Exome Sequencing Analysis in Severe, Early-Onset Chronic Obstructive Pulmonary Disease

Abstract

Rationale: Genomic regions identified by genome-wide association studies explain only a small fraction of heritability for chronic obstructive pulmonary disease (COPD). Alpha-1 antitrypsin deficiency shows that rare coding variants of large effect also influence COPD susceptibility. We hypothesized that exome sequencing in families identified through a proband with severe, early-onset COPD would identify additional rare genetic determinants of large effect.

Objectives: To identify rare genetic determinants of severe COPD.

Methods: We applied filtering approaches to identify potential causal variants for COPD in whole exomes from 347 subjects in 49 extended pedigrees from the Boston Early-Onset COPD Study. We assessed the power of this approach under different levels of genetic heterogeneity using simulations. We tested genes identified in these families using gene-based association tests in exomes of 204 cases with severe COPD and 195 resistant smokers from the COPDGene study. In addition, we examined previously described loci associated with COPD using these datasets.

Measurements and main results: We identified 69 genes with predicted deleterious nonsynonymous, stop, or splice variants that segregated with severe COPD in at least two pedigrees. Four genes (DNAH8, ALCAM, RARS, and GBF1) also demonstrated an increase in rare nonsynonymous, stop, and/or splice mutations in cases compared with resistant smokers from the COPDGene study; however, these results were not statistically significant. We demonstrate the limitations of the power of this approach under genetic heterogeneity through simulation.

Conclusions: Rare deleterious coding variants may increase risk for COPD, but multiple genes likely contribute to COPD susceptibility.

Trial registration: ClinicalTrials.gov NCT00608764.

Keywords: chronic obstructive pulmonary disease; genetic association studies; segregation analysis.

Figures

Figure 1.

A flow chart of the study design. COPD = chronic obstructive pulmonary disease; MAF = minor allele frequency.

Figure 2.

Effect of genetic heterogeneity on probability of identifying segregating variants. (A and B) The probability of identifying at least two (A) or four (B) segregating families is shown on the y-axis for different numbers of causal genes (x-axis) for 49 three-offspring (P-3O) or 49 one-parent with one-offspring (P-1O) scenarios under the alternative (H1) and null (H0) hypotheses. (C) Plot of the probability of observing at least n segregating P-1O families (x-axis) for different numbers of causal genes. numFam = number of segregating families; numGene = number of causal genes.

Figure 3.

Pedigree plots of the families with segregating variants in activated leukocyte cell adhesion molecule (ALCAM). Individuals colored in red are the cases of severe and very severe chronic obstructive pulmonary disease (COPD); individuals colored in blue are control subjects with normal spirometry, number of pack-years above 5, and age above 40 years. COPD severity (or GOLD [Global Initiative for Chronic Obstructive Lung Disease] 0, for those with normal spirometry) is indicated by solid symbols. An open circle/square indicates neither case nor control; “+” symbol under the circle indicates that the individual carries a segregating variant in the gene of interest; “−” symbol indicates the individual does not carry the variant; otherwise the variant status is unknown for the subject. Below the carrier status, phenotype FEV1% predicted, age, and pack-years (py) are shown for the sequenced subjects.

Figure 4.

Pedigree plots of the families with segregating variants in dynein, axonemal, heavy chain 8 (DNAH8). Individuals colored in red are the cases of severe and very severe chronic obstructive pulmonary disease (COPD); individuals colored in blue are control subjects with normal spirometry, number of pack-years above 5, and age above 40 years. COPD severity (or GOLD [Global Initiative for Chronic Obstructive Lung Disease] 0, for those with normal spirometry) is indicated by solid symbols. An open circle/square indicates neither case nor control; “+” symbol under the circle indicates that the individual carries a segregating variant in the gene of interest; “−” symbol indicates the individual does not carry the variant; otherwise the variant status is unknown for the subject. Below the carrier status, phenotype FEV1% predicted, age, and pack-years (py) are shown for the sequenced subjects.

Figure 5.

Pedigree plots of the families with segregating variants in arginyl-TRNA synthetase (RARS). Individuals colored in red are the cases of severe and very severe chronic obstructive pulmonary disease (COPD); individuals colored in blue are control subjects with normal spirometry, number of pack-years above 5, and age above 40 years. COPD severity (or GOLD [Global Initiative for Chronic Obstructive Lung Disease] 0, for those with normal spirometry) is indicated by solid symbols. An open circle/square indicates neither case nor control; “+” symbol under the circle indicates that the individual carries a segregating variant in the gene of interest; “−” symbol indicates the individual does not carry the variant; otherwise the variant status is unknown for the subject. Below the carrier status, phenotype FEV1% predicted, age, and pack-years (py) are shown for the sequenced subjects.

Figure 6.

Pedigree plots of the families with segregating variants in golgi brefeldin A resistant guanine nucleotide exchange factor 1 (GBF1). Individuals colored in red are the cases of severe and very severe chronic obstructive pulmonary disease (COPD); individuals colored in blue are control subjects with normal spirometry, number of pack-years above 5, and age above 40 years. COPD severity (or GOLD [Global Initiative for Chronic Obstructive Lung Disease] 0, for those with normal spirometry) is indicated by solid symbols. An open circle/square indicates neither case nor control; “+” symbol under the circle indicates that the individual carries a segregating variant in the gene of interest; “−” symbol indicates the individual does not carry the variant; otherwise the variant status is unknown for the subject. Below the carrier status, phenotype FEV1% predicted, age, and pack-years (py) are shown for the sequenced subjects.