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Genome-Wide Joint Meta-Analysis of SNP and SNP-by-Smoking Interaction Identifies Novel Loci for Pulmonary Function

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Hancock, Dana B., Artigas, María Soler, Gharib, Sina A., Henry, Amanda, Manichaikul, Ani, Ramasamy, Adaikalavan, Loth, Daan W., Imboden, Medea, Koch, Beate, McArdle, Wendy L., Smith, Albert V., Smolonska, Joanna, Sood, Akshay, Tang, Wenbo, Wilk, Jemma B., Zhai, Guangju, Zhao, Jing Hua, Aschard, Hugues, Burkart, Kristin M., Curjuric, Ivan, Eijgelsheim, Mark, Elliott, Paul, Gu, Xiangjun, Harris, Tamara B., Janson, Christer, Homuth, Georg, Hysi, Pirro G., Liu, Jason Z., Loehr, Laura R., Lohman, Kurt, Loos, Ruth J. F., Manning, Alisa K., Marciante, Kristin D., Obeidat, Ma'en, Postma, Dirkje S., Aldrich, Melinda C., Brusselle, Guy G., Chen, Ting-hsu, Eiriksdottir, Gudny, Franceschini, Nora, Heinrich, Joachim, Rotter, Jerome I., Wijmenga, Cisca, Williams, O. Dale, Bentley, Amy R., Hofman, Albert, Laurie, Cathy C., Lumley, Thomas, Morrison, Alanna C., Joubert, Bonnie R., Rivadeneira, Fernando, Couper, David J., Kritchevsky, Stephen B., Liu, Yongmei, Wjst, Matthias, Wain, Louise V., Vonk, Judith M., Uitterlinden, André G., Rochat, Thierry, Rich, Stephen S., Psaty, Bruce M., O'Connor, George T., North, Kari E., Mirel, Daniel B., Meibohm, Bernd, Launer, Lenore J., Khaw, Kay-Tee, Hartikainen, Anna-Liisa, Hammond, Christopher J., Gläser, Sven, Marchini, Jonathan, Kraft, Peter, Wareham, Nicholas J., Völzke, Henry, Stricker, Bruno H. C., Spector, Timothy D., Probst-Hensch, Nicole M., Jarvis, Deborah, Jarvelin, Marjo-Riitta, Heckbert, Susan R., Gudnason, Vilmundur, Boezen, H. Marike, Barr, R. Graham, Cassano, Patricia A., Strachan, David P., Fornage, Myriam, Hall, Ian P., Dupuis, Josée, Tobin, Martin D., London, Stephanie J.·2012·PLoS Genetics
DOI 10.1371/journal.pgen.1003098
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Abstract

Genome-wide association studies have identified numerous genetic loci for spirometic measures of pulmonary function, forced expiratory volume in one second (FEV(1)), and its ratio to forced vital capacity (FEV(1)/FVC). Given that cigarette smoking adversely affects pulmonary function, we conducted genome-wide joint meta-analyses (JMA) of single nucleotide polymorphism (SNP) and SNP-by-smoking (ever-smoking or pack-years) associations on FEV(1) and FEV(1)/FVC across 19 studies (total N = 50,047). We identified three novel loci not previously associated with pulmonary function. SNPs in or near DNER (smallest P(JMA = )5.00×10(-11)), HLA-DQB1 and HLA-DQA2 (smallest P(JMA = )4.35×10(-9)), and KCNJ2 and SOX9 (smallest P(JMA = )1.28×10(-8)) were associated with FEV(1)/FVC or FEV(1) in meta-analysis models including SNP main effects, smoking main effects, and SNP-by-smoking (ever-smoking or pack-years) interaction. The HLA region has been widely implicated for autoimmune and lung phenotypes, unlike the other novel loci, which have not been widely implicated. We evaluated DNER, KCNJ2, and SOX9 and found them to be expressed in human lung tissue. DNER and SOX9 further showed evidence of differential expression in human airway epithelium in smokers compared to non-smokers. Our findings demonstrated that joint testing of SNP and SNP-by-environment interaction identified novel loci associated with complex traits that are missed when considering only the genetic main effects.

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Metadata

Authors
Hancock, D. B., Artigas, M. S., Gharib, S. A., Henry, A., Manichaikul, A., Ramasamy, A., Loth, D. W., Imboden, M., Koch, B., McArdle, W. L., Smith, A. V., Smolonska, J., Sood, A., Tang, W., Wilk, J. B., Zhai, G., Zhao, J. H., Aschard, H., Burkart, K. M., Curjuric, I., Eijgelsheim, M., Elliott, P., Gu, X., Harris, T. B., Janson, C., Homuth, G., Hysi, P. G., Liu, J. Z., Loehr, L. R., Lohman, K., Loos, R. J. F., Manning, A. K., Marciante, K. D., Obeidat, M., Postma, D. S., Aldrich, M. C., Brusselle, G. G., Chen, T.-H., Eiriksdottir, G., Franceschini, N., Heinrich, J., Rotter, J. I., Wijmenga, C., Williams, O. D., Bentley, A. R., Hofman, A., Laurie, C. C., Lumley, T., Morrison, A. C., Joubert, B. R., Rivadeneira, F., Couper, D. J., Kritchevsky, S. B., Liu, Y., Wjst, M., Wain, L. V., Vonk, J. M., Uitterlinden, A. G., Rochat, T., Rich, S. S., Psaty, B. M., O'Connor, G. T., North, K. E., Mirel, D. B., Meibohm, B., Launer, L. J., Khaw, K.-T., Hartikainen, A.-L., Hammond, C. J., Gläser, S., Marchini, J., Kraft, P., Wareham, N. J., Völzke, H., Stricker, B. H. C., Spector, T. D., Probst-Hensch, N. M., Jarvis, D., Jarvelin, M.-R., Heckbert, S. R., Gudnason, V., Boezen, H. M., Barr, R. G., Cassano, P. A., Strachan, D. P., Fornage, M., Hall, I. P., Dupuis, J., Tobin, M. D., & London, S. J.
Venue
PLoS Genetics
Publisher
Public Library of Science (PLoS)
Published
2012-12-20
Volume
8
Issue
12
Pages
e1003098
ISSN
  • 1553-7390 (ISSN-L)
  • 1553-7404
DOI
10.1371/journal.pgen.1003098
OpenAlex
W2104443125
Cited by
166
References
11
FWCI
2.53
Type
journal article
Language
en
Open access
gold
Licence
creativecommons.org/publicdomain/zero/1.0/ (unspecified)

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Hancock, D. B., Artigas, M. S., Gharib, S. A., Henry, A., Manichaikul, A., Ramasamy, A., Loth, D. W., Imboden, M., Koch, B., McArdle, W. L., Smith, A. V., Smolonska, J., Sood, A., Tang, W., Wilk, J. B., Zhai, G., Zhao, J. H., Aschard, H., Burkart, K. M., . . . London, S. J. (2012). Genome-Wide Joint Meta-Analysis of SNP and SNP-by-Smoking Interaction Identifies Novel Loci for Pulmonary Function. PLoS Genetics. https://doi.org/10.1371/journal.pgen.1003098

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