Polygenic Score (PGS) ID: PGS000340

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

Score Construction
PGS Name LDL-Cpsp
Variants
Original Genome Build GRCh37
Number of Variants 28
Development Method
Name Genome-wide significant variants
Parameters Independent SNVs
PGS Source
PGS Catalog Publication (PGP) ID PGP000107
Citation (link to publication) Trinder M et al. Circ Genom Precis Med (2020)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST002222
EuropePMC: 24097068
94,595 individuals European

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 ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000925 PSS000465 PGP000107
Trinder M et al. (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
PPM000923 PSS000465 PGP000107
Trinder M et al. (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]
PPM000924 PSS000466 PGP000107
Trinder M et al. (2020)
Reported Trait: Low-density lipoprotein cholesterol levels β: 0.82 : 0.074 Age, sex

Evaluated Samples

PGS Sample Set ID
(PSS 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
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