Polygenic Score (PGS) ID: PGS002654

Predicted Trait
Reported Trait LDL cholesterol
Mapped Trait(s) low density lipoprotein cholesterol measurement (EFO_0004611)
Released in PGS Catalog: June 9, 2022
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name biochemistry_LDLdirect.PolyFun-pred
Development Method
Name PolyFun-pred
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 274,585
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000332
Citation (link to publication) Weissbrod O et al. Nat Genet (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
321,002 individuals (100%)
PGS Evaluation
African: 20%
East Asian: 20%
European: 20%
Multi-ancestry (including European): 20%
  • African
  • European
  • East Asian
  • South Asian
South Asian: 20%
5 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
— 321,002 individuals European 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
PPM014370 PSS009791|
African Ancestry|
6,068 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: LDL Cholesterol — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.1091 age, sex, age*sex, assessment center, genotyping array, 10 PCs See biochemistry_LDLdirect.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014419 PSS009792|
East Asian Ancestry|
875 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: LDL Cholesterol — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0724 age, sex, age*sex, assessment center, genotyping array, 10 PCs See biochemistry_LDLdirect.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014468 PSS009793|
European Ancestry|
41,139 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: LDL Cholesterol — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.1195 age, sex, age*sex, assessment center, genotyping array, 10 PCs See biochemistry_LDLdirect.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014517 PSS009794|
South Asian Ancestry|
7,638 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: LDL Cholesterol — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0528 age, sex, age*sex, assessment center, genotyping array, 10 PCs See biochemistry_LDLdirect.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM023042 PSS012103|
Multi-ancestry (including European)|
663 individuals
 PGP000763 |
Zou RS et al. J Am Heart Assoc (2024)
|Ext.		 Reported Trait: Plaque presence (on coronary computed tomography angiography) OR: 1.21 [1.01, 1.44] — — age, sex, and the first 10 principal components of ancestry —
PPM023043 PSS012103|
Multi-ancestry (including European)|
663 individuals
 PGP000763 |
Zou RS et al. J Am Heart Assoc (2024)
|Ext.		 Reported Trait: partially calcified plaque OR: 1.21 [1.01, 1.45] — — age, sex, and the first 10 principal components of ancestry —

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
PSS012103 — — 277 individuals — African unspecified — REPRIEVE —
PSS012103 — — 379 individuals — European — REPRIEVE —
PSS012103 — — 6 individuals — East Asian — REPRIEVE —
PSS012103 — — 1 individuals — South Asian — REPRIEVE —
PSS009791 — — 6,068 individuals — African unspecified — UKB —
PSS009792 — — 875 individuals — East Asian — UKB —
PSS009793 — — 41,139 individuals — European Non-British European UKB —
PSS009794 — — 7,638 individuals — South Asian — UKB —