PTPN22 Trp620 explains the association of chromosome 1p13 with type 1 diabetes and shows a statistical interaction with HLA class II genotypes

Diabetes

Volumn 57, Issue 6, 2008, Pages 1730-1737

  Smyth, Deborah J ^a   Cooper, Jason D ^a   Howson, Joanna M M ^a   Walker, Neil M ^a   Plagnol, Vincent ^a   Stevens, Helen ^a   Clayton, David G ^a   Todd, John A ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTOR RELATED PROTEIN COMPLEX 4 BETA1 SUBUNIT; DNA CROSS LINK REPAIR 1B; HLA ANTIGEN CLASS 2; NON RECEPTOR PROTEIN TYROSINE PHOSPHATASE 22; PUTATIVE HOMEODOMAIN TRANSCRIPTION FACTOR 1; ROUND SPERMATID BASIC PROTEIN 1; UNCLASSIFIED DRUG; ARGININE; HLA D ANTIGEN; PTPN22 PROTEIN, HUMAN; TRYPTOPHAN;

ARTICLE; CHROMOSOME 1; CHROMOSOME 1P; CONTROLLED STUDY; DISEASE ASSOCIATION; GENE LOCUS; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC HETEROGENEITY; GENOTYPE; HUMAN; HUMAN TISSUE; INSULIN DEPENDENT DIABETES MELLITUS; MAJOR CLINICAL STUDY; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; CHROMOSOME MAP; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC MARKER; GENETIC POLYMORPHISM; GENETICS; REFERENCE VALUE;

ARGININE; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN, PAIR 1; DIABETES MELLITUS, TYPE 1; GENE FREQUENCY; GENETIC MARKERS; GENOTYPE; HLA-D ANTIGENS; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 22; REFERENCE VALUES; TRYPTOPHAN;

EID: 48249152671     PISSN: 00121797     EISSN: 1939327X     Source Type: Journal    
DOI: 10.2337/db07-1131     Document Type: Article

References (46)

