Polygenic Score (PGS) ID: PGS000893

Predicted Trait
Reported Trait LDL cholesterol
Mapped Trait(s) low density lipoprotein cholesterol measurement (EFO_0004611)
Released in PGS Catalog: Dec. 10, 2021
Download Score FTP directory
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 GLGC_2021_EUR_LDL_PRS_weights_PT
Development Method
Name Pruning and Thresholding (P+T)
Parameters r2=0.1 distance=500kb p=5e-4
Variants
Original Genome Build hg19
Number of Variants 5,427
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)
European: 100%
831,666 individuals (100%)
PGS Evaluation
European: 33.3%
African: 22.2%
Hispanic or Latin American: 11.1%
Additional Asian Ancestries: 11.1%
East Asian: 11.1%
South Asian: 11.1%
9 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GLGC2021
 831,666 individuals European 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
PPM002565 PSS001151|
South Asian Ancestry|
15,242 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Max LDL cholesterol — — R²: 0.096 age, sex, and PC1-10 —
PPM002580 PSS001153|
African Ancestry|
1,341 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.058 sex, batch, PC1-4, and birth year —
PPM002581 PSS001154|
European Ancestry|
17,190 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.123 sex, batch, PC1-4, and birth year —
PPM002600 PSS001156|
African Ancestry|
18,251 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.042 sex, PC1-4, birth year, and mean age —
PPM002601 PSS001157|
Additional Asian Ancestries|
4,155 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.066 sex, PC1-4, birth year, and mean age —
PPM002602 PSS001158|
European Ancestry|
68,381 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.152 sex, PC1-4, birth year, and mean age —
PPM002603 PSS001159|
Hispanic or Latin American Ancestry|
7,669 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.106 sex, PC1-4, birth year, and mean age —
PPM002623 PSS001165|
European Ancestry|
389,158 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.176 sex, batch, age at initial assessment, PCs1-4 —
PPM002572 PSS001152|
East Asian Ancestry|
118,260 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.071 age, sex, and recruitment area —

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
PSS001151 — — 15,242 individuals — South Asian — G&H —
PSS001152 — — 118,260 individuals — East Asian — KoGES —
PSS001153 — — 1,341 individuals — African American or Afro-Caribbean — MGI —
PSS001154 — — 17,190 individuals — European — MGI —
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
PSS001165 — — 389,158 individuals — European — UKB —