Polygenic Score (PGS) ID: PGS000890

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_PRS-CS
Development Method
Name PRS-CS
Parameters 1000Genomes reference panel
Variants
Original Genome Build hg19
Number of Variants 1,029,158
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: 42.9%
African: 14.3%
Hispanic or Latin American: 14.3%
Additional Asian Ancestries: 14.3%
European: 14.3%
7 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
PPM002571 PSS001152|
East Asian Ancestry|
118,260 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.094 age, sex, and recruitment area —
PPM002596 PSS001156|
African Ancestry|
18,251 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.041 sex, PC1-4, birth year, and mean age —
PPM002598 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 —
PPM002599 PSS001159|
Hispanic or Latin American Ancestry|
7,669 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.063 sex, PC1-4, birth year, and mean age —
PPM002620 PSS001161|
East Asian Ancestry|
28,217 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.094 sex, age, recruitment method, and PC1-20 —
PPM002626 PSS001164|
East Asian Ancestry|
1,441 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Baseline LDL cholesterol — — R²: 0.113 sex, batch, age at initial assessment, PCs1-4 —
PPM002597 PSS001157|
Additional Asian Ancestries|
4,155 individuals
 PGP000230 |
Graham SE et al. Nature (2021)
 Reported Trait: Mean LDL cholesterol — — R²: 0.09 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
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
PSS001161 — — 28,217 individuals — East Asian — ToMMo Only participants from Miyagi Prefecture were included
PSS001164 — — 1,441 individuals — East Asian — UKB —