Polygenic Score (PGS) ID: PGS003786

Predicted Trait
Reported Trait LDL cholesterol
Mapped Trait(s) low density lipoprotein cholesterol measurement (EFO_0004611)
Released in PGS Catalog: Sept. 1, 2023
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Score Details

Score Construction
PGS Name LDL_AFR_CT
Development Method
Name Clumping and Thresholding (C+T)
Parameters clumping window size=500kb, clumping r2=0.1, p-value threshold = c(5E-08,5E-07,...,0.5,1)
Variants
Original Genome Build GRCh37
Number of Variants 188
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000489
Citation (link to publication) Zhang H et al. Nat Genet (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
African: 100%
87,760 individuals (100%)
Score Development/Training
African: 100%
4,293 individuals (100%)
PGS Evaluation
African: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 34887591
 87,760 individuals African American or Afro-Caribbean
(African American)		 NR
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 4,293 individuals,
42.0 % Male samples
 African American or Afro-Caribbean
(African American)		 UKB — Mean = 51.82 years
Sd = 8.06 years		 — — —

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
PPM018593 PSS011043|
African Ancestry|
4,292 individuals
 PGP000489 |
Zhang H et al. Nat Genet (2023)
 Reported Trait: Low-density lipoprotein cholesterol — — R²: 0.08924 — —

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
PSS011043 — — 4,292 individuals,
42.0 % Male samples
 Mean = 51.82 years
Sd = 8.06 years		 African American or Afro-Caribbean
(African American)		 — UKB —