Mixed lymphocyte cultures in rheumatoid arthritis. one), yielding a set of 372 cases with 372 controls. This analysis revealed the presence of at least two regions of association with RA in the class I region, independent of DRB1 genotype. SNP alleles found on the conserved A1-B8-DR3 (8.1) haplotype show the strongest evidence of positive association (p ~ 0.00005) clustered in the region around the HLA-C locus. In addition, we identified risk alleles that are not present on the 8.1 haplotype, with maximal association signals ( p~ 0.001C0.0027) located near the ZNF311 locus. This latter association is enriched PI-103 Hydrochloride in DRB1*0404 individuals. Finally, several additional association signals were found in the extreme centromeric portion of the MHC, in regions containing the DOB1, TAP2, DPB1 and COL11A2 genes. These data emphasize that further analysis of the MHC is likely to reveal genetic risk factors for rheumatoid arthritis that are independent of the DRB1 shared epitope alleles. strong class=”kwd-title” Keywords: Major histocompatibility complex, Rheumatoid arthritis, Genetics, Case-control studies INTRODUCTION Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disease characterized by joint inflammation and progressive joint destruction(1). Recently, several new genes with modest levels of risk for RA have been identified and replicated in various populations, including PTPN22(2), PADI4(3), TRAF1-C5(4, 5), STAT4(5) and 6q23/TNFAIP3(6). Nevertheless, numerous association studies and multiple genomewide linkage PI-103 Hydrochloride studies have shown that MHC region has the largest and most consistent genetic contribution in rheumatoid arthritis(7C9). Since the association of HLA with RA was first demonstrated in 1976(10), the vast majority of case-control association studies have focused on HLA-DRB1 locus encoding a group of risk alleles collectively referred to as the shared epitope (SE) alleles(11, 12). These alleles share a common sequence element containing Q/KCR-R-A-A at positions 70C74 of the DRB1 chain, with some minor variation from this canonical PI-103 Hydrochloride sequence in some risk alleles. Despite the appealing simplicity of the shared epitope as an explanation for disease association, it is quite apparent that there is a complex hierarchy of risk for the various DRB1 alleles that contain the shared epitope(13). In addition, certain genotypic combinations, PI-103 Hydrochloride such as DRB1*0401/0404 carry exceedingly high risk that cannot be simply explained by the number of shared epitope alleles PI-103 Hydrochloride that are present(12). This suggests that there may be haplotypic effects that modify the risk of particular shared epitope alleles. In addition, although the DRB1 locus is clearly of predominant importance, several reports over the years have suggested the presence of additional risk loci within the MHC(14C17). The arguments for these additional loci are often confounded by the complex patterns of linkage disequilibrium that are observed in this genetic region. By carefully matching cases and controls by DRB1 genotype, we now provide additional evidence for several new risk loci for RA located in the class I region of the MHC, as well in the region centromeric to the DRB1 locus METHODS Study populations RA cases and controls in the current analysis are largely taken from populations utilized for our previous whole genome association study using the Illumina 550K Beadchip(4). Briefly, RA cases were selected from four North American RA patient collections. The North American Rheumatoid Arthritis Consortium (NARAC) samples are from multiplex families (primarily affected sibling pairs); at least one sibling was required to have documented erosions on hand radiographs, with at least one sibling having disease onset between the ages of 18 and 60 years of age (18). The other collections include samples from the Wichita Rheumatic Disease Data Bank(19) (WRDDB, mean disease duration 10 years), the National Inception Cohort of Rheumatoid Arthritis Patients(20) (NICRAP), enrolled within 6 months of clinical diagnosis), and Study Of New Onset Rheumatoid Arthritis(21) (SONORA, enrolled within WAF1 3C12 months of clinical diagnosis). All cases were anticyclic citrullinated pepetide antibody positive ( CCP+) with reported European-American ancestry. The controls were taken from.