PGS Publication: PGP000221

Publication Information (EuropePMC)
Title A polygenic biomarker to identify patients with severe hypercholesterolemia of polygenic origin.
PubMed ID 32307928(Europe PMC)
doi 10.1002/mgg3.1248
Publication Date April 19, 2020
Journal Mol Genet Genomic Med
Author(s) Leal LG, Hoggart C, Jarvelin MR, Herzig KH, Sternberg MJE, David A.
Released in PGS Catalog: Aug. 26, 2021

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Multi-ancestry (including European)
Multi-ancestry (excluding European)
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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 Scoring File (FTP Link)
PGS000875
(PGS36_LDLc)
PGP000221 |
Leal LG et al. Mol Genet Genomic Med (2020)
Low-density lipoprotein cholesterol low density lipoprotein cholesterol measurement 36
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000875/ScoringFiles/PGS000875.txt.gz

External PGS Evaluated By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS000814
(GRS12_LDLc)
PGP000200 |
Talmud PJ et al. Lancet (2013)
Low-density lipoprotein cholesterol low density lipoprotein cholesterol measurement 12
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000814/ScoringFiles/PGS000814.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
PPM002500 PGS000875
(PGS36_LDLc)
PSS001124|
European Ancestry|
4,787 individuals
PGP000221 |
Leal LG et al. Mol Genet Genomic Med (2020)
Reported Trait: Low-density lipoprotein cholesterol : 0.08 Age, gender, body mass index, ancestry differences captured by the first two components from multidimensional scaling
PPM002501 PGS000875
(PGS36_LDLc)
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 PGS000875
(PGS36_LDLc)
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
PPM002503 PGS000814
(GRS12_LDLc)
PSS001124|
European Ancestry|
4,787 individuals
PGP000221 |
Leal LG et al. Mol Genet Genomic Med (2020)
|Ext.
Reported Trait: Low-density lipoprotein cholesterol AUROC: 0.65

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