Download PGS
(Variants and weights)

Polygenic Score (PGS) ID: PGS000016

Predicted Trait

Reported Trait: Atrial fibrillation
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): atrial fibrillation

Score Details

Name: GPS_AF

Original Genome Build: hg19
Number of Variants: 6,730,541

PGS Development Method: LDPred
PGS Development Details/Relevant Parameters: ρ = 0.003; LD panel = 503 1000G Europeans

Citation: Khera AV et al. Nat Genet (2018) | PGS Catalog Publication ID: PGP000006

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST004295
PubMed: 28416818
4,130 individuals East Asian
GWAS Catalog: GCST004295
PubMed: 28416818
5,875 individuals African American or Afro-Caribbean
GWAS Catalog: GCST004295
PubMed: 28416818
3,358 individuals Hispanic or Latin American
GWAS Catalog: GCST004295
PubMed: 28416818
118,755 individuals European
Score Development/Training
Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
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 120,280 individuals
[ 2,024 cases, 122,304 controls]
European UKB 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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000025 PSS000013 Khera AV et al. (2018) Reported Trait: Atrial fibrillation cases 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

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers 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 288,978 individuals
[ 4,576 cases, 293,554 controls]
European UKB UKB Phase 2