Allele and haplotype frequency distribution in PTPN22 gene across variable ethnic groups: Implications for genetic association studies for autoimmune diseases

References

• 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 phosphatase is associated with type I diabetes. Nat Genet. 2004; 36 4: 337–338.
   PubMed Web of Science ®Google Scholar
• Begovich AB, Carlton VE, Honigberg LA, Schrodi SJ, Chokkalingam AP, Alexander HC, Ardlie KG, Huang Q, Smith AM, Spoerke JM, . A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis. Am J Hum Genet. 2004; 75 2: 330–337.
   PubMed Web of Science ®Google Scholar
• 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. 2005; 66 1: 60–64.
   PubMed Web of Science ®Google Scholar
• Onengut-Gumuscu S, Ewens KG, Spielman RS, Concannon P. A functional polymorphism (1858C/T) in the PTPN22 gene is linked and associated with type I diabetes in multiplex families. Genes Immun. 2004; 5 8: 678–680.
   PubMed Web of Science ®Google Scholar
• Smyth D, Cooper JD, Collins JE, Heward JM, Franklyn JA, Howson JM, Vella A, Nutland S, Rance HE, Maier L, . 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. 2004; 53 11: 3020–3023.
   PubMed Web of Science ®Google Scholar
• Zheng W, She JX. Genetic association between a lymphoid tyrosine phosphatase (PTPN22) and type 1 diabetes. Diabetes. 2005; 54 3: 906–908.
   Google Scholar
• Zhernakova A, Eerligh P, Wijmenga C, Barrera P, Roep BO, Koeleman BP. Differential association of the PTPN22 coding variant with autoimmune diseases in a Dutch population. Genes Immun. 2005; 6 6: 459–461.
   Google Scholar
• Hinks A, Barton A, John S, Bruce I, Hawkins C, Griffiths CE, Donn R, Thomson W, Silman A, Worthington J. Association between the PTPN22 gene and rheumatoid arthritis and juvenile idiopathic arthritis in a UK population: Further support that PTPN22 is an autoimmunity gene. Arthritis Rheum. 2005; 52 6: 1694–1699.
   PubMed Web of Science ®Google Scholar
• Orozco G, Sanchez E, Gonzalez-Gay MA, Lopez-Nevot MA, Torres B, Caliz R, Ortego-Centeno N, Jimenez-Alonso J, Pascual-Salcedo D, Balsa A, . Association of a functional single-nucleotide polymorphism of PTPN22, encoding lymphoid protein phosphatase, with rheumatoid arthritis and systemic lupus erythematosus. Arthritis Rheum. 2005; 52 1: 219–224.
   Google Scholar
• Simkins HM, Merriman ME, Highton J, Chapman PT, O'Donnell JL, Jones PB, Gow PJ, McLean L, Pokorny V, Harrison AA, . Association of the PTPN22 locus with rheumatoid arthritis in a New Zealand Caucasian cohort. Arthritis Rheum. 2005; 52 7: 2222–2225.
   Google Scholar
• Kyogoku C, Langefeld CD, Ortmann WA, Lee A, Selby S, Carlton VE, Chang M, Ramos P, Baechler EC, Batliwalla FM, . Genetic association of the R620W polymorphism of protein tyrosine phosphatase PTPN22 with human SLE. Am J Hum Genet. 2004; 75 3: 504–507.
   PubMed Web of Science ®Google Scholar
• Skorka A, Bednarczuk T, Bar-Andziak E, Nauman J, Ploski R. Lymphoid tyrosine phosphatase (PTPN22/LYP) variant and Graves' disease in a Polish population: Association and gene dose-dependent correlation with age of onset. Clin Endocrinol (Oxf). 2005; 62 6: 679–682.
   PubMed Web of Science ®Google Scholar
• Velaga MR, Wilson V, Jennings CE, Owen CJ, Herington S, Donaldson PT, Ball SG, James RA, Quinton R, Perros P, . The codon 620 tryptophan allele of the lymphoid tyrosine phosphatase (LYP) gene is a major determinant of Graves' disease. J Clin Endocrinol Metab. 2004; 89 11: 5862–5865.
   PubMed Web of Science ®Google Scholar
• Viken MK, Amundsen SS, Kvien TK, Boberg KM, Gilboe IM, Lilleby V, Sollid LM, Forre OT, Thorsby E, Smerdel A, . Association analysis of the 1858C>T polymorphism in the PTPN22 gene in juvenile idiopathic arthritis and other autoimmune diseases. Genes Immun. 2005; 6 3: 271–273.
   PubMed Web of Science ®Google Scholar
• Gregersen PK, Lee HS, Batliwalla F, Begovich AB. PTPN22: Setting thresholds for autoimmunity. Semin Immunol. 2006; 18 4: 214–223.
   PubMed Web of Science ®Google Scholar
• Seldin MF, Shigeta R, Villoslada P, Selmi C, Tuomilehto J, Silva G, Belmont JW, Klareskog L, Gregersen PK. European population substructure: Clustering of northern and southern populations. PLoS Genet. 2006; 2 9: e143.
