Resequencing candidate genes implicates rare variants in asthma susceptibility

American Journal of Human Genetics

Volumn 90, Issue 2, 2012, Pages 273-281

  Torgerson, Dara G ^a,h   Capurso, Daniel ^a   Mathias, Rasika A ^b   Graves, Penelope E ^c   Hernandez, Ryan D ^d   Beaty, Terri H ^e   Bleecker, Eugene R ^f   Raby, Benjamin A ^g   Meyers, Deborah A ^f   Barnes, Kathleen C ^b   Weiss, Scott T ^g   Martinez, Fernando D ^c   Nicolae, Dan L ^a   Ober, Carole ^a  

^a UNIVERSITY OF CHICAGO   (United States)

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

^c UNIVERSITY OF ARIZONA   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^f WAKE FOREST SCHOOL OF MEDICINE   (United States)

^g BRIGHAM AND WOMEN S HOSPITAL   (United States)

^h UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APELIN RECEPTOR; DIPEPTIDYL PEPTIDASE; INTERLEUKIN 12 RECEPTOR; PROTEIN VARIANT;

ARTICLE; ASTHMA; CONTROLLED STUDY; DISEASE ASSOCIATION; DNA FLANKING REGION; EXON; GENETIC ASSOCIATION; GENETIC CODE; GENETIC SUSCEPTIBILITY; HUMAN; MAJOR CLINICAL STUDY; PRIORITY JOURNAL; STATISTICAL SIGNIFICANCE;

AFRICAN AMERICANS; ASTHMA; CASE-CONTROL STUDIES; EUROPEAN CONTINENTAL ANCESTRY GROUP; EXONS; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; HUMANS; OPEN READING FRAMES; SEQUENCE ANALYSIS, DNA; UNTRANSLATED REGIONS;

EID: 84856938156     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2012.01.008     Document Type: Article

References (43)

