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<i>HLA-DRB1</i> shared epitope (SE) alleles are important genetic contributors for the risk of developing anti-citrullinated protein antibodies (ACPA)-positive rheumatoid arthritis (RA), particularly in Caucasians. We aimed to analyze the contribution of HLA-DRB1 alleles and single nucleotide polymorphisms (SNPs) within the major histocompatibility complex (MHC) region to the susceptibility to develop ACPA-positive RA in a Latin American (LA) population with admixed ancestry. A total of 289 ACPA-positive RA patients and 510 controls were enrolled in this study. The presence of <i>HLA-DRB1*04:01</i>, <i>*09:01</i> and <i>*10:01</i> was increased in ACPA-positive RA patients compared with healthy controls (<i>p</i> < 0.0001, <i>p</i> < 0.001 and <i>p</i> < 0.01, respectively), whereas <i>DRB1*07:01</i> and <i>*08:02</i> was associated with a decreased risk of ACPA-positive RA (<i>p</i> < 0.001 and <i>p</i> < 0.01, respectively). These results showed a strong correlation with estimates from studies in Asians but not in Caucasian populations. The present study describes the protective effects of the <i>HLA-DRB1*07:01</i> and <i>*08:02</i> alleles in ACPA-positive RA patients in a LA population for the first time. Identifying relationships between <i>HLA-DRB1</i> alleles and RA is important for identifying disease associations in different ethnic groups in order to reach a better understanding of RA worldwide.