title: Do major histocompatibility complex tag single nucleotide polymorphisms accurately identify HLA-B27 in the Turkish population?
abstract: OBJECTIVE
  To evaluate the performance of human leukocyte antigen (HLA)-B27 tag single nucleotide polymorphisms (SNPs) by polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP).
  
  
  METHODS
  We genotyped three SNPs (rs116488202, rs13202464 and rs4349859). The primers were designed using Primer3 algorithm via primer-BLAST interface. PCR products were digested by using NlaIII, BmrI and TaqαI enzymes. Quality control was performed by DNA sequence analysis.
  
  
  RESULTS
  In total, 207 patients with ankylosing spondylitis and 32 healthy controls were included in the study. The sensitivity and specificity of SNPs rs116488202 and rs4349859 in identifying HLA-B27 were identical and adequate at 0.946 and 1.000, respectively. On the other hand, the sensitivity and specificity for rs13202464 was 0.878 and 0.934, respectively. The presence of another SNP (rs141774149) in close proximity to rs116488202 complicated the analysis for RFLP and required that we sequence all the T allele carrying samples.
  
  
  CONCLUSIONS
  The SNPs rs116488202 and rs4349859 may have a place in the identification of HLA-B27 in the Turkish population; however, methods other than PCR-RFLP should be considered.
authors.affiliation: Division of Rheumatology, Department of Internal Medicine, Izmir Katip Celebi University School of Medicine, Izmir, Turkey.
authors.forename: Servet
authors.initials: S
authors.lastname: Akar
authors.affiliation: Department of Medical Biology, School of Medicine, Gaziantep University, Gaziantep, Turkey.
authors.forename: Yusuf Z
authors.initials: YZ
authors.lastname: Igci
authors.affiliation: Department of Internal Medicine, Division of Rheumatology, Dokuz Eylul University School of Medicine, Izmir, Turkey.
authors.forename: Ismail
authors.initials: I
authors.lastname: Sari
authors.affiliation: Department of Medical Biology, School of Medicine, Gaziantep University, Gaziantep, Turkey.
authors.forename: Elif
authors.initials: E
authors.lastname: Pala
authors.affiliation: Department of Medical Biology, School of Medicine, Gaziantep University, Gaziantep, Turkey.
authors.forename: Esra
authors.initials: E
authors.lastname: Geyik
authors.affiliation: Department of Internal Medicine, Division of Rheumatology, Dokuz Eylul University School of Medicine, Izmir, Turkey.
authors.forename: Mehmet N
authors.initials: MN
authors.lastname: Tas
authors.affiliation: Department of Internal Medicine, Division of Rheumatology, Namik Kemal University School of Medicine, Tekirdag, Turkey.
authors.forename: Dilek
authors.initials: D
authors.lastname: Solmaz
authors.affiliation: Department of Internal Medicine, Division of Rheumatology, Dokuz Eylul University School of Medicine, Izmir, Turkey.
authors.forename: Pinar
authors.initials: P
authors.lastname: Çetin
authors.affiliation: Department of Internal Medicine, Division of Rheumatology, Dokuz Eylul University School of Medicine, Izmir, Turkey.
authors.forename: Nurullah
authors.initials: N
authors.lastname: Akkoc
mesh_terms: D000328:Adult; D054458:Amplified Fragment Length Polymorphism Analysis; D016022:Case-Control Studies; D005260:Female; D005787:Gene Frequency; D015796:HLA-B27 Antigen / Q000235:genetics* / Q000276:immunology; D006801:Humans; D008297:Male; D008875:Middle Aged; D012150:Polymorphism, Restriction Fragment Length; D020641:Polymorphism, Single Nucleotide; D011237:Predictive Value of Tests; D013167:Spondylitis, Ankylosing / Q000175:diagnosis / Q000235:genetics* / Q000276:immunology; D014421:Turkey
chemical_list: D015796:HLA-B27 Antigen
keywords: HLA-B27 antigen; ankylosing spondylitis; polymorphism; restriction fragment length polymorphism; single nucleotide polymorphism