Polygenic Score (PGS) ID: PGS000875

Predicted Trait
Reported Trait LDL cholesterol
Mapped Trait(s) low density lipoprotein cholesterol measurement (EFO_0004611)
Released in PGS Catalog: Aug. 26, 2021
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Score Details

Score Construction
PGS Name PGS36_LDLc
Development Method
Name Clumping and Thresholding (C+T)
Parameters R^2 = 0.078, p < 1e-20
Variants
Original Genome Build GRCh38
Number of Variants 36
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000221
Citation (link to publication) Leal LG et al. Mol Genet Genomic Med (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
94,595 individuals (100%)
Score Development/Training
European: 100%
2,197 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 23 cohorts
  • AGES
  • ,ARIC
  • ,B58C
  • ,BLSA
  • ,BRIGHT
  • ,CHS
  • ,CoLaus
  • ,DGI
  • ,EPIC-Norfolk
  • ,FHS
  • ,FINRISK
  • ,FUSION
  • ,Fenland
  • ,GENMETS
  • ,GenomEUtwin
  • ,InCHIANTI
  • ,KORA
  • ,LOLIPOP
  • ,MedSTAR
  • ,NFBC
  • ,PennCATH
  • ,RS
  • ,SUVIMAX
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
— 2,197 individuals,
49.0 % Male samples
 European eMERGE — Mean = 60.0 years
Sd = 11.5 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
PPM002500 PSS001124|
European Ancestry|
4,787 individuals
 PGP000221 |
Leal LG et al. Mol Genet Genomic Med (2020)
 Reported Trait: Low-density lipoprotein cholesterol — — R²: 0.08 Age, gender, body mass index, ancestry differences captured by the first two components from multidimensional scaling —
PPM002501 PSS001124|
European Ancestry|
4,787 individuals
 PGP000221 |
Leal LG et al. Mol Genet Genomic Med (2020)
 Reported Trait: Severe hypercholesterolemia — — Risk Ratio (RR, top 30% vs bottom 30%): 4.8 [2.6, 8.9] — —
PPM002502 PSS001124|
European Ancestry|
4,787 individuals
 PGP000221 |
Leal LG et al. Mol Genet Genomic Med (2020)
 Reported Trait: Low-density lipoprotein cholesterol — AUROC: 0.67 — — —

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
PSS001124 Individuals with severe hypercholesterolemia (HC) had a LDL-C level > 4.9 mmol/L. 124 individuals had severe HC, based on this criteria. Individuals with intermediate HC had a LDL-C level 3.0 ≤ LDL‐C ≤ 4.9 mmol/L. 1927 individuals had intermediate HC, based on this criteria. Individuals classified as having normal LDL-C levels had LDL-C levels < 3.0 mmol/L. 2733 individuals had normal LDL-C levels, based on this criteria. — 4,787 individuals,
48.0 % Male samples
 Mean = 31.0 years
Sd = 0.2 years		 European — NFBC —