Polygenic Score (PGS) ID: PGS004973

Predicted Trait
Reported Trait LDL cholesterol
Mapped Trait(s) low density lipoprotein cholesterol measurement (EFO_0004611)
Released in PGS Catalog: Oct. 8, 2024
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Score Details

Score Construction
PGS Name LDLC_Mean_INT_ldpred_METAss_amrld
Development Method
Name ldpred
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,286,612
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000679
Citation (link to publication) Gunn S et al. HGG Adv (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Multi-ancestry (including European): 50.3%
  • European
  • African
  • Hispanic or Latin American
  • Additional Asian Ancestries
European: 35.8%
African: 9.8%
Hispanic or Latin American: 4.1%
1,149,477 individuals (100%)
PGS Evaluation
African: 33.3%
Hispanic or Latin American: 33.3%
European: 33.3%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
— 113,034 individuals African American or Afro-Caribbean MVP
— 411,070 individuals European MVP
— 47,087 individuals Hispanic or Latin American MVP
— 578,286 individuals European, African American or Afro-Caribbean, Hispanic or Latin American, Asian unspecified MVP

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
PPM022095 PSS011816|
European Ancestry|
7,654 individuals
 PGP000679 |
Gunn S et al. HGG Adv (2024)
 Reported Trait: LDL cholesterol β: 0.274 [0.25, 0.3] — R²: 0.077 score previously adjusted for age, sex, 20 PCs —
PPM022101 PSS011796|
African Ancestry|
2,490 individuals
 PGP000679 |
Gunn S et al. HGG Adv (2024)
 Reported Trait: LDL cholesterol β: 0.292 [0.26, 0.33] — R²: 0.087 score previously adjusted for age, sex, 20 PCs —
PPM022107 PSS011806|
Hispanic or Latin American Ancestry|
1,000 individuals
 PGP000679 |
Gunn S et al. HGG Adv (2024)
 Reported Trait: LDL cholesterol β: 0.253 [0.19, 0.31] — R²: 0.065 score previously adjusted for age, sex, 20 PCs —

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
PSS011796 — — 2,490 individuals — African American or Afro-Caribbean — AllofUs —
PSS011806 — — 1,000 individuals — Hispanic or Latin American — AllofUs —
PSS011816 — — 7,654 individuals — European — AllofUs —