Predicted Trait | |
Reported Trait | Atrial fibrillation |
Mapped Trait(s) | atrial fibrillation (EFO_0000275) |
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) |
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 (Japanese) |
GWAS Catalog: GCST004295 EuropePMC: 28416818 |
118,755 individuals | European |
GWAS Catalog: GCST004295 EuropePMC: 28416818 |
3,358 individuals | Hispanic or Latin American |
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 |
---|---|---|---|---|---|---|---|
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 | — | [
|
— | European | — | UKB | UKB Phase 1 |
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 |
---|---|---|---|---|---|---|---|---|
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 | — |
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 | — |
PPM000389 | PSS000217 | PGP000057 Homburger JR et al. (2019) Ext. | Reported Trait: Atrial Fibrillation (personal history) | — | AUROC: 0.57 | — | — | — |
PGS Sample Set ID (PSS ID) |
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 | — | [
|
— | European | — | UKB | UKB Phase 2 |
PSS000217 | Phenotypic information was self-reported by the individual through an online, interactive health history tool | — | [ ,
17.1 % Male samples |
— | European | — | CG | Samples are individuals whose healthcare provider had ordered a Color Genomics multi-gene panel test |