Polygenic Score (PGS) ID: PGS000886

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_AFR_LDL_PRS_weights_PRS-CS
Development Method
Name PRS-CS
Parameters 1000Genomes reference panel
Variants
Original Genome Build hg19
Number of Variants 1,222,318
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)
African: 100%
87,760 individuals (100%)
PGS Evaluation
African: 66.7%
European: 33.3%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GLGC2021
 87,760 individuals African unspecified 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
PPM002576 PSS001153|
African Ancestry|
1,341 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.064 sex, batch, PC1-4, and birth year —
PPM002628 PSS001163|
African Ancestry|
6,863 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.112 sex, batch, age at initial assessment, PCs1-4 —
PPM002577 PSS001154|
European Ancestry|
17,190 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.056 sex, batch, PC1-4, and birth year —

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
PSS001154 — — 17,190 individuals — European — MGI —
PSS001163 — — 6,863 individuals — African unspecified — UKB —
PSS001153 — — 1,341 individuals — African American or Afro-Caribbean — MGI —