Author Correction: Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations (Nature Communications, (2019), 10, 1, (880), 10.1038/s41467-019-08469-7);Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations

Nature Communications

Volumn 10, Issue 1, 2019, Pages

  Daya, Michelle ^a   Rafaels, Nicholas ^a   Brunetti, Tonya M ^a   Chavan, Sameer ^a   Levin, Albert M ^b   Shetty, Aniket ^a   Gignoux, Christopher R ^a   Boorgula, Meher Preethi ^a   Wojcik, Genevieve ^c   Campbell, Monica ^a   Vergara, Candelaria ^d   Torgerson, Dara G ^e   Ortega, Victor E ^f   Doumatey, Ayo ^g   Johnston, Henry Richard ^h   Acevedo, Nathalie ⁱ   Araujo, Maria Ilma ^j   Avila, Pedro C ^k   Belbin, Gillian ^l   Bleecker, Eugene ^m   Bustamante, Carlos ^c   Caraballo, Luis ⁱ   Cruz, Alvaro ^j   Dunston, Georgia M ⁿ   Eng, Celeste ^e   Faruque, Mezbah U ⁿ   Ferguson, Trevor S ^o   Figueiredo, Camila ^j   Ford, Jean G ^p   Gan, Weiniu ^q   Gourraud, Pierre Antoine ^r   Hansel, Nadia N ^d   Hernandez, Ryan D ^s   Herrera Paz, Edwin Francisco ^t,u   Jiménez, Silvia ⁱ   Kenny, Eimear E ^l   Knight Madden, Jennifer ^o   Kumar, Rajesh ^k   Lange, Leslie A ^a   Lange, Ethan M ^a   Lizee, Antoine ^r   Maul, Pissamai ^v   Maul, Trevor ^v   Mayorga, Alvaro ^w   Meyers, Deborah ^m   Nicolae, Dan L ^x   O’Connor, Timothy D ^y   Oliveira, Ricardo Riccio ^z   Olopade, Christopher O ^x   Olopade, Olufunmilayo ^x   Qin, Zhaohui S ^aa   Rotimi, Charles ^g   Vince, Nicolas ^r   Watson, Harold ^v   Wilks, Rainford J ^o   Wilson, James G ^ab   Salzberg, Steven ^ac   Ober, Carole ^x   Burchard, Esteban G ^s   Williams, L Keoki ^b   Beaty, Terri H ^ad   Taub, Margaret A ^ad   Ruczinski, Ingo ^ad   Mathias, Rasika A ^d   Barnes, Kathleen C ^a   Adegnika, Ayola Akim ^ae   Arinola, Ganiyu ^af   Ateba Ngoa, Ulysse ^ae   Ayestas, Gerardo ^t   Bjarnadóttir, Hilda ^ag   Correa, Adolfo ^ab   Erazo, Said Omar Leiva ^t   Foreman, Marilyn G ^ah   Foster, Cassandra ^d   Gao, Li ^d   Gao, Jingjing ^ai   Grammer, Leslie ^k   Hansen, Mark ^aj   Hartert, Tina ^ak   Hu, Yijuan ^aa   Königsberg, Iain ^a   Kim, Kwang Youn A ^k   Landaverde Torres, Pamela ^t   Marrugo, Javier ⁱ   Martinez, Beatriz ⁱ   Martinez, Rosella ^t   Mayorga, Luis F ^t   Mejia Mejia, Delmy Aracely ^u   Meza, Catherine ⁱ   Musani, Solomon ^ab   Musharoff, Shaila ^c   Oluwole, Oluwafemi ^x   Pino Yanes, Maria ^e   Ramos, Hector ^t   Saenz, Allan ^t   Samms Vaughan, Maureen ^v   Schleimer, Robert ^k   Scott, Alan F ^d   Shringarpure, Suyash S ^c   Song, Wei ^y   Szpiech, Zachary A ^s   Torres, Raul ^s   Varela, Gloria ^t   Vasquez, Olga Marina ^al   Vega, Francisco M De La ^c   Ware, Lorraine B ^ak   Yazdanbakhsh, Maria ^am   more..

