Assessing pleiotropy and mediation in genetic loci associated with chronic obstructive pulmonary disease

Margaret M. Parker, Sharon M. Lutz, Brian D. Hobbs, Robert Busch, Merry Lynn N. McDonald, Peter J. Castaldi, Terri L Beaty, John E. Hokanson, Edwin K. Silverman, Michael H. Cho

Research output: Contribution to journalArticle

Abstract

Genetic association studies have increasingly recognized variant effects on multiple phenotypes. Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease with environmental and genetic causes. Multiple genetic variants have been associated with COPD, many of which show significant associations to additional phenotypes. However, it is unknown if these associations represent biological pleiotropy or if they exist through correlation of related phenotypes (“mediated pleiotropy”). Using 6,670 subjects from the COPDGene study, we describe the association of known COPD susceptibility loci with other COPD-related phenotypes and distinguish if these act directly on the phenotypes (i.e., biological pleiotropy) or if the association is due to correlation (i.e., mediated pleiotropy). We identified additional associated phenotypes for 13 of 25 known COPD loci. Tests for pleiotropy between genotype and associated outcomes were significant for all loci. In cases of significant pleiotropy, we performed mediation analysis to test if SNPs had a direct association to phenotype. Most loci showed a mediated effect through the hypothesized causal pathway. However, many loci also had direct associations, suggesting causal explanations (i.e., emphysema leading to reduced lung function) are incomplete. Our results highlight the high degree of pleiotropy in complex disease-associated loci and provide novel insights into the mechanisms underlying COPD.

Original languageEnglish (US)
Pages (from-to)318-329
Number of pages12
JournalGenetic epidemiology
Volume43
Issue number3
DOIs
StatePublished - Apr 1 2019

Fingerprint

Genetic Loci
Chronic Obstructive Pulmonary Disease
Phenotype
Disease Susceptibility
Emphysema
Genetic Association Studies
Single Nucleotide Polymorphism
Genotype
Lung

Keywords

  • causal inference
  • COPD
  • emphysema
  • GWAS
  • mediation
  • pleiotropy

ASJC Scopus subject areas

  • Epidemiology
  • Genetics(clinical)

Cite this

Parker, M. M., Lutz, S. M., Hobbs, B. D., Busch, R., McDonald, M. L. N., Castaldi, P. J., ... Cho, M. H. (2019). Assessing pleiotropy and mediation in genetic loci associated with chronic obstructive pulmonary disease. Genetic epidemiology, 43(3), 318-329. https://doi.org/10.1002/gepi.22192

Assessing pleiotropy and mediation in genetic loci associated with chronic obstructive pulmonary disease. / Parker, Margaret M.; Lutz, Sharon M.; Hobbs, Brian D.; Busch, Robert; McDonald, Merry Lynn N.; Castaldi, Peter J.; Beaty, Terri L; Hokanson, John E.; Silverman, Edwin K.; Cho, Michael H.

In: Genetic epidemiology, Vol. 43, No. 3, 01.04.2019, p. 318-329.

Research output: Contribution to journalArticle

Parker, MM, Lutz, SM, Hobbs, BD, Busch, R, McDonald, MLN, Castaldi, PJ, Beaty, TL, Hokanson, JE, Silverman, EK & Cho, MH 2019, 'Assessing pleiotropy and mediation in genetic loci associated with chronic obstructive pulmonary disease', Genetic epidemiology, vol. 43, no. 3, pp. 318-329. https://doi.org/10.1002/gepi.22192
Parker, Margaret M. ; Lutz, Sharon M. ; Hobbs, Brian D. ; Busch, Robert ; McDonald, Merry Lynn N. ; Castaldi, Peter J. ; Beaty, Terri L ; Hokanson, John E. ; Silverman, Edwin K. ; Cho, Michael H. / Assessing pleiotropy and mediation in genetic loci associated with chronic obstructive pulmonary disease. In: Genetic epidemiology. 2019 ; Vol. 43, No. 3. pp. 318-329.
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