Polygenic Score (PGS) ID: PGS003978

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

Score Construction
PGS Name meta_without-UKB_LDL
Development Method
Name PRS-CSx
Parameters default
Variants
Original Genome Build GRCh37
Number of Variants 348,056
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000514
Citation (link to publication) Hassanin E et al. medRxiv (2023) Preprint
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 79.8%
East Asian: 8.9%
African: 6%
Hispanic or Latin American: 2.9%
South Asian: 2.5%
1,654,960 individuals (100%)
PGS Evaluation
East Asian: 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: GCST90239655
Europe PMC: 34887591
 40,963 individuals South Asian NR
GWAS Catalog: GCST90239655
Europe PMC: 34887591
 48,057 individuals Hispanic or Latin American NR
GWAS Catalog: GCST90239655
Europe PMC: 34887591
 99,432 individuals African American or Afro-Caribbean, African unspecified NR
GWAS Catalog: GCST90239655
Europe PMC: 34887591
 146,492 individuals East Asian NR
GWAS Catalog: GCST90239655
Europe PMC: 34887591
 1,320,016 individuals European 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
PPM019139 PSS011207|
European Ancestry|
423,596 individuals
 PGP000514 |
Hassanin E et al. medRxiv (2023)
|Pre		 Reported Trait: LDL level — — R²: 10.5 % — —
PPM019141 PSS011203|
East Asian Ancestry|
1,480 individuals
 PGP000514 |
Hassanin E et al. medRxiv (2023)
|Pre		 Reported Trait: LDL level — — R²: 7.8 % — —
PPM019144 PSS011201|
East Asian Ancestry|
68,978 individuals
 PGP000514 |
Hassanin E et al. medRxiv (2023)
|Pre		 Reported Trait: LDL level — — R²: 6.7 % — —

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
PSS011201 — — 68,978 individuals,
31.2 % Male samples
 — East Asian — TWB —
PSS011203 — — 1,480 individuals,
36.8 % Male samples
 — East Asian — UKB —
PSS011207 — — 423,596 individuals,
45.9 % Male samples
 — European — UKB —