Polygenic Score (PGS) ID: PGS000035

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
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Score Details

Score Construction
PGS Name PRS_AF
Development Method
Name Pruning and Thresholding (P+T)
Parameters P < 10^-4; r2 < 0.5
Variants
Original Genome Build hg19
Number of Variants 1,168
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000022
Citation (link to publication) Weng LC et al. Circulation (2017)
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%
120,286 individuals (100%)
PGS Evaluation
Multi-ancestry (including European): 80%
  • European
  • Not Reported
European: 20%
5 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST004296
Europe PMC: 28416818
 5,875 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST004296
Europe PMC: 28416818
 4,130 individuals East Asian NR
GWAS Catalog: GCST004296
Europe PMC: 28416818
 118,755 individuals European NR
GWAS Catalog: GCST004296
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
—
[
  • 2,987 cases
  • , 117,299 controls
]
,
47.3 % Male samples
 European UKB AF was defined as a reported history of AF or atrial flutter, or if an individual had undergone a cardioversion, pulmonary vein isolation procedure, atrial flutter ablation, atrioventricular node ablation, or received an ICD code of 427.3 (ICD-9) or I48 (ICD-10). — — — —

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
PPM000079 PSS000053|
Multi-ancestry (including European)|
4,606 individuals
 PGP000022 |
Weng LC et al. Circulation (2017)
 Reported Trait: Incident atrial fibrillation HR: 1.14 [1.11, 1.16] — — Clinical risk (CHARGE-AF Score: height, weight, systolic and diastolic blood pressure, current smoking status, use of antihypertensive medication, diabetes mellitus, history of myocardial infarction and heart failure), age, sex, genotyping array, 1 PC of ancestry Unadjusted for Competing Risk of Death
PPM020778 PSS011403|
Multi-ancestry (including European)|
3,335 individuals
 PGP000586 |
Khurshid S et al. Circ Genom Precis Med (2021)
|Ext.		 Reported Trait: Incident atrial fibrillation HR: 1.49 [1.3, 1.71] C-index: 0.617 [0.574, 0.66] R²: 0.016 [0.004, 0.027] — —
PPM020775 PSS011406|
Multi-ancestry (including European)|
473,681 individuals
 PGP000586 |
Khurshid S et al. Circ Genom Precis Med (2021)
|Ext.		 Reported Trait: Incident atrial fibrillation HR: 1.34 [1.31, 1.37] C-index: 0.584 [0.577, 0.59] R²: 0.004 [0.004, 0.005] — —
PPM020776 PSS011404|
European Ancestry|
10,560 individuals
 PGP000586 |
Khurshid S et al. Circ Genom Precis Med (2021)
|Ext.		 Reported Trait: Incident atrial fibrillation HR: 1.48 [1.31, 1.66] C-index: 0.615 [0.579, 0.65] R²: 0.011 [0.004, 0.018] — —
PPM020777 PSS011405|
Multi-ancestry (including European)|
55,517 individuals
 PGP000586 |
Khurshid S et al. Circ Genom Precis Med (2021)
|Ext.		 Reported Trait: Incident atrial fibrillation HR: 1.28 [1.21, 1.35] C-index: 0.569 [0.554, 0.584] R²: 0.003 [0.002, 0.005] — —

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
PSS000053 Participants were classified as having AF if an arrhythmia was present on an ECG obtained at a study visit or encounter with external clinicians, Holter monitoring, or noted in hospital records during a median 9.4 years of follow-up. —
[
  • 580 cases
  • , 4,026 controls
]
,
45.9 % Male samples
 — European, NR FHS is principally composed of individuals of European ancestry FHS Samples were obtained from the following FHS cohorts: Original, Offspring, and Third Generation. Participants were eligible for inclusion if they were AF free at an average age of 55.
PSS011403 Cases were individuals with atrial fibrillation (AF). Individuals were classified as having AF if the arrhythmia was present on an ECG obtained at a study visit or encounter with external clinicians, Holter monitoring, or noted in hospital records. Study investigators reviewed all available records to determine dates of AF. Two physicians adjudicated first-detected AF events. —
[
  • 183 cases
  • , 3,152 controls
]
,
44.6 % Male samples
 Mean = 59.4 years
Sd = 15.5 years		 European, Not reported — FHS —
PSS011404 Cases were individuals with atrial fibrillation (AF). Cases were identified using ICD-10 code: I48 and ICD-9 code: 427.3. —
[
  • 299 cases
  • , 10,331 controls
]
,
47.7 % Male samples
 Mean = 57.0 years
Sd = 7.4 years		 European — FINRISK —
PSS011405 Cases were individuals with atrial fibrillation (AF). AF was defined as a clinically reported finding of AF or atrial flutter from a 12- lead ECG or a diagnosis of AF or atrial flutter applied to two or more inpatient or outpatient encounters or on the patient problem list from the institutional electronic health record. Diagnosis codes used to define AF included ICD10: I48.0, I48.1, I48.2, I48.3 and I48.91); ICD9: 427.31; and 92 separate internal codes. —
[
  • 1,336 cases
  • , 54,181 controls
]
,
34.2 % Male samples
 Mean = 47.3 years
Sd = 15.2 years		 European, Not reported — MyCode —
PSS011406 Cases were individuals with atrial fibrillation (AF). Cases were identified using using self-report, ICD 9/10 codes, or cause of death records and where available, codes for specific AF-related procedures (e.g., percutaneous transluminal ablation of pulmonary vein) were also utilized in the AF definition. The complete list of clinical factor definitions is shown in supplemental Table I. —
[
  • 7,192 cases
  • , 466,489 controls
]
,
45.3 % Male samples
 Mean = 56.9 years
Sd = 8.1 years		 European, Not reported — UKB Possible sample overlap between this dataset and the dataset used to develop/train PGS000035.