Ethnic-specific associations of rare and low-frequency DNA sequence variants with asthma

Nature Communications

Volumn 6, Issue , 2015, Pages

  Igartua, Catherine ^a   Myers, Rachel A ^a   Mathias, Rasika A ^b   Pino Yanes, Maria ^c,d   Eng, Celeste ^c   Graves, Penelope E ^e   Levin, Albert M ^f   Del Rio Navarro, Blanca E ^g   Jackson, Daniel J ^h   Livne, Oren E ^a   Rafaels, Nicholas ⁱ   Edlund, Christopher K ^j   Yang, James J ^k   Huntsman, Scott ^c   Salam, Muhammad T ^j   Romieu, Isabelle ^l   Mourad, Raphael ^a   Gern, James E ^h   Lemanske, Robert F ^h   Wyss, Annah ^m   Hoppin, Jane A ^m,n   Barnes, Kathleen C ^b   Burchard, Esteban G ^c   Gauderman, W James ^j   Martinez, Fernando D ^e   Raby, Benjamin A ^o   Weiss, Scott T ^o   Williams, L Keoki ^f   London, Stephanie J ^m   Gilliland, Frank D ^j   Nicolae, Dan L ^a   Ober, Carole ^a   more..

^a UNIVERSITY OF CHICAGO   (United States)

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

^c UNIVERSITY OF CALIFORNIA   (United States)

^d INSTITUTO DE SALUD CARLOS III   (Spain)

^e UNIVERSITY OF ARIZONA   (United States)

^f HENRY FORD HEALTH SYSTEM   (United States)

^g HOSPITAL INFANTIL DE MÉXICO FEDERICO GÓMEZ   (Mexico)

^h UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

ⁱ JOHNS HOPKINS UNIVERSITY   (United States)

^j UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^k UNIVERSITY OF MICHIGAN   (United States)

^l INTERNATIONAL AGENCY FOR RESEARCH ON CANCER   (France)

^m NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

ⁿ NORTH CAROLINA STATE UNIVERSITY   (United States)

^o HARVARD MEDICAL SCHOOL   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ANCESTRY; ASTHMA; DNA; GENETIC ANALYSIS; HERITABILITY; RISK ASSESSMENT;

AFRICAN AMERICAN; AFRICAN CARIBBEAN; ARTICLE; ASTHMA; CHROMOSOME 17Q; CONTROLLED STUDY; DNA SEQUENCE; ETHNICITY; EUROPEAN AMERICAN; FEMALE; GENE; GENE FREQUENCY; GENE LOCUS; GENETIC ASSOCIATION; GENETIC RISK; GENETIC VARIABILITY; GRASP GENE; GSDMB GENE; HERITABILITY; HUMAN; MAJOR CLINICAL STUDY; MALE; MISSENSE MUTATION; MTHFR GENE; GENE LINKAGE DISEQUILIBRIUM; GENETIC PREDISPOSITION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; PROCEDURES;

CARRIER PROTEIN; GRASP PROTEIN, HUMAN; GSDMB PROTEIN, HUMAN; MEMBRANE PROTEIN; TUMOR PROTEIN;

ASTHMA; CARRIER PROTEINS; FEMALE; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LINKAGE DISEQUILIBRIUM; MALE; MEMBRANE PROTEINS; NEOPLASM PROTEINS;

EID: 84922746494     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms6965     Document Type: Article

References (46)

