Polygenic Score (PGS) ID: PGS000340

Predicted Trait
Reported Trait LDL cholesterol
Mapped Trait(s) low density lipoprotein cholesterol measurement (EFO_0004611)
Released in PGS Catalog: Nov. 20, 2020
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Score Details

Score Construction
PGS Name LDL-Cpsp
Development Method
Name Genome-wide significant variants
Parameters Independent SNVs
Variants
Original Genome Build GRCh37
Number of Variants 28
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000107
Citation (link to publication) Trinder M et al. Circ Genom Precis Med (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
94,595 individuals (100%)
PGS Evaluation
European: 50%
Multi-ancestry (including European): 50%
  • European
  • Not Reported
2 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

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
PPM000924 PSS000466|
European Ancestry|
389,127 individuals
 PGP000107 |
Trinder M et al. Circ Genom Precis Med (2020)
 Reported Trait: Low-density lipoprotein cholesterol levels β: 0.82 (0.006) — R²: 0.074 Age, sex —
PPM000923 PSS000465|
Multi-ancestry (including European)|
1,120 individuals
 PGP000107 |
Trinder M et al. Circ Genom Precis Med (2020)
 Reported Trait: Low-density lipoprotein cholesterol levels in familial hypercholesterolemia mutation carriers — — Beta (per 20% increase in PGS): 0.13 [0.072, 0.19] — —
PPM000925 PSS000465|
Multi-ancestry (including European)|
1,120 individuals
 PGP000107 |
Trinder M et al. Circ Genom Precis Med (2020)
 Reported Trait: Atherosclerotic cardiovascular disease in familial hypercholesterolemia mutation carriers — — Odds Ratio (OR; top 20% vs. rest): 1.48 [1.02, 2.14] sex —

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
PSS000465 Individuals ≥18 years with clinically diagnosed heterozygous familial hypercholesterolemia (FH) from the BCFH cohort. Individuals who were positive for the common French Canadian variant in the LDLR gene including del.15 kb of the promoter and exon 1, del.5 kb of exons 2 and 3, p.W66G (exon 3), p.E207K (exon 4), p.Y468X (exon 10), or p.C646Y (exon 14) in this study. Fasting clinical lipid profiles were obtained following a 4-week washout of any cholesterol-lowering medications from the CNMA cohort. Individuals who were positive for a LDLR, APOB, or PCSK9 variant that was deemed to cause FH in the UKB cohort.Any atherosclerotic cardiovascular disease (ASCVD) event, which was defined as myocardial infarction, coronary artery disease or carotid revascularization, transient ischemic attack or stroke. For the UK Biobank, retrospecitvie ASCVD was self reported and prospective ASCVD were defined using hospital episode statistics and 10th revision of the International Statistical Classification of Diseases and Related Health Problems diagnosis codes and OPCS Classification of Interventions and Procedures version 4 procedure codes — 1,120 individuals,
40.4 % Male samples
 Mean = 41.36 years European, NR European (94%), Not reported (6%) BCFH, CNMA, UKB —
PSS000466 Any atherosclerotic cardiovascular disease (ASCVD) event, which was defined as myocardial infarction, coronary artery disease or carotid revascularization, transient ischemic attack or stroke. For the UK Biobank, retrospecitvie ASCVD was self reported and prospective ASCVD were defined using hospital episode statistics and 10th revision of the International Statistical Classification of Diseases and Related Health Problems diagnosis codes and OPCS Classification of Interventions and Procedures version 4 procedure codes — 389,127 individuals — European — UKB —