Genome-wide Study of Atrial Fibrillation Identifies Seven Risk Loci and Highlights Biological Pathways and Regulatory Elements Involved in Cardiac Development

Abstract

Atrial fibrillation (AF) is a common cardiac arrhythmia and a major risk factor for stroke, heart failure, and premature death. The pathogenesis of AF remains poorly understood, which contributes to the current lack of highly effective treatments. To understand the genetic variation and biology underlying AF, we undertook a genome-wide association study (GWAS) of 6,337 AF individuals and 61,607 AF-free individuals from Norway, including replication in an additional 30,679 AF individuals and 278,895 AF-free individuals. Through genotyping and dense imputation mapping from whole-genome sequencing, we tested almost nine million genetic variants across the genome and identified seven risk loci, including two novel loci. One novel locus (lead single-nucleotide variant [SNV] rs12614435; p = 6.76 × 10^-18) comprised intronic and several highly correlated missense variants situated in the I-, A-, and M-bands of titin, which is the largest protein in humans and responsible for the passive elasticity of heart and skeletal muscle. The other novel locus (lead SNV rs56202902; p = 1.54 × 10^-11) covered a large, gene-dense chromosome 1 region that has previously been linked to cardiac conduction. Pathway and functional enrichment analyses suggested that many AF-associated genetic variants act through a mechanism of impaired muscle cell differentiation and tissue formation during fetal heart development.

Keywords: CDKN2C; DMRTA2; GWAS; TTN; atrial fibrillation; cardiomyopathy; fetal; genetic risk score; heart; pathway.

Figure 1

Regional Plots at the Two AF-Associated Loci Identified in Chromosomal Regions 1p32 and 2q31 in This Study The dots represent SNVs, whose positions are based on genomic build GRCh37 and whose −log₁₀(p values) are based on association tests within the HUNT discovery cohort. The SNVs reaching the highest level of statistical significance at the two loci are marked with reference numbers. The strength of the pairwise LD (r²) between the lead SNV and all other SNVs was computed on the basis of genotyped and imputed markers and is indicated by a gradient from red to green to blue. The blue line indicates estimated recombination rates.

Figure 2

Polygenic Risk Scores and Estimates of Statistical Power for AF-Associated Loci (A) Polygenic risk scores stratified by age of disease onset. White dots represent medians, black boxes represent interquartile ranges, black whiskers represent 1.5× the interquartile range, and colored areas show the probability density of the data. The vertical gray dotted line represents the median score for control individuals. (B) Statistical-power estimates stratified by age of disease onset. The upper panel shows the necessary statistical power to detect risk loci (each represented by a dot) on the basis of the observed allele frequencies within subgroups, the number of case (bottom panel) and control (n = 61,607) individuals, and α = 5 × 10⁻⁸.

Figure 3

Tissues and Reconstituted Gene Sets Significantly Enriched with AF-Associated Loci (A) On the basis of expression patterns across 37,427 human mRNA microarrays, DEPICT predicted genes within AF-associated loci to be highly expressed in various muscle tissues. Tissues are grouped by type and significance. The horizontal dotted line represents the experiment-wide significance threshold (p = 5 × 10⁻³). (B) Reconstituted gene sets found to be significantly (p < 5 × 10⁻⁶; FDR < 5%) and marginally (p < 5 × 10⁻⁵) significantly enriched by DEPICT are represented by nodes colored according to the permutation p value; the pairwise overlap of genes is denoted by the width of connecting lines.

Figure 4

Enrichment of AF-Associated Loci within DNaseI Hypersensitivity Sites across 424 Cell Types Available from ENCODE and the Roadmap Epigenomics Project Enrichment tests were performed independently across markers that reached one of eight different GWAS p value thresholds (p < 1 × 10⁻¹ to < 1 × 10⁻⁸). The radial axis shows fold enrichment calculated at each of the eight thresholds, each indicated by a different color, for each of the 424 cell types. Cell types are sorted by tissue, represented along the outside edge of the plot; font size is proportional to the number of cell types from that tissue. The outer line and dots next to the tissue labels are colored with respect to tissue type. Dots along the inside edge of the plot denote significant enrichment (if any) for a given cell type at a GWAS p value threshold < 1 × 10⁻⁵ (outermost dot) to a GWAS p value threshold < 1 × 10⁻⁸ (innermost dot). Of all tissues examined, the strongest enrichment was seen for DNaseI hypersensitivity sites in the fetal heart.