1. Thomsen, S. F., van der Sluis, S., Kyvik, K. O., Skytthe, A. & Backer, V. Estimates of asthma heritability in a large twin sample. Clin. Exp. Allergy 40, 1054-1061 (2010).
2. Duffy, D. L., Martin, N. G., Battistutta, D., Hopper, J. L. & Mathews, J. D. Genetics of asthma and hay fever in Australian twins. Am. Rev. Respir. Dis. 142, 1351-1358 (1990).
3. Palmer, L. J., Burton, P. R., James, A. L., Musk, A. W. & Cookson, W. O. Familial aggregation and heritability of asthma-associated quantitative traits in a population-based sample of nuclear families. Eur. J. Hum. Genet. 8, 853-860 (2000).
4. Torgerson, D. G. et al. Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations. Nat. Genet. 43, 887-892 (2011).
5. Moffatt, M. F. et al. A large-scale, consortium-based genomewide association study of asthma. N. Engl. J. Med. 363, 1211-1221 (2010).
6. Bonnelykke, K. et al. A genome-wide association study identifies CDHR3 as a susceptibility locus for early childhood asthma with severe exacerbations. Nat. Genet. 46, 51-55 (2014).
7. Hirota, T. et al. Genome-wide association study identifies three new susceptibility loci for adult asthma in the Japanese population. Nat. Genet. 43, 893-896 (2011).
8. Manolio, T. A. et al. Finding the missing heritability of complex diseases. Nature 461, 747-753 (2009).
9. Ober, C. & Vercelli, D. Gene-environment interactions in human disease: nuisance or opportunity? Trends Genet. 27, 107-115 (2011).
10. Myers, R. A. et al. Further replication studies of the EVE Consortium metaanalysis identifies 2 asthma risk loci in European Americans. J. Allergy Clin. Immunol. 130, 1294-1301 (2012).
11. Alavanja, M. C. et al. The Agricultural Health Study. Environ. Health Perspect. 104, 362-369 (1996).
12. Halapi, E. et al. A sequence variant on 17q21 is associated with age at onset and severity of asthma. Eur. J. Hum. Genet. 18, 902-908 (2010).
13. Lluis, A. et al. Asthma-associated polymorphisms in 17q21 influence cord blood ORMDL3 and GSDMA gene expression and IL-17 secretion. J. Allergy Clin. Immunol. 127, 1587-94.e6 (2011).
14. Moffatt, M. F. et al. Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma. Nature 448, 470-473 (2007).
15. Zhou, X. & Stephens, M. Genome-wide efficient mixed-model analysis for association studies. Nat. Genet. 44, 821-824 (2012).
16. Horvath, S., Xu, X. & Laird, N. M. The family based association test method: strategies for studying general genotype-phenotype associations. Eur. J. Hum. Genet. 9, 301-306 (2001).
17. DeWan, A. T. et al. Whole-exome sequencing of a pedigree segregating asthma. BMC Med. Genet. 13, 95 (2012).
18. Himes, B. E. et al. Genome-wide association analysis identifies PDE4D as an asthma-susceptibility gene. Am. J. Hum. Genet. 84, 581-593 (2009).
19. Galanter, J. M. et al. Genome-wide association study and admixture mapping identify different asthma-associated loci in Latinos: The Genes-environments & Admixture in Latino Americans study. J. Allergy Clin. Immunol. 134, 295-305 (2014).
20. Granell, R. et al. Examination of the relationship between variation at 17q21 and childhood wheeze phenotypes. J. Allergy Clin. Immunol. 131, 685-694 (2013).
21. Calskan, M. et al. Rhinovirus wheezing illness and genetic risk of childhoodonset asthma. N. Engl. J. Med. 368, 1398-1407 (2013).
22. Hao, K. et al. Lung eQTLs to help reveal the molecular underpinnings of asthma. PLoS Genet. 8, e1003029 (2012).
23. Murphy, A. et al. Mapping of numerous disease-associated expression polymorphisms in primary peripheral blood CD4 lymphocytes. Hum. Mol. Genet 19, 4745-4757 (2010).
24. Sharma, S. et al. A genome-wide survey of CD4() lymphocyte regulatory genetic variants identifies novel asthma genes. J. Allergy Clin. Immunol. 134, 1153-1162 (2014).
25. Zuk, O. et al. Searching for missing heritability: designing rare variant association studies. Proc. Natl Acad. Sci. USA 111, E455-E464 (2014).
26. Torgerson, D. G. et al. Resequencing candidate genes implicates rare variants in asthma susceptibility. Am. J. Hum. Genet. 90, 273-281 (2012).
27. Cirulli, E. T. & Goldstein, D. B. Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat. Rev. Genet. 11, 415-425 (2010).
28. Lee, S., Teslovich, T. M., Boehnke, M. & Lin, X. General framework for metaanalysis of rare variants in sequencing association studies. Am. J. Hum. Genet. 93, 42-53 (2013).
29. Adzhubei, I. A. et al. A method and server for predicting damaging missense mutations. Nat. Methods 7, 248-249 (2010).
30. Huyghe, J. R. et al. Exome array analysis identifies new loci and low-frequency variants influencing insulin processing and secretion. Nat. Genet. 45, 197-201 (2013).
31. Kirke, P. N. et al. Impact of the MTHFR C677T polymorphism on risk of neural tube defects: case-control study. BMJ 328, 1535-1536 (2004).
32. Newton-Cheh, C. et al. Genome-wide association study identifies eight loci associated with blood pressure. Nat. Genet. 41, 666-676 (2009).
33. Wu, X. et al. Association between the MTHFR C677T polymorphism and recurrent pregnancy loss: a meta-analysis. Genet. Test Mol. Biomarkers 16, 806-811 (2012).
34. Husemoen, L. L. N. et al. The association between atopy and factors influencing folate metabolism: is low folate status causally related to the development of atopy? Int. J. Epidemiol. 35, 954-961 (2006).
35. Thuesen, B. H., Husemoen, L. L. N., Fenger, M. & Linneberg, A. Lack of association between the MTHFR (C677T) polymorphism and atopic disease. Clin. Respir. J. 3, 102-108 (2009).
36. Granell, R. et al. The association between mother and child MTHFR C677T polymorphisms, dietary folate intake and childhood atopy in a population-based, longitudinal birth cohort. Clin. Exp. Allergy 38, 320-328 (2008).
37. Haberg, S. E. et al. Maternal folate levels in pregnancy and asthma in children at age 3 years. J. Allergy Clin. Immunol. 127, 262-4-264.e1 (2011).
38. Haberg, S. E., London, S. J., Stigum, H., Nafstad, P. & Nystad, W. Folic acid supplements in pregnancy and early childhood respiratory health. Arch. Dis. Child. 94, 180-184 (2009).
39. Nevrivy, D. J. et al. Interaction of GRASP, a protein encoded by a novel retinoic acid-induced gene, with members of the cytohesin family of guanine nucleotide exchange factors. J. Biol. Chem. 275, 16827-16836 (2000).
40. Zhang, Y. et al. Roles of scaffolding protein Gab1 in regulation of myeloid dentritic cell-mediated allergic asthma (HYP7P.281). J. Immunol. 192, 119.4-119.4 (2014).
41. Walker, J. K. L. et al. Beta-arrestin-2 regulates the development of allergic asthma. J. Clin. Invest. 112, 566-574 (2003).
42. Verlaan, D. J. et al. Targeted screening of cis-regulatory variation in human haplotypes. Genome Res. 19, 118-127 (2009).
43. Morrison, F. S. et al. The splice site variant rs11078928 may be associated with a genotype-dependent alteration in expression of GSDMB transcripts. BMC Genomics 14, 627 (2013).
44. Saeki, N. et al. Distinctive expression and function of four GSDM family genes (GSDMA-D) in normal and malignant upper gastrointestinal epithelium. Genes Chromosomes Cancer 48, 261-271 (2009).
45. Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575 (2007).
46. Gibbs, R. A. et al. The International HapMap Project. Nature 426, 789-796 (2003).