Common polygenic variation in coeliac disease and confirmation of ZNF335 and NIFA as disease susceptibility loci

European Journal of Human Genetics

Volumn 24, Issue 2, 2016, Pages 291-297

  Coleman, Ciara ^a   Quinn, Emma M ^a   Ryan, Anthony W ^a   Conroy, Judith ^b   Trimble, Valerie ^a   Mahmud, Nasir ^a   Kennedy, Nicholas ^a   Corvin, Aiden P ^c   Morris, Derek W ^d   Donohoe, Gary ^d   O'Morain, Colm ^e   MacMathuna, Padraic ^f   Byrnes, Valerie ^g   Kiat, Clifford ^g   Trynka, Gosia ^h   Wijmenga, Cisca ⁱ   Kelleher, Dermot ^a,j   Ennis, Sean ^b   Anney, Richard J L ^c   McManus, Ross ^a  

^a ST JAMES S HOSPITAL   (Ireland)

^b UNIVERSITY COLLEGE DUBLIN   (Ireland)

^c TRINITY COLLEGE DUBLIN   (Ireland)

^d NATIONAL UNIVERSITY OF IRELAND   (Ireland)

^e ADELAIDE AND MEATH HOSPITAL   (Ireland)

^f MATER MISERICORDIAE UNIVERSITY HOSPITAL   (Ireland)

^g UNIVERSITY HOSPITAL GALWAY   (Ireland)

^h WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

ⁱ UNIVERSITY MEDICAL CENTER GRONINGEN   (Netherlands)

^j IMPERIAL COLLEGE LONDON   (United Kingdom)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ASSESSMENT OF HUMANS; CELIAC DISEASE; CONTROLLED STUDY; DISEASE PREDISPOSITION; GENE; GENE LOCUS; GENETIC ASSOCIATION; GENETIC RISK; GENETIC VARIABILITY; GENOTYPE; HLA SYSTEM; HUMAN; HUMAN TISSUE; MAJOR CLINICAL STUDY; NIFA GENE; POLYGENE RISK SCORE; PRIORITY JOURNAL; ZNF335 GENE; ALLELE; GENETIC PREDISPOSITION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; IMMUNE SYSTEM; IMMUNOLOGY; INTESTINE MUCOSA; META ANALYSIS; PATHOLOGY;

GLIADIN; HLA DQ ANTIGEN; NUCLEAR PROTEIN; SIGNAL PEPTIDE; ZNF335 PROTEIN, HUMAN;

ALLELES; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; GLIADIN; HLA-DQ ANTIGENS; HUMANS; IMMUNE SYSTEM; INTESTINAL MUCOSA; INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS; NUCLEAR PROTEINS;

EID: 84954398045     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2015.87     Document Type: Article

References (38)

