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Large-scale genome-wide association studies and meta-analyses of longitudinal change in adult lung function

Wenbo Tang, Matthew Kowgier, Daan W Loth, María Soler Artigas, Bonnie R Joubert, Emily Hodge, Sina A Gharib, Albert V Smith, Ingo Ruczinski, Vilmundur Gudnason, et al. (2014) PLOS ONE. 9(7).
abstract
Background: Genome-wide association studies (GWAS) have identified numerous loci influencing cross-sectional lung function, but less is known about genes influencing longitudinal change in lung function. Methods: We performed GWAS of the rate of change in forced expiratory volume in the first second (FEV1) in 14 longitudinal, population-based cohort studies comprising 27,249 adults of European ancestry using linear mixed effects model and combined cohort-specific results using fixed effect meta-analysis to identify novel genetic loci associated with longitudinal change in lung function. Gene expression analyses were subsequently performed for identified genetic loci. As a secondary aim, we estimated the mean rate of decline in FEV1 by smoking pattern, irrespective of genotypes, across these 14 studies using meta-analysis. Results: The overall meta-analysis produced suggestive evidence for association at the novel IL16/STARD5/TMC3 locus on chromosome 15 (P = 5.71 x 10(-7)). In addition, meta-analysis using the five cohorts with >= 3 FEV1 measurements per participant identified the novel ME3 locus on chromosome 11 (P = 2.18 x 10(-8)) at genome-wide significance. Neither locus was associated with FEV1 decline in two additional cohort studies. We confirmed gene expression of IL16, STARD5, and ME3 in multiple lung tissues. Publicly available microarray data confirmed differential expression of all three genes in lung samples from COPD patients compared with controls. Irrespective of genotypes, the combined estimate for FEV1 decline was 26.9, 29.2 and 35.7 mL/year in never, former, and persistent smokers, respectively. Conclusions: In this large-scale GWAS, we identified two novel genetic loci in association with the rate of change in FEV1 that harbor candidate genes with biologically plausible functional links to lung function.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
INTERLEUKIN-16, GENE, EXPRESSION, ASTHMA, HEARING-LOSS, MALIC ENZYME, GLOBAL BURDEN, FUNCTION DECLINE, OBSTRUCTIVE PULMONARY-DISEASE, EPIDERMODYSPLASIA-VERRUCIFORMIS
journal title
PLOS ONE
PLoS One
volume
9
issue
7
article number
e100776
pages
13 pages
Web of Science type
Article
Web of Science id
000339635000039
JCR category
MULTIDISCIPLINARY SCIENCES
JCR impact factor
3.234 (2014)
JCR rank
9/57 (2014)
JCR quartile
1 (2014)
ISSN
1932-6203
DOI
10.1371/journal.pone.0100776
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
5771697
handle
http://hdl.handle.net/1854/LU-5771697
date created
2014-12-04 14:50:57
date last changed
2016-12-21 15:42:42
@article{5771697,
  abstract     = {Background: Genome-wide association studies (GWAS) have identified numerous loci influencing cross-sectional lung function, but less is known about genes influencing longitudinal change in lung function. 
Methods: We performed GWAS of the rate of change in forced expiratory volume in the first second (FEV1) in 14 longitudinal, population-based cohort studies comprising 27,249 adults of European ancestry using linear mixed effects model and combined cohort-specific results using fixed effect meta-analysis to identify novel genetic loci associated with longitudinal change in lung function. Gene expression analyses were subsequently performed for identified genetic loci. As a secondary aim, we estimated the mean rate of decline in FEV1 by smoking pattern, irrespective of genotypes, across these 14 studies using meta-analysis. 
Results: The overall meta-analysis produced suggestive evidence for association at the novel IL16/STARD5/TMC3 locus on chromosome 15 (P = 5.71 x 10(-7)). In addition, meta-analysis using the five cohorts with {\textrangle}= 3 FEV1 measurements per participant identified the novel ME3 locus on chromosome 11 (P = 2.18 x 10(-8)) at genome-wide significance. Neither locus was associated with FEV1 decline in two additional cohort studies. We confirmed gene expression of IL16, STARD5, and ME3 in multiple lung tissues. Publicly available microarray data confirmed differential expression of all three genes in lung samples from COPD patients compared with controls. Irrespective of genotypes, the combined estimate for FEV1 decline was 26.9, 29.2 and 35.7 mL/year in never, former, and persistent smokers, respectively. 
