Polygenic Score (PGS) ID: PGS001263

Predicted Trait
Reported Trait Atrial flutter
Mapped Trait(s) atrial flutter (EFO_0003911)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC440
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
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_HC440
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 2,087
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. medRxiv (2021) Preprint
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
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
[
  • 12,386 cases
  • , 257,318 controls
]
European white British ancestry UKB

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
PPM008820 PSS004501|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Atrial flutter AUROC: 0.76033 [0.71757, 0.80309] : 0.10534
Incremental AUROC (full-covars): 0.00055
PGS R2 (no covariates): 0.00351
PGS AUROC (no covariates): 0.54665 [0.4962, 0.5971]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008821 PSS004502|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Atrial flutter AUROC: 0.82631 [0.7516, 0.90103] : 0.15678
Incremental AUROC (full-covars): 0.02031
PGS R2 (no covariates): 0.01354
PGS AUROC (no covariates): 0.59968 [0.4662, 0.73316]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008822 PSS004503|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Atrial flutter AUROC: 0.78179 [0.76842, 0.79516] : 0.1422
Incremental AUROC (full-covars): 0.02171
PGS R2 (no covariates): 0.02517
PGS AUROC (no covariates): 0.61716 [0.59934, 0.63498]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008823 PSS004504|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Atrial flutter AUROC: 0.73743 [0.69955, 0.77531] : 0.09462
Incremental AUROC (full-covars): -0.00059
PGS R2 (no covariates): 0.00793
PGS AUROC (no covariates): 0.57035 [0.52788, 0.61283]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008824 PSS004505|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Atrial flutter AUROC: 0.76368 [0.75572, 0.77165] : 0.12819
Incremental AUROC (full-covars): 0.02207
PGS R2 (no covariates): 0.02215
PGS AUROC (no covariates): 0.60821 [0.59797, 0.61845]
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
PSS004501
[
  • 128 cases
  • , 6,369 controls
]
African unspecified UKB
PSS004502
[
  • 24 cases
  • , 1,680 controls
]
East Asian UKB
PSS004503
[
  • 983 cases
  • , 23,922 controls
]
European non-white British ancestry UKB
PSS004504
[
  • 186 cases
  • , 7,645 controls
]
South Asian UKB
PSS004505
[
  • 3,114 cases
  • , 64,311 controls
]
European white British ancestry UKB Testing cohort (heldout set)