Polygenic Score (PGS) ID: PGS000016

Predicted Trait
Reported Trait Atrial fibrillation
Mapped Trait(s) atrial fibrillation (EFO_0000275)
Released in PGS Catalog: Oct. 14, 2019
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Terms and Licenses
Freely available to the academic community for research use. Parties interested in using the scores for commercial purposes should contact the Broad Office of Strategic Alliances and Partnering (partnering@broadinstitute.org).

Score Details

Score Construction
PGS Name GPS_AF
Development Method
Name LDpred
Parameters ρ = 0.003; LD panel = 503 1000G Europeans
Variants
Original Genome Build hg19
Number of Variants 6,730,541
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000006
Citation (link to publication) Khera AV et al. Nat Genet (2018)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 89.9%
African: 4.4%
East Asian: 3.1%
Hispanic or Latin American: 2.5%
132,118 individuals (100%)
Score Development/Training
European: 100%
120,280 individuals (100%)
PGS Evaluation
European: 60%
Not Reported: 20%
Multi-ancestry (excluding European): 20%
  • East Asian
  • South Asian
  • Hispanic or Latin American
  • Additional Asian Ancestries
5 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST004295
Europe PMC: 28416818
5,875 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST004295
Europe PMC: 28416818
4,130 individuals East Asian
(Japanese)
NR
GWAS Catalog: GCST004295
Europe PMC: 28416818
118,755 individuals European NR
GWAS Catalog: GCST004295
Europe PMC: 28416818
3,358 individuals Hispanic or Latin American NR
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
[
  • 2,024 cases
  • , 118,256 controls
]
European UKB Atrial fibrillation ascertainment was based on self-report of atrial fibrillation, atrial flutter, or cardioversion in an interview with a trained nurse, an ICD-9 code of 427.3 or ICD-10 code of I48.X in hospitalization records, or a history of a percutaneous ablation or cardioversion based on the OPCS-4 coded procedure (K57.1, K62.1, K62.2, K62.3, or K 62.4), as performed previously UKB Phase 1

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
PPM000385 PSS000217|
European Ancestry|
10,303 individuals
PGP000057 |
Homburger JR et al. Genome Med (2019)
|Ext.
Reported Trait: Atrial Fibrillation (personal history) OR: 1.277 [1.12, 1.46] AUROC: 0.78 age, sex
PPM000025 PSS000013|
European Ancestry|
288,978 individuals
PGP000006 |
Khera AV et al. Nat Genet (2018)
Reported Trait: Atrial fibrillation AUROC: 0.77 [0.76, 0.77] Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment): 0.029 age; sex; Ancestry PC 1-4; genotyping chip
PPM000389 PSS000217|
European Ancestry|
10,303 individuals
PGP000057 |
Homburger JR et al. Genome Med (2019)
|Ext.
Reported Trait: Atrial Fibrillation (personal history) AUROC: 0.57
PPM002019 PSS000998|
Ancestry Not Reported|
368 individuals
PGP000182 |
Tadros R et al. Nat Genet (2021)
|Ext.
Reported Trait: Atrial fibrillation or atrial flutter in individuals with a pathogenic or likely pathogenic sarcomeric variant HR: 1.5 [1.17, 1.91]
β: 0.402 (0.124)
Genetic relatedness matrix, sex
PPM014988 PSS009946|
European Ancestry|
36,662 individuals
PGP000368 |
Marston NA et al. Eur Heart J (2022)
|Ext.
Reported Trait: Atrial fibrillation HR: 1.4 [1.32, 1.49]
PPM014989 PSS009947|
Multi-ancestry (excluding European)|
4,873 individuals
PGP000368 |
Marston NA et al. Eur Heart J (2022)
|Ext.
Reported Trait: Atrial fibrillation HR: 2.15 [1.57, 2.95]

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
PSS000013 Atrial fibrillation ascertainment was based on self-report of atrial fibrillation, atrial flutter, or cardioversion in an interview with a trained nurse, an ICD-9 code of 427.3 or ICD-10 code of I48.X in hospitalization records, or a history of a percutaneous ablation or cardioversion based on the OPCS-4 coded procedure (K57.1, K62.1, K62.2, K62.3, or K 62.4), as performed previously
[
  • 4,576 cases
  • , 284,402 controls
]
European UKB UKB Phase 2
PSS000998 All individuals were carriers of a pathogenic or likely pathogenic variant (MYBPC3 truncating variant, MYBPC3 non-truncating variant, MYH7 variant, MYL2 variant, other genetic variant). Cases included individuals who had experienced atrial fibrillation, defined as: time to atrial fibrillation or flutter.
[
  • 70 cases
  • , 298 controls
]
Not reported ERSPC
PSS009946 36,662 individuals,
75.0 % Male samples
Mean = 64.1 years European FOURIER, PEGASUS, SAVOR-TIMI_53, SOLID-TIMI_52
PSS009947 674 individuals Asian unspecified FOURIER, PEGASUS, SAVOR-TIMI_53, SOLID-TIMI_52
PSS009947 791 individuals East Asian FOURIER, PEGASUS, SAVOR-TIMI_53, SOLID-TIMI_52
PSS009947 687 individuals South Asian FOURIER, PEGASUS, SAVOR-TIMI_53, SOLID-TIMI_52
PSS009947 2,721 individuals Hispanic or Latin American
(Mixed American)
FOURIER, PEGASUS, SAVOR-TIMI_53, SOLID-TIMI_52
PSS000217 Phenotypic information was self-reported by the individual through an online, interactive health history tool
[
  • 239 cases
  • , 10,064 controls
]
,
17.1 % Male samples
European CG Samples are individuals whose healthcare provider had ordered a Color Genomics multi-gene panel test