Polygenic Score (PGS) ID: PGS000891

Predicted Trait
Reported Trait LDL cholesterol
Mapped Trait(s) low density lipoprotein cholesterol measurement (EFO_0004611)
Released in PGS Catalog: Dec. 10, 2021
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Score Details

Score Construction
PGS Name GLGC_2021_EAS_LDL_PRS_weights_PT
Development Method
Name Pruning and Thresholding (P+T)
Parameters r2=0.1 distance=500kb p=5e-9
Variants
Original Genome Build hg19
Number of Variants 66
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000230
Citation (link to publication) Graham SE et al. Nature (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
East Asian: 100%
82,587 individuals (100%)
PGS Evaluation
East Asian: 33.3%
African: 16.7%
Hispanic or Latin American: 16.7%
Additional Asian Ancestries: 16.7%
European: 16.7%
6 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GLGC2021
 82,587 individuals East Asian NR

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
PPM002570 PSS001152|
East Asian Ancestry|
118,260 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.098 age, sex, and recruitment area —
PPM002592 PSS001156|
African Ancestry|
18,251 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.056 sex, PC1-4, birth year, and mean age —
PPM002593 PSS001157|
Additional Asian Ancestries|
4,155 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.098 sex, PC1-4, birth year, and mean age —
PPM002594 PSS001158|
European Ancestry|
68,381 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.083 sex, PC1-4, birth year, and mean age —
PPM002595 PSS001159|
Hispanic or Latin American Ancestry|
7,669 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.057 sex, PC1-4, birth year, and mean age —
PPM002627 PSS001164|
East Asian Ancestry|
1,441 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.1 sex, batch, age at initial assessment, PCs1-4 —

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
PSS001152 — — 118,260 individuals — East Asian — KoGES —
PSS001156 — — 18,251 individuals — African American or Afro-Caribbean — MVP Subset not used in discovery dataset
PSS001157 — — 4,155 individuals — Asian unspecified — MVP Subset not used in discovery dataset
PSS001158 — — 68,381 individuals — European — MVP Subset not used in discovery dataset
PSS001159 — — 7,669 individuals — Hispanic or Latin American — MVP Subset not used in discovery dataset
PSS001164 — — 1,441 individuals — East Asian — UKB —