Genome-wide genetic and transcriptomic investigation of variation in antibody response to dietary antigens

Genetic Epidemiology

Volumn 38, Issue 5, 2014, Pages 439-446

  Rubicz, Rohina ^a,b   Yolken, Robert ^c   Alaedini, Armin ^d   Drigalenko, Eugene ^a   Charlesworth, Jac C ^e   Carless, Melanie A ^a   Severance, Emily G ^c   Krivogorsky, Bogdana ^c   Dyer, Thomas D ^a   Kent, Jack W ^a   Curran, Joanne E ^a   Johnson, Matthew P ^a   Cole, Shelley A ^a   Almasy, Laura ^a   Moses, Eric K ^f   Blangero, John ^a   Göring, Harald H H ^a  

^a SOUTHWEST FOUNDATION FOR BIOMEDICAL RESEARCH   (United States)

^b USA   (United States)

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

^d Department of Medicine   (United States)

^e UNIVERSITY OF TASMANIA   (Australia)

^f UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

Association; Gliadin; IgG antibody; Integrative genomics; Pedigree study; Transcriptional profiling

Indexed keywords

ARMC9 PROTEIN; BOVINE SERUM ALBUMIN; BOVINE SERUM ALBUMIN A; BOVINE SERUM ALBUMIN B; BTNL2 PROTEIN; C15ORF32 PROTEIN; CASEIN; CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN; GLIADIN; GLIADIN ANTIBODY; GPR65 PROTEIN; HLA DQ2 ANTIGEN; HLA DQ8 ANTIGEN; HLA DR ANTIGEN; IMMUNOGLOBULIN G ANTIBODY; KCNK10 PROTEIN; NOTCH4 RECEPTOR; PEPTIDES AND PROTEINS; UNCLASSIFIED DRUG; ANTIBODY; BTNL2 PROTEIN, HUMAN; IMMUNOGLOBULIN G; MEMBRANE PROTEIN; MESSENGER RNA;

ADOLESCENT; ADULT; AGED; ALLELE; ANTIBODY RESPONSE; ARTICLE; CELIAC DISEASE; CONTROLLED STUDY; ENZYME LINKED IMMUNOSORBENT ASSAY; FEMALE; GENETIC ASSOCIATION; GENETIC DIFFERENCE; GENETIC VARIABILITY; HERITABILITY; HUMAN; MALE; ANIMAL; BOVINE; ENVIRONMENT; FOOD ALLERGY; GENE EXPRESSION PROFILING; GENETICS; GENOME-WIDE ASSOCIATION STUDY; IMMUNOLOGY; MEXICAN AMERICAN; PEDIGREE; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; ANTIBODIES; CASEINS; CATTLE; CELIAC DISEASE; ENVIRONMENT; ENZYME-LINKED IMMUNOSORBENT ASSAY; FOOD HYPERSENSITIVITY; GENE EXPRESSION PROFILING; GENOME-WIDE ASSOCIATION STUDY; GLIADIN; HLA-DR ANTIGENS; HUMANS; IMMUNOGLOBULIN G; MEMBRANE GLYCOPROTEINS; MEXICAN AMERICANS; PEDIGREE; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA, MESSENGER; SERUM ALBUMIN, BOVINE;

EID: 84902995993     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.21817     Document Type: Article

References (47)

