Meta-analysis and imputation identifies a 109kb risk haplotype spanning TNFAIP3 associated with lupus nephritis and hematologic manifestations

Genes and Immunity

Volumn 10, Issue 5, 2009, Pages 470-477

  Bates, J S ^a   Lessard, C J ^a,b   Leon, J M ^a   Nguyen, T ^a   Battiest, L J ^a   Rodgers, J ^a   Kaufman, K M ^a,b,c   James, J A ^a   Gilkeson, G S ^d   Kelly, J A ^a   Humphrey, M B ^b   Harley, J B ^a   Gray McGuire, C ^a   Moser, K L ^a   Gaffney, P M ^a  

^a OKLAHOMA MEDICAL RESEARCH FOUNDATION   (United States)

^b UNIVERSITY OF OKLAHOMA COLLEGE OF MEDICINE   (United States)

^c VETERANS AFFAIRS MEDICAL CENTER   (United States)

^d MEDICAL UNIVERSITY OF SOUTH CAROLINA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN TNFAIP3; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN;

ALLELE; ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; GENETIC ASSOCIATION; GENETIC IDENTIFICATION; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HAPLOTYPE MAP; HETEROZYGOSITY; HOMOZYGOSITY; HUMAN; LUPUS ERYTHEMATOSUS NEPHRITIS; MAJOR CLINICAL STUDY; PHENOTYPE; POPULATION BASED CASE CONTROL STUDY; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SYSTEMIC LUPUS ERYTHEMATOSUS;

GENOME-WIDE ASSOCIATION STUDY; HAPLOTYPES; INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS; LUPUS NEPHRITIS; NUCLEAR PROTEINS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 67849116005     PISSN: 14664879     EISSN: 14765470     Source Type: Journal    
DOI: 10.1038/gene.2009.31     Document Type: Article

References (26)

1. Harley JB, Alarcon-Riquelme ME, Criswell LA, Jacob CO, Kimberly RP, Moser KL et al. Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat Genet 2008; 40: 204-210.
2. Graham RR, Cotsapas C, Davies L, Hackett R, Lessard CJ, Leon JM et al Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus. Nat Genet 2008; 40: 1059-1061.
3. Hom G, Graham RR, Modrek B, Taylor KE, Ortmann W, Garnier S et al. Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX. N Engl J Med 2008; 358: 900-909.
4. Kozyrev SV, Abelson AK, Wojcik J, Zaghlool A, Linga Reddy MV, Sanchez E et al. Functional variants in the B-cell gene BANK1 are associated with systemic lupus erythematosus. Nat Genet 2008; 40: 211-216.
5. Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 2007; 447: 661-678.
6. Thomson W, Barton A, Ke X, Eyre S, Hinks A, Bowes J et al. Rheumatoid arthritis association at 6q23. Nat Genet 2007; 39 1431-1433.
7. Plenge RM, Cotsapas C, Davies L, Price AL, de Bakker PI, Maller J et al. Two independent alleles at 6q23 associated with risk of rheumatoid arthritis. Nat Genet 2007; 39: 1477-1482.
8. Musone SL, Taylor KE, Lu TT, Nititham J, Ferreira RC, Ortmann W et al Multiple polymorphisms in the TNFAIP3 region are independently associated with systemic lupus erythematosus. Nat Genet 2008; 40: 1062-1064.
9. Hitotsumatsu O, Ahmad RC, Tavares R, Wang M, Philpott D, Turer EE et al. The ubiquitin-editing enzyme A20 restricts nucleotide-binding oligomerization domain containing 2-triggered signals. Immunity 2008; 28: 381-390.
10. Lee EG, Boone DL, Chai S, Libby SL, Chien M, Lodolce JP et al. Failure to regulate TNF-induced NF-kappaB and cell death responses in A20-deficient mice. Science 2000; 289: 2350-2354.
11. Boone DL, Turer EE, Lee EG, Ahmad RC, Wheeler MT, Tsui C et al. The ubiquitin-modifying enzyme A20 is required for termination of Toll-like receptor responses. Nat Immunol 2004; 5: 1052-1060.
12. Wertz IE, O'Rourke KM, Zhou H, Eby M, Aravind L, Seshagiri S et al De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling. Nature 2004; 430: 694-699.
13. Jaattela M, Mouritzen H, Elling F, Bastholm L. A20 zinc finger protein inhibits TNF and IL-1 signaling. J Immunol 1996; 156: 1166-1173.
14. Evans PC, Ovaa H, Hamon M, Kilshaw PJ, Hamm S, Bauer S et al. Zinc-finger protein A20, a regulator of inflammation and cell survival, has de-ubiquitinating activity. Biochem J 2004; 378 (Pt 3): 727-734.
15. Mauro C, Pacifico F, Lavorgna A, Mellone S, Iannetti A, Acquaviva R et al. ABIN-1 binds to NEMO/IKKgamma and co-operates with A20 in inhibiting NF-kappaB. J Biol Chem 2006; 281: 18482-18488.
16. Fernando MM, Stevens CR, Walsh EC, De Jager PL, Goyette P, Plenge RM et al. Defining the role of the MHC in autoimmunity: A review and pooled analysis. PLoS Genet 2008; 4: E1000024.
17. Graham RR, Kozyrev SV, Baechler EC, Reddy MV, Plenge RM, Bauer JW et al. A common haplotype of interferon regulatory factor 5 (IRF5) regulates splicing and expression and is associated with increased risk of systemic lupus erythematosus. Nat Genet 2006; 38: 550-555.
18. Remmers EF, Plenge RM, Lee AT, Graham RR, Hom G, Behrens TW et al. STAT4 and the risk of rheumatoid arthritis and systemic lupus erythematosus. N Engl J Med 2007; 357: 977-986.
19. Nath SK, Han S, Kim-Howard X, Kelly JA, Viswanathan P, Gilkeson GS et al. A nonsynonymous functional variant in integrin-alpha(M) (encoded by ITGAM) is associated with systemic lupus erythematosus. Nat Genet 2008; 40: 152-154.
20. de Bakker PI, McVean G, Sabeti PC, Miretti MM, Green T, Marchini J et al. A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nat Genet 2006; 38: 1166-1172.
21. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D et al. PLINK: A tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007; 81: 559-575.
22. Hochberg MC. Updating the American College of Rheumatology revised criteria for the classification of systemic lupus erythematosus. Arthritis Rheum 1997; 40: 1725.
23. Tan EM, Cohen AS, Fries JF, Masi AT, McShane DJ, Rothfield NF et al The 1982 revised criteria for the classification of systemic lupus erythematosus. Arthritis Rheum 1982; 25: 1271-1277.
24. Gaffney PM, Langefeld CD, Graham RR, Ortmann WA, Williams AH, Rodine PR et al. Fine-mapping chromosome 20 in 230 systemic lupus erythematosus sib pair and multiplex families: Evidence for genetic epistasis with chromosome 16q12. Am J Hum Genet 2006; 78: 747-758.
25. Fisher RA. Statistical Methods for Research Workers 13th edn. Oliver and Lloyd: London, 1925.
26. Marchini J, Howie B, Myers S, McVean G, Donnelly P. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet 2007; 39: 906-913.