Polygenic Score (PGS) ID: PGS000895

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_HIS_LDL_PRS_weights_PT
Development Method
Name Pruning and Thresholding (P+T)
Parameters r2=0.1 distance=500kb p=5e-7
Variants
Original Genome Build hg19
Number of Variants 76
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)
Hispanic or Latin American: 100%
46,040 individuals (100%)
PGS Evaluation
Hispanic or Latin American: 40%
African: 20%
Additional Asian Ancestries: 20%
European: 20%
5 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GLGC2021
 46,040 individuals Hispanic or Latin American 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
PPM002609 PSS001157|
Additional Asian Ancestries|
4,155 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.079 sex, PC1-4, birth year, and mean age —
PPM002610 PSS001158|
European Ancestry|
68,381 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.119 sex, PC1-4, birth year, and mean age —
PPM002611 PSS001159|
Hispanic or Latin American Ancestry|
7,669 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.102 sex, PC1-4, birth year, and mean age —
PPM002633 PSS001155|
Hispanic or Latin American Ancestry|
360 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.088 sex, batch, PC1-4, and birth year —
PPM002608 PSS001156|
African Ancestry|
18,251 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.1 sex, PC1-4, birth year, and mean age —

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
PSS001155 — — 360 individuals — Hispanic or Latin American — 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