PGS Publication: PGP000775

Publication Information (EuropePMC)
Title Genetic variants and polygenic risk scores associated with paroxysmal atrial fibrillation in the Japanese population.
PubMed ID 42081549(Europe PMC)
doi 10.1371/journal.pone.0344360
Publication Date May 4, 2026
Journal PLoS One
Author(s) Shiomi M, Nagata Y, Sudo T, Takahashi K, Higuchi C, Ihara K, Asada K, Tanaka Y, Yamauchi Y, Sasaki T, Hachiya H, Imai Y, Fujita H, Sasano T, Furukawa T, Tanaka T.
Released in PGS Catalog: June 17, 2026

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
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Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS005388
(PAF_PRS)
 PGP000775 |
Shiomi M et al. PLoS One (2026)
 Paroxysmal atrial fibrillation Paroxysmal atrial fibrillation 122
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005388/ScoringFiles/PGS005388.txt.gz

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		Evaluated Score PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM023426 PGS005388
(PAF_PRS)
 PSS012177|
East Asian Ancestry|
179 individuals
 PGP000775 |
Shiomi M et al. PLoS One (2026)
 Reported Trait: Paroxysmal atrial fibrillation — AUROC: 0.702 [0.624, 0.77] AUPRC: 0.776
F1: 0.698		 — Best PRS-only model (Light Gradient Boosting Machine, LGBM) using the 122-SNP PAF_PRS at P < 1 × 10-5 and r2 > 0.3; performance evaluated on the 10% test dataset (PAF_JPN_test) with 1,000 bootstrap resamples.
PPM023427 PGS005388
(PAF_PRS)
 PSS012177|
East Asian Ancestry|
179 individuals
 PGP000775 |
Shiomi M et al. PLoS One (2026)
 Reported Trait: Paroxysmal atrial fibrillation — AUROC: 0.737 [0.668, 0.804] AUPRC: 0.781
F1: 0.748		 sex, smoking, alcohol consumption, history of hypertension, diabetes mellitus, dyslipidemia, cerebral infarction, and family history of AF Best additive model (Extreme Gradient Boosting, XGB) with the 122-SNP PAF_PRS and the listed clinical covariates; same P-value and LD r2 thresholds and test dataset as the PRS-only model; performance metrics obtained from 1,000 bootstrap resamples.

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS012177 Paroxysmal atrial fibrillation (PAF) cases and controls recruited from cardiology departments. Exclusion criteria were: (1) missing clinical information, (2) AF other than PAF, (3) history of heart failure, (4) coronary artery disease, or (5) valvular heart disease. Phenotypes based on clinical records and ECG findings. —
[
  • 104 cases
  • , 75 controls
]
,
65.0 % Male samples
 — East Asian
(Japanese)		 — PAF_JPN Held-out 10% test dataset obtained by stratified sampling to preserve the case-control ratio.