1. Cucca F, Lampis R, Congia M, Angius E, Nutland S, Bain SC, Barnett AH, Todd JA: A correlation between the relative predisposition of MHC class II alleles to type 1 diabetes and the structure of their proteins. Hum Mol Genet 10:2025-2037, 2001
2. Nejentsev S, Howson JM, Walker NM, Szeszko J, Field SF, Stevens HE, Reynolds P, Hardy M, King E, Masters J, Hulme J, Maier LM, Smyth D, Bailey R, Cooper JD, Ribas G, Campbell RD, Clayton DG, Todd JA; Wellcome Trust Case Control Consortium: Localization of type 1 diabetes susceptibility to the MHC class I genes HLA-B and HLA-A. Nature, 450:887-892, 2007
3. Bell GI, Horita S, Karam JH: A polymorphic locus near the human insulin gene is associated with insulin-dependent diabetes mellitus. Diabetes 33:176-183, 1984
4. Barratt BJ, Payne F, Lowe CE, Hermann R, Healy BC, Harold D, Concan-non P, Gharani N, McCarthy MI, Olavesen MG, McCormack R, Guja C, Ionescu-Tirgoviste C, Undlien DE, Ronningen KS, Gillespie KM, Tuom-ilehto-Wolf E, Tuomilehto J, Bennett ST, Clayton DG, Cordell HJ, Todd JA: Remapping the insulin gene/IDDM2 locus in type 1 diabetes. Diabetes 53:1884-1889, 2004
5. Nistico L, Buzzetti R, Pritchard LE, Van der Auwera B, Giovannini C, Bosi E, Larrad MT, Rios MS, Chow CC, Cockram CS, Jacobs K, Mijovic C, Bain SC, Barnett AH, Vandewalle CL, Schuit F, Gorus FK, Tosi R, Pozzilli P, Todd JA: The CTLA-4 gene region of chromosome 2q33 is linked to, and associated with, type 1 diabetes: Belgian Diabetes Registry. Hum Mol Genet 5:1075-1080, 1996
6. Ueda H, Howson JM, Esposito L, Heward J, Snook H, Chamberlain G, Rainbow DB, Hunter KM, Smith AN, Di Genova G, Herr MH, Dahlman I, Payne F, Smyth D, Lowe C, Twells RC, Howlett S, Healy B, Nutland S, Rance HE, Everett V, Smink LJ, Lam AC, Cordell HJ, Walker NM, Bordin C, Hulme J, Motzo C, Cucca F, Hess JF, Metzker ML, Rogers J, Gregory S, Allahabadia A, Nithiyananthan R, Tuomilehto-Wolf E, Tuomilehto J, Bing-ley P, Gillespie KM, Undlien DE, Ronningen KS, Guja C, Ionescu-Tirgoviste C, Savage DA, Maxwell AP, Carson DJ, Patterson CC, Franklyn JA, Clayton DG, Peterson LB, Wicker LS, Todd JA, Gough SC: Association of the T-cell regulatory gene CTLA4 with susceptibility to autoimmune disease. Nature 423:506-511, 2003
7. Bottini N, Musumeci L, Alonso A, Rahmouni S, Nika K, Rostamkhani M, MacMurray J, Meloni GF, Lucarelli P, Pellecchia M, Eisenbarth GS, Comings D, Mustelin T: A functional variant of lymphoid tyrosine phos-phatase is associated with type I diabetes. Nat Genet 36:337-338, 2004
8. Lowe CE, Cooper JD, Brusko T, Walker NM, Smyth DJ, Bailey R, Bourget K, Plagnol V, Field S, Atkinson M, Clayton DG, Wicker LS, Todd JA: Large-scale genetic fine mapping and genotype-phenotype associations implicate polymorphism in the IL2RA region in type 1 diabetes. Nat Genet, 39:1074-1082, 2007
9. Vella A, Cooper JD, Lowe CE, Walker N, Nutland S, Widmer B, Jones R, Ring SM, McArdle W, Pembrey ME, Strachan DP, Dunger DB, Twells RC, Clayton DG, Todd JA: Localization of a type 1 diabetes locus in the IL2RA/CD25 region by use of tag single-nucleotide polymorphisms. Am J Hum Genet 76:773-779, 2005
10. Qu HQ, Montpetit A, Ge B, Hudson TJ, Polychronakos C: Toward further mapping of the association between the IL2RA locus and type 1 diabetes. Diabetes 56:1174-1176, 2007
11. Smyth DJ, Cooper JD, Bailey R, Field S, Burren O, Smink LJ, Guja C, Ionescu-Tirgoviste C, Widmer B, Dunger DB, Savage DA, Walker NM, Clayton DG, Todd JA: A genome-wide association study of nonsynony-mous SNPs identifies a type 1 diabetes locus in the interferon-induced helicase (IFIH1) region. Nat Genet 38:617-619, 2006
12. WTCCC: Genome-wide association study of14,000 cases ofseven common diseases and 3,000 shared controls. Nature 447:661-678, 2007
