Polygenic Score (PGS) ID: PGS003856

Predicted Trait
Reported Trait HDL cholesterol
Mapped Trait(s) high density lipoprotein cholesterol measurement (EFO_0004612)
Released in PGS Catalog: Sept. 1, 2023
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Score Details

Score Construction
PGS Name PRS59_HDL
Development Method
Name Genome-wide significant SNPs
Parameters NR
Variants
Original Genome Build NR
Number of Variants 59
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000493
Citation (link to publication) Li J et al. JAMA Netw Open (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
East Asian: 100%
81,045 individuals (100%)
PGS Evaluation
East Asian: 100%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST004234
Europe PMC: 28334899
 25,169 individuals East Asian NR
GWAS Catalog: GCST003215
Europe PMC: 26582766
 8,344 individuals East Asian NR
Europe PMC: 29083407
 47,532 individuals East Asian 12 cohorts
  • CHNS
  • ,CLHNS
  • ,FAMHES
  • ,GBTDS
  • ,NHAPC
  • ,PUUMA
  • ,SBCS
  • ,SIMES
  • ,SMHS
  • ,SP2
  • ,SWHS
  • ,TUDR

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
PPM018688 PSS011066|
East Asian Ancestry|
37,317 individuals
 PGP000493 |
Li J et al. JAMA Netw Open (2023)
 Reported Trait: Estimated annual change of HDL cholesterol — — p-value (inferior to): 0.001 — —
PPM018692 PSS011068|
East Asian Ancestry|
15,664 individuals
 PGP000493 |
Li J et al. JAMA Netw Open (2023)
 Reported Trait: Estimated annual change of HDL cholesterol — — p-value (inferior to): 0.001 — —
PPM018696 PSS011067|
East Asian Ancestry|
21,653 individuals
 PGP000493 |
Li J et al. JAMA Netw Open (2023)
 Reported Trait: Estimated annual change of HDL cholesterol — — p-value (inferior to): 0.001 — —

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
PSS011066 — — 37,317 individuals,
41.98 % Male samples
 Mean = 51.37 years
Sd = 10.82 years		 East Asian — InterASIA China MUCA, CIMIC
PSS011067 — — 21,653 individuals,
41.98 % Male samples
 Mean = 51.22 years
Sd = 10.78 years		 East Asian — InterASIA China MUCA, CIMIC
PSS011068 — — 15,664 individuals,
41.98 % Male samples
 Mean = 51.57 years
Sd = 10.87 years		 East Asian — InterASIA China MUCA, CIMIC