1. D.B. Hancock, I. Romieu, M. Shi, J.J. Sienra-Monge, H. Wu, G.Y. Chiu, H. Li, B.E. del Rio-Navarro, S.A. Willis-Owen, and S.T. Weiss Genome-wide association study implicates chromosome 9q21.31 as a susceptibility locus for asthma in mexican children PLoS Genet. 5 2009 e1000623
2. B.E. Himes, G.M. Hunninghake, J.W. Baurley, N.M. Rafaels, P. Sleiman, D.P. Strachan, J.B. Wilk, S.A. Willis-Owen, B. Klanderman, and J. Lasky-Su Genome-wide association analysis identifies PDE4D as an asthma-susceptibility gene Am. J. Hum. Genet. 84 2009 581 593
3. X. Li, T.D. Howard, S.L. Zheng, T. Haselkorn, S.P. Peters, D.A. Meyers, and E.R. Bleecker Genome-wide association study of asthma identifies RAD50-IL13 and HLA-DR/DQ regions J. Allergy Clin. Immunol. 125 2010 328-335.e11
4. R.A. Mathias, A.V. Grant, N. Rafaels, T. Hand, L. Gao, C. Vergara, Y.J. Tsai, M. Yang, M. Campbell, and C. Foster A genome-wide association study on African-ancestry populations for asthma J. Allergy Clin. Immunol. 125 2010 336-346.e4
5. M.F. Moffatt, I.G. Gut, F. Demenais, D.P. Strachan, E. Bouzigon, S. Heath, E. von Mutius, M. Farrall, M. Lathrop, W.O. Cookson GABRIEL Consortium A large-scale, consortium-based genomewide association study of asthma N. Engl. J. Med. 363 2010 1211 1221
6. M.F. Moffatt, M. Kabesch, L. Liang, A.L. Dixon, D. Strachan, S. Heath, M. Depner, A. von Berg, A. Bufe, and E. Rietschel Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma Nature 448 2007 470 473 (Pubitemid 47123521)
7. P.M. Sleiman, J. Flory, M. Imielinski, J.P. Bradfield, K. Annaiah, S.A. Willis-Owen, K. Wang, N.M. Rafaels, S. Michel, and K. Bonnelykke Variants of DENND1B associated with asthma in children N. Engl. J. Med. 362 2010 36 44
8. D.G. Torgerson, E.J. Ampleford, G.Y. Chiu, W.J. Gauderman, C.R. Gignoux, P.E. Graves, B.E. Himes, A.M. Levin, R.A. Mathias, D.B. Hancock Mexico City Childhood Asthma Study (MCAAS) Children's Health Study (CHS) and HARBORS study Genetics of Asthma in Latino Americans (GALA) Study, Study of Genes-Environment and Admixture in Latino Americans (GALA2) and Study of African Americans, Asthma, Genes & Environments (SAGE) Childhood Asthma Research and Education (CARE) Network Childhood Asthma Management Program (CAMP) Study of Asthma Phenotypes and Pharmacogenomic Interactions by Race-Ethnicity (SAPPHIRE) Genetic Research on Asthma in African Diaspora (GRAAD) Study Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations Nat. Genet. 43 2011 887 892
9. M.A. Ferreira, M.C. Matheson, D.L. Duffy, G.B. Marks, J. Hui, P. Le Souëf, P. Danoy, S. Baltic, D.R. Nyholt, M. Jenkins Australian Asthma Genetics Consortium Identification of IL6R and chromosome 11q13.5 as risk loci for asthma Lancet 378 2011 1006 1014
10. T. Hirota, A. Takahashi, M. Kubo, T. Tsunoda, K. Tomita, S. Doi, K. Fujita, A. Miyatake, T. Enomoto, and T. Miyagawa Genome-wide association study identifies three new susceptibility loci for adult asthma in the Japanese population Nat. Genet. 43 2011 893 896
11. J.K. Pritchard Are rare variants responsible for susceptibility to complex diseases? Am. J. Hum. Genet. 69 2001 124 137 (Pubitemid 32614025)
12. J.C. Cohen, R.S. Kiss, A. Pertsemlidis, Y.L. Marcel, R. McPherson, and H.H. Hobbs Multiple rare alleles contribute to low plasma levels of HDL cholesterol Science 305 2004 869 872 (Pubitemid 39038422)
13. S. Romeo, L.A. Pennacchio, Y. Fu, E. Boerwinkle, A. Tybjaerg-Hansen, H.H. Hobbs, and J.C. Cohen Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL Nat. Genet. 39 2007 513 516 (Pubitemid 46514768)