13. Todd JA, Walker NM, Cooper JD, Smyth DJ, Downes K, Plagnol V, Bailey R, Nejentsev S, Field SF, Payne F, Lowe CE, Szeszko JS, Hafler JP, Zeitels L, Yang JH, Vella A, Nutland S, Stevens HE, Schuilenburg H, Coleman G, Maisuria M, Meadows W, Smink LJ, Healy B, Burren OS, Lam AA, Ovington NR, Allen J, Adlem E, Leung HT, Wallace C, Howson JM, Guja C, Ionescu-Tirgoviste C, Simmonds MJ, Heward JM, Gough SC, Dunger DB, Wicker LS, Clayton DG: Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. Nat Genet, 39:857-864, 2007
14. Hakonarson H, Grant SF, Bradfield JP, Marchand L, Kim CE, Glessner JT, Grabs R, Casalunovo T, Taback SP, Frackelton EC, Lawson ML, Robinson LJ, Skraban R, Lu Y, Chiavacci RM, Stanley CA, Kirsch SE, Rappaport EF, Orange JS, Monos DS, Devoto M, Qu HQ, Polychronakos C: A genome-wide association study identifies KIAA0350 as a type 1 diabetes gene. Nature 448:591-594, 2007
15. Smyth D, Cooper JD, Collins JE, Heward JM, Franklyn JA, Howson JM, Vella A, Nutland S, Rance HE, Maier L, Barratt BJ, Guja C, Ionescu-Tirgoviste C, Savage DA, Dunger DB, Widmer B, Strachan DP, Ring SM, Walker N, Clayton DG, Twells RC, Gough SC, Todd JA: Replication of an association between the lymphoid tyrosine phosphatase locus (LYP/PTPN22) with type 1 diabetes and evidence for its role as a general autoimmunity locus. Diabetes 53:3020-3023, 2004
16. Ladner MB, Bottini N, Valdes AM, Noble JA: Association of the single nucleotide polymorphism C1858T of the PTPN22 gene with type 1 diabetes. Hum, Immunol 66:60-64, 2005
17. Qu H, Tessier MC, Hudson TJ, Polychronakos C: Confirmation of the association of the R620W polymorphism in the protein tyrosine phosphatase PTPN22 with type 1 diabetes in a family based study. J Med Genet 42:266-270, 2005
18. Zheng W, She JX: Genetic association between a lymphoid tyrosine phosphatase (PTPN22) and type 1 diabetes. Diabetes 54:906-908, 2005
19. Vang T, Congia M, Macis MD, Musumeci L, Orru V, Zavattari P, Nika K, Tautz L, Tasken K, Cucca F, Mustelin T, Bottini N: Autoimmune-associated lymphoid tyrosine phosphatase is a gain-of-function variant. Nat Genet 37:1317-1319, 2005
20. Bottini N, Vang T, Cucca F, Mustelin T: Role of PTPN22 in type 1 diabetes and other autoimmune diseases. Semin Immunol 18:207-213, 2006
21. Aarnisalo J, Treszl A, Svec P, Marttila J, Oling V, Simell O, Knip M, Korner A, Madacsy L, Vasarhelyi B, Ilonen J, Hermann R: Reduced CD4+T cell activation in children with type 1 diabetes carrying the PTPN22Lyp620Trp variant. J Autoimmun, 2008. DOI: 10.1016.jaut.2008.01.001
22. Steer S, Abkevich V, Gutin A, Cordell HJ, Gendall KL, Merriman ME, Rodger RA, Rowley KA, Chapman P, Gow P, Harrison AA, Highton J, Jones PB, O'Donnell J, Stamp L, Fitzgerald L, Iliev D, Kouzmine A, Tran T, Skolnick MH, Timms KM, Lanchbury JS, Merriman TR: Genomic DNA pooling for whole-genome association scans in complex disease: empirical demonstration of efficacy in rheumatoid arthritis. Genes Immun 8:57-68, 2007
23. Onengut-Gumuscu S, Buckner JH, Concannon P: A haplotype-based analysis of the PTPN22 locus in type 1 diabetes. Diabetes 55:2883-2889, 2006
24. Carlton VE, Hu X, Chokkalingam AP, Schrodi SJ, Brandon R, Alexander HC, Chang M, Catanese JJ, Leong DU, Ardlie KG, Kastner DL, Seldin MF, Criswell LA, Gregersen PK, Beasley E, Thomson G, Amos CI, Begovich AB: PTPN22 genetic variation: evidence for multiple variants associated with rheumatoid arthritis. Am J Hum Genet 77:567-581, 2005
25. Kawasaki E, Awata T, Ikegami H, Kobayashi T, Maruyama T, Nakanishi K, Shimada A, Uga M, Kurihara S, Kawabata Y, Tanaka S, Kanazawa Y, Lee I, Eguchi K: Systematic search for single nucleotide polymorphisms in a lymphoid tyrosine phosphatase gene (PTPN22): association between a promoter polymorphism and type 1 diabetes in Asian populations. Am J Med Genet A 140:586-593, 2006
26. Viken MK, Olsson M, Flam ST, Forre O, Kvien TK, Thorsby E, Lie BA: The PTPN22 promoter polymorphism -1123G>C association cannot be distinguished from the 1858C>T association in a Norwegian rheumatoid arthritis material. Tissue Antigens 70:190-197, 2007
