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Further Evidence of a Primary, Causal Association of the PTPN22 620W Variant With Type 1 Diabetes

Magdalena Zoledziewska^1,2, Chiara Perra^2,, Valeria Orrù^1,3, Loredana Moi², Paola Frongia⁴, Mauro Congia², Nunzio Bottini³, and Francesco Cucca¹

¹ Dipartimento di Scienze Biomediche, University of Sassari, Sassari, Italy
² Laboratorio di Immunogenetica, Ospedale Microcitemico, Cagliari, Italy
³ Institute for Genetic Medicine, University of Southern California, Los Angeles, California
⁴ Divisione Pediatrica, Ospedale Brotzu, Cagliari, Italy

Address correspondence and reprint requests to Francesco Cucca, Cattedra di Genetica Medica, Dipartimento di Scienze Biomediche, Università di Sassari, Viale S. Pietro, 07100 Sassari, Italy. E-mail: fcucca{at}uniss.it

Key Words: AFBAC, affected family–based control • DIP, deletion insertion polymorphism • HLA, human leukocyte antigen • Lyp, lymphoid protein tyrosine phosphatase • MAF, minor allele frequency • SNP, single nucleotide polymorphism • TDT, transmission disequilibrium test

OBJECTIVE— The minor allele of the nonsynonymous single nucleotide polymorphism (SNP) +1858C>T within the PTPN22 gene is positively associated with type 1 diabetes and other autoimmune diseases. Genetic and functional data underline its causal effect, but some studies suggest that this polymorphism does not entirely explain disease association of the PTPN22 region. The aim of this study was to evaluate type 1 diabetes association within this gene in the Sardinian population.

RESEARCH DESIGN AND METHODS— We resequenced the exons and potentially relevant portions of PTPN22 and detected 24 polymorphisms (23 SNPs and 1 deletion insertion polymorphism [DIP]), 8 of which were novel. A representative set of 14 SNPs and the DIP were sequentially genotyped and assessed for disease association in 794 families, 490 sporadic patients, and 721 matched control subjects.

RESULTS— The +1858C>T variant, albeit rare in the general Sardinian population (allele frequency 0.014), was positively associated with type 1 diabetes (P_{one tail} = 3.7 x 10^–3). In contrast, the background haplotype in which this mutation occurred was common (haplotype frequency 0.117) and neutrally associated with disease. We did not confirm disease associations reported in other populations for non +1858C>T variants (rs2488457, rs1310182, and rs3811021), although they were present in appreciable frequencies in Sardinia. Additional weak disease associations with rare variants were detected in the Sardinian families but not confirmed in independent case-control sample sets and are most likely spurious.

CONCLUSIONS— We provide further evidence that the +1858C>T polymorphism is primarily associated with type 1 diabetes and exclude major contributions from other purportedly relevant variants within this gene.

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