This study was to investigate whether autoimmune encephalitis is associated with the human leukocyte antigen (HLA) genotypes in Chinese Han population. We compared and analyzed the HLA genotypes of 101 patients with autoimmune encephalitis (77 anti-NMDAR, 11 anti-LGI1 and 13 anti-GABABR antibody, respectively) to the 200 healthy control groups. Our results showed that the DRB1*03:01 or DQB1*02:01 allele and the extended DRB1*03:01 ~ DQB1*02:01 haplotype represented the strong susceptibility locus for anti-LGI1 encephalitis (OR = 18.84, 95% CI = 5.01–70.89, Pc = 0.004; OR = 18.84, 95% CI = 5.01–70.89, Pc = 0.004; OR = 18.84, 95% CI = 5.01–70.89, Pc = 0.001). Additionally, the DRB1*08:03 ~ DQB1*06:01 or B*08:01 ~ C*07:02 haplotype was likely to be associated with anti-LGI1 encephalitis (OR = 10.23, 95% CI = 2.87–36.42, Pc = 0.039; OR = 74.62, 95% CI = 6.97–799.06, Pc = 0.043). No statistically significant differences were found for HLA association between patients with anti-NMDAR or anti-GABABR encephalitis and healthy controls. These results indicated that HLA subtypes were only associated with anti-LGI1 encephalitis.
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