14. J.C. Cohen, A. Pertsemlidis, S. Fahmi, S. Esmail, G.L. Vega, S.M. Grundy, and H.H. Hobbs Multiple rare variants in NPC1L1 associated with reduced sterol absorption and plasma low-density lipoprotein levels Proc. Natl. Acad. Sci. USA 103 2006 1810 1815 (Pubitemid 43228775)
15. I.K. Kotowski, A. Pertsemlidis, A. Luke, R.S. Cooper, G.L. Vega, J.C. Cohen, and H.H. Hobbs A spectrum of PCSK9 alleles contributes to plasma levels of low-density lipoprotein cholesterol Am. J. Hum. Genet. 78 2006 410 422 (Pubitemid 43291224)
16. C.T. Johansen, J. Wang, M.B. Lanktree, H. Cao, A.D. McIntyre, M.R. Ban, R.A. Martins, B.A. Kennedy, R.G. Hassell, and M.E. Visser Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemia Nat. Genet. 42 2010 684 687
17. C. Ober, and S. Hoffjan Asthma genetics 2006: The long and winding road to gene discovery Genes Immun. 7 2006 95 100 (Pubitemid 43336051)
18. D. Vercelli Advances in asthma and allergy genetics in 2007 J. Allergy Clin. Immunol. 122 2008 267 271
19. C. Ober, and T.C. Yao The genetics of asthma and allergic disease: A 21st century perspective Immunol. Rev. 242 2011 10 30
20. R. Blekhman, O. Man, L. Herrmann, A.R. Boyko, A. Indap, C. Kosiol, C.D. Bustamante, K.M. Teshima, and M. Przeworski Natural selection on genes that underlie human disease susceptibility Curr. Biol. 18 2008 883 889
21. C.D. Bustamante, A. Fledel-Alon, S. Williamson, R. Nielsen, M.T. Hubisz, S. Glanowski, D.M. Tanenbaum, T.J. White, J.J. Sninsky, and R.D. Hernandez Natural selection on protein-coding genes in the human genome Nature 437 2005 1153 1157 (Pubitemid 41509352)
22. D.G. Torgerson, A.R. Boyko, R.D. Hernandez, A. Indap, X. Hu, T.J. White, J.J. Sninsky, M. Cargill, M.D. Adams, C.D. Bustamante, and A.G. Clark Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence PLoS Genet. 5 2009 e1000592
23. T.W. Guilbert, W.J. Morgan, M. Krawiec, R.F.J. Lemanske Jr., C. Sorkness, S.J. Szefler, G. Larsen, J.D. Spahn, R.S. Zeiger, G. Heldt Prevention of Early Asthma in Kids Study,Childhood Asthma Research and Education Network The Prevention of Early Asthma in Kids study: Design, rationale and methods for the Childhood Asthma Research and Education network Control. Clin. Trials 25 2004 286 310 (Pubitemid 38626165)
24. L.A. Lester, S.S. Rich, M.N. Blumenthal, A. Togias, S. Murphy, F. Malveaux, M.E. Miller, G.M. Dunston, J. Solway, R.L. Wolf Collaborative Study on the Genetics of Asthma Ethnic differences in asthma and associated phenotypes: Collaborative study on the genetics of asthma J. Allergy Clin. Immunol. 108 2001 357 362 (Pubitemid 32881055)
25. W.C. Moore, E.R. Bleecker, D. Curran-Everett, S.C. Erzurum, B.T. Ameredes, L. Bacharier, W.J. Calhoun, M. Castro, K.F. Chung, M.P. Clark National Heart, Lung, Blood Institute's Severe Asthma Research Program Characterization of the severe asthma phenotype by the National Heart, Lung, and Blood Institute's Severe Asthma Research Program J. Allergy Clin. Immunol. 119 2007 405 413 (Pubitemid 46210080)
26. American Thoracic Society Proceedings of the ATS workshop on refractory asthma: Current understanding, recommendations, and unanswered questions Am. J. Respir. Crit. Care Med. 162 2000 2341 2351
27. W.C. Moore, D.A. Meyers, S.E. Wenzel, W.G. Teague, H. Li, X. Li, R.J. D'Agostino Jr., M. Castro, D. Curran-Everett, A.M. Fitzpatrick National Heart, Lung, and Blood Institute's Severe Asthma Research Program Identification of asthma phenotypes using cluster analysis in the Severe Asthma Research Program Am. J. Respir. Crit. Care Med. 181 2010 315 323
