Evidence for gene-gene epistatic interactions among susceptibility loci for systemic lupus erythematosus

Arthritis and Rheumatism

Volumn 64, Issue 2, 2012, Pages 485-492

  Hughes, Travis ^a   Adler, Adam ^a   Kelly, Jennifer A ^a   Kaufman, Kenneth M ^b   Williams, Adrienne H ^c   Langefeld, Carl D ^c   Brown, Elizabeth E ^d   Alarcõn, Graciela S ^d   Kimberly, Robert P ^d   Edberg, Jeffrey C ^d   Ramsey Goldman, Rosalind ^e   Petri, Michelle ^f   Boackle, Susan A ^g   Stevens, Anne M ^h   Reveille, John D ⁱ   Sanchez, Elena ^a   Martín, Javier ^j   Niewold, Timothy B ^k   Vilá, Luis M ^l   Scofield, R Hal ^b   Gilkeson, Gary S ^m   Gaffney, Patrick M ^a   Criswell, Lindsey A ⁿ   Moser, Kathy L ^a   Merrill, Joan T ^o   Jacob, Chaim O ^p   Tsao, Betty P ^q   James, Judith A ^o   Vyse, Timothy J ^r   Alarcõn Riquelme, Marta E ^s   Harley, John B ^t   Richardson, Bruce C ^u   Sawalha, Amr H ^b   more..

^a OKLAHOMA MEDICAL RESEARCH FOUNDATION   (United States)

^b UNIVERSITY OF OKLAHOMA HEALTH SCIENCES CENTER   (United States)

^c WAKE FOREST UNIVERSITY HEALTH SCIENCES   (United States)

^d UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^e NORTHWESTERN UNIVERSITY   (United States)

^f JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^g UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^h UNIVERSITY OF WASHINGTON   (United States)

ⁱ UNIVERSITY OF TEXAS   (United States)

^j INSTITUTO DE PARASITOLOGÍA Y BIOMEDICINA LÓPEZ NEYRA   (Spain)

^k UNIVERSITY OF CHICAGO   (United States)

^l UNIVERSITY OF PUERTO RICO   (Puerto Rico)

^m MEDICAL UNIVERSITY OF SOUTH CAROLINA   (United States)

ⁿ UNIVERSITY OF CALIFORNIA   (United States)

^o UNIVERSITY OF OKLAHOMA   (United States)

^p UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^q UNIVERSITY OF CALIFORNIA   (United States)

^r KING'S COLLEGE LONDON   (United Kingdom)

^s CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER   (United States)

^t UNIVERSITY OF MICHIGAN   (United States)

^u JUNTA DE ANDALUCÍA   (Spain)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA INTEGRIN; CYTOTOXIC T LYMPHOCYTE ANTIGEN 4; INTEGRIN ALPHA M; INTERFERON REGULATORY FACTOR 5; INTERLEUKIN 21; PROGRAMMED DEATH 1 RECEPTOR; UNCLASSIFIED DRUG;

ALLELE; ARTICLE; CONTROLLED STUDY; GENE INTERACTION; GENE LOCUS; GENETIC EPISTASIS; GENETIC RISK; GENETIC SUSCEPTIBILITY; GENOTYPE; HLA SYSTEM; HUMAN; MAJOR CLINICAL STUDY; MULTIFACTOR DIMENSIONALITY REDUCTION; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SYSTEMIC LUPUS ERYTHEMATOSUS;

ADULT; ALLELES; EPISTASIS, GENETIC; FEMALE; GENETIC LOCI; GENETIC PREDISPOSITION TO DISEASE; GENOTYPE; HUMANS; LUPUS ERYTHEMATOSUS, SYSTEMIC; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84863026696     PISSN: 00043591     EISSN: 15290131     Source Type: Journal    
DOI: 10.1002/art.33354     Document Type: Article

References (37)

