title: Haplotype analysis revealed no association between the PTPN22 gene and RA in a Japanese population.
abstract: OBJECTIVE
  The protein tyrosine phosphatase non-receptor type 22 (PTPN22) gene is a member of the PTPs that negatively regulate T-cell activation. A missense single nucleotide polymorphism (SNP) in the PTPN22 gene known as R620W was recently reported to be associated with several autoimmune diseases including rheumatoid arthritis (RA). The association was confirmed repeatedly in the populations of North European ancestry. However, the SNP was reported to be non-polymorphic in the Asian populations. Because the gene confers an impact on autoimmune diseases, we attempt to explore an association between PTPN22 gene and RA in a Japanese population without restricting to the SNP, R620W.
  
  
  METHODS
  We studied 1128 RA patients and 455 controls. In addition to the SNP, R620W, we selected eight testing SNPs spanning 45 kb over the PTPN22 gene using the International HapMap Project. Genotyping was performed using the TaqMan fluorogenic 5' nuclease assay. Associations between RA and each of the SNPs were estimated by the Fisher's exact test. Haplotype was constructed using the expectation-maximization algorithm.
  
  
  RESULTS
  R620W was not polymorphic enough in both the patients and the controls, and was therefore excluded from further analysis. Each allele frequency for the eight other SNPs in both groups was compared and no association was detected. Haplotype analysis also revealed that PTPN22 gene was not associated with RA in a Japanese population.
  
  
  CONCLUSIONS
  We found no association between PTPN22 and RA in a Japanese population. The result suggests that the PTPN22 gene is associated with RA only in a specific ethnic group.
authors.affiliation: Institute of Rheumatology, Tokyo Women's Medical University, 10-22 Kawada, Tokyo 162-0054, Japan. kikari@ior.twmu.ac.jp
authors.forename: K
authors.initials: K
authors.lastname: Ikari
authors.forename: S
authors.initials: S
authors.lastname: Momohara
authors.forename: E
authors.initials: E
authors.lastname: Inoue
authors.forename: T
authors.initials: T
authors.lastname: Tomatsu
authors.forename: M
authors.initials: M
authors.lastname: Hara
authors.forename: H
authors.initials: H
authors.lastname: Yamanaka
authors.forename: N
authors.initials: N
authors.lastname: Kamatani
mesh_terms: D001172:Arthritis, Rheumatoid / Q000235:genetics*; D044466:Asian People / Q000235:genetics*; D005260:Female; D005787:Gene Frequency; D020022:Genetic Predisposition to Disease; D005838:Genotype; D006239:Haplotypes; D006801:Humans; D007564:Japan; D015810:Linkage Disequilibrium; D008297:Male; D020641:Polymorphism, Single Nucleotide; D054596:Protein Tyrosine Phosphatase, Non-Receptor Type 22; D017027:Protein Tyrosine Phosphatases / Q000235:genetics*
chemical_list: C516765:PTPN22 protein, human; D054596:Protein Tyrosine Phosphatase, Non-Receptor Type 22; D017027:Protein Tyrosine Phosphatases