Polygenic Score (PGS) ID: PGS003405

Predicted Trait
Reported Trait LDL cholesterol
Mapped Trait(s) low density lipoprotein cholesterol measurement (EFO_0004611)
Released in PGS Catalog: Jan. 19, 2023
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Score Details

Score Construction
Development Method
Name Genome-wide significant SNPs
Parameters LD: --clump-r2 0.1 & --clump-kb 250
Original Genome Build GRCh38
Number of Variants 165
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000422
Citation (link to publication) Vanhoye X et al. Transl Res (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
427,099 individuals (100%)
Score Development/Training
European: 100%
1,082 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST002222
Europe PMC: 24097068
94,595 individuals European NR
GWAS Catalog: GCST009148
Europe PMC: 29083408
237,050 individuals European NR
GWAS Catalog: GCST000759
Europe PMC: 20686565
95,454 individuals European 23 cohorts
  • AGES
  • ,ARIC
  • ,B58C
  • ,BLSA
  • ,CHS
  • ,CoLaus
  • ,DGI
  • ,EPIC-Norfolk
  • ,FHS
  • ,Fenland
  • ,GenomEUtwin
  • ,KORA
  • ,MedSTAR
  • ,NFBC
  • ,PennCATH
  • ,RS
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
1,082 individuals,
46.7 % Male samples
European MONA-LISA Mean = 53.8 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
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM017044 PSS010104|
European Ancestry|
89,528 individuals
PGP000422 |
Vanhoye X et al. Transl Res (2022)
Reported Trait: LDL-c blood concentration β: 0.31 [0.3, 0.31] AUROC: 0.6901 [0.684, 0.696] : 0.1979 Age, BMI, sex, age

Evaluated Samples

PGS Sample Set ID
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
PSS010104 89,528 individuals European UKB