1. Flesher DL, Sun X, Behrens TW, Graham RR, Criswell LA,. Recent advances in the genetics of systemic lupus erythematosus. Expert Rev Clin Immunol 2010; 6: 461-79.
2. Hellquist A, Jarvinen TM, Koskenmies S, Zucchelli M, Orsmark-Pietras C, Berglind L, et al. Evidence for genetic association and interaction between the TYK2 and IRF5 genes in systemic lupus erythematosus. J Rheumatol 2009; 36: 1631-8.
3. Suarez-Gestal M, Calaza M, Gonzalez A,. Lack of interaction between systemic lupus erythematosus-associated polymorphisms in TYK2 and IRF5. J Rheumatol 2010; 37: 676-7.
4. 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: 204-10. (Pubitemid 351171405)
5. Graham RR, Kyogoku C, Sigurdsson S, Vlasova IA, Davies LR, Baechler EC, et al. Three functional variants of IFN regulatory factor 5 (IRF5) define risk and protective haplotypes for human lupus. Proc Natl Acad Sci U S A 2007; 104: 6758-63. (Pubitemid 47175574)
6. 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: 1271-7. (Pubitemid 13221242)
7. Hochberg MC, for the Diagnostic and Therapeutic Criteria Committee of the American College of Rheumatology. Updating the American College of Rheumatology revised criteria for the classification of systemic lupus erythematosus [letter]. Arthritis Rheum 1997; 40: 1725.
8. Yang N, Li H, Criswell LA, Gregersen PK, Alarcon-Riquelme ME, Kittles R, et al. 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: 382-92. (Pubitemid 43101691)
9. Tian C, Hinds DA, Shigeta R, Adler SG, Lee A, Pahl MV, et al. A genomewide single-nucleotide-polymorphism panel for Mexican American admixture mapping. Am J Hum Genet 2007; 80: 1014-23. (Pubitemid 47579339)
10. Kosoy R, Nassir R, Tian C, White PA, Butler LM, Silva G, et al. Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America. Hum Mutat 2009; 30: 69-78.
11. Sanchez E, Webb RD, Rasmussen A, Kelly JA, Riba L, Kaufman KM, et al. Genetically determined Amerindian ancestry correlates with increased frequency of risk alleles for systemic lupus erythematosus. Arthritis Rheum 2010; 62: 3722-9.
12. 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: 559-75. (Pubitemid 47330214)
13. Ritchie MD, Hahn LW, Roodi N, Bailey LR, Dupont WD, Parl FF, et al. Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. Am J Hum Genet 2001; 69: 138-47. (Pubitemid 32614026)
14. Moore JH,. Detecting, characterizing, and interpreting nonlinear gene-gene interactions using multifactor dimensionality reduction. Adv Genet 2010; 72: 101-16.
15. Benjamini Y, Hochberg Y,. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B 1995; 57: 289-300.
16. Lage-Castellanos A, Martinez-Montes E, Hernandez-Cabrera JA, Galan L,. False discovery rate and permutation test: an evaluation in ERP data analysis. Stat Med 2010; 29: 63-74.
17. Yang Q, Khoury MJ, Sun F, Flanders WD,. Case-only design to measure gene-gene interaction. Epidemiology 1999; 10: 167-70. (Pubitemid 29093954)
18. Cordell HJ,. Detecting gene-gene interactions that underlie human diseases. Nat Rev Genet 2009; 10: 392-404.
19. Janeway CA, Travers P, Walport M, Shlomchik MJ,. T cell-mediated immunity. In: Immunobiology: the immune system in health and disease. 6th ed. New York: Garland Sciences; 2005. p. 319-65.
20. 2. J Biol Chem 2003; 278: 34395-402. (Pubitemid 37553285)
21. Fagerholm SC, Varis M, Stefanidakis M, Hilden TJ, Gahmberg CG,. α-Chain phosphorylation of the human leukocyte CD11b/CD18 (Mac-1) integrin is pivotal for integrin activation to bind ICAMs and leukocyte extravasation. Blood 2006; 108: 3379-86.
22. DiPlacido LD, Craft J,. Emerging from the shadows: follicular helper T cells in autoimmunity [editorial]. Arthritis Rheum 2010; 62: 6-8.
23. McHeyzer-Williams LJ, Pelletier N, Mark L, Fazilleau N, McHeyzer-Williams MG,. Follicular helper T cells as cognate regulators of B cell immunity. Curr Opin Immunol 2009; 21: 266-73.
24. Good-Jacobson KL, Szumilas CG, Chen L, Sharpe AH, Tomayko MM, Shlomchik MJ,. PD-1 regulates germinal center B cell survival and the formation and affinity of long-lived plasma cells. Nat Immunol 2010; 11: 535-42.
25. Simpson N, Gatenby PA, Wilson A, Malik S, Fulcher DA, Tangye SG, et al. Expansion of circulating T cells resembling follicular helper T cells is a fixed phenotype that identifies a subset of severe systemic lupus erythematosus. Arthritis Rheum 2010; 62: 234-44.
26. 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: 211-6. (Pubitemid 351171404)
27. 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: 900-9. (Pubitemid 351397089)
28. Barreto M, Santos E, Ferreira R, Fesel C, Fontes MF, Pereira C, et al. Evidence for CTLA4 as a susceptibility gene for systemic lupus erythematosus. Eur J Hum Genet 2004; 12: 620-6. (Pubitemid 39172422)
29. Magnusson V, Johanneson B, Lima G, Odeberg J, Alarcon-Segovia D, Alarcon-Riquelme ME,. Both risk alleles for FcγRIIA and FcγRIIIA are susceptibility factors for SLE: a unifying hypothesis. Genes Immun 2004; 5: 130-7. (Pubitemid 38967642)
30. Sawalha AH, Kaufman KM, Kelly JA, Adler AJ, Aberle T, Kilpatrick J, et al. Genetic association of interleukin-21 polymorphisms with systemic lupus erythematosus. Ann Rheum Dis 2008; 67: 458-61. (Pubitemid 351498423)
31. M (encoded by ITGAM) is associated with systemic lupus erythematosus. Nat Genet 2008; 40: 152-4. (Pubitemid 351171399)
32. Lee YH, Witte T, Momot T, Schmidt RE, Kaufman KM, Harley JB, et al. The mannose-binding lectin gene polymorphisms and systemic lupus erythematosus: two case-control studies and a meta-analysis. Arthritis Rheum 2005; 52: 3966-74. (Pubitemid 41798236)
33. Prokunina L, Castillejo-Lopez C, Oberg F, Gunnarsson I, Berg L, Magnusson V, et al. A regulatory polymorphism in PDCD1 is associated with susceptibility to systemic lupus erythematosus in humans. Nat Genet 2002; 32: 666-9. (Pubitemid 35435182)
34. Lee YH, Rho YH, Choi SJ, Ji JD, Song GG, Nath SK, et al. The PTPN22 C1858T functional polymorphism and autoimmune diseases: a meta-analysis. Rheumatology (Oxford) 2007; 46: 49-56. (Pubitemid 44932783)
35. 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: 977-86. (Pubitemid 47367077)
36. Graham DS, Graham RR, Manku H, Wong AK, Whittaker JC, Gaffney PM, et al. Polymorphism at the TNF superfamily gene TNFSF4 confers susceptibility to systemic lupus erythematosus. Nat Genet 2008; 40: 83-9.
37. Velez DR, White BC, Motsinger AA, Bush WS, Ritchie MD, Williams SM, et al. A balanced accuracy function for epistasis modeling in imbalanced datasets using multifactor dimensionality reduction. Genet Epidemiol 2007; 31: 306-15. (Pubitemid 46642095)