PGS Publication: PGP000107

Publication Information (EuropePMC)
Title Polygenic Contribution to Low-Density Lipoprotein Cholesterol Levels and Cardiovascular Risk in Monogenic Familial Hypercholesterolemia.
PubMed ID 33079599(Europe PMC)
doi 10.1161/circgen.120.002919
Publication Date Aug. 13, 2020
Journal Circ Genom Precis Med
Author(s) Trinder M, Paquette M, Cermakova L, Ban MR, Hegele RA, Baass A, Brunham LR.
Released in PGS Catalog: Nov. 20, 2020

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
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Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000340
(LDL-Cpsp)
 PGP000107 |
Trinder M et al. Circ Genom Precis Med (2020)
 LDL cholesterol low density lipoprotein cholesterol measurement 28
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000340/ScoringFiles/PGS000340.txt.gz

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) 		Evaluated Score 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 PGS000340
(LDL-Cpsp)
 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 PGS000340
(LDL-Cpsp)
 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 PGS000340
(LDL-Cpsp)
 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 —