Polygenic Score (PGS) ID: PGS019822

Predicted Trait
Reported Trait HDL cholesterol
Mapped Trait(s) LDL cholesterol (EFO_0004195)
Released in PGS Catalog: July 29, 2026
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Score Details

Score Construction
PGS Name TPMI_HDL-C_LDPred2
Development Method
Name LDPred2
Parameters NR
Variants
Original Genome Build GRCh38
Number of Variants 939,781
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000835
Citation (link to publication) Chen HH et al. Nature (2025)
Ancestry Distribution
Source of Variant
Associations (GWAS)
East Asian: 100%
194,120 individuals (100%)
Score Development/Training
East Asian: 100%
52,970 individuals (100%)
PGS Evaluation
East Asian: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
— 194,120 individuals,
42.45 % Male samples
 East Asian
(Han Chinese)		 TPMI
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
— 52,970 individuals,
45.27 % Male samples
 East Asian
(Han Chinese)		 TPMI 0 — — — —

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
PPM038004 PSS013734|
East Asian Ancestry|
8,059 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: High-density lipoprotein cholesterol — AUROC: 0.62244 R²: 0.13809 sex, age, array, PCs 1-10 —

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
PSS013734 — — 8,059 individuals,
46.28 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —