Genome-wide association studies in asthma; perhaps, the end of the beginning

Current Opinion in Allergy and Clinical Immunology

Volumn 13, Issue 5, 2013, Pages 463-469

  Lockett, Gabrielle A ^a   Holloway, John W ^a  

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

Author keywords

Asthma; Genetic; Genome wide association study

Indexed keywords

HLA DPB1 ANTIGEN; HLA DQB1 ANTIGEN; HLA DR ANTIGEN; IMMUNOGLOBULIN E ANTIBODY; INTERLEUKIN 1 RECEPTOR TYPE I; INTERLEUKIN 18 RECEPTOR; INTERLEUKIN 33;

ALLELE; ALLERGIC ASTHMA; ASPIRIN EXACERBATED RESPIRATORY DISEASE; ASTHMA; CASE CONTROL STUDY; COPY NUMBER VARIATION; CORTICOSTEROID THERAPY; ENVIRONMENTAL EXPOSURE; ENVIRONMENTAL FACTOR; EPIGENETICS; GENE EXPRESSION; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOTYPE; GENOTYPE ENVIRONMENT INTERACTION; HEREDITY; HERITABILITY; HUMAN; LUNG FUNCTION; NONHUMAN; OCCUPATIONAL ASTHMA; PHENOTYPE; POPULATION RISK; PRIORITY JOURNAL; REPRODUCIBILITY; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL SIGNIFICANCE;

ANIMALS; ASTHMA; GENETIC LOCI; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS;

EID: 84883598850     PISSN: 15284050     EISSN: 14736322     Source Type: Journal    
DOI: 10.1097/ACI.0b013e328364ea5f     Document Type: Review

References (50)

