Polygenic Score (PGS) ID: PGS004932

Predicted Trait
Reported Trait HDL cholesterol
Mapped Trait(s) high density lipoprotein cholesterol measurement (EFO_0004612)
Additional Trait Information Above 60 mg/dL or 1.5 mmol/Lhigh
Released in PGS Catalog: Sept. 19, 2024
Download Score FTP directory
Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name high_density_lipoprotein_cholesterol_measurement_combined
Development Method
Name SnpNet
Parameters lambda = 200; alpha=1; ncores=20
Variants
Original Genome Build hg19
Number of Variants 17,151
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000665
Citation (link to publication) Moreno-Grau S et al. Human Genomics (2024)
Ancestry Distribution
Score Development/Training
European: 100%
249,496 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 100,148 cases
  • , 149,348 controls
]
,
46.0 % Male samples
 European
(British)		 UKB — Mean = 56.74 years
Sd = 8.02 years		 — — —

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
PPM021720 PSS011762|
European Ancestry|
8,417 individuals
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
 Reported Trait: High density lipoprotein cholesterol level OR: 1.02 [0.94, 1.11] AUROC: 0.6 — — —

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
PSS011762 — — 8,417 individuals — European — BBofA —