   Google Scholar
• Kawasaki E, Awata T, Ikegami H, Kobayashi T, Maruyama T, Nakanishi K, Shimada A, Uga M, Kurihara S, Kawabata Y, . 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. 2006; 140 6: 586–593.
   PubMed Web of Science ®Google Scholar
• Mori M, Yamada R, Kobayashi K, Kawaida R, Yamamoto K. Ethnic differences in allele frequency of autoimmune-disease-associated SNPs. J Hum Genet. 2005; 50 5: 264–266.
   PubMed Web of Science ®Google Scholar
• Zhang ZH, Chen F, Zhang XL, Jin Y, Bai J, Fu SB. PTPN22 allele polymorphisms in 15 Chinese populations. Int J Immunogenet. 2008; 35 6: 433–437.
   Google Scholar
• Carlton VE, Hu X, Chokkalingam AP, Schrodi SJ, Brandon R, Alexander HC, Chang M, Catanese JJ, Leong DU, Ardlie KG, . PTPN22 genetic variation: Evidence for multiple variants associated with rheumatoid arthritis. Am J Hum Genet. 2005; 77 4: 567–581.
   PubMed Web of Science ®Google Scholar
• Tang H, Quertermous T, Rodriguez B, Kardia SL, Zhu X, Brown A, Pankow JS, Province MA, Hunt SC, Boerwinkle E, . Genetic structure, self-identified race/ethnicity, and confounding in case-control association studies. Am J Hum Genet. 2005; 76 2: 268–275.
   PubMed Web of Science ®Google Scholar
• Devlin B, Roeder K. Genomic control for association studies. Biometrics. 1999; 55 4: 997–1004.
   PubMed Web of Science ®Google Scholar
• Pritchard JK, Donnelly P. Case-control studies of association in structured or admixed populations. Theor Popul Biol. 2001; 60 3: 227–237.
   Google Scholar
• Smith MW, Patterson N, Lautenberger JA, Truelove AL, McDonald GJ, Waliszewska A, Kessing BD, Malasky MJ, Scafe C, Le E, . A high-density admixture map for disease gene discovery in african americans. Am J Hum Genet. 2004; 74 5: 1001–1013.
   Google Scholar
• Yang N, Li H, Criswell LA, Gregersen PK, Alarcon-Riquelme ME, Kittles R, Shigeta R, Silva G, Patel PI, Belmont JW, . Examination of ancestry and ethnic affiliation using highly informative diallelic DNA markers: Application to diverse and admixed populations and implications for clinical epidemiology and forensic medicine. Hum Genet. 2005; 118 3–4: 382–392.
   Web of Science ®Google Scholar
• Lins TC, Nogueira LR, Lima RM, Gentil P, Oliveira RJ, Pereira RW. A multiplex single-base extension protocol for genotyping Cdx2, FokI, BsmI, ApaI, and TaqI polymorphisms of the vitamin D receptor gene. Genet Mol Res. 2007; 6 2: 216–224.
   Google Scholar
• Lins TC, Vieira RG, Abreu BS, Grattapaglia D, Pereira RW. Genetic composition of Brazilian population samples based on a set of twenty eight ancestry informative SNPs. Am J Hum Biol 2009; Epub(2009/07/28): DOI 10.1002/ajhb.20976.
   Google Scholar
• Peakall R, Smouse PE. Genalex 6: Genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecol Notes. 2006; 6 1: 288–295.
   Web of Science ®Google Scholar
• Excoffier L, Laval G, Schneider S. Arlequin version 3.0: An integrated software package for population genetics data analysis. Evol BioinformOnline. 2005; 1:47–50.
   PubMed Web of Science ®Google Scholar
• Kimmel G, Shamir R. GERBIL: Genotype resolution and block identification using likelihood. Proc Natl Acad Sci USA. 2005; 102 1: 158–162.
   Google Scholar
• Lins TC, Abreu BS, Pereira RW. TagSNP transferability and relative loss of variability prediction from HapMap to an admixed population. J Biomed Sci. 2009; 16:73.
   Google Scholar
• Tsai HJ, Choudhry S, Naqvi M, Rodriguez-Cintron W, Burchard EG, Ziv E. Comparison of three methods to estimate genetic ancestry and control for stratification in genetic association studies among admixed populations. Hum Genet. 2005; 118 3–4: 424–433.
   Web of Science ®Google Scholar
• Purcell S, Daly MJ, Sham PC. WHAP: Haplotype-based association analysis. Bioinformatics. 2007; 23 2: 255–256.
   Google Scholar
• De Bakker P, Graham R, Altshuler D, Henderson B, Haiman C. Transferability of tag SNPs to capture common genetic variation in DNA repair genes across multiple populations. Pac Symp Biocomput. 2006478–486.