1. Sandford A, Weir T, Paré P. The genetics of asthma. Am J Respir Crit Care Med 1996; 153:1749-1765.
2. Marsh DG, Bias WB, Hsu SH, Goodfriend L. Association of the HL-A7 crossreacting group with a specific reaginic antibody response in allergic man. Science 1973; 179:691-693.
3. Holloway JW, Yang IA, Holgate ST.Genetics of allergic disease. J Allergy Clin Immunol 2010; 125:S81-S94.
4. Michel S, Liang L, Depner M, et al. Unifying candidate gene and GWAS approaches in asthma. PLoS One 2010; 5:e13894.
5. Moffatt MF, Kabesch M, Liang L, et al. Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma. Nature 2007; 448:470-473.
6. Wan YI, Shrine NRG, Soler Artigas M, et al. Genome-wide association study to identify genetic determinants of severe asthma. Thorax 2012; 67:762-768.
7. Karunas AS, Iunusbaev BB, Fedorova I, et al. Genome-wide association study of bronchial asthma in the Volga-Ural region of Russia. Mol Biol (Mosk) 2011; 45:992-1003.
8. Sleiman PMA, Flory J, Imielinski M, et al. Variants of DENND1B associated with asthma in children. N Engl J Med 2010; 362:36-44.
9. Torgerson DG, Ampleford EJ, Chiu GY, et al. Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations. Nat Genet 2011; 43:887-892.
10. Ferreira MAR, Matheson MC, Duffy DL, et al. Identification of IL6R and chromosome 11q13.5 as risk loci for asthma. Lancet 2011; 378:1006-1014.
11. Moffatt MF,Gut IG,Demenais F, et al.Alarge-scale, consortium-based genomewide association study of asthma. N Engl J Med 2010; 363:1211-1221.
12. Gudbjartsson DF, Bjornsdottir US, Halapi E, et al. Sequence variants affecting eosinophil numbers associate with asthma and myocardial infarction. Nat Genet 2009; 41:342-347.
13. Noguchi E, Sakamoto H, Hirota T, et al. Genome-Wide association study identifies HLA-DP as a susceptibility gene for pediatric asthma in Asian populations. PLoS Genet 2011; 7:e1002170.
14. Park B, Kim T-H, Kim J-H, et al. Genome-wide association study of aspirinexacerbated respiratory disease in a Korean population. Hum Genet 2013; 132:313-321.
15. Lasky-Su J, Himes BE, Raby BA, et al. HLA-DQ strikes again: Genome-wide association study further confirms HLA-DQ in the diagnosis of asthma among adults. Clin Exp Allergy 2012; 42:1724-1733.
16. Li X, Howard TD, Zheng SL, et al. Genome-wide association study of asthma identifies RAD50-IL13 and HLA-DR/DQ regions. J Allergy Clin Immunol 2010; 125:328-335; e311.
17. Hirota T, Takahashi A, Kubo M, et al. Genome-wide association study identifies three new susceptibility loci for adult asthma in the Japanese population. Nat Genet 2011; 43:893-896.
18. Ramasamy A, Kuokkanen M, Vedantam S, et al. Genome-wide association studies of asthma in population-based cohorts confirm known and suggested loci and identify an additional association near HLA. PLoS One 2012; 7:e44008.
19. Li X, Ampleford EJ, Howard TD, et al. Genome-wide association studies of asthma indicate opposite immunopathogenesis direction from autoimmune diseases. J Allergy Clin Immunol 2012; 130:861-868; e867.
20. Ober C, Yao T. The genetics of asthma and allergic disease: A 21st century perspective. Immunol Rev 2011; 242:10-30.
21. Schauberger EM, Ewart SL, Arshad SH, et al. Identification of ATPAF1 as a novel candidate gene for asthma in children. J Allergy Clin Immunol 2011; 128:753-760; e711.
22. Du R, Litonjua AA, Tantisira KG, et al. Genome-wide association study reveals class I MHC-restricted T cell-associated molecule gene (CRTAM) variants interact with vitamin D levels to affect asthma exacerbations. J Allergy Clin Immunol 2012; 129:368-373; e365.
23. Kim SH, Cho BY, Park CS, et al. Alpha-T-catenin (CTNNA3) gene was identified as a risk variant for toluene diisocyanate-induced asthma by genome-wide association analysis. Clin Exp Allergy 2009; 39:203-212.
24. Forno E, Lasky-Su J, Himes B, et al. Genome-wide association study of the age of onset of childhood asthma. J Allergy Clin Immunol 2012; 130:83-90; e84.
25. Weidinger S, Gieger C, Rodriguez E, et al. Genome-wide scan on total serum IgE levels identifies FCER1A as novel susceptibility locus. PLoS Genet 2008; 4:e1000166.
26. Levin AM, Mathias RA, Huang L, et al. A meta-analysis of genomewide association studies for serum total IgE in diverse study populations. J AllergyClin Immunol 2013; 131:1176-1184.
27. Esparza-Gordillo J, Weidinger S, Folster-Holst R, et al. A common variant on chromosome 11q13 is associated with atopic dermatitis. NatGenet 2009; 41:596-601.
28. Sun L-D, Xiao F-L, Li Y, et al. Genome-wide association study identifies two new susceptibility loci for atopic dermatitis in the Chinese Han population. Nat Genet 2011; 43:690-694.
29. Paternoster L, Standl M, Chen C-M, et al. Meta-analysis of genomewide association studies identifies three new risk loci for atopic dermatitis. Nat Genet 2012; 44:187-192.
30. Tomita K, Sakashita M, Hirota T, et al. Variants in the 17q21 asthma susceptibility locus are associated with allergic rhinitis in the Japanese population. Allergy 2013; 68:92-100.
31. Anantharaman R, Andiappan A, Nilkanth P, et al. Genome-wide association study identifies PERLD1 as asthma candidate gene. BMC Med Genet 2011; 12:170.
32. Himes BE, Jiang X, Hu R, et al. Genome-wide association analysis in asthma subjects identifies SPATS2L as a novel bronchodilator response gene. PLoS Genet 2012; 8:e1002824.
33. Tantisira KG, Damask A, Szefler SJ, et al. Genome-wide association identifies the T Gene as a novel asthma pharmacogenetic locus. Am J Respir Crit Care Med 2012; 185:1286-1291.
34. Tantisira KG, Lasky-Su J, Harada M, et al. Genomewide association between GLCCI1 and response to glucocorticoid therapy in asthma. N Engl J Med 2011; 365:1173-1183.
35. Manolio TA, Collins FS, Cox NJ, et al. Finding the missing heritability of complex diseases. Nature 2009; 461:747-753.
36. Wjst M, Sargurupremraj M, Arnold M. Genome-wide association studies in asthma: What they really told us about pathogenesis. CurrOpinion Allergy Clin Immunol 2013; 13:112-118.
37. Spycher BD, Henderson J, Granell R, et al. Genome-wide prediction of childhood asthma and related phenotypes in a longitudinal birth cohort. J Allergy Clin Immunol 2012; 130:503-509; e507.
38. Rogers AJ, Chu JH, Darvishi K, et al. Copy number variation prevalence in known asthma genes and their impact on asthma susceptibility. Clin Exp Allergy 2013; 43:455-462.
39. DeWan A, Egan KB, Hellenbrand K, et al. Whole-exome sequencing of a pedigree segregating asthma. BMC Med Genet 2012; 13:95.
40. Ege MJ, Strachan DP, CooksonWOCM, et al. Gene-environment interaction for childhood asthma and exposure to farming in Central Europe. J Allergy Clin Immunol 2011; 127:138-144; e134.
41. Ober C, Vercelli D. Gene-environment interactions in human disease: Nuisance or opportunity?. Trends Genet 2011; 27:107-115.
42. Lockett GA, Wilkes F, Maleszka R. Brain plasticity, memory and neurological disorders: An epigenetic perspective. NeuroReport 2010; 21:909-913.
43. Karmaus W, Ziyab AH, Everson T, Holloway JW. Epigenetic mechanisms and models in the origins of asthma. Curr Opin Allergy Clin Immunol 2013; 13:63-69.
44. Soto-Rami'rez N, Arshad SH, Holloway JW, et al. The interaction of genetic variants and DNA methylation of the interleukin-4 receptor gene increase the risk of asthma at age 18 years. Clin Epigenet 2013; 5:1.
45. Rakyan VK, Down TA, Balding DJ, Beck S. Epigenome-wide association studies for common human diseases. Nat Rev Genet 2011; 12:529-541.
46. Relton CL, Davey Smith G. Two-step epigenetic Mendelian randomization: A strategy for establishing the causal role of epigenetic processes in pathways to disease. Int J Epidemiol 2012; 41:161-176.
47. Gerasimova A, Chavez L, Li B, et al. Predicting cell types and genetic variations contributing to disease by combining GWAS and epigenetic data. PLoS One 2013; 8:e54359.
48. Himes BE, Sheppard K, Berndt A, et al. Integration of mouse and human genome-wide association data identifies KCNIP4 as an asthma gene. PLoS ONE 2013; 8:e56179.
49. Song GG, Lee YH. Pathway analysis of genome-wide association study on asthma. Hum Immunol 2013; 74:256-260.
50. Christodoulou K, Wiskin AE, Gibson J, et al. Next generation exome sequencing of paediatric inflammatory bowel disease patients identifies rare and novel variants in candidate genes. Gut 2013; 62:977-984. Diseases