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      Genetic Analysis with the Immunochip Platform in Behçet Disease. Identification of Residues Associated in the HLA Class I Region and New Susceptibility Loci

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          Abstract

          Behcet's disease (BD) is an immuno-mediated vasculitis in which knowledge of its etiology and genetic basis is limited. To improve the current knowledge, a genetic analysis performed with the Immunochip platform was carried out in a population from Spain. A discovery cohort comprising 278 BD cases and 1,517 unaffected controls were genotyped using the Immunochip platform. The validation step was performed on an independent replication cohort composed of 130 BD cases and 600 additional controls. The strongest association signals were observed in the HLA class I region, being HLA-B*51 the highest peak (overall P = 6.82E-32, OR = 3.82). A step-wise conditional logistic regression with classical alleles identified HLA-B*57 and HLA-A*03 as additional independent markers. The amino acid model that best explained the association, includes the position 97 of the HLA-B molecule and the position 66 of the HLA-A. Among the non-HLA loci, the most significant in the discovery analysis were: IL23R (rs10889664: P = 3.81E-12, OR = 2.00), the JRKL/CNTN5 region (rs2848479: P = 5.00E-08, OR = 1.68) and IL12A (rs1874886: P = 6.67E-08, OR = 1.72), which were confirmed in the validation phase ( JRKL/CNTN5 rs2848479: P = 3.29E-10, OR = 1.66; IL12A rs1874886: P = 1.62E-08, OR = 1.61). Our results confirm HLA-B*51 as a primary-association marker in predisposition to BD and suggest additional independent signals within the class I region, specifically in the genes HLA-A and HLA-B. Regarding the non-HLA genes, in addition to IL-23R, previously reported in our population; IL12A, described in other populations, was found to be a BD susceptibility factor also in Spaniards; finally, a new associated locus was found in the JRKL/CNTN5 region.

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          Most cited references27

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          Behçet's disease.

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            A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC.

            The proteins encoded by the classical HLA class I and class II genes in the major histocompatibility complex (MHC) are highly polymorphic and are essential in self versus non-self immune recognition. HLA variation is a crucial determinant of transplant rejection and susceptibility to a large number of infectious and autoimmune diseases. Yet identification of causal variants is problematic owing to linkage disequilibrium that extends across multiple HLA and non-HLA genes in the MHC. We therefore set out to characterize the linkage disequilibrium patterns between the highly polymorphic HLA genes and background variation by typing the classical HLA genes and >7,500 common SNPs and deletion-insertion polymorphisms across four population samples. The analysis provides informative tag SNPs that capture much of the common variation in the MHC region and that could be used in disease association studies, and it provides new insight into the evolutionary dynamics and ancestral origins of the HLA loci and their haplotypes.
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              HLA-B51/B5 and the risk of Behçet's disease: a systematic review and meta-analysis of case-control genetic association studies.

              To quantify by meta-analysis the genetic effect of the HLA-B5 or HLA-B51 (HLA-B51/B5) allele on the risk of developing Behçet's disease (BD) and to look for potential effect modifiers. Relevant studies were identified using the PubMed Medline database and manual searches of the literature. Pooled odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated by using the random-effects model. Subgroup meta-analyses and meta-regression analyses were undertaken to investigate the effects of selected study-level parameters on the pooled OR. Heterogeneity was assessed using the I2 statistic. Pooled results were used to calculate population-attributable risks (PAR) for BD in relationship to HLA-B51/B5. A total of 4,800 patients with BD and 16,289 controls from 78 independent studies (published 1975-2007) were selected. The pooled OR of HLA-B51/B5 allele carriers to develop BD compared with noncarriers was 5.78 (95% CI 5.00-6.67), with moderate between-study heterogeneity (I2 = 61%). The subgroup analyses stratifying studies by geographic locations (Eastern Asia, Middle East/North Africa, Southern Europe, Northern/Eastern Europe) yielded consistent OR ranges (5.31-7.20), with I2 ranges of 52-70%. Univariate random-effects meta-regression indicated the percentage of male BD cases (P = 0.008) as a source of heterogeneity. The PAR within the various geographic areas were estimated at 32-52%. The strength of the association between BD and HLA-B51/B5, and its consistency across populations of various ethnicities, lends further support to this allele being a primary and causal risk determinant for BD. Variations according to sex support an interaction of this allele with BD characteristics.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                22 August 2016
                2016
                : 11
                : 8
                : e0161305
                Affiliations
                [1 ]Department of Immunology, Hospital Universitario Virgen del Rocío (IBiS, CSIC, US), Sevilla, 41013, Spain
                [2 ]Instituto de Parasitología y Biomedicina “López-Neyra”, CSIC, PTS Granada, Granada, 18016, Spain
                [3 ]Department of Internal Medicine, Hospital Clínico San Cecilio, Granada, 18003, Spain
                [4 ]Department of Internal Medicine, Hospital Universitario Virgen del Rocío, Sevilla, 41003, Spain
                [5 ]Department Autoimmune Diseases, Hospital Universitari Clínic, Barcelona, 08036, Spain
                [6 ]Department of Rheumatology, Complejo Hospitalario Universitario A Coruña, A Coruña, 15006, Spain
                [7 ]Department of Rheumatology, Hospital Universitario de Valme, Sevilla, 41014, Spain
                [8 ]Department of Immunology, Hospital Universitari Son Espases, Palma de Mallorca, 07120, Spain
                [9 ]Department of Internal Medicine, Autoimmune Systemic Diseases Unit, Hospital Vall d’Hebron, Universidad Autonoma de Barcelona, Barcelona, 08035, Spain
                [10 ]Department of Rheumatology, Hospital Universitario Marqués de Valdecilla, Santander, 39008, Spain
                [11 ]Department of Internal Medicine, Complejo Hospitalario Torrecárdenas, Almería, 04009, Spain
                [12 ]Department of Internal Medicine, Hospital Universitario Central de Asturias, Asturias, 33011, Spain
                [13 ]Department of Internal Medicine, Hospital Virgen del Camino, Pamplona, 31008, Spain
                [14 ]Deparment of Internal Medicine, Hospital Universitari Mútua Terrassa, Terrassa, 08221, Spain
                [15 ]Department of Rheumatology, Hospital Clínico San Carlos, Madrid, 28040, Spain
                [16 ]Department of Internal Medicine, Hospital Regional Universitario de Málaga, Málaga, 29010, Spain
                [17 ]Department of Rheumatology, Hospital de la Princesa, IIS-Princesa, Madrid, 28006, Spain
                [18 ]Department of Rheumatology, Hospital Universitario Doctor Peset, Valencia, 46017, Spain
                Keio University, JAPAN
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                • Conceptualization: MAMC JRGL MFGE.

