Polygenic Score (PGS) ID: PGS002814

Predicted Trait
Reported Trait Atrial fibrillation
Mapped Trait(s) atrial fibrillation (EFO_0000275)
Additional Trait Information Atrial flutter
Released in PGS Catalog: Jan. 19, 2023
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Terms and Licenses
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Score Details

Score Construction
PGS Name AF-PRS
Development Method
Name Pruning and Thresholding (P+T)
Parameters 1KG-EUR for LD reference, 0.5 for r2, and 5.0 x 10-4 for p-value threshold
Variants
Original Genome Build GRCh37
Number of Variants 4,520
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000392
Citation (link to publication) Miyazawa K et al. Nat Genet (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Multi-ancestry (including European): 100%
  • East Asian
  • European
1,150,799 individuals (100%)
Score Development/Training
Multi-ancestry (including European): 100%
  • East Asian
  • European
1,150,799 individuals (100%)
PGS Evaluation
East Asian: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90204201
[
  • 74,754 cases
  • , 1,076,045 controls
]
 East Asian, European
(Japanese, European)		 8 cohorts
  • AFGen
  • ,BBJ
  • ,FinnGen
  • ,HUNT
  • ,MGI
  • ,MyCode
  • ,UKB
  • ,deCODE
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
GWAS Catalog: GCST90204201
[
  • 74,754 cases
  • , 1,076,045 controls
]
 East Asian, European
(Japanese, European)		 8 cohorts
  • AFGen
  • ,BBJ
  • ,FinnGen
  • ,HUNT
  • ,MGI
  • ,MyCode
  • ,UKB
  • ,deCODE
 ICD48 — — — —

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) 		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
PPM015602 PSS009995|
East Asian Ancestry|
24,147 individuals
 PGP000392 |
Miyazawa K et al. Nat Genet (2023)
 Reported Trait: Atrial fibrillation OR: 1.94332
β: 0.66		 AUROC: 0.74 Nagelkerke’s pseudo R2: 0.14 age, sex, and the top 20 PCs We assessed the PRS performance using logistic regression model adjusted for covariates using glm in R.

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
PSS009995 ICD48 —
[
  • 2,953 cases
  • , 21,194 controls
]
 — East Asian
(Japanese)		 — BBJ —