1. Abecasis GR, Cherny SS, Cookson WO, Cardon LR. 2002. Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 30(1):97-101.
2. Almasy L, Blangero J. 1998. Multipoint quantitative-trait linkage analysis in general pedigrees. Am J Hum Genet 62(5):1198-1211.
3. Boehnke M, Moll PP, Lange K, Weidman WH, Kottke BA. 1986. Univariate and bivariate analyses of cholesterol and triglyceride levels in pedigrees. Am J Med Genet 23(3):775-792.
4. Briani C, Samaroo D, Alaedini A. 2008. Celiac disease: from gluten to autoimmunity. Autoimmun Rev 7(8):644-650.
5. Campos Alberto EJ, Shimojo N, Suzuki Y, Mashimo Y, Arima T, Matsuura T, Inoue Y, Yamaide A, Tomiita M, Fujii K and others 2008. IL-10 gene polymorphism, but not TGF-beta1 gene polymorphisms, is associated with food allergy in a Japanese population. Pediatr Allergy Immunol 19(8):716-721.
6. Cheng ML, Woodford SC, Hilburn JL, VandeBerg JL. 1986. A novel system for storage of sera frozen in small aliquots. J Biochem Biophys Methods 13(1):47-51.
7. Cosnes J, Cellier C, Viola S, Colombel JF, Michaud L, Sarles J, Hugot JP, Ginies JL, Dabadie A, Mouterde O and others. 2008. Incidence of autoimmune diseases in celiac disease: protective effect of the gluten-free diet. Clin Gastroenterol Hepatol 6(7):753-758.
8. Dubois PC, Trynka G, Franke L, Hunt KA, Romanos J, Curtotti A, Zhernakova A, Heap GA, Adany R, Aromaa A and others. 2010. Multiple common variants for celiac disease influencing immune gene expression. Nat Genet 42(4):295-302.
9. Fasano A, Berti I, Gerarduzzi T, Not T, Colletti RB, Drago S, Elitsur Y, Green PH, Guandalini S, Hill ID and others. 2003. Prevalence of celiac disease in at-risk and not-at-risk groups in the United States: a large multicenter study. Arch Intern Med 163(3):286-292.
10. Festen EA, Goyette P, Green T, Boucher G, Beauchamp C, Trynka G, Dubois PC, Lagace C, Stokkers PC, Hommes DW and others. 2011. A meta-analysis of genome-wide association scans identifies IL18RAP, PTPN2, TAGAP, and PUS10 as shared risk loci for Crohn's disease and celiac disease. PLoS Genet 7(1):e1001283.
11. Goring HH, Curran JE, Johnson MP, Dyer TD, Charlesworth J, Cole SA, Jowett JB, Abraham LJ, Rainwater DL, Comuzzie AG and others. 2007. Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes. Nat Genet 39(10):1208-1216.
12. Henderson KN, Tye-Din JA, Reid HH, Chen Z, Borg NA, Beissbarth T, Tatham A, Mannering SI, Purcell AW, Dudek NL and others. 2007. A structural and immunological basis for the role of human leukocyte antigen DQ8 in celiac disease. Immunity 27(1):23-34.
13. Hong X, Tsai HJ, Wang X. 2009. Genetics of food allergy. Curr Opin Pediatr 21(6):770-776.
14. Howell WM, Turner SJ, Hourihane JO, Dean TP, Warner JO. 1998. HLA class II DRB1, DQB1 and DPB1 genotypic associations with peanut allergy: evidence from a family-based and case-control study. Clin Exp Allergy 28(2):156-162.
15. Ingenuity Systems, http://www.ingenuity.com.
16. Kim CY, Quarsten H, Bergseng E, Khosla C, Sollid LM. 2004. Structural basis for HLA-DQ2-mediated presentation of gluten epitopes in celiac disease. Proc Natl Acad Sci USA 101(12):4175-4179.
17. Kiyohara C, Tanaka K, Miyake Y. 2008. Genetic susceptibility to atopic dermatitis. Allergol Int 57(1):39-56.
18. Kusunoki T, Okafuji I, Yoshioka T, Saito M, Nishikomori R, Heike T, Sugai M, Shimizu A, Nakahata T. 2005. SPINK5 polymorphism is associated with disease severity and food allergy in children with atopic dermatitis. J Allergy Clin Immunol 115(3):636-638.
19. Lange K, Boehnke M. 1983. Extensions to pedigree analysis. IV. Covariance components models for multivariate traits. Am J Med Genet 14(3):513-524.
20. Liu X, Zhang S, Tsai HJ, Hong X, Wang B, Fang Y, Pongracic JA, Wang X. 2009. Genetic and environmental contributions to allergen sensitization in a Chinese twin study. Clin Exp Allergy 39(7):991-998.
21. Louka AS, Sollid LM. 2003. HLA in coeliac disease: unravelling the complex genetics of a complex disorder. Tissue Antigens 61(2):105-117.
22. Lundin KE, Alaedini A. 2012. Non-celiac gluten sensitivity. Gastrointest Endosc Clin N Am 22(4):723-734.
23. McGovern DP, Gardet A, Torkvist L, Goyette P, Essers J, Taylor KD, Neale BM, Ong RT, Lagace C, Li C and others. 2010. Genome-wide association identifies multiple ulcerative colitis susceptibility loci. Nat Genet 42(4):332-337.
24. Mitchell BD, Kammerer CM, Blangero J, Mahaney MC, Rainwater DL, Dyke B, Hixson JE, Henkel RD, Sharp RM, Comuzzie AG and others. 1996. Genetic and environmental contributions to cardiovascular risk factors in Mexican Americans. The San Antonio Family Heart Study. Circulation 94(9):2159-2170.
