Polygenic Score (PGS) ID: PGS002409

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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Score Details

Score Construction
PGS Name biochemistry_LDLdirect.P+T.0.0001
Development Method
Name Pruning and Thresholding (P+T)
Parameters p < 0.0001
Variants
Original Genome Build GRCh37
Number of Variants 7,626
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: 25%
East Asian: 25%
European: 25%
South Asian: 25%
4 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
PPM013390 PSS009791|
African Ancestry|
6,068 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: LDL Cholesterol — — Incremental R2 (full model vs. covariates alone): 0.0019 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM013439 PSS009792|
East Asian Ancestry|
875 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: LDL Cholesterol — — Incremental R2 (full model vs. covariates alone): 0.0268 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM013488 PSS009793|
European Ancestry|
41,139 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: LDL Cholesterol — — Incremental R2 (full model vs. covariates alone): 0.0733 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM013537 PSS009794|
South Asian Ancestry|
7,638 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: LDL Cholesterol — — Incremental R2 (full model vs. covariates alone): 0.0203 age, sex, age*sex, assessment center, genotyping array, 10 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
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 —