^a UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^b HENRY FORD HEALTH SYSTEM   (United States)

^c STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

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

^e UNIVERSITY OF CALIFORNIA   (United States)

^f WAKE FOREST SCHOOL OF MEDICINE   (United States)

^g NATIONAL INSTITUTES OF HEALTH   (United States)

^h EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

ⁱ UNIVERSIDAD DE CARTAGENA   (Colombia)

^j FEDERAL UNIVERSITY OF BAHIA   (Brazil)

^k NORTHWESTERN UNIVERSITY   (United States)

^l MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^m UNIVERSITY OF ARIZONA COLLEGE OF MEDICINE   (United States)

ⁿ HOWARD UNIVERSITY COLLEGE OF MEDICINE   (United States)

^o UNIVERSITY OF THE WEST INDIES   (Jamaica)

^p EINSTEIN MEDICAL CENTER   (United States)

^q NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

^r UNIVERSITÉ DE NANTES   (France)

^s UNIVERSITY OF CALIFORNIA   (United States)

^t Facultad de Medicina   (Honduras)

^u UNIVERSIDAD TECNOLÓGICA CENTROAMERICANA UNITEC   (Honduras)

^v UNIVERSITY OF THE WEST INDIES   (Jamaica)

^w Centro de Neumologia y Alergia   (Honduras)

^x UNIVERSITY OF CHICAGO   (United States)

^y UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

^z INSTITUTO OSWALDO CRUZ   (Brazil)

^aa EMORY UNIVERSITY   (United States)

^ab UNIVERSITY OF MISSISSIPPI SCHOOL OF MEDICINE   (United States)

^ac JOHNS HOPKINS UNIVERSITY   (United States)

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

^ae German Center for Infection Research CERMEL   (Gabon)

^af UNIVERSITY OF IBADAN   (Nigeria)

^ag UNIVERSITY OF ICELAND   (Iceland)

^ah MOREHOUSE SCHOOL OF MEDICINE   (United States)

^ai ABBVIE INC   (United States)

^aj ILLUMINA INC   (United States)

^ak VANDERBILT UNIVERSITY   (United States)

^al Faculty of Medicine   (Honduras)

^am LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

more..

Author keywords

[No Author keywords available]

Indexed keywords

IMMUNOGLOBULIN E; STAT6 PROTEIN;

AFRICAN AMERICAN; ANCESTRY; ASTHMA; CHROMOSOME; GENOME; HEALTH RISK; IDENTIFICATION METHOD; META-ANALYSIS; PUBLIC HEALTH;

ARTICLE; ASTHMA; CHROMOSOME 17; CONTROLLED STUDY; EXPRESSION QUANTITATIVE TRAIT LOCUS; GENE FREQUENCY; GENE LOCUS; GENE STRUCTURE; GENETIC RISK; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HAPLOTYPE; HUMAN; IMMUNOGLOBULIN BLOOD LEVEL; POLLEN ALLERGY; SINGLE NUCLEOTIDE POLYMORPHISM; AFRICAN AMERICAN; CHROMOSOME 12; CHROMOSOME 8; GENETIC PREDISPOSITION; GENETICS; HISPANIC; META ANALYSIS; UNITED STATES;

AFRICAN AMERICANS; ASTHMA; CHROMOSOMES, HUMAN, PAIR 12; CHROMOSOMES, HUMAN, PAIR 17; CHROMOSOMES, HUMAN, PAIR 8; GENETIC LOCI; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HISPANIC AMERICANS; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; UNITED STATES;

EID: 85061908861     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/s41467-019-12158-w     Document Type: Erratum

References (73)

1. Moorman, J. E. et al. National surveillance of asthma: United States, 2001–2010. Vital Health Stat. 3, 1–58 (2012).
2. Moorman, J. E. et al. National surveillance for asthma—United States, 1980–2004. Mmwr. Surveill. Summ. 56, 1–54 (2007).
3. Keet, C. A. et al. Neighborhood poverty, urban residence, race/ethnicity, and asthma: rethinking the inner-city asthma epidemic. J. Allergy Clin. Immunol. 135, 655–662 (2015).
4. Mathias, R. A. et al. A genome-wide association study on African-ancestry populations for asthma. J. Allergy Clin. Immunol. 125, 336–346 e4 (2010).
5. Almoguera, B. et al. Identification of four novel loci in asthma in European American and African American populations. Am. J. Respir. Crit. Care. Med. 195, 456–463 (2017).
6. 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).
7. Demenais, F. et al. Multiancestry association study identifies new asthma risk loci that colocalize with immune-cell enhancer marks. Nat. Genet. 50, 42–53 (2018).
8. White, M. J. et al. Novel genetic risk factors for asthma in African American children: precision medicine and the SAGE II study. Immunogenetics 68, 391–400 (2016).
9. Mathias, R. A. et al. A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome. Nat. Commun. 7, 12522 (2016).
10. Johnston, H. R. et al. Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome. Sci. Rep. 7, 46398 (2017).
11. Magi, R. et al. Trans-ethnic meta-regression of genome-wide association studies accounting for ancestry increases power for discovery and improves fine-mapping resolution. Hum. Mol. Genet. 26, 3639–3650 (2017).
12. MacArthur, J. et al. The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog). Nucleic Acids Res. 45, D896–D901 (2017).
13. Stein, M. M. et al. A decade of research on the 17q12–21 asthma locus: piecing together the puzzle. J. Allergy Clin. Immunol. 142, 749–764 (2018).
14. Schmitt, A. D. et al. A compendium of chromatin contact maps reveals spatially active regions in the human genome. Cell Rep. 17, 2042–2059 (2016).
15. Martin, J. S. et al. HUGIn: Hi-C unifying genomic interrogator. Bioinformatics 33, 3793–3795 (2017).
16. Ay, F., Bailey, T. L. & Noble, W. S. Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome Res. 24, 999–1011 (2014).
17. Singh, D. et al. Altered gene expression in blood and sputum in COPD frequent exacerbators in the ECLIPSE cohort. PLoS One 9, e107381 (2014).
18. Pinto, S. M. et al. Quantitative phosphoproteomic analysis of IL-33-mediated signaling. Proteomics 15, 532–544 (2015).
19. Yao, T. C. et al. Genome-wide association study of lung function phenotypes in a founder population. J. Allergy Clin. Immunol. 133, 248–255 e1–10 (2014).
20. Centers for Disease Control and Prevention (CDC) National Asthma Control Program. Asthma in Puerto Rico. State Data Profiles https://www.cdc.gov/asthma/stateprofiles/Asthma_in_PR.pdf (2011).
21. Dragon, S., Hirst, S. J., Lee, T. H. & Gounni, A. S. IL-17A mediates a selective gene expression profile in asthmatic human airway smooth muscle cells. Am. J. Respir. Cell Mol. Biol. 50, 1053–1063 (2014).
22. Goenka, S. & Kaplan, M. H. Transcriptional regulation by STAT6. Immunol. Res. 50, 87–96 (2011).
23. Wain, L. V. et al. Genome-wide association analyses for lung function and chronic obstructive pulmonary disease identify new loci and potential druggable targets. Nat. Genet. 49, 416–425 (2017).
24. Soler Artigas, M. et al. Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function. Nat. Genet. 43, 1082–1090 (2011).
25. The Collaborative Study on the Genetics of Asthma (CSGA). A genome-wide search for asthma susceptibility loci in ethnically diverse populations. Nat. Genet. 15, 389–392 (1997).
