Polygenic Score (PGS) ID: PGS002056

Predicted Trait
Reported Trait Phlebitis and thrombophlebitis
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_451
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 114,679
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
PPM011310 PSS009319|
European Ancestry|
18,164 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): 0.0561 [0.0416, 0.0706] sex, age, birth date, deprivation index, 16 PCs
PPM011311 PSS009093|
European Ancestry|
3,734 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): 0.0729 [0.0408, 0.1048] sex, age, birth date, deprivation index, 16 PCs
PPM011312 PSS008647|
European Ancestry|
6,014 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): 0.0469 [0.0216, 0.0722] sex, age, birth date, deprivation index, 16 PCs
PPM011313 PSS008421|
Greater Middle Eastern Ancestry|
1,102 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): 0.085 [0.0256, 0.1439] sex, age, birth date, deprivation index, 16 PCs
PPM011314 PSS008201|
South Asian Ancestry|
5,719 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): 0.0284 [0.0025, 0.0543] sex, age, birth date, deprivation index, 16 PCs
PPM011315 PSS007983|
East Asian Ancestry|
1,622 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): -0.0188 [-0.0677, 0.0302] sex, age, birth date, deprivation index, 16 PCs
PPM011316 PSS007766|
African Ancestry|
2,283 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): -0.001 [-0.0422, 0.0402] sex, age, birth date, deprivation index, 16 PCs
PPM011317 PSS008870|
African Ancestry|
3,611 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): -0.0043 [-0.037, 0.0284] 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
PSS009093 3,734 individuals European Poland (NE Europe) UKB
PSS008421 1,102 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008647 6,014 individuals European Italy (South Europe) UKB
PSS009319 18,164 individuals European UK (+ Ireland) UKB
PSS008201 5,719 individuals South Asian India (South Asia) UKB
PSS008870 3,611 individuals African unspecified Nigeria (West Africa) UKB
PSS007983 1,622 individuals East Asian China (East Asia) UKB
PSS007766 2,283 individuals African American or Afro-Caribbean Carribean UKB