Rs2476601 T Allele (R620W) Defines High-Risk PTPN22 Type I Diabetes-Associated Haplotypes with Preliminary Evidence for an Additional Protective Haplotype
Genes and Immunity (2009) 10, S21–S26 & 2009 Macmillan Publishers Limited All rights reserved 1466-4879/09 $32.00 www.nature.com/gene ORIGINAL ARTICLE rs2476601 T allele (R620W) defines high-risk PTPN22 type I diabetes-associated haplotypes with preliminary evidence for an additional protective haplotype AK Steck1, EE Baschal1, JM Jasinski1, BO Boehm2, N Bottini3, P Concannon4, C Julier5, G Morahan6, JA Noble7, C Polychronakos8, JX She9, GS Eisenbarth1 and the Type I Diabetes Genetics Consortium 1Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, CO, USA; 2Department of Internal Medicine, Ulm University, Ulm, Germany; 3Institute for Genetic Medicine, University of Southern California, Los Angeles, CA, USA; 4Department of Biochemistry and Molecular Genetics and Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA; 5Ge´ne´tique des Maladies Infectieuses et Autoimmunes, Institut Pasteur, Paris, France; 6Western Australian Institute for Medical Research, The University of Western Australia, Perth, Australia; 7Children’s Hospital Oakland Research Institute, Oakland, CA, USA; 8Department of Human Genetics, The McGill University Health Center, Montreal, Quebec, Canada and 9Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta, GA, USA Protein tyrosine phosphatase non-receptor type 22 (PTPN22) is the third major locus affecting risk of type I diabetes (T1D), after HLA-DR/DQ and INS. The most associated single-nucleotide polymorphism (SNP), rs2476601, has a C-4T variant and results in an arginine (R) to tryptophan (W) amino acid change at position 620. To assess whether this, or other specific variants, are responsible for T1D risk, the Type I Diabetes Genetics Consortium analyzed 28 PTPN22 SNPs in 2295 affected sib-pair (ASP) families.
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