NBDC Research ID: hum0495.v1
SUMMARY
Aims: Atrial fibrillation (AF) is the most prevalent arrhythmia in the world and can cause serious complications such as stroke or heart failure. Paroxysmal atrial fibrillation (PAF), a subtype of AF, accounts for approximately 25% of AF cases and is estimated to affect approximately 30 million people worldwide. Despite extensive genetic research on AF, the genetic factors involved in PAF in East Asian populations remain unidentified. The aim of our study is to identify genetic factors associated with PAF in the Japanese population, contributing to our understanding of the genetic architecture of AF in Japanese populations.
Methods: We performed whole exome sequencing and processed the sequencing data according to the best practices described in the Genome Analysis Toolkit (GATK). We also performed gene-based association tests, specifically burden tests, sequence kernel association test (SKAT), and SKAT-O.
Participants/Materials: 1,176 PAF patients and 1,172 non-PAF patients
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| hum0495.v1.gwas.v1 | GWAS for PAF using whole exome sequencing data | Unrestricted-access | 2025/02/13 |
*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more
MOLECULAR DATA
| Participants/Materials |
PAF (ICD10: I48.0): 1,176 cases non-PAF (control) : 1,172 individuals |
| Targets | Exome / Genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNA extracted from peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | SureSelectXT Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Genotype Call Methods (software) | GATK HaplotypeCaller |
| Association Analysis & Meta Analysis (software) | Burden, SKAT, SKATO (R:package SKAT) |
| Filtering Methods |
Sample QC: (1) Sample call rate < 0.97 (2) Samples with sex mismatches were excluded. (3) One sample for each pair of second degree or closer relatives (kinship coefficient >0.088) was removed. (4) Samples with outliers in sample size, heterozygosity and missing rates were excluded. Variant QC: (1) genotype quality >= 20 (2) depth >=10 (3) allele balance (4) variant call rate >= 0.97 (5) Hardy‒Weinberg equilibrium P-values >1 × 10−8 (6) PCA |
| Marker Number (after QC) | 518,621 |
| NBDC Dataset ID |
(Click the gwas number to download files) |
| Total Data Volume | 822 KB (tsv) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Toshihiro Tanaka
Affiliation: Department of Human Genetics and Disease Diversity, Institute of Science Tokyo
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Project for Medical Device and Healthcare, Japan Agency for Medical Research and Development (AMED) | Establishment of intelligent infrastructure of prevention and detection of atrial fibrillation | JP21he2102002 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | |||
| 2 |