1. Abadie V, Sollid LM, Barreiro LB, Jabri B: Integration of genetic and immunological insights into a model of celiac disease pathogenesis. Ann Rev Immunol 2011; 29: 493-525.
2. Sollid LM, Jabri B: Triggers and drivers of autoimmunity: lessons from coeliac disease. Nat Rev Immunol 2013; 13: 294-302.
3. Greco L, Romino R, Coto I et al: The first large population based twin study of coeliac disease. Gut 2002; 50: 624-628.
4. Nisticò L, Fagnani C, Coto I et al: Concordance, disease progression, and heritability of coeliac disease in Italian twins. Gut 2006; 55: 803-808.
5. Bevan S, Popat S, Braegger CP et al: Contribution of the MHC region to the familial risk of coeliac disease. J Med Genet 1999; 36: 687-690.
6. Karell K, Louka AS, Moodie SJ et al: HLA types in celiac disease patients not carrying the DQA1∗05-DQB1∗02 (DQ2) heterodimer: results from the European Genetics Cluster on Celiac Disease. Hum Immunol 2003; 64: 469-477.
7. Margaritte-Jeannin P, Babron MC, Bourgey M et al: HLA-DQ relative risks for coeliac disease in European populations: a study of the European Genetics Cluster on Coeliac Disease. Tissue Antigens 2004; 63: 562-567.
8. Trynka G, Wijmenga C, van Heel DA: A genetic perspective on coeliac disease. Trends Mol Med 2010; 16: 537-550.
9. Megiorni F, Mora B, Bonamico M et al: HLA-DQ and risk gradient for celiac disease. Hum Immunol 2009; 70: 55-59.
10. van Heel DA, Franke L, Hunt KA et al: A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21. Nat Genet 2007; 39: 827-829.
11. Dubois PCA, Trynka G, Franke L et al: Multiple common variants for celiac disease influencing immune gene expression. Nat Genet 2010; 42: 295-302.
12. Hunt KA, Zhernakova A, Turner G et al: Newly identified genetic risk variants for celiac disease related to the immune response. Nat Genet 2008; 40: 395-402.
13. Parkes M, Cortes A, van Heel DA, Brown MA: Genetic insights into common pathways and complex relationships among immune-mediated diseases. Nat Rev Genet 2013; 14: 661-673.
14. Trynka G, Hunt KA, Bockett NA et al: Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease. Nat Genet 2011; 43: 1193-1201.
15. Purcell SM, Wray NR, Stone JL et al. The International Schizophrenia Consortium Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature 2009; 460: 748-752.
16. Cross-Disorder Group of the Psychiatric Genomics Consortium: Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis. Lancet 2013; 381: 1371-1379.
17. Bush WS, Sawcer SJ, de Jager PL et al. The International Multiple Sclerosis Genetics Consortium Evidence for polygenic susceptibility to multiple sclerosis - the shape of things to come. Am J Hum Genet 2010; 86: 621-625.
18. Simonson MA, Wills AG, Keller MC, McQueen MB: Recent methods for polygenic analysis of genome-wide data implicate an important effect of common variants on cardiovascular disease risk. BMC Med Genet 2011; 12: 146.
19. Romanos J, Rosén A, Kumar V et al: Improving coeliac disease risk prediction by testing non-HLA variants additional to HLA variants. Gut 2014; 63: 415-422.
20. Abraham G, Tye-Din JA, Bhalala OG, Kowalczyk A, Zobel J, Inouye M: Accurate and robust genomic prediction of celiac disease using statistical learning. PLoS Genet 2014; 10: e1004137.
21. Purcell S, Neale B, Todd-Brown K et al: PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007; 81: 559-575.
22. Beck T, Hastings RK, Gollapudi S, Free RC, Brookes AJ: GWAS Central: a comprehensive resource for the comparison and interrogation of genome-wide association studies. Eur J Hum Genet 2014; 22: 949-952.
23. Willer CJ, Li Y, Abecasis GR: METAL: fast and efficient meta-analysis of genomewide association scans. Bioinformatics 2010; 26: 2190-2191.
24. Sollid LM: Molecular basis of celiac disease. Ann Rev Immunol 2000; 18: 53-81.
25. Liu Y-J, Papasian CJ, Liu J-F, Hamilton J, Deng H-W: Is replication the gold standard for validating genome-wide association findings? PLoS ONE 2008; 3: e4037.
26. Lindquist KJ, Jorgenson E, Hoffmann TJ, Witte JS: The impact of improved microarray coverage and larger sample sizes on future genome-wide association studies. Genet Epidemiol 2013; 37: 383-392.
27. Wood AR, Esko T, Yang J et al: Defining the role of common variation in the genomic and biological architecture of adult human height. Nat Genet 2014; 46: 1173-1186, advance online publication.
28. Jostins L, Ripke S, Weersma RK et al: Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 2012; 491: 119-124.
29. Schizophrenia Working Group of the Psychiatric Genomics C: Biological insights from 108 schizophrenia-associated genetic loci. Nature 2014; 511: 421-427.
30. Starnes LM, Sorrentino A, Ferracin M et al: A transcriptome-wide approach reveals the key contribution of NFI-A in promoting erythroid differentiation of human CD34+ progenitors and CML cells. Leukemia 2010; 24: 1220-1223.
31. Mahajan MA, Murray A, Samuels HH: NRC-interacting factor 1 is a novel cotransducer that interacts with and regulates the activity of the nuclear hormone receptor coactivator NRC. Mol Cell Biol 2002; 22: 6883-6894.
32. Garapaty S, Xu C-F, Trojer P, Mahajan MA, Neubert TA, Samuels HH: Identification and characterization of a novel nuclear protein complex involved in nuclear hormone receptor-mediated gene regulation. JBiolChem2009; 284: 7542-7552.
33. Yang Yawei J, Baltus Andrew E, Mathew Rebecca S et al: Microcephaly gene links trithorax and REST/NRSF to control neural stem cell proliferation and differentiation. Cell 2012; 151: 1097-1112.
34. Kumar V, Wijmenga C, Withoff S: From genome-wide association studies to disease mechanisms: celiac disease as a model for autoimmune diseases. Semin Immunopathol 2012; 34: 567-580.
35. Hunt KA, Mistry V, Bockett NA et al: Negligible impact of rare autoimmune-locus coding-region variants on missing heritability. Nature 2013; 498: 232-235.
36. Strange A, Capon F, Spencer CC et al. Genetic Analysis of Psoriasis Consortium & the Wellcome Trust Case Control Consortium 2 A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1. Nat Genet 2010; 42: 985-990.
37. Lincoln MR, Ramagopalan SV, Chao MJ et al: Epistasis among HLA-DRB1, HLA-DQA1, and HLA-DQB1 loci determines multiple sclerosis susceptibility. Proc Natl Acad Sci USA 2009; 106: 7542-7547.
38. Wei Z, Wang W, Bradfield J et al: Large sample size, wide variant spectrum, and advanced machine-learning technique boost risk prediction for inflammatory bowel disease. Am J Hum Genet 2013; 92: 1008-1012.