28. Standards for the diagnosis and care of patients with chronic obstructive pulmonary disease (COPD) and asthma. This official statement of the American Thoracic Society was adopted by the ATS Board of Directors, November 1986 Am. Rev. Respir. Dis. 136 1987 225 244
29. Worldwide variations in the prevalence of asthma symptoms: The International Study of Asthma and Allergies in Childhood (ISAAC) Eur. Respir. J. 12 1998 315 335
30. C. Ober, Z. Tan, Y. Sun, J.D. Possick, L. Pan, R. Nicolae, S. Radford, R.R. Parry, A. Heinzmann, and K.A. Deichmann Effect of variation in CHI3L1 on serum YKL-40 level, risk of asthma, and lung function N. Engl. J. Med. 358 2008 1682 1691 (Pubitemid 351549915)
31. C.D. Bustamante, R. Nielsen, S.A. Sawyer, K.M. Olsen, M.D. Purugganan, and D.L. Hartl The cost of inbreeding in Arabidopsis Nature 416 2002 531 534 (Pubitemid 34288853)
32. M. Tzetis, A. Efthymiadou, S. Strofalis, P. Psychou, A. Dimakou, E. Pouliou, S. Doudounakis, and E. Kanavakis CFTR gene mutations - including three novel nucleotide substitutions - and haplotype background in patients with asthma, disseminated bronchiectasis and chronic obstructive pulmonary disease Hum. Genet. 108 2001 216 221 (Pubitemid 32297568)
33. M. Allen, A. Heinzmann, E. Noguchi, G. Abecasis, J. Broxholme, C.P. Ponting, S. Bhattacharyya, J. Tinsley, Y. Zhang, and R. Holt Positional cloning of a novel gene influencing asthma from chromosome 2q14 Nat. Genet. 35 2003 258 263 (Pubitemid 37363180)
34. S. Purcell, B. Neale, K. Todd-Brown, L. Thomas, M.A. Ferreira, D. Bender, J. Maller, P. Sklar, P.I. de Bakker, M.J. Daly, and P.C. Sham PLINK: A tool set for whole-genome association and population-based linkage analyses Am. J. Hum. Genet. 81 2007 559 575 (Pubitemid 47330214)
35. K.A. Frazer, D.G. Ballinger, D.R. Cox, D.A. Hinds, L.L. Stuve, R.A. Gibbs, J.W. Belmont, A. Boudreau, P. Hardenbol, S.M. Leal International HapMap Consortium A second generation human haplotype map of over 3.1 million SNPs Nature 449 2007 851 861 (Pubitemid 47598626)
36. R.M. Durbin, G.R. Abecasis, D.L. Altshuler, A. Auton, L.D. Brooks, R.M. Durbin, R.A. Gibbs, M.E. Hurles, G.A. McVean 1000 Genomes Project Consortium A map of human genome variation from population-scale sequencing Nature 467 2010 1061 1073
37. D. Karolchik, R. Baertsch, M. Diekhans, T.S. Furey, A. Hinrichs, Y.T. Lu, K.M. Roskin, M. Schwartz, C.W. Sugnet, D.J. Thomas University of California Santa Cruz The UCSC Genome Browser Database Nucleic Acids Res. 31 2003 51 54 (Pubitemid 36150331)
38. W.J. Kent, C.W. Sugnet, T.S. Furey, K.M. Roskin, T.H. Pringle, A.M. Zahler, and D. Haussler The human genome browser at UCSC Genome Res. 12 2002 996 1006 (Pubitemid 34662293)
39. A. Agresti An Introduction to Categorical Data Analysis (Wiley Series in Probability and Statistics) Second Edition 2007 John Wiley & Sons Hoboken, NJ
40. S. Sankararaman, S. Sridhar, G. Kimmel, and E. Halperin Estimating local ancestry in admixed populations Am. J. Hum. Genet. 82 2008 290 303 (Pubitemid 351726099)
41. B.M. Neale, M.A. Rivas, B.F. Voight, D. Altshuler, B. Devlin, M. Orho-Melander, S. Kathiresan, S.M. Purcell, K. Roeder, and M.J. Daly Testing for an unusual distribution of rare variants PLoS Genet. 7 2011 e1001322
42. A.R. Boyko, S.H. Williamson, A.R. Indap, J.D. Degenhardt, R.D. Hernandez, K.E. Lohmueller, M.D. Adams, S. Schmidt, J.J. Sninsky, and S.R. Sunyaev Assessing the evolutionary impact of amino acid mutations in the human genome PLoS Genet. 4 2008 e1000083
43. J. Yang, B. Benyamin, B.P. McEvoy, S. Gordon, A.K. Henders, D.R. Nyholt, P.A. Madden, A.C. Heath, N.G. Martin, and G.W. Montgomery Common SNPs explain a large proportion of the heritability for human height Nat. Genet. 42 2010 565 569