Polygenic Score (PGS) ID: PGS002048

Predicted Trait
Reported Trait Coronary atherosclerosis
Mapped Trait(s) coronary atherosclerosis (MONDO_0021661)
Additional Trait Information circulatory system
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_411.4
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 762,124
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
PPM011246 PSS009311|
European Ancestry|
19,308 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Coronary atherosclerosis — — Partial Correlation (partial-r): 0.1078 [0.0938, 0.1217] sex, age, birth date, deprivation index, 16 PCs —
PPM011247 PSS009085|
European Ancestry|
4,021 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Coronary atherosclerosis — — Partial Correlation (partial-r): 0.1435 [0.113, 0.1737] sex, age, birth date, deprivation index, 16 PCs —
PPM011248 PSS008639|
European Ancestry|
6,492 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Coronary atherosclerosis — — Partial Correlation (partial-r): 0.1061 [0.0819, 0.1301] sex, age, birth date, deprivation index, 16 PCs —
PPM011250 PSS008193|
South Asian Ancestry|
6,070 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Coronary atherosclerosis — — Partial Correlation (partial-r): 0.1246 [0.0997, 0.1493] sex, age, birth date, deprivation index, 16 PCs —
PPM011251 PSS007975|
East Asian Ancestry|
1,794 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Coronary atherosclerosis — — Partial Correlation (partial-r): 0.0522 [0.0057, 0.0985] sex, age, birth date, deprivation index, 16 PCs —
PPM011252 PSS007758|
African Ancestry|
2,396 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Coronary atherosclerosis — — Partial Correlation (partial-r): 0.0358 [-0.0044, 0.0759] sex, age, birth date, deprivation index, 16 PCs —
PPM011253 PSS008862|
African Ancestry|
3,793 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Coronary atherosclerosis — — Partial Correlation (partial-r): 0.01 [-0.0219, 0.0419] sex, age, birth date, deprivation index, 16 PCs —
PPM011249 PSS008413|
Greater Middle Eastern Ancestry|
1,158 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Coronary atherosclerosis — — Partial Correlation (partial-r): 0.0727 [0.0146, 0.1302] 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
PSS007975 — — 1,794 individuals — East Asian China (East Asia) UKB —
PSS008413 — — 1,158 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS007758 — — 2,396 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008639 — — 6,492 individuals — European Italy (South Europe) UKB —
PSS009085 — — 4,021 individuals — European Poland (NE Europe) UKB —
PSS008862 — — 3,793 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009311 — — 19,308 individuals — European UK (+ Ireland) UKB —
PSS008193 — — 6,070 individuals — South Asian India (South Asia) UKB —