Evaluating validity of (TAG) single nucleotide polymorphism,which thougt represents major histocompatibility gene area in defining HLA-B27

ABSTRACT Background: Ankylosing spondylitis (AS) is strongly associated with HLA-B27. Although AS and HLA-B27 interaction is one of the best known disease association and has been recognized since 1973, accurate HLA-B27 typing is technically challenging. Previously major histocompatibility complex (MHC) tag single nucleotide polymorphisms (SNPs) rs4349859 and rs13202464 were shown to be able to identify HLA-B27 in European and Asian AS patients. Objectives: Therefore the objective of this study was to evaluate the sensitivity and specificity of these SNPs in identifying HLA-B27 allele. Methods: We genotyped two SNPs (rs13202464 and rs4349859) by using polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP). The primers were designed using Primer3 algorithm via primer-BLAST interface. PCR products were digested by using BmrI, and Taq?I restriction endonuclease enzymes. Some of the samples were also sequenced by using ABI 3130 automated DNA sequencer in order to prevent misleading results. HLA-B*27 analysis for patient group was performed by using commercially used SSP-typing kit. SSP-typing results were visualized on 2% agarose gel electrophoresis. Results: In total 207 patients (72% male, mean age 42.3 ± 10.8 years and 146 [71%] was HLA-B27 positive) with AS according to the modified New York criteria and 32 healthy controls (78%male, mean age 52.7 ± 10.8 years and 2 [6%] was HLA-B27 positive) were included in the study. The effect alleles of SNPs rs4349859 (A) showed a high specificity (1.000). However sensitivity figure for HLA-B27 were 0.469. The effect allele of SNP rs13202464 (G) has a specificity of 0.967 and a sensitivity of 0.530. Conclusion: Our results suggest that the SNPs which previously reported as strongly tagged to HLA-B27 do not have any advantage over the HLA-B27 typing in Turkish population. Further research is needed to identify SNPs that may have stronger association with HLA-B27 in our population.