 x 10-18, respectively. 2431697, PCombined=1.1 x 10-8; rs10088247 and rs7007032 in 8p23.2 (CSMD1), PCombined 4.5 * 10-9 and 3.8 x 10-8, rs3751385, PCombined=8.6 * 10-8 (PGWAS+Replication1=1.7 * 10-10) in 13q12.11 (GJB2); Combined=2.1 x 10-9.
Three, the Uygur population (verification 3), German population (verification 4), American population (verification 5) and 254 core families (verification 6) were analyzed statistically. The results showed that rs3751385 in 13q12.11 (GJB2) and rs151823 in 5q15 (ERAP1) were associated with psoriasis in German and Chinese Uygur populations (P=3.6 x 10-3, O). R=1.26; P=2.9 * 10-5, OR=1.45).ZNF816A showed a consistent association in the Han population (P=2.1 * 10-9, OR=0.88), Chinese Uygur population (P=1.7 x 10-3, OR=0.77) and German population (P=7.9 x 10-3, OR=0.84). The associated evidence (P=1.6 * 10-2, OR=0.90) was suggested in the United States population (5). Combined analysis of the Caucasus population (verification 4 and 5), The newly discovered SNP locus is not associated with psoriasis in Caucasian populations.
Four, the Han population combined with typing data suggested that ZNF816A (rs9304742) and ERAP1 (rs151823) may be associated with early onset psoriasis (P=1.5 * 10-3, OR=0.85; P=6.5 x 10-3, OR=0.88).
conclusion
Six new susceptibility loci of psoriasis were found in the Chinese Han population, and it was confirmed that the susceptible locus 5q33.1 reported by the Caucasus also played a role in the Han population..ZNF816A and GJB2 were associated with psoriasis in the German population..ERAP1 and ZNF816A were significantly related to the occurrence of I psoriasis in the Han people. The results were abundant. The genetic risk factors of psoriasis suggest that the genetic factors may lead to the difference in the age of the disease, and that the genetic susceptibility to psoriasis is heterogeneous in the Chinese and European population, and provides new potential biological evidence for the pathogenesis of psoriasis.
【学位授予单位】：安徽医科大学
【学位级别】：博士
【学位授予年份】：2010
【分类号】：R758.63
【引证文献】
相关期刊论文 前1条
1 罗轶波;杨利蓉;王婷婷;陈吉辉;;延续护理对银屑病患者的影响探究[J];中国地方病防治杂志;2014年S2期
相关硕士学位论文 前1条
1 孙海波;CSMD1基因和BRG1基因与喉鳞状细胞癌发生的相关性研究[D];吉林大学;2012年
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