                • Data curation: LOF MFGE.

                • Formal analysis: LOF FDC MFGE.

                • Funding acquisition: MFGE.

                • Investigation: LOF FDC MAMC JRGL JM MFGE.

                • Methodology: LOF FDC JM MFGE.

                • Project administration: MFGE.

                • Resources: LOF FDC MAMC JRGL MCJ NOC MJC GE GGG JSB MRJ RS RB ACBM RGDLT PF MRC LRR TC SC JJAS JM MFGE.

                • Software: LOF FDC.

                • Supervision: MFGE.

                • Validation: LOF FDC MFGE.

                • Visualization: LOF FDC MFGE.

                • Writing - original draft: LOF FDC MFGE.

                • Writing - review & editing: LOF FDC MAMC JRGL MCJ NOC MJC GE GGG JSB MRJ RS RB ACBM RGDLT PF MRC LRR TC SC JJAS JM MFGE.

                Author information
                http://orcid.org/0000-0003-1336-0163
                http://orcid.org/0000-0001-9041-8117
                http://orcid.org/0000-0002-2869-7861
                Article
                PONE-D-16-13712
                10.1371/journal.pone.0161305
                4993481
                27548383
                491ea8a7-5e5b-46c0-8e6a-6dfb6e7f2603
                © 2016 Ortiz-Fernández et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 7 April 2016
                : 3 August 2016
                Page count
                Figures: 4, Tables: 3, Pages: 17
                Funding
                Funded by: Fondo de Investigaciones Sanitarias, Instituto de Salud Carlos III
                Award ID: 13/01118
                Funded by: Fondo de Investigaciones Sanitarias, Instituto de Salud Carlos III
                Award ID: FI11/00547
                Award Recipient :
                Funded by: Fondo de Investigaciones Sanitarias, Instituto de Salud Carlos III
                Award ID: RD12/0009/0013
                Award Recipient :
                Funded by: Fondos FEDER and Plan Andaluz de Investigación
                Award ID: CTS-0197
                This work was supported by Fondo de Investigaciones Sanitarias, Instituto de Salud Carlos III (ISCIII, 13/01118), Fondos FEDER and Plan Andaluz de Investigación (CTS-0197). LOF is the recipient of a fellowship (ISCIII, FI11/00547) and FDC was funded by the RETICS Program (RIER, ISCIII, RD12/0009/0013). All these are public institutions from Spain and the funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Molecular Biology Assays and Analysis Techniques
                Amino Acid Analysis
                Research and Analysis Methods
                Molecular Biology Techniques
                Molecular Biology Assays and Analysis Techniques
                Amino Acid Analysis
                Biology and Life Sciences
                Genetics
                Genetic Loci
                Alleles
                Biology and Life Sciences
                Genetics
                Genetics of Disease
                People and Places
                Geographical Locations
                Europe
                Spain
                Biology and Life Sciences
                Genetics
                Genetic Loci
                Biology and Life Sciences
                Genetics
                Genetics of Disease
                Genetic Predisposition
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Genotyping
                Research and Analysis Methods
                Molecular Biology Techniques
                Genotyping
                Biology and Life Sciences
                Computational Biology
                Genome Analysis
                Genome-Wide Association Studies
                Biology and Life Sciences
                Genetics
                Genomics
                Genome Analysis
                Genome-Wide Association Studies
                Biology and Life Sciences
                Genetics
                Human Genetics
                Genome-Wide Association Studies
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