Polygenic Score (PGS) ID: PGS002057

Predicted Trait
Reported Trait Varicose veins
Mapped Trait(s) Varicose veins (HP_0002619)
Additional Trait Information circulatory system
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_454
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 760,630
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
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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM011318 PSS009320|
European Ancestry|
18,550 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Varicose veins — — Partial Correlation (partial-r): 0.0824 [0.0681, 0.0967] sex, age, birth date, deprivation index, 16 PCs —
PPM011319 PSS009094|
European Ancestry|
3,835 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Varicose veins — — Partial Correlation (partial-r): 0.083 [0.0514, 0.1145] sex, age, birth date, deprivation index, 16 PCs —
PPM011320 PSS008648|
European Ancestry|
6,131 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Varicose veins — — Partial Correlation (partial-r): 0.0666 [0.0416, 0.0915] sex, age, birth date, deprivation index, 16 PCs —
PPM011321 PSS008422|
Greater Middle Eastern Ancestry|
1,116 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Varicose veins — — Partial Correlation (partial-r): -0.0216 [-0.0807, 0.0377] sex, age, birth date, deprivation index, 16 PCs —
PPM011322 PSS008202|
South Asian Ancestry|
5,823 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Varicose veins — — Partial Correlation (partial-r): 0.0802 [0.0546, 0.1057] sex, age, birth date, deprivation index, 16 PCs —
PPM011323 PSS007984|
East Asian Ancestry|
1,639 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Varicose veins — — Partial Correlation (partial-r): 0.0953 [0.0468, 0.1434] sex, age, birth date, deprivation index, 16 PCs —
PPM011324 PSS007767|
African Ancestry|
2,295 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Varicose veins — — Partial Correlation (partial-r): 0.0038 [-0.0373, 0.0449] sex, age, birth date, deprivation index, 16 PCs —
PPM011325 PSS008871|
African Ancestry|
3,619 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Varicose veins — — Partial Correlation (partial-r): 0.0324 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
PSS009094 — — 3,835 individuals — European Poland (NE Europe) UKB —
PSS008422 — — 1,116 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009320 — — 18,550 individuals — European UK (+ Ireland) UKB —
PSS008648 — — 6,131 individuals — European Italy (South Europe) UKB —
PSS008202 — — 5,823 individuals — South Asian India (South Asia) UKB —
PSS008871 — — 3,619 individuals — African unspecified Nigeria (West Africa) UKB —
PSS007984 — — 1,639 individuals — East Asian China (East Asia) UKB —
PSS007767 — — 2,295 individuals — African American or Afro-Caribbean Carribean UKB —