A Genome-wide Association Study For Coding Variants Of Systemic Lupus Erythematosus

Background: Systemic lupus erythematosus(SLE,MIM 152700)is an inflammatory,autoimmune,and multisystemic disorder of the connective tissue characterized by autoantibody production and tissue injury.Women of childbearing age are most affected,and with significant gender differneces between male to female ratio is about 1:9.The prevalence of SLE varies among different ethnic and geographical populations,with Europeans showing lower prevalence compared with individuals of African or Asian ancestry.SLE global average of prevalence is about 12 to 39/100,000,and 30 to 70/100,000 in China.Etiology and pathogenesis for SLE are not clear,generally,it is considered that genetic factors,immune abnormalities,sex hormones and environmental factors are associated with SLE and caused by genetic and environmental interactions,which belongs to a complex disease with involving multi-susceptibility genes.Since 2008,genome-wide association studies(GWAS)have successfully identified 81 genomic loci for the risk of SLE with genome-wide significance(P < 5 × 10-8).However,these discovered loci in total cannot fully account for the observed genetic variation for SLE,suggesting that additional genetic factors have not yet to be discovered.Furthermore,the majority of associated variants exert relatively small effect size and lie within noncoding sequence,and thus provide few clues as to the functional mechanism.Coding variants that have been rarely investigated in GWAS have been hypothesized and discovered to explain part of the “missing heritability” for complex diseases.Recently,exome array has been designed in order to study the role of coding variants in human complex diseases systematically and cost-effectively,and it has been applied in the studies for age-related macular degeneration,multiple sclerosis,psoriasis,and multiple other complex diseases.These applications increase the number of novel susceptibility findings,and more importantly,these studies observe several coding variants directly associated with the risk of complex diseases,then provide a great opportunity to study their biological mechanisms underlying diseases.Object: We aim to systematically investigate the role of coding variants in SLE in a genome-wide exome study and further identifiy low-frequency variants association with this disease.Methods: In this study,we genotyped 5,004 cases and 8,179 controls in Han Chinese population by using Illumina Human Exome Asian Bead Chip.After quality control,SNPs were filtered for further analysis.To validate these findings,we put them forward for genotyping in an independent cohort of 5,099 cases and 8,147 controls using the Sequenom Mass ARRAY system.We perform linkage disequilibrium analysis and e QTL analysis to screen susceptibility genes/loci of SLE in Chinese Han population.Results: We put forward 39 SNPs with suggestive association of P < 1.00 × 10-03 in the discovery stage for an independent genotyping in a cohort of 13,246 samples(5,099 cases and 8,147 controls)using the Sequenom Mass ARRAY system.In this validation samples,21 of them were shown consistent and supportive association evidence(P < 0.05).The meta-analysis between two stages identified six novel common SNPs within or around six genes: CD58(rs1335532,P = 5.80 × 10-09,OR = 1.11),LCT(rs2322659,P = 1.80 × 10-17,OR = 1.17),TPCN2(rs10750836,P = 3.85 × 10-11,OR = 1.13),OAS1(rs1051042,P = 1.77 × 10-11,OR = 0.87),AHNAK2(rs4465542,P = 1.70 × 10-11,OR = 0.85),and TNFRSF13B(rs4792801,P = 1.15 × 10-10,OR = 0.89).Among the six novel findings,three SNPs rs2322659(p.Asn1639 Ser,LCT),rs1051042(p.Arg361 Thr,OAS1),and rs4465542(p.Thr4664 Ala,AHNAK2)are nonsynonymous variants.Two other novel SNPs rs1335532,and rs4792801 are located in introns at genes CD58 and TNFRSF13 B,respectively.The last novel SNP rs10750836 is the only intergenic variant discovered in the present study.It is 841 bp upstream of gene TPCN2 on chromosome 11.They tended to be enriched among gene regulatory elements,and exhibited e QTL effects on genes CD58,TPCN2,TNFRSF13 B,and OAS1 in immune cells.The newly implicated genes suggest several pathways relevant to immune response and response to stimuli in the risk of SLE.Conclusions: This is the first large-scale exome chip genotyping array to systematically search the coding variants in 10,103 SLE cases and 16,326 healthy controls and we identified six new SLE susceptibility genes(CD58,LCT,TPCN2,OAS1,AHNAK2,TNFRSF13B).These susceptibility genes increase the number of known genetic risk factors.Findings in this study broaden our understanding of the genetic structure of SLE and also extend the functional spectrum of genetic variation underlying SLE susceptibility.