Polygenic Score (PGS) ID: PGS002055

Predicted Trait
Reported Trait Peripheral vascular disease, unspecified
Mapped Trait(s) peripheral vascular disease (EFO_0003875)
Additional Trait Information circulatory system
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_443.9
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 599,514
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
PPM011302 PSS009318|
European Ancestry|
19,668 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Peripheral vascular disease, unspecified Partial Correlation (partial-r): 0.0175 [0.0035, 0.0315] sex, age, birth date, deprivation index, 16 PCs
PPM011304 PSS008646|
European Ancestry|
6,566 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Peripheral vascular disease, unspecified Partial Correlation (partial-r): 0.0261 [0.0018, 0.0503] sex, age, birth date, deprivation index, 16 PCs
PPM011305 PSS008420|
Greater Middle Eastern Ancestry|
1,189 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Peripheral vascular disease, unspecified Partial Correlation (partial-r): -0.0296 [-0.0868, 0.0278] sex, age, birth date, deprivation index, 16 PCs
PPM011306 PSS008200|
South Asian Ancestry|
6,258 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Peripheral vascular disease, unspecified Partial Correlation (partial-r): 0.0061 [-0.0187, 0.0309] sex, age, birth date, deprivation index, 16 PCs
PPM011307 PSS007982|
East Asian Ancestry|
1,794 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Peripheral vascular disease, unspecified Partial Correlation (partial-r): -0.0276 [-0.074, 0.019] sex, age, birth date, deprivation index, 16 PCs
PPM011308 PSS007765|
African Ancestry|
2,444 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Peripheral vascular disease, unspecified Partial Correlation (partial-r): -0.0324 [-0.0721, 0.0074] sex, age, birth date, deprivation index, 16 PCs
PPM011309 PSS008869|
African Ancestry|
3,878 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Peripheral vascular disease, unspecified Partial Correlation (partial-r): 0.0345 [0.003, 0.066] sex, age, birth date, deprivation index, 16 PCs
PPM011303 PSS009092|
European Ancestry|
4,063 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Peripheral vascular disease, unspecified Partial Correlation (partial-r): 0.011 [-0.0198, 0.0418] 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
PSS008420 1,189 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008869 3,878 individuals African unspecified Nigeria (West Africa) UKB
PSS009318 19,668 individuals European UK (+ Ireland) UKB
PSS008646 6,566 individuals European Italy (South Europe) UKB
PSS008200 6,258 individuals South Asian India (South Asia) UKB
PSS009092 4,063 individuals European Poland (NE Europe) UKB
PSS007982 1,794 individuals East Asian China (East Asia) UKB
PSS007765 2,444 individuals African American or Afro-Caribbean Carribean UKB