Polygenic Score (PGS) ID: PGS001339

Predicted Trait
Reported Trait Atrial fibrillation and flutter (time-to-event)
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC964
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_HC964
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 2,142
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
[
  • 13,747 cases
  • , 255,957 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
PPM009181 PSS004746|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE atrial fibrillation and flutter AUROC: 0.75135 [0.70951, 0.7932] : 0.09804
Incremental AUROC (full-covars): -0.00345
PGS R2 (no covariates): 0.00273
PGS AUROC (no covariates): 0.53955 [0.48964, 0.58946]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009182 PSS004747|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE atrial fibrillation and flutter AUROC: 0.8247 [0.75141, 0.898] : 0.15451
Incremental AUROC (full-covars): 0.0187
PGS R2 (no covariates): 0.01158
PGS AUROC (no covariates): 0.59663 [0.46689, 0.72636]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009183 PSS004748|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE atrial fibrillation and flutter AUROC: 0.77656 [0.76352, 0.7896] : 0.14023
Incremental AUROC (full-covars): 0.02188
PGS R2 (no covariates): 0.02447
PGS AUROC (no covariates): 0.613 [0.59591, 0.6301]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009184 PSS004749|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE atrial fibrillation and flutter AUROC: 0.73999 [0.70422, 0.77576] : 0.09669
Incremental AUROC (full-covars): -0.00357
PGS R2 (no covariates): 0.00629
PGS AUROC (no covariates): 0.56035 [0.51988, 0.60082]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009185 PSS004750|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE atrial fibrillation and flutter AUROC: 0.76362 [0.75604, 0.7712] : 0.133
Incremental AUROC (full-covars): 0.02354
PGS R2 (no covariates): 0.0246
PGS AUROC (no covariates): 0.6108 [0.60113, 0.62048]
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
PSS004746
[
  • 136 cases
  • , 6,361 controls
]
African unspecified UKB
PSS004747
[
  • 24 cases
  • , 1,680 controls
]
East Asian UKB
PSS004748
[
  • 1,090 cases
  • , 23,815 controls
]
European non-white British ancestry UKB
PSS004749
[
  • 200 cases
  • , 7,631 controls
]
South Asian UKB
PSS004750
[
  • 3,483 cases
  • , 63,942 controls
]
European white British ancestry UKB Testing cohort (heldout set)