   Google Scholar
• De Bakker P, Yelensky R, Pe'er I, Gabriel S, Daly M, Altshuler D. Efficiency and power in genetic association studies. Nat Genet. 2005; 37 11: 1217–1223.
   PubMed Web of Science ®Google Scholar
• Wigginton JE, Cutler DJ, Abecasis GR. A note on exact tests of Hardy-Weinberg equilibrium. Am J Hum Genet. 2005; 76 5: 887–893.
   PubMed Web of Science ®Google Scholar
• Heward JM, Brand OJ, Barrett JC, Carr-Smith JD, Franklyn JA, Gough SC. Association of PTPN22 haplotypes with Graves' disease. J Clin Endocrinol Metab. 2007; 92 2: 685–690.
   PubMed Web of Science ®Google Scholar
• Ikari K, Momohara S, Inoue E, Tomatsu T, Hara M, Yamanaka H, Kamatani N. Haplotype analysis revealed no association between the PTPN22 gene and RA in a Japanese population. Rheumatology (Oxford). 2006; 45 11: 1345–1348.
   PubMed Web of Science ®Google Scholar
• Zoledziewska M, Perra C, Orru V, Moi L, Frongia P, Congia M, Bottini N, Cucca F. Further evidence of a primary, causal association of the PTPN22 620W variant with type 1 diabetes. Diabetes. 2008; 57 1: 229–234.
   PubMed Web of Science ®Google Scholar
• Kochi Y, Suzuki A, Yamada R, Yamamoto K. Genetics of rheumatoid arthritis: Underlying evidence of ethnic differences. J Autoimmun. 2009; 32 3–4: 158–162.
   PubMed Web of Science ®Google Scholar
• Dieude P, Teixeira VH, Pierlot C, Cornelis F, Petit-Teixeira E. Testing for linkage and association with rheumatoid arthritis a PTPN22 promoter polymorphism reported to be associated and linked with type 1 diabetes in the Caucasian population. Ann Rheum Dis. 2008; 67 6: 900–901.
   Google Scholar
• Cooper JD, Smyth DJ, Smiles AM, Plagnol V, Walker NM, Allen JE, Downes K, Barrett JC, Healy BC, Mychaleckyj JC, . Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. Nat Genet. 2008; 40 12: 1399–1401.
   PubMed Web of Science ®Google Scholar
• Raychaudhuri S, Remmers EF, Lee AT, Hackett R, Guiducci C, Burtt NP, Gianniny L, Korman BD, Padyukov L, Kurreeman FA, . Common variants at CD40 and other loci confer risk of rheumatoid arthritis. Nat Genet. 2008; 40 10: 1216–1223.
   PubMed Web of Science ®Google Scholar
• WTCCC. Genome-wide association study of 14,000 cases of seven common diseases and 3000 shared controls. Nature. 2007; 447 7145: 661–678.
   PubMed Web of Science ®Google Scholar
• Ray D, Tomar N, Gupta N, Goswami R. Protein tyrosine phosphatase non-receptor type 22 (PTPN22) gene R620W variant and sporadic idiopathic hypoparathyroidism in Asian Indians. Int J Immunogenet. 2006; 33 4: 237–240.
   Google Scholar
• Mastana S, Gilmour A, Ghelani A, Smith H, Samanta A. Association of PTPN22 with rheumatoid arthritis among South Asians in the UK. J Rheumatol. 2007; 34 10: 1984–1986.
   Web of Science ®Google Scholar
• Baca V, Velazquez-Cruz R, Salas-Martinez G, Espinosa-Rosales F, Saldana-Alvarez Y, Orozco L. Association analysis of the PTPN22 gene in childhood-onset systemic lupus erythematosus in Mexican population. Genes Immun. 2006; 7 8: 693–695.
   Google Scholar
• Gomez LM, Anaya JM, Gonzalez CI, Pineda-Tamayo R, Otero W, Arango A, Martin J. PTPN22 C1858T polymorphism in Colombian patients with autoimmune diseases. Genes Immun. 2005; 6 7: 628–631.
   Google Scholar
• 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. 2006; 7 5: 274–278.
   PubMed Web of Science ®Google Scholar
• Tsai HJ, Kho JY, Shaikh N, Choudhry S, Naqvi M, Navarro D, Matallana H, Castro R, Lilly CM, Watson HG, . Admixture-matched case-control study: A practical approach for genetic association studies in admixed populations. Hum Genet. 2006; 118 5: 626–639.
   Google Scholar
• Callegari-Jacques SM, Grattapaglia D, Salzano FM, Salamoni SP, Crossetti SG, Ferreira ME, Hutz MH. Historical genetics: Spatiotemporal analysis of the formation of the Brazilian population. Am J Hum Biol. 2003; 15 6: 824–834.
   Google Scholar
• Suarez-Kurtz G, Vianna-Jorge R, Perini JA, Pena SD. Detection of CYP2C9*5 in a white Brazilian subject. Clin Pharmacol Ther. 2005; 77 6: 587–588.
   Google Scholar