Conclusions: In this large-scale GWAS, we identified two novel genetic loci in association with the rate of change in FEV1 that harbor candidate genes with biologically plausible functional links to lung function.},
  articleno    = {e100776},
  author       = {Tang, Wenbo and Kowgier, Matthew and Loth, Daan W and Artigas, Mar{\'i}a Soler and Joubert, Bonnie R and Hodge, Emily and Gharib, Sina A and Smith, Albert V and Ruczinski, Ingo and Gudnason, Vilmundur and Mathias, Rasika A and Harris, Tamara B and Hansel, Nadia N and Launer, Lenore J and Barnes, Kathleen C and Hansen, Joyanna G and Albrecht, Eva and Aldrich, Melinda C and Allerhand, Michael and Barr, R Graham and Brusselle, Guy and Couper, David J and Curjuric, Ivan and Davies, Gail and Deary, Ian J and Dupuis, Jos{\'e}e and Fall, Tove and Foy, Millennia and Franceschini, Nora and Gao, Wei and Gl{\"a}ser, Sven and Gu, Xiangjun and Hancock, Dana B and Heinrich, Joachim and Hofman, Albert and Imboden, Medea and Ingelsson, Erik and James, Alan and Karrasch, Stefan and Koch, Beate and Kritchevsky, Stephen B and Kumar, Ashish and Lahousse, Lies and Li, Guo and Lind, Lars and Lindgren, Cecilia and Liu, Yongmei and Lohman, Kurt and Lumley, Thomas and McArdle, Wendy L and Meibohm, Bernd and Morris, Andrew P and Morrison, Alanna C and Musk, Bill and North, Kari E and Palmer, Lyle J and Probst-Hensch, Nicole M and Psaty, Bruce M and Rivadeneira, Fernando and Rotter, Jerome I and Schulz, Holger and Smith, Lewis J and Sood, Akshay and Starr, John M and Strachan, David P and Teumer, Alexander and Uitterlinden, Andr{\'e} G and V{\"o}lzke, Henry and Voorman, Arend and Wain, Louise V and Wells, Martin T and Wilk, Jemma B and Williams, O Dale and Heckbert, Susan R and Stricker, Bruno H and London, Stephanie J and Fornage, Myriam and Tobin, Martin D and O'Connor, George T and Hall, Ian P and Cassano, Patricia A},
  issn         = {1932-6203},
  journal      = {PLOS ONE},
  keyword      = {INTERLEUKIN-16,GENE,EXPRESSION,ASTHMA,HEARING-LOSS,MALIC ENZYME,GLOBAL BURDEN,FUNCTION DECLINE,OBSTRUCTIVE PULMONARY-DISEASE,EPIDERMODYSPLASIA-VERRUCIFORMIS},
  language     = {eng},
  number       = {7},
  pages        = {13},
  title        = {Large-scale genome-wide association studies and meta-analyses of longitudinal change in adult lung function},
  url          = {http://dx.doi.org/10.1371/journal.pone.0100776},
  volume       = {9},
  year         = {2014},
}

Chicago
Tang, Wenbo, Matthew Kowgier, Daan W Loth, María Soler Artigas, Bonnie R Joubert, Emily Hodge, Sina A Gharib, et al. 2014. “Large-scale Genome-wide Association Studies and Meta-analyses of Longitudinal Change in Adult Lung Function.” Plos One 9 (7).
APA
Tang, W., Kowgier, M., Loth, D. W., Artigas, M. S., Joubert, B. R., Hodge, E., Gharib, S. A., et al. (2014). Large-scale genome-wide association studies and meta-analyses of longitudinal change in adult lung function. PLOS ONE, 9(7).
Vancouver
1.
Tang W, Kowgier M, Loth DW, Artigas MS, Joubert BR, Hodge E, et al. Large-scale genome-wide association studies and meta-analyses of longitudinal change in adult lung function. PLOS ONE. 2014;9(7).
MLA
Tang, Wenbo, Matthew Kowgier, Daan W Loth, et al. “Large-scale Genome-wide Association Studies and Meta-analyses of Longitudinal Change in Adult Lung Function.” PLOS ONE 9.7 (2014): n. pag. Print.