ADAM19 and HTR4 variants and pulmonary function: Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium Targeted Sequencing Study

Abstract

Background: The pulmonary function measures of forced expiratory volume in 1 second (FEV1) and its ratio to forced vital capacity (FVC) are used in the diagnosis and monitoring of lung diseases and predict cardiovascular mortality in the general population. Genome-wide association studies (GWASs) have identified numerous loci associated with FEV1 and FEV1/FVC, but the causal variants remain uncertain. We hypothesized that novel or rare variants poorly tagged by GWASs may explain the significant associations between FEV1/FVC and 2 genes: ADAM19 and HTR4.

Methods and results: We sequenced ADAM19 and its promoter region along with the ≈21-kb portion of HTR4 harboring GWAS single-nucleotide polymorphisms for pulmonary function and analyzed associations with FEV1/FVC among 3983 participants of European ancestry from Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium. Meta-analysis of common variants in each region identified statistically significant associations (316 tests; P<1.58×10(-4)) with FEV1/FVC for 14 ADAM19 single-nucleotide polymorphisms and 24 HTR4 single-nucleotide polymorphisms. After conditioning on the sentinel GWASs hit in each gene (ADAM19 rs1422795, minor allele frequency=0.33 and HTR4 rs11168048, minor allele frequency=0.40], 1 single-nucleotide polymorphism remained statistically significant (ADAM19 rs13155908, minor allele frequency=0.12; P=1.56×10(-4)). Analysis of rare variants (minor allele frequency <1%) using sequence kernel association test did not identify associations with either region.

Conclusions: Sequencing identified 1 common variant associated with FEV1/FVC independent of the sentinel ADAM19 GWAS hit and supports the original HTR4 GWAS findings. Rare variants do not seem to underlie GWAS associations with pulmonary function for common variants in ADAM19 and HTR4.

Keywords: Airway Obstruction; genome-wide association study; lung; polymorphism, genetic; pulmonary disease, chronic obstructive; respiratory function tests; sequence analysis, DNA.

Figure 1

Regional association plot for common SNPs identified by sequencing in loci investigated for FEV1/FVC and FEV1. The two loci are ADAM19 on 5q33.3 and HTR4 on 5q.31.1. The P values for association with the trait (FEV1/FVC or FEV1) from the unconditional analysis are represented by circles and those from the conditional analysis, accounting for the sentinel SNP in each locus, are denoted by squares. For each locus, correlations in the combined study sample between the sentinel SNP from the GWAS and other SNPs identified by sequencing in the region are depicted in red when 0.8 ≤ r² < 1, orange when 0.5 ≤ r²< 0.8, yellow when 0.2 ≤ r²< 0.5 and white when r²< 0.2. Gene annotations are shown in green, and estimated recombination rates from HapMap are shown in light blue. The sentinel SNP (rs1422795 for ADAM19 and rs11168048 for HTR4) is annotated with its unconditional association P value for the trait. (a) FEV1/FVC, ADAM19 locus (b) FEV1, ADAM19 locus (c) FEV1/FVC, HTR4 locus (d) FEV1, HTR4 locus

Figure 1

Regional association plot for common SNPs identified by sequencing in loci investigated for FEV1/FVC and FEV1. The two loci are ADAM19 on 5q33.3 and HTR4 on 5q.31.1. The P values for association with the trait (FEV1/FVC or FEV1) from the unconditional analysis are represented by circles and those from the conditional analysis, accounting for the sentinel SNP in each locus, are denoted by squares. For each locus, correlations in the combined study sample between the sentinel SNP from the GWAS and other SNPs identified by sequencing in the region are depicted in red when 0.8 ≤ r² < 1, orange when 0.5 ≤ r²< 0.8, yellow when 0.2 ≤ r²< 0.5 and white when r²< 0.2. Gene annotations are shown in green, and estimated recombination rates from HapMap are shown in light blue. The sentinel SNP (rs1422795 for ADAM19 and rs11168048 for HTR4) is annotated with its unconditional association P value for the trait. (a) FEV1/FVC, ADAM19 locus (b) FEV1, ADAM19 locus (c) FEV1/FVC, HTR4 locus (d) FEV1, HTR4 locus

Figure 1

Regional association plot for common SNPs identified by sequencing in loci investigated for FEV1/FVC and FEV1. The two loci are ADAM19 on 5q33.3 and HTR4 on 5q.31.1. The P values for association with the trait (FEV1/FVC or FEV1) from the unconditional analysis are represented by circles and those from the conditional analysis, accounting for the sentinel SNP in each locus, are denoted by squares. For each locus, correlations in the combined study sample between the sentinel SNP from the GWAS and other SNPs identified by sequencing in the region are depicted in red when 0.8 ≤ r² < 1, orange when 0.5 ≤ r²< 0.8, yellow when 0.2 ≤ r²< 0.5 and white when r²< 0.2. Gene annotations are shown in green, and estimated recombination rates from HapMap are shown in light blue. The sentinel SNP (rs1422795 for ADAM19 and rs11168048 for HTR4) is annotated with its unconditional association P value for the trait. (a) FEV1/FVC, ADAM19 locus (b) FEV1, ADAM19 locus (c) FEV1/FVC, HTR4 locus (d) FEV1, HTR4 locus

Figure 1

Regional association plot for common SNPs identified by sequencing in loci investigated for FEV1/FVC and FEV1. The two loci are ADAM19 on 5q33.3 and HTR4 on 5q.31.1. The P values for association with the trait (FEV1/FVC or FEV1) from the unconditional analysis are represented by circles and those from the conditional analysis, accounting for the sentinel SNP in each locus, are denoted by squares. For each locus, correlations in the combined study sample between the sentinel SNP from the GWAS and other SNPs identified by sequencing in the region are depicted in red when 0.8 ≤ r² < 1, orange when 0.5 ≤ r²< 0.8, yellow when 0.2 ≤ r²< 0.5 and white when r²< 0.2. Gene annotations are shown in green, and estimated recombination rates from HapMap are shown in light blue. The sentinel SNP (rs1422795 for ADAM19 and rs11168048 for HTR4) is annotated with its unconditional association P value for the trait. (a) FEV1/FVC, ADAM19 locus (b) FEV1, ADAM19 locus (c) FEV1/FVC, HTR4 locus (d) FEV1, HTR4 locus