Identification of genetic variants by using a whole exome sequencing approach in Taiwanese patients with Brugada Syndrome
Authors: Juang J , Lu K , Tseng H , Lu T 
Published: October 2024

Abstract

Background
Brugada Syndrome (BrS) is a life-threatening arrhythmia disease primarily affecting young men. Many genetic studies have been conducted mainly in Caucasian BrS patients to identify potential genetic drivers. SCN5A mutations are less common in Asian BrS patients (around 10%) compared to Caucasian patients (20-30%). This means the pathogenic process of more than 70% of BrS patients remains unclear. With the advancement in NGS technologies, we can conduct genome-wide screening of DNA variants in BrS patients efficiently.

Purpose
Since less than 30% of the BrS patients have known genetic drivers for the disease, we aimed to identify more DNA variants in BrS patients by using the whole exome sequencing (WES) approach. Furthermore, we evaluated the landscape of DNA variants in the two groups of BrS patients according to whether they have SCN5A mutations or not.

Methods
A total of 201 BrS patients were recruited for the WES experiments. After obtaining the raw sequencing data, we performed the quality check procedures using the multiQC and Trimmomatic softwares (Figure 1). For reads passing the quality check, the BWA algorithm was used for the alignment. Next, the samtools, bamtools, and Picard methods were used to remove duplicates and perform the sorting. Subsequently, those sorted sequencing files were used to call the DNA variants by using the GATK approach and annotate them using the ANNOVAR method. The 201 BrS patients were classified into two different groups based on their mutation status of SCN5A, presentation of sudden cardiac death (SCD), and SCD along with syncope. The gene-based algorithm, SKAT, was used to analyze the summarized effects of DNA variants located in a single gene. For each DNA variant, Fisher's exact test was used to compare the allele frequency in the BrS patients under their groupings.

Results
The WES approach in the 201 BrS patients revealed a total of 205,454 variants, which were further categorized into two groups, common variants (51,867) and rare variants (153,587), based on their allele frequencies (5%). The SKAT algorithm was performed in the 30 genes that have been previously reported to be associated with BrS. No significant differences were observed in any gene in BrS patients for the common variants. Intriguingly, KCNJ8, SCN1B, ZFPM2, MAPRE2, and KCNE5 showed significant differences in allele frequencies between the SCN5A+ and SCN5A- patients (Figure 2). Fisher's exact test further revealed that three DNA variants (chr19:35524980, chr12:21926440, chr6:126210346) were significantly enriched in SCN5A+ patients. The 5 DNA variants located in ZFPM2 showed a linkage disequilibrium block and were enriched in SCN5A+ patients.

Conclusions
The WES approach in BrS patients revealed DNA variants that were reported in previous studies. Several DNA variants were significantly enriched in SCN5A+ patients, suggesting that the genome-wide mutation landscape was different in SCN5A+ and SCN5A- BrS patients.Figure 1Figure 2