25. Monsuur AJ, de Bakker PI, Zhernakova A, Pinto D, Verduijn W, Romanos J, Auricchio R, Lopez A, van Heel DA, Crusius JB and others. 2008. Effective detection of human leukocyte antigen risk alleles in celiac disease using tag single nucleotide polymorphisms. PloS One 3(5):e2270.
26. Niebuhr DW, Li Y, Cowan DN, Weber NS, Fisher JA, Ford GM, Yolken R. 2011. Association between bovine casein antibody and new onset schizophrenia among US military personnel. Schizophr Res 128(1-3):51-55.
27. Nistico L, Fagnani C, Coto I, Percopo S, Cotichini R, Limongelli MG, Paparo F, D'Alfonso S, Giordano M, Sferlazzas C and others. 2006. Concordance, disease progression, and heritability of coeliac disease in Italian twins. Gut 55(6):803-808.
28. Parmar AS, Lappalainen M, Paavola-Sakki P, Halme L, Farkkila M, Turunen U, Kontula K, Aromaa A, Salomaa V, Peltonen L and others. 2012. Association of celiac disease genes with inflammatory bowel disease in Finnish and Swedish patients. Genes Immun 13(6):474-480.
29. Patel DA, Holdford DA, Edwards E, Carroll NV. 2011. Estimating the economic burden of food-induced allergic reactions and anaphylaxis in the United States. J Allergy Clin Immunol 128(1):110-115.
30. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. 2006. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38(8):904-909.
31. R Development Core Team: R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria, 2011. URL http://www.R-project.org/.
32. Rubicz R, Yolken R, Drigalenko E, Carless MA, Dyer TD, Bauman L, Melton PE, Kent JW, Jr., Harley JB, Curran JE and others. 2013. A genome-wide integrative genomic study localizes genetic factors influencing antibodies against Epstein-Barr virus nuclear antigen 1 (EBNA-1). PLoS Genetics 9(1):e1003147.
33. Rybicki BA, Walewski JL, Maliarik MJ, Kian H, Iannuzzi MC. 2005. The BTNL2 gene and sarcoidosis susceptibility in African Americans and Whites. Am J Hum Genet 77(3):491-499.
34. Samaroo D, Dickerson F, Kasarda DD, Green PH, Briani C, Yolken RH, Alaedini A. 2010. Novel immune response to gluten in individuals with schizophrenia. Schizophr Res 118(1-3):248-255.
35. Senechal H, Geny S, Desvaux FX, Busson M, Mayer C, Aron Y, Oster JP, Bessot JC, Peltre G, Pauli G and others. 1999. Genetics and specific immune response in allergy to birch pollen and food: evidence of a strong, positive association between atopy and the HLA class II allele HLA-DR7. J Allergy Clin Immunol 104:395-401.
36. Severance EG, Lin J, Sampson HA, Gimenez G, Dickerson FB, Halling M, Gressitt K, Haile L, Stallings CR, Origoni AE and others. 2011. Dietary antigens, epitope recognition, and immune complex formation in recent onset psychosis and long-term schizophrenia. Schizophr Res 126(1-3):43-50.
37. Sheridan JW, Simmons RJ. 1983. Pancreatin-EDTA treatment affects buoyancy of cells in Cohn fraction V protein density gradients without residual effect on cell size. Aust J Exp Biol Med Sci 61:727-737.
38. Skypala I. 2011. Adverse food reactions-an emerging issue for adults. J Am Diet Assoc 111(12):1877-1891.
39. Sobel E, Papp JC, Lange K. 2002. Detection and integration of genotyping errors in statistical genetics. Am J Hum Genet 70(2):496-508.
40. Sollid LM, Markussen G, Ek J, Gjerde H, Vartdal F, Thorsby E. 1989. Evidence for a primary association of celiac disease to a particular HLA-DQ alpha/beta heterodimer. J Exp Med 169(1):345-350.
41. Sollid LM, Qiao SW, Anderson RP, Gianfrani C, Koning F. 2012. Nomenclature and listing of celiac disease relevant gluten T-cell epitopes restricted by HLA-DQ molecules. Immunogenetics 64(6):455-460.
42. Spence MA, Westlake J, Lange K. 1977. Estimation of the variance components for dermal ridge count. Ann Hum Genet 41(1):111-115.
43. Tan RA, Corren J. 2011. The relationship of rhinitis and asthma, sinusitis, food allergy, and eczema. Immunol Allergy Clin North Am 31(3):481-491.
44. Trynka G, Hunt KA, Bockett NA, Romanos J, Mistry V, Szperl A, Bakker SF, Bardella MT, Bhaw-Rosun L, Castillejo G and others. 2011. Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease. Nat Genet 43(12):1193-1201.
45. Tsai HJ, Kumar R, Pongracic J, Liu X, Story R, Yu Y, Caruso D, Costello J, Schroeder A, Fang Y and others. 2009. Familial aggregation of food allergy and sensitization to food allergens: a family-based study. Clin Exp Allergy 39(1):101-109.
46. Vojdani A. 2009. Detection of IgE, IgG, IgA and IgM antibodies against raw and processed food antigens. Nutr Metab 12:6-22.
47. Woo JG, Assa'ad A, Heizer AB, Bernstein JA, Hershey GK. 2003. The -159 C->T polymorphism of CD14 is associated with nonatopic asthma and food allergy. J Allergy Clin Immunol 112(2):438-444.