PGS Publication: PGP000422

Publication Information (EuropePMC)
Title A new 165-SNP low-density lipoprotein cholesterol polygenic risk score based on next generation sequencing outperforms previously published scores in routine diagnostics of familial hypercholesterolemia.
PubMed ID 36528340(Europe PMC)
doi 10.1016/j.trsl.2022.12.002
Publication Date Dec. 15, 2022
Journal Transl Res
Author(s) Vanhoye X, Bardel C, Rimbert A, Moulin P, Rollat-Farnier PA, Muntaner M, Marmontel O, Dumont S, Charrière S, Cornélis F, Ducluzeau PH, Fonteille A, Nobecourt E, Peretti N, Schillo F, Wargny M, Cariou B, Meirhaeghe A, Di Filippo M.
Released in PGS Catalog: Jan. 19, 2023

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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Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
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)
PGS003405
(165SNP_PRS)
 PGP000422 |
Vanhoye X et al. Transl Res (2022)
 LDL cholesterol low density lipoprotein cholesterol measurement 169
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003405/ScoringFiles/PGS003405.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
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS003403
(PRS28_LDL)
 PGP000420 |
Trinder M et al. J Am Coll Cardiol (2019)
 LDL cholesterol low density lipoprotein cholesterol measurement 28
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003403/ScoringFiles/PGS003403.txt.gz
PGS003404
(wGRS)
 PGP000421 |
Wang J et al. Arterioscler Thromb Vasc Biol (2016)
 LDL cholesterol low density lipoprotein cholesterol measurement 10
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003404/ScoringFiles/PGS003404.txt.gz
PGS000814
(GRS12_LDLc)
 PGP000200 |
Talmud PJ et al. Lancet (2013)
 LDL cholesterol low density lipoprotein cholesterol measurement 16
-
 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
PPM017044 PGS003405
(165SNP_PRS)
 PSS010104|
European Ancestry|
89,528 individuals
 PGP000422 |
Vanhoye X et al. Transl Res (2022)
 Reported Trait: LDL-c blood concentration β: 0.31 [0.3, 0.31] AUROC: 0.6901 [0.684, 0.696] R²: 0.1979 Age, BMI, sex, age —
PPM017045 PGS000814
(GRS12_LDLc)
 PSS010104|
European Ancestry|
89,528 individuals
 PGP000422 |
Vanhoye X et al. Transl Res (2022)
|Ext.		 Reported Trait: LDL-c blood concentration β: 0.25 [0.25, 0.26] AUROC: 0.6503 [0.644, 0.657] R²: 0.1055 Age, BMI, sex, age —
PPM017046 PGS003403
(PRS28_LDL)
 PSS010104|
European Ancestry|
89,528 individuals
 PGP000422 |
Vanhoye X et al. Transl Res (2022)
|Ext.		 Reported Trait: LDL-c blood concentration β: 0.18 [0.18, 0.18] AUROC: 0.6233 [0.617, 0.63] R²: 0.1055 Age, BMI, sex, age —
PPM017047 PGS003404
(wGRS)
 PSS010104|
European Ancestry|
89,528 individuals
 PGP000422 |
Vanhoye X et al. Transl Res (2022)
|Ext.		 Reported Trait: LDL-c blood concentration β: 0.16 [0.15, 0.16] AUROC: 0.6072 [0.6, 0.614] R²: 0.09317 Age, BMI, sex, age —

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
PSS010104 — — 89,528 individuals — European — UKB —