26. Barnes, K. C. et al. Dense mapping of chromosome 12q13.12–q23.3 and linkage to asthma and atopy. J. Allergy Clin. Immunol. 104, 485–491 (1999).
27. Barnes, K. C. et al. Linkage of asthma and total serum IgE concentration to markers on chromosome 12q: evidence from Afro-Caribbean and Caucasian populations. Genomics 37, 41–50 (1996).
28. Nickel, R. et al. Evidence for linkage of chromosome 12q15–q24.1 markers to high total serum IgE concentrations in children of the German Multicenter Allergy Study. Genomics 46, 159–162 (1997).
29. Kavalar, M. S. et al. Association of ORMDL3, STAT6 and TBXA2R gene polymorphisms with asthma. Int. J. Immunogenet. 39, 20–25 (2012).
30. Duetsch, G. et al. STAT6 as an asthma candidate gene: polymorphism-screening, association and haplotype analysis in a Caucasian sib-pair study. Hum. Mol. Genet. 11, 613–621 (2002).
31. Wang, Q. et al. Association of polymorphisms of STAT6 and SO(2) with Chinese childhood asthma: a case-control study. Biomed. Environ. Sci. 24, 670–677 (2011).
32. Godava, M., Vrtel, R. & Vodicka, R. STAT6—polymorphisms, haplotypes and epistasis in relation to atopy and asthma. Biomed. Pap. Med. Fac. Univ. Palacky. Olomouc Czech. Repub. 157, 172–180 (2013).
33. Yan, Q. et al. A meta-analysis of genome-wide association studies of asthma in Puerto Ricans. Eur. Respir. J. 49, 1601505 (2017).
34. Kreiner-Moller, E. et al. 17q21 gene variation is not associated with asthma in adulthood. Allergy 70, 107–114 (2015).
35. Esnault, S. et al. Identification of genes expressed by human airway eosinophils after an in vivo allergen challenge. PLoS One 8, e67560 (2013).
36. Lima, L. C. et al. Genetic variants in RORA are associated with asthma and allergy markers in an admixed population. Cytokine 113, 177–184 (2019).
37. Sunyer, J., Anto, J. M., Castellsague, J., Soriano, J. B. & Roca, J. Total serum IgE is associated with asthma independently of specific IgE levels. The Spanish Group of the European Study of Asthma. Eur. Respir. J. 9, 1880–1884 (1996).
38. Sears, M. R. et al. Relation between airway responsiveness and serum IgE in children with asthma and in apparently normal children. N. Engl. J. Med. 325, 1067–1071 (1991).
39. Palmer, L. J. et al. Independent inheritance of serum immunoglobulin E concentrations and airway responsiveness. Am. J. Respir. Crit. Care. Med. 161, 1836–1843 (2000).
40. Levin, A. M. et al. A meta-analysis of genome-wide association studies for serum total IgE in diverse study populations. J. Allergy Clin. Immunol. 131, 1176–1184 (2013).
41. Burrows, B., Martinez, F. D., Halonen, M., Barbee, R. A. & Cline, M. G. Association of asthma with serum IgE levels and skin-test reactivity to allergens. N. Engl. J. Med. 320, 271–277 (1989).
42. 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).
43. Vaillancourt, V. T., Bordeleau, M., Laviolette, M. & Laprise, C. From expression pattern to genetic association in asthma and asthma-related phenotypes. BMC Res. Notes 5, 630 (2012).
44. Gould, W. et al. Factors predicting inhaled corticosteroid responsiveness in African American patients with asthma. J. Allergy Clin. Immunol. 126, 1131–1138 (2010).
45. Sulovari, A., Chen, Y. H., Hudziak, J. J. & Li, D. Atlas of human diseases influenced by genetic variants with extreme allele frequency differences. Hum. Genet. 136, 39–54 (2017).
46. Morales, J. et al. A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog. Genome Biol. 19, 21 (2018).
47. West, K. M., Blacksher, E. & Burke, W. Genomics, health disparities, and missed opportunities for the nation’s research agenda. JAMA 317, 1831–1832 (2017).
48. Popejoy, A. B. & Fullerton, S. M. Genomics is failing on diversity. Nature 538, 161–164 (2016).
