Sarcoidosis is a multiorgan inflammatory disorder with heritability estimates up to 66%. Previous studies have shown the major histocompatibility complex (MHC) region to be associated with sarcoidosis, suggesting a functional role for antigen-presenting molecules and immune mediators in the disease pathogenesis. To detect variants predisposing to sarcoidosis and to identify genetic differences between patient subgroups, we studied four genes in the MHC Class III region (LTA, TNF, AGER, BTNL2) and HLA-DRA with tag-SNPs and their relation to HLA-DRB1 alleles. We present results from a joint analysis of four study populations (Finnish, Swedish, Dutch, and Czech). Patients with sarcoidosis (n = 805) were further subdivided based on the disease activity and the presence of Löfgren's syndrome. In a joint analysis, seven SNPs were associated with non-Löfgren sarcoidosis (NL; the strongest association with rs3177928, P = 1.79E-07, OR = 1.9) and eight with Löfgren's syndrome [Löfgren syndrome (LS); the strongest association with rs3129843, P = 3.44E-12, OR = 3.4] when compared with healthy controls (n = 870). Five SNPs were associated with sarcoidosis disease course (the strongest association with rs3177928, P = 0.003, OR = 1.9). The high linkage disequilibrium (LD) between SNPs and an HLA-DRB1 challenged the result interpretation. When the SNPs and HLA-DRB1 alleles were analyzed together, independent association was observed for four SNPs in the HLA-DRA/BTNL2 region: rs3135365 (NL; P = 0.015), rs3177928 (NL; P < 0.001), rs6937545 (LS; P = 0.012), and rs5007259 (disease activity; P = 0.002). These SNPs act as expression quantitative trait loci (eQTL) for HLA-DRB1 and/or HLA-DRB5. In conclusion, we found novel SNPs in BTNL2 and HLA-DRA regions associating with sarcoidosis. Our finding further establishes that polymorphisms in the HLA-DRA and BTNL2 have a role in sarcoidosis susceptibility. This multi-population study demonstrates that at least a part of these associations are HLA-DRB1 independent (e.g., not due to LD) and shared across ancestral origins. The variants that were independent of HLA-DRB1 associations acted as eQTL for HLA-DRB1 and/or -DRB5, suggesting a role in regulating gene expression.

Analytical and Translational Genetics Unit Department of Medicine Massachusetts General Hospital Harvard Medical School Boston MA USA

Department of Immunology Faculty of Medicine and Dentistry Palacky University Olomouc Olomouc Czech Republic

Department of Pathological Physiology and Institute of Molecular and Translational Medicine Faculty of Medicine and Dentistry Palacky University Olomouc Olomouc Czech Republic

Department of Pathological Physiology Faculty of Medicine and Dentistry Palacky University Olomouc Olomouc Czech Republic

Department of Pulmonology St Antonius Hospital Nieuwegein Heart and Lung Center University Medical Center Utrecht Utrecht Netherlands

Department of Respiratory Medicine Faculty of Medicine and Dentistry Palacky University Olomouc Olomouc Czech Republic

Institute for Molecular Medicine Finland University of Helsinki Helsinki Finland

Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA USA

Raasepori Health Care Centre Raasepori Finland

Rare Disease Center Children's Hospital and Adult Immunodeficiency Unit Inflammation Center Helsinki University and Helsinki University Hospital Helsinki Finland

Respiratory Medicine Unit Department of Medicine Solna and CMM Karolinska Institutet Karolinska University Hospital Solna Sweden

Rheumatology Unit Department of Medicine Karolinska Institutet Karolinska University Hospital Stockholm Sweden

Transplantation Laboratory Medicum University of Helsinki Helsinki Finland

University of Helsinki Helsinki Finland

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Next-Generation Sequencing Based HLA Typing: Deciphering Immunogenetic Aspects of Sarcoidosis