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PTPN22 Trp(620) explains the association of chromosome 1p13 with type 1 diabetes and shows a statistical interaction with HLA class II genotypes

Smyth, DJ; Cooper, JD; Howson, JMM; Walker, NM; Plagnol, V; Stevens, H; ... Todd, JA; + view all (2008) PTPN22 Trp(620) explains the association of chromosome 1p13 with type 1 diabetes and shows a statistical interaction with HLA class II genotypes. DIABETES , 57 (6) 1730 - 1737. 10.2337/db07-1131.

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Abstract

OBJECTIVE-The disease association of the common 1858C>T Arg620Trp (rs2476601) nonsynonymous single nucleotide polymorphism (SNP) of protein tyrosine phosphatase; nonreceptor type 22 (PTPN22) on chromosome 1p13 has been confirmed in type 1 diabetes and also in other autoimmune diseases, including rheumatoid arthritis and Graves' disease. Some studies have reported additional associated SNPs independent of rs2476601/Trp(620), suggesting that it may not be the sole causal variant in the region and that the relative risk of rs2476601/Trp(620) is greater in lower risk by HLA class II genotypes than in the highest risk class II risk category.RESEARCH DESIGN AND METHODS-We resequenced PTPN22 and used these and other data to provide > 150 SNPs to evaluate the association of the PTPN22 gene and its flanking chromosome region with type 1 diabetes in a minimum of 2,000 case subjects and 2,400 control subjects.RESULTS-Due to linkage disequilibrium, we were unable to distinguish between rs2476601/Trp(620) (P = 2.11 X 10(-87)) and rs6679677 (P = 3.21 X 10(-17)), an intergenic SNP between the genes putative homeodomain transcription factor I and round spermatid basic protein 1. None of the previously reported disease-associated SNPs proved to be independent of rs2476601/Trp(620) We did not detect any interaction with age at diagnosis or sex. However, we found that rs2476601/Trp(620) has a higher relative risk in type 1 diabetic case subjects carrying lower risk HLA class II genotypes than in those carrying higher risk ones (P = 1.36 X 10(-4) in a test of interaction).CONCLUSIONS-In our datasets, there was no evidence for allelic heterogeneity at the PTPN22 locus in type 1 diabetes, indicating that the SNP rs247660 1/Trp(620) remains the best candidate in this chromosome region in European populations. The heterogeneity of rs2476601/Trp(620) disease risk by HLA class II genotype is consistent with previous studies, and the joint effect of the two loci is still greater in the high-risk group.

Type:Article
Title:PTPN22 Trp(620) explains the association of chromosome 1p13 with type 1 diabetes and shows a statistical interaction with HLA class II genotypes
DOI:10.2337/db07-1131
Keywords:LYMPHOID TYROSINE PHOSPHATASE, GENOME-WIDE ASSOCIATION, SINGLE-NUCLEOTIDE POLYMORPHISMS, RHEUMATOID-ARTHRITIS, GENETIC ASSOCIATION, PROMOTER POLYMORPHISM, FUNCTIONAL VARIANT, LARGE-SCALE, LOCUS, DISEASE
UCL classification:UCL > School of Life and Medical Sciences > Faculty of Life Sciences > Biosciences (Division of) > Genetics, Evolution and Environment > UCL Genetics Institute

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