Targeted Sequencing Approach to Identifying Rare Genetic Variants Associated with Atrial Fibrillation

Abstract

Purpose Atrial fibrillation (AF) is the most common cardiac arrhythmia in clinical practice and is associated with considerable morbidity and mortality. Multiple genes and genetic loci affecting AF susceptibility have been identified using positional cloning and candidate gene approaches The extent to which such polymorphisms contribute to AF is unknown. The aim of this study was to determine the spectrum and prevalence of rare amino acid coding (AAC) variants in candidate AF genes in a cohort of unrelated AF patients from Kazakhstan. Methods We sequenced 96 candidate genes in 102 Kazakhstani patients with AF using customized targeted gene panel (Haloplex, Agilent Technologies). Variants detected were compared with variants observed in the Exome Sequencing Project (ESP) to identify very rare (minor allele frequency 0.04%) AAC variants. ACMG/AMP guidelines were applied for variant interpretation of clinical significance - pathogenic (P), possibly pathogenic (PP), variant of uncertain significance (VUS), possibly benign (PB), benign (B). The ClinVar, Varsome and HGMD databases were also used. Results Median age at AF onset was 47.0 years, and 31.3% had a family history of AF. Totally 456 variants were identified in 74 genes for the overall study group. Variants included one in/del variant, four splice-site variants and 451 single-nucleotide variants (SNV) within the coding exonic regions. 168 HGMD mutations (61 unique) were observed in 37 genes. Classification of 456 variants according to ACMG guidelines showed that 13(2.9%) variants were classified as pathogenic, 13(2.9%) - likely pathogenic, 145 (31.9%) - uncertain significance, 109 (23.8%) likely benign and 175 (38.4%) benign. 31 rare AAC variants were identified in 20 of 102 AF patients. Among them three pathogenic variants KCNQ1 c.477+1G>A, KCNJ2 R218Q and KCNE2 T10K C29A (PP) were identified. Conclusion Our study shows that individuals presenting with AF carry rare mutations and potentially pathogenetic sequence variants in classical cardiac risk genes in almost 20%. No very rare AAC variants were identified in 80% of AF patients. Potential reasons for the lack of very rare AAC variants include a complex pattern of inheritance, variants in as yet unidentified AF genes or in noncoding regions, and environmental factors.