Polygenic Score (PGS) ID: PGS001340

Predicted Trait
Reported Trait Atrial fibrillation
Mapped Trait(s) atrial fibrillation (EFO_0000275)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC281
Released in PGS Catalog: Oct. 21, 2021
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_HC281
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 2,955
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
269,704 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

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
—
[
  • 12,795 cases
  • , 256,909 controls
]
 European UKB — — — white British ancestry —

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
PPM009186 PSS004413|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Atrial fibrillation — AUROC: 0.75367 [0.71087, 0.79646] R²: 0.10139
Incremental AUROC (full-covars): -0.00517
PGS R2 (no covariates): 0.00295
PGS AUROC (no covariates): 0.5427 [0.49184, 0.59356]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009187 PSS004414|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Atrial fibrillation — AUROC: 0.82329 [0.75147, 0.89511] R²: 0.15391
Incremental AUROC (full-covars): 0.01729
PGS R2 (no covariates): 0.01132
PGS AUROC (no covariates): 0.5932 [0.45826, 0.72815]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009188 PSS004415|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Atrial fibrillation — AUROC: 0.77562 [0.76201, 0.78924] R²: 0.13687
Incremental AUROC (full-covars): 0.02036
PGS R2 (no covariates): 0.02331
PGS AUROC (no covariates): 0.61305 [0.59537, 0.63074]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009189 PSS004416|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Atrial fibrillation — AUROC: 0.73506 [0.69832, 0.7718] R²: 0.09299
Incremental AUROC (full-covars): -0.00714
PGS R2 (no covariates): 0.00594
PGS AUROC (no covariates): 0.56086 [0.51842, 0.60331]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009190 PSS004417|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Atrial fibrillation — AUROC: 0.76157 [0.75368, 0.76945] R²: 0.12768
Incremental AUROC (full-covars): 0.02194
PGS R2 (no covariates): 0.02239
PGS AUROC (no covariates): 0.60727 [0.59722, 0.61733]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS004413 — —
[
  • 132 cases
  • , 6,365 controls
]
 — African unspecified — UKB —
PSS004414 — —
[
  • 24 cases
  • , 1,680 controls
]
 — East Asian — UKB —
PSS004415 — —
[
  • 1,017 cases
  • , 23,888 controls
]
 — European non-white British ancestry UKB —
PSS004416 — —
[
  • 189 cases
  • , 7,642 controls
]
 — South Asian — UKB —
PSS004417 — —
[
  • 3,228 cases
  • , 64,197 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)