Polygenic Score (PGS) ID: PGS002955

Predicted Trait
Reported Trait HDL cholesterol
Mapped Trait(s) high density lipoprotein cholesterol measurement (EFO_0004612)
Additional Trait Information HDL cholesterol (quantile); Quantitative
Released in PGS Catalog: Nov. 23, 2022
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Score Details

Score Construction
PGS Name ExPRSweb_HDL_30760-irnt_PT_MGI_20211120
Development Method
Name Pruning and Thresholding (P+T)
Parameters LD Clumping (using Plink to calculate LD, MAF >= 1%, r^2 <= 0.1) & P-value threshold <=3.98e-03
Variants
Original Genome Build GRCh37
Number of Variants 16,393
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000393
Citation (link to publication) Ma Y et al. Am J Hum Genet (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
315,133 individuals (100%)
Score Development/Training
European: 100%
9,319 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
315,133 individuals European UKB
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
— 9,319 individuals European MGI HIGH DENSITY LIPOPROTEIN CHOL (LOINC: 2085-9); Quantitative — — — —

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
PPM015836 PSS010006|
European Ancestry|
9,320 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: HDL β: 4.39 (0.127) — R²: 0.0903 SEX,AGE,Batch,PC1,PC2,PC3,PC4 —

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
PSS010006 HIGH DENSITY LIPOPROTEIN CHOL (LOINC: 2085-9); Quantitative — 9,320 individuals — European — MGI —