Polygenic Score (PGS) ID: PGS002059

Predicted Trait
Reported Trait Circulatory disease NEC
Mapped Trait(s) vascular disease (EFO_0004264)
Additional Trait Information circulatory system
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_459.9
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 604,572
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
PPM011334 PSS009322|
European Ancestry|
19,705 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Circulatory disease NEC — — Partial Correlation (partial-r): 0.0497 [0.0358, 0.0636] sex, age, birth date, deprivation index, 16 PCs —
PPM011335 PSS009096|
European Ancestry|
4,066 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Circulatory disease NEC — — Partial Correlation (partial-r): 0.0288 [-0.002, 0.0596] sex, age, birth date, deprivation index, 16 PCs —
PPM011336 PSS008650|
European Ancestry|
6,570 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Circulatory disease NEC — — Partial Correlation (partial-r): 0.0323 [0.0081, 0.0565] sex, age, birth date, deprivation index, 16 PCs —
PPM011337 PSS008424|
Greater Middle Eastern Ancestry|
1,182 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Circulatory disease NEC — — Partial Correlation (partial-r): -0.0502 [-0.1074, 0.0073] sex, age, birth date, deprivation index, 16 PCs —
PPM011339 PSS007986|
East Asian Ancestry|
1,790 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Circulatory disease NEC — — Partial Correlation (partial-r): 0.0257 [-0.0209, 0.0722] sex, age, birth date, deprivation index, 16 PCs —
PPM011340 PSS007769|
African Ancestry|
2,467 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Circulatory disease NEC — — Partial Correlation (partial-r): 0.0063 [-0.0333, 0.0459] sex, age, birth date, deprivation index, 16 PCs —
PPM011338 PSS008204|
South Asian Ancestry|
6,220 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Circulatory disease NEC — — Partial Correlation (partial-r): 0.0197 [-0.0052, 0.0446] sex, age, birth date, deprivation index, 16 PCs —
PPM011341 PSS008873|
African Ancestry|
3,882 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Circulatory disease NEC — — Partial Correlation (partial-r): 0.0041 [-0.0275, 0.0356] 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
PSS009096 — — 4,066 individuals — European Poland (NE Europe) UKB —
PSS008424 — — 1,182 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009322 — — 19,705 individuals — European UK (+ Ireland) UKB —
PSS008650 — — 6,570 individuals — European Italy (South Europe) UKB —
PSS008204 — — 6,220 individuals — South Asian India (South Asia) UKB —
PSS008873 — — 3,882 individuals — African unspecified Nigeria (West Africa) UKB —
PSS007986 — — 1,790 individuals — East Asian China (East Asia) UKB —
PSS007769 — — 2,467 individuals — African American or Afro-Caribbean Carribean UKB —