27. Chelala C, Duchatelet S, Joffret ML, Bergholdt R, Dubois-Laforgue D, Ghandil P, Pociot F, Caillat-Zucman S, Timsit J, Julier C: PTPN22 R620W functional variant in type 1 diabetes and autoimmunity related traits. Diabetes 56:522-526, 2007
28. Heward JM, Brand OJ, Barrett JC, Carr-Smith JD, Franklyn JA, Gough SC:Association of PTPN22 haplotypes with Graves' disease. J Clin Endocrinol Metab 92:685-690, 2007
29. Hermann R, Lipponen K, Kiviniemi M, Kakko T, Veijola R, Simell O, Knip M, Ilonen J: Lymphoid tyrosine phosphatase (LYP/PTPN22) Arg620Trp variant regulates insulin autoimmunity and progression to type 1 diabetes. Diabetologia 49:1198-1208, 2006
30. Steck AK, Liu SY, McFann K, Barriga KJ, Babu SR, Eisenbarth GS, Rewers MJ, She JX: Association of the PTPN22/LYP gene with type 1 diabetes. Pediatr Diabetes 7:274-278, 2006
31. Clayton DG, Walker NM, Smyth DJ, Pask R, Cooper JD, Maier LM, Smink LJ, Lam AC, Ovington NR, Stevens HE, Nutland S, Howson JM, Faham M, Moorhead M, Jones HB, Falkowski M, Hardenbol P, Willis TD, Todd JA:Population structure, differential bias and genomic control in a large-scale, case-control association study. Nat Genet 37:1243-1246, 2005
32. Consortium TIH: A haplotype map of the human genome. Nature 437:1299-1320, 2005
33. Hardenbol P, Yu F, Belmont J, Mackenzie J, Bruckner C, Brundage T, Boudreau A, Chow S, Eberle J, Erbilgin A, Falkowski M, Fitzgerald R, Ghose S, Iartchouk O, Jain M, Karlin-Neumann G, Lu X, Miao X, Moore B, Moorhead M, Namsaraev E, Pasternak S, Prakash E, Tran K, Wang Z, Jones HB, Davis RW, Willis TD, Gibbs RA: Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay. Genome Res 15:269-275, 2005
34. Plagnol V, Cooper JD, Todd JA, Clayton DG: A method to address differential bias in genotyping in large-scale association studies. PLoS Genet 3: e74, 2007
35. Cordell HJ, Clayton DG: A unified stepwise regression procedure for evaluating the relative effects of polymorphisms within a gene using case/control or family data: application to HLA in type 1 diabetes. Am J Hum Genet 70:124-141, 2002
36. Chapman J, Clayton D: Detecting association using epistatic information. Genet Epidemiol 31:894-909, 2007
37. Cordell HJ: Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans. Hum Mol Genet 11:2463-2468, 2002
38. Weinberg CR, Umbach DM: Choosing a retrospective design to assess joint genetic and environmental contributions to risk. Am J Epidemiol 152:197-203, 2000
39. Koeleman BP, Lie BA, Undlien DE, Dudbridge F, Thorsby E, de Vries RR, Cucca F, Roep BO, Giphart MJ, Todd JA: Genotype effects and epistasis in type 1 diabetes and HLA-DQ trans dimer associations with disease. Genes Immun 5:381-388, 2004
40. Umbach DM, Weinberg CR: Designing and analysing case-control studies to exploit independence of genotype and exposure. Stat Med 16:1731-1743, 1997
41. Hill RJ, Zozulya S, Lu YL, Ward K, Gishizky M, Jallal B: The lymphoid protein tyrosine phosphatase Lyp interacts with the adaptor molecule Grb2 and functions as a negative regulator of T-cell activation. Exp Hematol 30:237-244, 2002
42. Cordell HJ, Barratt BJ, Clayton DG: Case/pseudocontrol analysis in genetic association studies: a unified framework for detection of genotype and haplotype associations, gene-gene and gene-environment interactions, and parent-of-origin effects. Genet Epidemiol 26:167-185, 2004
43. Howson JM, Barratt BJ, Todd JA, Cordell HJ: Comparison of population-and family-based methods for genetic association analysis in the presence of interacting loci. Genet Epidemiol 29:51-67, 2005
44. Bennett ST, Barnes C, Cox A, Davies L, Brown C: Toward the 1,000 dollars human genome. Pharmacogenomics 6:373-382, 2005
45. Bentley DR: Whole-genome re-sequencing. Curr Opin Genet Dev 16:545-552, 2006
46. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM: Genome sequencing in microfabricated high-density picoli-tre reactors. Nature 437:376-380, 2005