49. Ferreira, M. A. et al. Shared genetic origin of asthma, hay fever and eczema elucidates allergic disease biology. Nat. Genet. 49, 1752–1757 (2017).
50. Wolford, B. N., Willer, C. J. & Surakka, I. Electronic health records: the next wave of complex disease genetics. Hum. Mol. Genet. 27, R14–R21 (2018).
51. National Institutes of Health. Health Disparities (NIH, UK, 2010).
52. Brody, J. A. et al. Analysis commons, a team approach to discovery in a big-data environment for genetic epidemiology. Nat. Genet. 49, 1560–1563 (2017).
53. Schlauch, D., Glass, K., Hersh, C. P., Silverman, E. K. & Quackenbush, J. Estimating drivers of cell state transitions using gene regulatory network models. BMC Syst. Biol. 11, 139 (2017).
54. Ferreira, M. A. et al. Gene-based analysis of regulatory variants identifies 4 putative novel asthma risk genes related to nucleotide synthesis and signaling. J. Allergy Clin. Immunol. 139, 1148–1157 (2017).
55. Gamazon, E. R. et al. A gene-based association method for mapping traits using reference transcriptome data. Nat. Genet. 47, 1091–1098 (2015).
56. Mao, X. et al. A genomewide admixture mapping panel for Hispanic/Latino populations. Am. J. Hum. Genet. 80, 1171–1178 (2007).
57. Conomos, M. P., Miller, M. B. & Thornton, T. A. Robust inference of population structure for ancestry prediction and correction of stratification in the presence of relatedness. Genet. Epidemiol. 39, 276–293 (2015).
58. Conomos, M. P., Reiner, A. P., Weir, B. S. & Thornton, T. A. Model-free estimation of recent genetic relatedness. Am. J. Hum. Genet. 98, 127–148 (2016).
59. Chang, C. C. et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4, 7 (2015).
60. 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).
61. Liu, E. Y. et al. Genotype imputation of Metabochip SNPs using a study-specific reference panel of ~4,000 haplotypes in African Americans from the Women’s Health Initiative. Genet. Epidemiol. 36, 107–117 (2012).
62. Zhou, B., Shi, J. & Whittemore, A. S. Optimal methods for meta-analysis of genome-wide association studies. Genet. Epidemiol. 35, 581–591 (2011).
63. Lettre, G. et al. Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project. PLoS Genet. 7, e1001300 (2011).
64. Friedman, G. D. et al. CARDIA: study design, recruitment, and some characteristics of the examined subjects. J. Clin. Epidemiol. 41, 1105–1116 (1988).
65. Bild, D. E. et al. Multi-Ethnic Study of Atherosclerosis: objectives and design. Am. J. Epidemiol. 156, 871–881 (2002).
66. The ARIC investigators. The Atherosclerosis Risk in Communities (ARIC) Study: design and objectives. Am. J. Epidemiol. 129, 687–702 (1989).
67. Pasaniuc, B. et al. Fast and accurate imputation of summary statistics enhances evidence of functional enrichment. Bioinformatics 30, 2906–2914 (2014).
68. Barrett, J. C., Fry, B., Maller, J. & Daly, M. J. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263–265 (2005).
69. Gabriel, S. B. et al. The structure of haplotype blocks in the human genome. Science 296, 2225–2229 (2002).
70. Maples, B. K., Gravel, S., Kenny, E. E. & Bustamante, C. D. RFMix: a discriminative modeling approach for rapid and robust local-ancestry inference. Am. J. Hum. Genet. 93, 278–288 (2013).
71. Gao, X., Starmer, J. & Martin, E. R. A multiple testing correction method for genetic association studies using correlated single nucleotide polymorphisms. Genet. Epidemiol. 32, 361–369 (2008).
72. Johnson, J. L. & Abecasis, G. R. GAS Power Calculator: web-based power calculator for genetic association studies. Preprint at bioRxiv https://doi.org/10.1101/164343 (2017).
73. Yang, Y. et al. Effective sample size: quick estimation of the effect of related samples in genetic case-control association analyses. Comput. Biol. Chem. 35, 40–49 (2011).