Polygenic Score (PGS) ID: PGS002050

Predicted Trait
Reported Trait Atrial fibrillation and flutter
Mapped Trait(s)
Additional Trait Information circulatory system
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_427.2
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 554,908
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 Sample Sets

Development Samples

Score Development/Training
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
391,124 individuals European UK (+ Ireland) UKB

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
PPM011263 PSS009087|
European Ancestry|
3,980 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Atrial fibrillation and flutter Partial Correlation (partial-r): 0.0689 [0.0379, 0.0999] sex, age, birth date, deprivation index, 16 PCs
PPM011264 PSS008641|
European Ancestry|
6,397 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Atrial fibrillation and flutter Partial Correlation (partial-r): 0.0839 [0.0594, 0.1082] sex, age, birth date, deprivation index, 16 PCs
PPM011265 PSS008415|
Greater Middle Eastern Ancestry|
1,151 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Atrial fibrillation and flutter Partial Correlation (partial-r): 0.0983 [0.0402, 0.1557] sex, age, birth date, deprivation index, 16 PCs
PPM011266 PSS008195|
South Asian Ancestry|
6,001 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Atrial fibrillation and flutter Partial Correlation (partial-r): 0.043 [0.0177, 0.0683] sex, age, birth date, deprivation index, 16 PCs
PPM011267 PSS007977|
East Asian Ancestry|
1,768 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Atrial fibrillation and flutter Partial Correlation (partial-r): 0.041 [-0.0059, 0.0877] sex, age, birth date, deprivation index, 16 PCs
PPM011268 PSS007760|
African Ancestry|
2,381 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Atrial fibrillation and flutter Partial Correlation (partial-r): 0.0475 [0.0072, 0.0877] sex, age, birth date, deprivation index, 16 PCs
PPM011269 PSS008864|
African Ancestry|
3,769 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Atrial fibrillation and flutter Partial Correlation (partial-r): 0.0418 [0.0098, 0.0737] sex, age, birth date, deprivation index, 16 PCs
PPM011262 PSS009313|
European Ancestry|
19,230 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Atrial fibrillation and flutter Partial Correlation (partial-r): 0.1034 [0.0894, 0.1174] sex, age, birth date, deprivation index, 16 PCs

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
PSS009087 3,980 individuals European Poland (NE Europe) UKB
PSS007977 1,768 individuals East Asian China (East Asia) UKB
PSS007760 2,381 individuals African American or Afro-Caribbean Carribean UKB
PSS009313 19,230 individuals European UK (+ Ireland) UKB
PSS008415 1,151 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008864 3,769 individuals African unspecified Nigeria (West Africa) UKB
PSS008641 6,397 individuals European Italy (South Europe) UKB
PSS008195 6,001 individuals South Asian India (South Asia) UKB