Polygenic Score (PGS) ID: PGS003791

Predicted Trait
Reported Trait LDL cholesterol
Mapped Trait(s) low density lipoprotein cholesterol measurement (EFO_0004611)
Released in PGS Catalog: Sept. 1, 2023
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Score Details

Score Construction
PGS Name LDL_EAS_CT
Development Method
Name Clumping and Thresholding (C+T)
Parameters clumping window size=500kb, clumping r2=0.1, p-value threshold = c(5E-08,5E-07,...,0.5,1)
Variants
Original Genome Build GRCh37
Number of Variants 80
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000489
Citation (link to publication) Zhang H et al. Nat Genet (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
East Asian: 100%
82,587 individuals (100%)
Score Development/Training
East Asian: 100%
950 individuals (100%)
PGS Evaluation
East Asian: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 34887591
 82,587 individuals East Asian NR
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
— 950 individuals,
32.0 % Male samples
 East Asian UKB — Mean = 52.47 years
Sd = 7.81 years		 — — —

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
PPM018598 PSS011044|
East Asian Ancestry|
970 individuals
 PGP000489 |
Zhang H et al. Nat Genet (2023)
 Reported Trait: Low-density lipoprotein cholesterol — — R²: 0.02274 — —

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
PSS011044 — — 970 individuals,
32.0 % Male samples
 Mean = 52.47 years
Sd = 7.81 years		 East Asian — UKB —