Polygenic Score (PGS) ID: PGS000016

Predicted Trait
Reported Trait Atrial fibrillation
Mapped Trait(s) atrial fibrillation (EFO_0000275)
Released in PGS: Oct. 14, 2019

Score Details

Score Construction
PGS Name GPS_AF
Variants
Original Genome Build hg19
Number of Variants 6,730,541
Development Method
Name LDPred
Parameters ρ = 0.003; LD panel = 503 1000G Europeans
PGS Source
PGS Catalog Publication (PGP) ID PGP000006
Citation (link to publication) Khera AV et al. Nat Genet (2018)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST004295
EuropePMC: 28416818
5,875 individuals African American or Afro-Caribbean
GWAS Catalog: GCST004295
EuropePMC: 28416818
4,130 individuals East Asian
GWAS Catalog: GCST004295
EuropePMC: 28416818
118,755 individuals European
GWAS Catalog: GCST004295
EuropePMC: 28416818
3,358 individuals Hispanic or Latin American
Score Development/Training
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants 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
[
  • 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 ID
(PPM ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000025 PSS000013 PGP000006
Khera AV et al. (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
PPM000385 PSS000217 PGP000057
Homburger JR et al. (2019)
Ext.
Reported Trait: Atrial Fibrillation (personal history) OR: 1.277[1.12, 1.46] AUROC: 0.78 age, sex
PPM000389 PSS000217 PGP000057
Homburger JR et al. (2019)
Ext.
Reported Trait: Atrial Fibrillation (personal history) AUROC: 0.57

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description 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
  • , 293,554 controls
]
European UKB UKB Phase 2
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